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Sample records for site-specific photoelectron diffraction

  1. Photoelectron diffraction

    NASA Astrophysics Data System (ADS)

    Fadley, Charles S.

    1987-01-01

    The use of core-level photoelectron diffraction for structural studies of surfaces and epitaxial overlayers is discussed. Photoelectron diffraction is found to provide several direct and rather unique types of structural information, including the sites and positions of adsorbed atoms; the orientations of small molecules or fragments bound to surfaces; the orientations, layer thicknesses, vertical lattice constants, and degrees of short-range order of epitaxial or partially-epitaxial overlayers; and the presence of short-range spin order in magnetic materials. Specific systems considered are the reaction of oxygen with Ni(001), the growth of epitaxial Cu on Ni(001), the well-defined test case S on Ni(001), and short-range spin order in the antiferromagnet KMnF3. A rather straightforward single scattering cluster (SSC) model also proves capable of quantitatively describing such data, particularly for near-surface species and with corrections for spherical-wave scattering effects and correlated vibrational motion. Promising new directions in such studies also include measurements with high angular resolution and the expanded use of synchrotron radiation.

  2. Oxygen as a site specific structural probe in neutron diffraction

    SciTech Connect

    Neuefeind, Joerg C; Simonson, J Michael {Mike}; Salmon, Phil; Zeidler, Anita; Fischer, Henry E; Rauch, Helmut; Markland, Thomas; Lemmel, Hartmut

    2011-01-01

    Oxygen is a ubiquitous element, playing an essential role in most scientific and technological disciplines, and is often incorporated within a structurally disordered material where examples include molten silicates in planetary science, glasses used for lasers and optical communication, and water in biological processes. Establishing the structure of a liquid or glassy oxide and thereby its relation to the functional properties of a material is not, however, a trivial task owing to the complexity associated with atomic disorder. Here we approach this challenge by measuring the bound coherent neutron scattering lengths of the oxygen isotopes with the sensitive technique of neutron interferometry. We find that there is a small but finite contrast of 0.204(6) fm between the scattering lengths of the isotope 18O and oxygen of natural isotopic abundance natO, contrary to tables of recommended values. This has enabled us to investigate the structure of both light and heavy water by exploiting, for the first time, the method of oxygen isotope substitution in neutron diffraction, thus circumventing many of the significant problems associated with more traditional methods in which hydrogen is substituted by deuterium. We find a difference of ~0.5% between the O-H and O-D intra-molecular bond distances which is much smaller than recent estimates based on diffraction data and is found to be in excellent agreement with path integral molecular dynamics simulations made with a flexible polarisable water model. Our results demonstrate the potential for using oxygen isotope substitution as a powerful and effective site specific probe in a plethora of materials, of pertinence as instrumentation at next generation neutron sources comes online

  3. Observation of spin-polarized photoelectron diffraction

    NASA Astrophysics Data System (ADS)

    Sinković, B.; Hermsmeier, B.; Fadley, C. S.

    1985-09-01

    We report the first observation of spin-polarized photoelectron diffraction in core-level emission from anti-ferromagnetic KMnF3. The Mn 3s multiplet splitting provides an internal source of polarized electrons, and spin polarized photoelectron diffraction effects of up to 17% are seen in the 5/ 7S intensity ratio. These effects are found to be very sensitive to both emission direction and temperature. Short-range antiferromagnetic order is found to persist up to approximately three times the Neél temperature.

  4. Theory of spin polarized photoelectron diffraction

    NASA Astrophysics Data System (ADS)

    Sinković, B.; Friedman, D. J.; Fadley, C. S.

    1991-01-01

    We discuss several aspects of the theory of spin-polarized photoelectron diffraction (SPPD). This method makes use of multiplet splittings of core-level binding energies to produce photoelectron peaks with high spin polarization (for example, the two principal peaks associated with Mn 3s emission from Mn 2+). We consider three possible mechanisms for spin-dependent photoelectron scattering and diffraction: exchange scattering by valence electrons (3d 5 for Mn 2+), spin-orbit scattering (which is not expected to yield large effects if the sample does not have a net magnetization), and spin-dependent inelastic scattering (which cannot yet be dealt with in a fully quantitative way, but is estimated to be less important than the other two). The fact that SPPD involves internal sources of polarized electrons references to their respective emitters implies that it can be employed to study magnetic order in both anti-ferromagnets and ferromagnets and at temperatures above their respective Néel or Curie points. The effects of exchange scattering on Mn 3s emission from Mn 2+ in KMnF 3 have been incorporated into a single-scattering cluster model of the diffraction process via either the Dirac-Hara or Kohn-Sham local density approximations. This model is applied to several cases: a single Mn 2+ scatterer, small clusters of Mn 2+ scatterers, and full clusters appropriate to the (110) surface of KMnF 3, with all atoms included. These calculations demonstrate that SPPD should be a short-range probe of magnetic order, a result consistent with conclusions reached in several prior studies of photoelectron diffraction without spin resolution. They also illustrate the perturbative nature of these effects, which are only about ca. 5-15% of the total intensity; this in turn leads to several possible simplifications in the theory. We have in addition phenomenologically modelled the decreases of short-range order with increasing temperature by using a Gaussian modulation of spins; this

  5. Intramolecular photoelectron diffraction in the gas phase

    NASA Astrophysics Data System (ADS)

    Ueda, K.; Miron, C.; Plésiat, E.; Argenti, L.; Patanen, M.; Kooser, K.; Ayuso, D.; Mondal, S.; Kimura, M.; Sakai, K.; Travnikova, O.; Palacios, A.; Decleva, P.; Kukk, E.; Martín, F.

    2013-09-01

    We report unambiguous experimental and theoretical evidence of intramolecular photoelectron diffraction in the collective vibrational excitation that accompanies high-energy photoionization of gas-phase CF4, BF3, and CH4 from the 1s orbital of the central atom. We show that the ratios between vibrationally resolved photoionization cross sections (v-ratios) exhibit pronounced oscillations as a function of photon energy, which is the fingerprint of electron diffraction by the surrounding atomic centers. This interpretation is supported by the excellent agreement between first-principles static-exchange and time-dependent density functional theory calculations and high resolution measurements, as well as by qualitative agreement at high energies with a model in which atomic displacements are treated to first order of perturbation theory. The latter model allows us to rationalize the results for all the v-ratios in terms of a generalized v-ratio, which contains information on the structure of the above three molecules and the corresponding molecular cations. A fit of the measured v-ratios to a simple formula based on this model suggests that the method could be used to obtain structural information of both neutral and ionic molecular species.

  6. Intramolecular photoelectron diffraction in the gas phase.

    PubMed

    Ueda, K; Miron, C; Plésiat, E; Argenti, L; Patanen, M; Kooser, K; Ayuso, D; Mondal, S; Kimura, M; Sakai, K; Travnikova, O; Palacios, A; Decleva, P; Kukk, E; Martín, F

    2013-09-28

    We report unambiguous experimental and theoretical evidence of intramolecular photoelectron diffraction in the collective vibrational excitation that accompanies high-energy photoionization of gas-phase CF4, BF3, and CH4 from the 1s orbital of the central atom. We show that the ratios between vibrationally resolved photoionization cross sections (v-ratios) exhibit pronounced oscillations as a function of photon energy, which is the fingerprint of electron diffraction by the surrounding atomic centers. This interpretation is supported by the excellent agreement between first-principles static-exchange and time-dependent density functional theory calculations and high resolution measurements, as well as by qualitative agreement at high energies with a model in which atomic displacements are treated to first order of perturbation theory. The latter model allows us to rationalize the results for all the v-ratios in terms of a generalized v-ratio, which contains information on the structure of the above three molecules and the corresponding molecular cations. A fit of the measured v-ratios to a simple formula based on this model suggests that the method could be used to obtain structural information of both neutral and ionic molecular species.

  7. Spherical-wave effects in photoelectron diffraction

    NASA Astrophysics Data System (ADS)

    Sagurton, M.; Bullock, E. L.; Saiki, R.; Kaduwela, A.; Brundle, C. R.; Fadley, C. S.; Rehr, J. J.

    1986-02-01

    The influence of spherical-wave (SW) effects on the analysis of photoelectron diffraction (PD) data is considered by comparing full SW single-scattering calculations with similar calculations based upon the plane-wave (PW) approximation and a new approximation for including SW effects (SW(1)) due to Rehr, Albers, Natoli, and Stern, as well as with experimental data involving both scanned-energy and scanned-angle measurements. In general, SW effects are found to be much more important in forward scattering and to explain prior empirical adjustments of PW x-ray PD scattering amplitudes at higher energies of >~500 eV. The more easily used SW(1) approximation is also seen to allow very well for SW effects. Not all PD data are expected to be equally sensitive to SW corrections. For example, scanned-energy data for S/Ni(001) emphasizing backscattering events are about equally well described by the PW and SW models, whereas higher-energy azimuthal-scan data for O/Ni(001) in which forward scattering is dominant require SW corrections to describe some, but not all, directions of emission quantitatively.

  8. Ultrafast molecular orbital imaging based on attosecond photoelectron diffraction.

    PubMed

    Li, Yang; Qin, Meiyan; Zhu, Xiaosong; Zhang, Qingbin; Lan, Pengfei; Lu, Peixiang

    2015-04-20

    We present ab initio numerical study of ultrafast ionization dynamics of H(2)(+) as well as CO(2) and N(2) exposed to linearly polarized attosecond extreme ultraviolet pulses. When the molecules are aligned perpendicular to laser polarization direction, photonionization of these molecules show clear and distinguishing diffraction patterns in molecular attosecond photoelectron momentum distributions. The internuclear distances of the molecules are related to the position of the associated diffraction patterns, which can be determined with high accuracy. Moreover, the relative heights of the diffraction fringes contain fruitful information of the molecular orbital structures. We show that the diffraction spectra can be well produced using the two-center interference model. By adopting a simple inversion algorithm which takes into account the symmetry of the initial molecular orbital, we can retrieve the molecular orbital from which the electron is ionized. Our results offer possibility for imaging of molecular structure and orbitals by performing molecular attosecond photoelectron diffraction.

  9. Imaging scatterer planes by photoelectron diffraction

    NASA Astrophysics Data System (ADS)

    Seelmann-Eggebert, M.

    1997-04-01

    A novel direct crystallographic method CHRISDA (combined holographic real-space imaging by superimposed dimer function algorithm) is proposed which permits an assessment of the near-surface structure of a solid sample by analysis of a single core-level photoemission or Auger emission diffraction pattern (XPD or AED) recorded over the hemisphere of electron escape angles. Combining the elements of holography and real-space triangulation, the approach achieves a high spatial resolution (≈0.1 Å) and requires a knowledge of only a few non-structural parameters. To demonstrate the experimental efficacy of CHRISDA, a Sn film deposited on a CdTe(111) substrate is analyzed and yields the diamond structure characteristic of α-Sn.

  10. Theory and Application of Auger and Photoelectron Diffraction and Holography

    NASA Astrophysics Data System (ADS)

    Chen, Xiang

    This dissertation addresses the theories and applications of three important surface analysis techniques: Auger electron diffraction (AED), x-ray photoelectron diffraction (XPD), and Auger and photoelectron holography. A full multiple-scattering scheme for the calculations of XPD, AED, and Kikuchi electron diffraction pattern from a surface cluster is described. It is used to simulate 64 eV M_{2,3}VV and 913 eV L_3VV AED patterns from Cu(001) surfaces, in order to test assertions in the literature that they are explicable by a classical "blocking" and channeling model. We find that this contention is not valid, and that only a quantum mechanical multiple-scattering calculation is able to simulate these patterns well. The same multiple scattering simulation scheme is also used to investigate the anomalous phenomena of peak shifts off the forward-scattering directions in photo -electron diffraction patterns of Mg KLL (1180 eV) and O 1s (955 eV) from MgO(001) surfaces. These shifts are explained by calculations assuming a short electron mean free path. Similar simulations of XPD from a CoSi_2(111) surface for Co-3p and Si-2p normal emission agree well with experimental diffraction patterns. A filtering process aimed at eliminating the self -interference effect in photoelectron holography is developed. A better reconstructed image from Si-2p XPD from a Si(001) (2 times 1) surface is seen at atomic resolution. A reconstruction algorithm which corrects for the anisotropic emitter waves as well as the anisotropic atomic scattering factors is used for holographic reconstruction from a Co-3p XPD pattern from a CoSi_2 surface. This new algorithm considerably improves the reconstructed image. Finally, a new reconstruction algorithm called "atomic position recovery by iterative optimization of reconstructed intensities" (APRIORI), which takes account of the self-interference terms omitted by the other holographic algorithms, is developed. Tests on a Ni-C-O chain and Si(111

  11. Photoelectron diffraction of magnetic ultrathin films: Fe/Cu(001)

    SciTech Connect

    Tobin, J.G. ); Wagner, M.K. . Dept. of Chemistry); Guo, X.Q.; Tong, S.Y. . Dept. of Physics)

    1991-01-03

    The preliminary results of an ongoing investigation of Fe/Cu(001) are presented here. Energy dependent photoelectron diffraction, including the spin-dependent variant using the multiplet split Fe3s state, is being used to investigate the nanoscale structures formed by near-monolayer deposits of Fe onto Cu(001). Core-level photoemission from the Fe3p and Fe3s states has been generated using synchrotron radiation as the tunable excitation source. Tentatively, a comparison of the experimental Fe3p cross section measurements with multiple scattering calculations indicates that the Fe is in a fourfold hollow site with a spacing of 3.6{Angstrom} between it and the atom directly beneath it, in the third layer. This is consistent with an FCC structure. The possibility of utilizing spin-dependent photoelectron diffraction to investigate magnetic ultrathin films will be demonstrated, using our preliminary spectra of the multiplet-split Fe3s os near-monolayer Fe/Cu(001). 18 refs., 10 figs.

  12. Application of a Novel Multiple-Scattering Approach to Photoelectron Diffraction and Auger Electron Diffraction.

    NASA Astrophysics Data System (ADS)

    Kaduwela, Ajith P.

    We apply a new separable-Green's-function matrix method due to Rehr and Albers (Phys. Rev. B4l (1990) 8139) to a multiple scattering treatment of photoelectron diffraction and Auger electron diffraction. This cluster -based method permits building up successive orders of scattering and judging the approach to convergence in a convenient and time-saving way. We include multiple scattering up to tenth order and can treat photoelectron emission form any initial state (s, p, d, or f) with full final-state interference. This new approach is used to simulate emission from linear and bent chains of atoms, from epitaxial overlayers and multilayer substrates and from atomic and molecular adsorbates, and various conclusions are drawn concerning the range of utility of the method and the geometric structures for which multiple scattering effects must be considered.

  13. Global search algorithms in surface structure determination using photoelectron diffraction

    NASA Astrophysics Data System (ADS)

    Duncan, D. A.; Choi, J. I. J.; Woodruff, D. P.

    2012-02-01

    Three different algorithms to effect global searches of the variable-parameter hyperspace are compared for application to the determination of surface structure using the technique of scanned-energy mode photoelectron diffraction (PhD). Specifically, a new method not previously used in any surface science methods, the swarm-intelligence-based particle swarm optimisation (PSO) method, is presented and its results compared with implementations of fast simulated annealing (FSA) and a genetic algorithm (GA). These three techniques have been applied to experimental data from three adsorption structures that had previously been solved by standard trial-and-error methods, namely H2O on TiO2(110), SO2 on Ni(111) and CN on Cu(111). The performance of the three algorithms is compared to the results of a purely random sampling of the structural parameter hyperspace. For all three adsorbate systems, the PSO out-performs the other techniques as a fitting routine, although for two of the three systems studied the advantage relative to the GA and random sampling approaches is modest. The implementation of FSA failed to achieve acceptable fits in these tests.

  14. The interfacial and surface properties of thin Fe and Gd films grown on W(110) as studied by scanning tunneling microscopy, site-resolved photoelectron diffraction, and spin polarized photoelectron diffraction

    SciTech Connect

    Tober, Eric D.

    1997-06-01

    Combined scanning tunneling microscopy (STM) and low energy electron diffraction (LEED) measurements from Gd films grown on W(110) prepared with and without annealing have been used to provide a detailed picture of the growth of such films, permitting a quantitative structural explanation for previously-measured magnetic properties and the identification of a new two-dimensional structure for the first monolayer. The analysis of the film roughness of room-temperature-grown films as a function of coverage and lateral length scale reveals that the growing Gd surface follows scaling laws for a self-affine surface. Annealing these as-deposited films at elevated temperatures is found to drastically alter the morphology of the films, as seen by both STM and LEED. Nanometer-scale islands of relatively well-defined size and shape are observed under certain conditions. Finally, the first monolayer of Gd is observed to form a (7x14) superstructure with pseudo-(7x7) symmetry that is consistent with a minimally-distorted hexagonal two-dimensional Gd(0001) film. Furthermore, a new beamline and photoelectron spectrometer/diffractometer at the Advanced Light Source have been used to obtain full-solid-angle and site-specific photoelectron diffraction (PD) data from interface W atoms just beneath (1x1) Fe and (7x14) Gd monolayers on W(110) by utilizing the core level shift in the W 4f7/2 spectrum. A comparison of experiment with multiple scattering calculations permits determining the Fe adsorption site and the relative interlayer spacing to the first and second W layers. These Fe results are also compared to those from the very different Gd overlayer and from the clean W(110) surface. Such interface PD measurements show considerable promise for future studies. Finally, the rare-earth ferromagnetic system of Gd(0001) has been examined through the use of spin polarized photoelectron diffraction from the Gd 4s and 5s photoelectron multiplets.

  15. Imaging molecular structure through femtosecond photoelectron diffraction on aligned and oriented gas-phase molecules.

    PubMed

    Boll, Rebecca; Rouzée, Arnaud; Adolph, Marcus; Anielski, Denis; Aquila, Andrew; Bari, Sadia; Bomme, Cédric; Bostedt, Christoph; Bozek, John D; Chapman, Henry N; Christensen, Lauge; Coffee, Ryan; Coppola, Niccola; De, Sankar; Decleva, Piero; Epp, Sascha W; Erk, Benjamin; Filsinger, Frank; Foucar, Lutz; Gorkhover, Tais; Gumprecht, Lars; Hömke, André; Holmegaard, Lotte; Johnsson, Per; Kienitz, Jens S; Kierspel, Thomas; Krasniqi, Faton; Kühnel, Kai-Uwe; Maurer, Jochen; Messerschmidt, Marc; Moshammer, Robert; Müller, Nele L M; Rudek, Benedikt; Savelyev, Evgeny; Schlichting, Ilme; Schmidt, Carlo; Scholz, Frank; Schorb, Sebastian; Schulz, Joachim; Seltmann, Jörn; Stener, Mauro; Stern, Stephan; Techert, Simone; Thøgersen, Jan; Trippel, Sebastian; Viefhaus, Jens; Vrakking, Marc; Stapelfeldt, Henrik; Küpper, Jochen; Ullrich, Joachim; Rudenko, Artem; Rolles, Daniel

    2014-01-01

    This paper gives an account of our progress towards performing femtosecond time-resolved photoelectron diffraction on gas-phase molecules in a pump-probe setup combining optical lasers and an X-ray free-electron laser. We present results of two experiments aimed at measuring photoelectron angular distributions of laser-aligned 1-ethynyl-4-fluorobenzene (C(8)H(5)F) and dissociating, laser-aligned 1,4-dibromobenzene (C(6)H(4)Br(2)) molecules and discuss them in the larger context of photoelectron diffraction on gas-phase molecules. We also show how the strong nanosecond laser pulse used for adiabatically laser-aligning the molecules influences the measured electron and ion spectra and angular distributions, and discuss how this may affect the outcome of future time-resolved photoelectron diffraction experiments.

  16. Spin-polarized photoelectron diffraction from magnetically-ordered solids and surfaces

    NASA Astrophysics Data System (ADS)

    Sinković, B.; Hermsmeier, B.; Fadley, C. S.

    1986-02-01

    We report the first experimental observation of Spin-Polarized Photoelectron Diffraction (SPPD), an effect which shows considerable promise for studying short-range order in magnetic solids and surfaces. The detection of photoelectron spin polarization in this experiment is provided by 3s-level multiplet splittings in 3d metals and their compounds; thus no external spin detector is required. Measurements on antiferromagnetic KMnF 3 show spin asymmetries of as high as 17% due to short-range order.

  17. Site-specific recoil-induced effects on inner-shell photoionization of linear triatomic molecules: N 1 s photoelectron spectra of N2 O

    NASA Astrophysics Data System (ADS)

    Krivosenko, Yu. S.; Pavlychev, A. A.

    2016-11-01

    We investigate hard X-ray ionization of linear triatomic molecules accenting recoil-induced effects on the dynamics of molecular frame. This dynamics is studied within the two-springs and harmonic approximations. The mode-channel relationship connecting the excitations of vibrational, rotational and translational degrees of freedom with the Σ → Σ and Σ → Π photoionization channels is applied to compute the N 1s-1 photoelectron spectra of molecular N2 O for various photon energies. The distinct ionized-site- and molecular-orientation-specific changes in the vibration structure of the 1 s photoelectron lines of terminal and central nitrogen atoms are revealed and discussed.

  18. Femtosecond photoelectron diffraction: a new approach to image molecular structure during photochemical reactions

    NASA Astrophysics Data System (ADS)

    Rolles, Daniel; Boll, Rebecca; Tamrakar, Samyak R.; Anielski, Denis; Bomme, Cédric

    2014-09-01

    Continuing technical advances in the creation of (sub-) femtosecond VUV and X-ray pulses with Free-Electron Lasers and laser-based high-harmonic-generation sources have created new opportunities for studying ultrafast dynamics during chemical reactions. Here, we present an approach to image the geometric structure of gas-phase molecules with fewfemtosecond temporal and sub-Ångström spatial resolution using femtosecond photoelectron diffraction. This technique allows imaging the molecules "from within" by analyzing the diffraction of inner-shell photoelectrons that are created by femtosecond VUV and X-ray pulses. Using pump-probe schemes, ultrafast structural changes during photochemical reactions can thus be directly visualized with a temporal resolution that is only limited by the pulse durations of the pump and the probe pulse and the synchronization of the two light pulses. Here, we illustrate the principle of photoelectron diffraction using a simple, geometric scattering model and present results from photoelectron diffraction experiments on laser-aligned molecules using X-ray pulses from a Free-Electron Laser.

  19. Photoelectron dynamics in x-ray free-electron-laser diffractive imaging of biological samples.

    PubMed

    Hau-Riege, Stefan P

    2012-06-08

    X-ray free electron lasers hold the promise of enabling atomic-resolution diffractive imaging of single biological molecules. We develop a hybrid continuum-particle model to describe the x-ray induced damage and find that the photoelectron dynamics and electrostatic confinement strongly affect the time scale of the damage processes. These phenomena are not fully captured in hydrodynamic modeling approaches.

  20. X-Ray Photoelectron Diffraction Studies of Structural and Magnetic Disordering Transitions Near Surfaces

    NASA Astrophysics Data System (ADS)

    Tran, Thuy Thu

    This thesis deals with order/disorder transitions near solid surfaces as studied by x-ray photoelectron diffraction and photoelectron holography. Transitions involving both atomic positional order and magnetic order have been studied. Further evidence for a reversible high-temperature surface-disordering phase transition on Ge(111) has been found using Ge 3p x-ray photoelectron diffraction (a short -range-order probe of surface structure) and photoelectron holography. Azimuthal diffraction data at takeoff angles with respect to the surface of theta = 19^circ and theta = 55^circ show abrupt drops in intensity of ~30%-40% over the temperature interval of 900-1200 K. Photoelectron holographic near-neighbor images at temperatures below and above the transition region furthermore indicate an identical near-neighbor structure for all atoms present in ordered sites. These combined diffraction and holography data show that by 1200 K, the Ge(111) surface is covered by a completely disordered overlayer of about 2 Ge monolayers in thickness. The rate of growth of this overlayer with increasing temperature is in excellent agreement with recent medium-energy ion scattering results, although the thickness we find for the overlayer is 1.5-2.0x larger than that derived from ion scattering. Based on these data, a disordering model for the Ge(111) surface phase transition occurring at 1050 K is discussed. Spin-polarized photoelectron diffraction is a recently developed and promising application of photoelectron diffraction to the study of the magnetic structure near surfaces. This technique is based on an internal source of spin-polarized electrons as produced in core-level multiplet splittings and it is thus sensitive to the short-range magnetic order around a given type of emitter in the crystal. In prior studies, it has been applied to two antiferromagnets, KMnF_3 and MnO, and the effects seen at temperatures well above the Neel (or long-range -order) temperature have been

  1. Beyond hard x-ray photoelectron spectroscopy: Simultaneous combination with x-ray diffraction

    SciTech Connect

    Rubio-Zuazo, Juan; Castro, German R.

    2013-05-15

    Hard x-ray photoelectron spectroscopy (HAXPES) is a powerful and novel emerging technique for the nondestructive determination of electronic properties and chemical composition of bulk, buried interfaces and surfaces. It benefits from the exceptionally large escape depth of high kinetic energy photoelectrons, increasing the information depth up to several tens of nanometers. Complementing HAXPES with an atomic structure sensitive technique (such as x-ray diffraction) opens a new research field with major applications for materials science. At SpLine, the Spanish CRG beamline at the European Synchrotron Radiation Facility, we have developed a novel experimental set-up that combines HAXPES and x-ray diffraction (x-ray reflectivity, surface x-ray diffraction, grazing incidence x-ray diffraction, and reciprocal space maps). Both techniques can be operated simultaneously on the same sample and using the same excitation source. The set-up includes a robust 2S + 3D diffractometer hosting a ultrahigh vacuum chamber equipped with a unique photoelectron spectrometer (few eV < electron kinetic energy < 15 keV), x-ray tube (Mg/Ti), 15 keV electron gun, and auxiliary standard surface facilities (molecular beam epitaxy evaporator, ion gun, low energy electron diffraction, sample heating/cooling system, leak valves, load-lock sample transfer, etc.). This end-station offers the unique possibility of performing simultaneous HAXPES + x-ray diffraction studies. In the present work, we describe the experimental set-up together with two experimental examples that emphasize its outstanding capabilities: (i) nondestructive characterization of the Si/Ge and HfO{sub 2}/SiO{sub 2} interfaces on Ge-based CMOS devices, and (ii) strain study on La{sub 0.7}Ca{sub 0.3}MnO{sub 3} ultrathin films grown on SrTiO{sub 3}(001) substrate.

  2. Convergent N2-scaling iterative method of photoelectron diffraction and low-energy electron diffraction for ordered or disordered systems

    NASA Astrophysics Data System (ADS)

    Wu, Huasheng; Tong, S. Y.

    1999-01-01

    We present results of a convergent iterative method of photoelectron diffraction and low-energy electron diffraction. The computation time of this method scales as N2, where N is the dimension of the propagator matrix, rather than N3 as in conventional Gaussian substitutional methods. We show that the Rehr-Albers separable-representation cluster approach or slab-type nonseparable methods can all be cast in this iterative form. The convergence of this method is demonstrated for different materials. With the substantial savings in computational time and no loss in numerical accuracy, this method will be very useful in future applications of multiple-scattering theory, particularly for systems either involving very large unit cells (200-700 atoms) or where no long-range order is present.

  3. Linear dimerized Se chains in cancrinite nanochannels: X-ray diffraction and photoelectron spectra

    NASA Astrophysics Data System (ADS)

    Poborchii, V. V.; Sato, M.; Shchukarev, A. V.

    1997-09-01

    Cancrinite crystals containing adsorbed selenium in 1-dimensional nanochannels (Can-Se) have been examined by X-ray diffraction, X-ray photoelectron spectroscopy and polarized infrared spectroscopy. It is found that adsorbed selenium forms Se 22- anions substituting OH - groups inside channels. Se 22- dimers are located in the center of the cancrinite channel and oriented along the channel. They interact with Na + cations located in the channels and with each other giving rise to a linear chain incommensurate to the cancrinite matrix. The arrangement of the dimers in the chain has been found to be dependent on the temperature.

  4. Is the Separable Propagator Perturbation Approach Accurate in Calculating Angle Resolved Photoelectron Diffraction Spectra?

    NASA Astrophysics Data System (ADS)

    Ng, C. N.; Chu, T. P.; Wu, Huasheng; Tong, S. Y.; Huang, Hong

    1997-03-01

    We compare multiple scattering results of angle-resolved photoelectron diffraction spectra between the exact slab method and the separable propagator perturbation method. In the slab method,footnote C.H. Li, A.R. Lubinsky and S.Y. Tong, Phys. Rev. B17, 3128 (1978). the source wave and multiple scattering within the strong scattering atomic layers are expanded in spherical waves while interlayer scattering is expressed in plane waves. The transformation between spherical waves and plane waves is done exactly. The plane waves are then matched across the solid-vacuum interface to a single outgoing plane wave in the detector's direction. The separable propagator perturbation approach uses two approximations: (i) A separable representation of the Green's function propagator and (ii) A perturbation expansion of multiple scattering terms. Results of c(2x2) S-Ni(001) show that this approximate method fails to converge due to the very slow convergence of the separable representation for scattering angles less than 90^circ. However, this method is accurate in the backscattering regime and may be applied to XAFS calculations.(J.J. Rehr and R.C. Albers, Phys. Rev. B41, 8139 (1990).) The use of this method for angle-resolved photoelectron diffraction spectra is substantially less reliable.

  5. Scanned-energy mode photoelectron diffraction measurements at beamline 7.0.1

    SciTech Connect

    Toomes, R.; Booth, N.A.; Woodruff, D.P.

    1997-04-01

    This report covers the results of the authors first experimental run, in May 1996, conducted to explore the advantages offered by the high spectral resolution available at the SpectroMicroscopy Facility on beam line 7.0 to conduct scanned-energy mode photoelectron diffraction (PhD). This technique is now a well-established method for the determination of local structure of atomic and molecular adsorbates on well-characterised surfaces. The directly-emitted component of an adsorbate core-level photoelectron wavefield interferes coherently with components of the same wavefield elastically scattered by surrounding atoms, leading to a modulation in the photoemission intensity as a function of kinetic energy in any specific emission direction. A series of such PhD modulation spectra, each typically covering energies from 50-500 eV, for a series of different emission directions, provides the basis for a quantitative structure determination of the emitter-scatterer geometry. Within the last years the authors have developed an integrated approach to extract the structural information from these photoelectron diffraction (PhD) spectra in a quantitative way. A direct data inversion technique (the so-called Projection method) provides a first-order estimate of the local adsorbate geometry in the form of an `image` of the scatterer atoms which are nearest neighbours to the emitter. This information is then used as a starting model for optimisation of the structural parameters by comparing the experimental PhD spectra with the results of multiple scattering simulations using a code developed by Fritzsche. The optimisation uses an automated trial-and-error procedure by minimising a reliability factor which provides an objective measure of the quality of agreement between experiment and theory. The authors have successfully applied this approach to the structure determination of about 30 adsorption systems.

  6. Photoelectron diffraction k-space volumes of the c(2x2) Mn/Ni(100) structure

    SciTech Connect

    Banerjee, S.; Denlinger, J.; Chen, X.

    1997-04-01

    Traditionally, x-ray photoelectron diffraction (XPD) studies have either been done by scanning the diffraction angle for fixed kinetic energy (ADPD), or scanning the kinetic energy at fixed exit angle (EDPD). Both of these methods collect subsets of the full diffraction pattern, or volume, which is the intensity of photoemission as a function of momentum direction and magnitude. With the high density available at the Spectromicroscopy Facility (BL 7.0) {open_quotes}ultraESCA{close_quotes} station, the authors are able to completely characterize the photoelectron diffraction patterns of surface structures, up to several hundred electron volts kinetic energy. This large diffraction `volume` can then be analyzed in many ways. The k-space volume contains as a subset the energy dependent photoelectron diffraction spectra along all emission angles. It also contains individual, hemispherical, diffraction patterns at specific kinetic energies. Other `cuts` through the data set are also possible, revealing new ways of viewing photoelectron diffraction data, and potentially new information about the surface structure being studied. In this article the authors report a brief summary of a structural study being done on the c(2x2) Mn/Ni(100) surface alloy. This system is interesting for both structural and magnetic reasons. Magnetically, the Mn/Ni(100) surface alloy exhibits parallel coupling of the Mn and Ni moments, which is opposite to the reported coupling for the bulk, disordered, alloy. Structurally, the Mn atoms are believed to lie well above the surface plane.

  7. GaN quantum dot polarity determination by X-ray photoelectron diffraction

    NASA Astrophysics Data System (ADS)

    Romanyuk, O.; Bartoš, I.; Brault, J.; Mierry, P. De; Paskova, T.; Jiříček, P.

    2016-12-01

    Growth of GaN quantum dots (QDs) on polar and semipolar GaN substrates is a promising technology for efficient nitride-based light emitting diodes (LED). The QDs crystal orientation typically repeats the polarity of the substrate. In case of non-polar or semipolar substrates, the polarity of QDs is not obvious. In this article, the polarity of GaN QDs and of underlying layers was investigated nondestructively by X-ray photoelectron diffraction (XPD). Polar and semipolar GaN/Al0.5Ga0.5N heterostructures were grown on the sapphire substrates with (0001) and (1 1 bar 00) orientations by molecular beam epitaxy (MBE). Polar angle dependence of N 1s core-level photoelectron intensities were measured from GaN QDs and compared with the corresponding experimental curves from free-standing GaN crystals. It is confirmed experimentally, that the crystalline orientation of polar (0001) GaN QDs follows the orientation of the (0001) sapphire substrate. In case of semipolar GaN QDs grown on (1 1 bar 00) sapphire substrate, the (11 2 bar 2) polarity of QDs was determined.

  8. Surface structure of lithiated graphite by X-ray photoelectron diffraction

    NASA Astrophysics Data System (ADS)

    Lee, Choong Man; Yang, S.-H.; Mun, B.-J.; Ross, Philip N.

    2001-04-01

    The surface composition and structure of a stage-one lithium intercalation compound (Li-GIC) was studied by X-ray photoelectron diffraction (XPD) from Li 1s and C 1s core levels. The Li-GIC was prepared in situ by vapor phase intercalation of lithium into highly oriented pyrolitic graphite (HOPG) in an ultra-high vacuum system. Stage-one Li-GIC, LiC 6, having a characteristic golden color, was obtained using Li evaporation onto a HOPG substrate at 400 K, while a metallic lithium overlayer was observed at depositions below room temperature. XPD patterns of Li 1s and C 1s intensities as a function of the polar emission angle were obtained at a fixed photon energy of 1253.6 eV. The experimental XPD patterns on the HOPG and the stage-one Li-GIC were both in quite good agreement with calculated XPD patterns based on Rehr-Albers separable representation for scattering of the emitted photoelectrons. The structural model for the surface of the Li-GIC producing the best fit to the experimental data has the bulk LiC 6 lattice with surface termination in the graphene plane.

  9. The Rh oxide ultrathin film on Rh(100): an x-ray photoelectron diffraction study.

    PubMed

    Zhan, Rong Rong; Vesselli, Erik; Baraldi, Alessandro; Lizzit, Silvano; Comelli, Giovanni

    2010-12-07

    The surface and interface structure of the RhO(2) ultrathin film grown on Rh(100) is investigated by means of x-ray photoelectron diffraction. Experimental and simulated one- and two-dimensional angular distribution intensities of the O1s and Rh3d(5/2) chemically shifted core levels are quantitatively analyzed. The previously proposed O-Rh-O trilayer model is independently confirmed. A rippled buckling of the metal surface is observed at the oxide-metal interface, with a mean interfacial Rh-O distance which is 0.2 Å larger with respect to previous findings. The link between the local atomic rearrangement and the overall geometric and electronic properties of the oxide is discussed on the basis of a thorough comparison with the corresponding RhO(2) rutile structure.

  10. Spin-polarized photoelectron diffraction: A new probe of short-range magnetic order (invited) (abstract)

    NASA Astrophysics Data System (ADS)

    Fadley, C. S.; Sinkovic, B.; Hermsmeier, B. D.; Osterwalder, J.

    1988-04-01

    It has recently been pointed out theoretically and subsequently observed experimentally that core-level multiplet splittings can be used to yield a spin-polarized form of photoelectron diffraction (SPPD). This internally referenced source of electrons that are highly polarized with both orientations of spin thus eliminates the need for an external spin detector, permits studying both ferromagnetic and antiferromagnetic specimens, and can, in principle, detect short-range magnetic or for temperatures above the Curie or Néel temperature. In the first measurements of this type on the antiferromagnet KMnF3, an abrupt loss of short-range order at a transition temperature considerably above the bulk Néel temperature of the material was observed. More recent theoretical diffraction calculations have pointed out several ways in which SPPD should permit deriving unique information on short-range spin-order structures at and near the surfaces of magnetic materials. New experimental results have also been obtained for the antiferromagnet MnO. This paper will discuss these new developments, will review the advantages and disadvantages of SPPD, and also will consider some interesting future directions of investigation.

  11. X-Ray photoelectron diffraction and photoelectron holography as methods for investigating the local atomic structure of the surface of solids

    NASA Astrophysics Data System (ADS)

    Kuznetsov, M. V.; Ogorodnikov, I. I.; Vorokh, A. S.

    2014-01-01

    The state-of-the-art theory and experimental applications of X-ray photoelectron diffraction (XPD) and photoelectron holography (PH) are discussed. These methods are rapidly progressing and serve to examine the surface atomic structure of solids, including nanostructures formed on surfaces during adsorption of gases, epitaxial film growth, etc. The depth of analysis by these methods is several nanometres, which makes it possible to characterize the positions of atoms localized both on and beneath the surface. A remarkable feature of the XPD and PH methods is their sensitivity to the type of examined atoms and, in the case of high energy resolution, to the particular chemical form of the element under study. The data on experimental applications of XPD and PH to studies of various surface structures are analyzed and generalized. The bibliography includes 121 references.

  12. Normal emission photoelectron diffraction: a new technique for determining surface structure

    SciTech Connect

    Kevan, S.D.

    1980-05-01

    One technique, photoelectron diffraction (PhD) is characterized. It has some promise in surmounting some of the problems of LEED. In PhD, the differential (angle-resolved) photoemission cross-section of a core level localized on an adsorbate atom is measured as a function of some final state parameter. The photoemission final state consists of two components, one of which propagates directly to the detector and another which scatters off the surface and then propagates to the detector. These are added coherently, and interference between the two manifests itself as cross-section oscillations which are sensitive to the local structure around the absorbing atom. We have shown that PhD deals effectively with two- and probably also three-dimensionally disordered systems. Its non-damaging and localized, atom-specific nature gives PhD a good deal of promise in dealing with molecular overlayer systems. It is concluded that while PhD will never replace LEED, it may provide useful, complementary and possibly also more accurate surface structural information.

  13. Sensitivity of photoelectron diffraction to conformational changes of adsorbed molecules: Tetra-tert-butyl-azobenzene/Au(111)

    PubMed Central

    Schuler, A.; Greif, M.; Seitsonen, A. P.; Mette, G.; Castiglioni, L.; Osterwalder, J.; Hengsberger, M.

    2017-01-01

    Electron diffraction is a standard tool to investigate the atomic structure of surfaces, interfaces, and adsorbate systems. In particular, photoelectron diffraction is a promising candidate for real-time studies of structural dynamics combining the ultimate time resolution of optical pulses and the high scattering cross-sections for electrons. In view of future time-resolved experiments from molecular layers, we studied the sensitivity of photoelectron diffraction to conformational changes of only a small fraction of molecules in a monolayer adsorbed on a metallic substrate. 3,3′,5,5′-tetra-tert-butyl-azobenzene served as test case. This molecule can be switched between two isomers, trans and cis, by absorption of ultraviolet light. X-ray photoelectron diffraction patterns were recorded from tetra-tert-butyl-azobenzene/Au(111) in thermal equilibrium at room temperature and compared to patterns taken in the photostationary state obtained by exposing the surface to radiation from a high-intensity helium discharge lamp. Difference patterns were simulated by means of multiple-scattering calculations, which allowed us to determine the fraction of molecules that underwent isomerization. PMID:28217715

  14. Sensitivity of photoelectron diffraction to conformational changes of adsorbed molecules: Tetra-tert-butyl-azobenzene/Au(111).

    PubMed

    Schuler, A; Greif, M; Seitsonen, A P; Mette, G; Castiglioni, L; Osterwalder, J; Hengsberger, M

    2017-01-01

    Electron diffraction is a standard tool to investigate the atomic structure of surfaces, interfaces, and adsorbate systems. In particular, photoelectron diffraction is a promising candidate for real-time studies of structural dynamics combining the ultimate time resolution of optical pulses and the high scattering cross-sections for electrons. In view of future time-resolved experiments from molecular layers, we studied the sensitivity of photoelectron diffraction to conformational changes of only a small fraction of molecules in a monolayer adsorbed on a metallic substrate. 3,3',5,5'-tetra-tert-butyl-azobenzene served as test case. This molecule can be switched between two isomers, trans and cis, by absorption of ultraviolet light. X-ray photoelectron diffraction patterns were recorded from tetra-tert-butyl-azobenzene/Au(111) in thermal equilibrium at room temperature and compared to patterns taken in the photostationary state obtained by exposing the surface to radiation from a high-intensity helium discharge lamp. Difference patterns were simulated by means of multiple-scattering calculations, which allowed us to determine the fraction of molecules that underwent isomerization.

  15. Fourier transform photoelectron diffraction and its application to molecular orbitals and surface structure

    SciTech Connect

    Zhou, Xin

    1998-11-30

    Photoemission intensities from the molecular orbitals of c(2x2)CO/Pt(111) over a wide photon energy range were measured and analyzed by the same methods developed for structural studies using core levels. The 4{sigma} orbital center of gravity is found to be concentrated between the C and O atoms, while that of the 5{sigma} orbital lies between the C atom and the Pt surface. The C 1s photoelectron diffraction was used to determine the adsorption geometry. The earlier ambiguity that multiple scattering is needed to correctly model a {chi} curve while single scattering is sufficient for understanding major peaks in the ARPEFS-FTS is clarified by studying the clean Ni(111) surface. In the normal emission case, several different combinations of scattering events have similar path length differences (PLDs), and can either cancel each other or enhance the corresponding FT peak. In the off-normal case the degeneracy is greatly reduced due to the lower degree of symmetry. In normal emission AR PEFS, up to third order multiple scattering is needed to describe fully both the {chi} curve and its FT spectrum. To improve the spectral resolution in the ARPEFS-FT analysis, several new spectral analysis methods are introduced. With both autocorrelation autoregression (ACAR) and autocorrelation eigenvector (ACE), we can produce a reliable power spectrum by following the order-closing procedure. The best spectra are usually obtained when the autocorrelation sequence is computed with lags up to half the data range. A simple way of determining surface adsorption sites is proposed as follows: First use a single scattering cluster for possible adsorption sites to construct the geometrical PLDs from the strong backscattering events; then compare these PLDs with those obtained from the ARPEFS-FT analysis of the experimental data. After the preferred adsorption site is determined, fine tune the interlayer distances according to the positional R-factor.

  16. Cluster-Based Methods of Modeling Photoelectron Diffraction Data: Comparisons and Applications to Adsorption and Epitaxial Growth

    NASA Astrophysics Data System (ADS)

    van Hove, M. A.; Chen, Y.; Wu, H.; Chassé, A.; García de Abajo, F. J.; Shirley, D. A.; Hussain, Z.; Kaduwela, A. P.; Ynzunza, R. X.; Fadley, C. S.

    1998-03-01

    Photoelectron diffraction (PD) is a widely used probe of surface structures, and its most accurate modeling requires multiple scattering theory. A cluster method has been applied to PD simulations previously, using the accurate separable Green's function approach of Rehr and Albers in 2nd order. The more recent implementation has improved the approximation up to 4th order and computation speed by over an order of magnitude, in particular by allowing quick rotations of incident and exit angles in any combination. These approaches will be described and compared to calculations from more exact, albeit slower, cluster methods. Their application to experimental data recently obtained at the Advanced Light Source will also be presented, such as for photoelectron diffraction data obtained from clean and adsorbate-covered metal surfaces - W(110) and O/W(110) - and from a clean compound surface - MnO - using both scanned-angle and scanned-energy data. Work supported by DOE.

  17. Spin-polarized photoelectron diffraction and valence-band photoemission from MnO(001)

    NASA Astrophysics Data System (ADS)

    Hermsmeier, B.; Osterwalder, J.; Friedman, D. J.; Sinkovic, B.; Tran, T.; Fadley, C. S.

    1990-12-01

    Spin-polarized photoelectron diffraction (SPPD) has previously been proposed as a technique for studying short-range magnetic order in magnetic materials, and the first experimental study of this kind was performed on the ionic antiferromagnetic KMnF3 [B. Sinkovic, B. Hermsmeier, and C. S. Fadley, Phys. Rev. Lett. 55, 1227 (1985)]. We present here a much more detailed study of SPPD for the antiferromagnetic transition-metal oxide MnO with a (001) surface orientation. The Mn 3s and Mn 3p multiplets have been studied using both low-energy (192.6 eV) and high-energy (1486.7 eV) x-ray excitation and the intensity ratios I(5S(↑))/I(7S(↓)) and I(5P(↑))/I(7P(↓)) have been measured as a function of both direction and temperature. Data obtained with the lower excitation energy and resulting in kinetic energies of 50-100 eV show an abrupt change or step in both the I(5S(↑))/I(7S(↓)) and I(5P(↑))/I(7P(↓)) intensity ratios at ~=530+/-20 K or ~=4.5 times the Néel temperature TN. This change is interpreted to be a new type of short-range-order transition occurring at what is denoted TSR. Also, these same quintet or septet intensity ratios show a weak peak at TN, suggesting for the first time that SPPD has sensitivity to long-range magnetic order. Data obtained for the I(5S(↑))/I(7S(↓)) intensity ratio with the higher excitation energy show no such effects, a result consistent with the much weaker exchange scattering expected at such energies. Additional x-ray photoelectron spectroscopy spectra and azimuthal scans of Mn and O core-level intensities are considered and these establish that (i) the sample surface had good stoichiometry and was very clean and well ordered, (ii) the SPPD effects observed at TSR are not due to any surface structural change, and (iii) a single-scattering cluster (SSC) theoretical model is at least a qualitatively reasonable starting point for describing such effects. We also compare experimental results for the magnitudes of these

  18. High-energy non-Franck-Condon vibrational excitation of CH4 by intramolecular photoelectron diffraction

    NASA Astrophysics Data System (ADS)

    Argenti, L.; Plésiat, E.; Kukk, E.; Ueda, K.; Decleva, P.; Martín, F.

    2012-11-01

    Distinct oscillations in vibrationally resolved cross section ratios for the photoionization of CH4 from the C 1s orbital at photon energies as high as 1keV are predicted. The oscillations are attributed to the different relative vibrational excitation due to the scattering of the photoelectron by the peripheral hydrogen atoms. The latter effect is also responsible for the well known EXAFS oscillations in the integrated photoelectron spectrum. The calculations are performed with an ab-initio DFT method [1], as well as with a single-particle semi-analytical model, which incorporate both the effect of the nuclear recoil and of the Coulomb corrections.

  19. Photoelectron diffraction study of the Si -rich 3C-SiC(001)-(3×2) structure

    NASA Astrophysics Data System (ADS)

    Tejeda, A.; Dunham, D.; García de Abajo, F. J.; Denlinger, J. D.; Rotenberg, E.; Michel, E. G.; Soukiassian, P.

    2004-07-01

    The structure of the Si -rich 3C-SiC(001)-(3×2) surface reconstruction is determined using soft x-ray photoelectron diffraction. Photoelectrons are detected along a full hemispherical sector for different photon energies. A comparison between the experimental data and multiple scattering calculations of the competing models favors a modified version of the two-adlayer asymmetric dimer model. An R -factor analysis has been employed to refine this model. We determine the interlayer spacings of the last six atomic layers and find a corrugation of (0.25±0.10) Å for the atoms in the outermost dimer. Atoms in the second layer dimerize as well, forming rows of long and short dimers.

  20. The (3 × 2) β -SiC(001) surface reconstruction investigated by photoelectron diffraction in the backscattering regime

    NASA Astrophysics Data System (ADS)

    Michel, E. G.; Dunham, D.; Tejeda, A.; Soukiassian, P.; Rotenberg, E.; Denlinger, J. D.

    2006-03-01

    The atomic positions of the (3× 2) reconstruction of the cubic polytype of SiC(001) are determined by using photoelectron diffraction in the backscattering regime. The comparison of multiple scattering spherical wave calculations with experimental data favours a modified version of the two-adlayer asymmetric dimer model. The atomic positions in the reconstructed layers are obtained from an R-factor refinement analysis. Atoms in the outermost layer form asymmetric dimers with a corrugation of (0.25 ± 0.10) Å. The second layer is also dimerized and originates rows of long and short dimers.

  1. Variable growth modes of CaF2 on Si(111) determined by x-ray photoelectron diffraction

    NASA Astrophysics Data System (ADS)

    Denlinger, J. D.; Rotenberg, Eli; Hessinger, Uwe; Leskovar, M.; Olmstead, Marjorie A.

    1993-04-01

    Chemical discrimination of bulk and interface Ca 2p x-ray photoelectron diffraction modulations is used to identify three growth regimes during the initial stages of CaF2 epitaxy on Si(111). Low flux, high temperature conditions produce island growth atop a nonwetting, chemically reacted Ca-F interface layer. Changing the growth kinetics by increasing the flux produces more laminar growth. Lowering the substrate temperature produces a more stoichiometric CaF2 interface layer that results in immediate wetting and laminar growth.

  2. Time-and-state resolved spectroscopy, diffraction, and circular dichroism in core photoelectron emission from clean and oxygen-covered W(110)

    SciTech Connect

    Ynzunza, Ramon Xavier

    1998-10-01

    Several aspects of core-level photoelectron emission fi-om solid surfaces as excited by high-brightness variable-polarization synchrotrons radiation have been studied with a new beamline and experimental station at the Advanced Light Source in Berkeley. These include: resolution of different chemical states and site types via high-resolution photoelectron spectroscopy (PS), the use of state-resolved photoelectron difllaction (PD) to determine local atomic geometries, and the observation and analysis of circular dichroism (CD) effects in photoelectron diffraction. These methods have been applied to clean and oxygen-exposed surfaces of W(110). Full-solid-angle photoelectron diffraction from clean W(110) was measured, with the surface and bulk atoms being clearly resolved.

  3. Non-destructive assessment of the polarity of GaN nanowire ensembles using low-energy electron diffraction and x-ray photoelectron diffraction

    SciTech Connect

    Romanyuk, O. Jiříček, P.; Bartoš, I.; Fernández-Garrido, S.; Geelhaar, L.; Brandt, O.; Paskova, T.

    2015-01-12

    We investigate GaN nanowire ensembles spontaneously formed in plasma-assisted molecular beam epitaxy by non-destructive low-energy electron diffraction (LEED) and x-ray photoelectron diffraction (XPD). We show that GaN nanowire ensembles prepared on AlN-buffered 6H-SiC(0001{sup ¯}) substrates with well-defined N polarity exhibit similar LEED intensity-voltage curves and angular distribution of photo-emitted electrons as N-polar free-standing GaN layers. Therefore, as in the case of GaN layers, LEED and XPD are found to be suitable techniques to assess the polarity of GaN nanowire ensembles on a macroscopic scale. The analysis of GaN nanowire ensembles prepared on bare Si(111) allows us to conclude that, on this non-polar substrate, the majority of nanowires is also N-polar.

  4. Structure of the c(2x2) Mn/Ni(001) surface alloy by quantitative photoelectron diffraction

    SciTech Connect

    Banerjee, S.; Denlinger, J.; Chen, X.

    1997-04-01

    Surface alloys are two-dimensional metallic systems that can have structures that are unique to the surface, and have no counterpart in the bulk binary phase diagram. A very unusual structure was reported for the Mn-Ni system, based on a quantitative LEED structure determination, which showed that the Mn atoms were displaced out of the surface by a substantial amount. This displacement was attributed to a large magnetic moment on the Mn atoms. The structure of the Mn-Ni surface alloy was proposed to be based on a bulk termination model. Magnetic measurements on the Mn-Ni surface alloys, however, showed conclusively that the magnetic structure of these surface alloys is completely different from the bulk alloy analogs. For example, bulk MnNi is an antiferromagnet, whereas the surface alloy is ferromagnetic. This suggests that the proposed structure based on bulk termination, may not be correct. X-ray Photoelectron Diffraction (XPD) techniques were used to investigate this structure, using both a comparison to multiple scattering calculations and photoelectron holography. In this article the authors present some of the results from the quantitative analysis of individual diffraction patterns by comparison to theory.

  5. Convergence and reliability of the Rehr-Albers formalism in multiple-scattering calculations of photoelectron diffraction

    NASA Astrophysics Data System (ADS)

    Chen, Y.; García de Abajo, F. J.; Chassé, A.; Ynzunza, R. X.; Kaduwela, A. P.; van Hove, M. A.; Fadley, C. S.

    1998-11-01

    The Rehr-Albers (RA) separable Green's-function formalism, which is based on an expansion series, has been successful in speeding up multiple-scattering cluster calculations for photoelectron diffraction simulations, particularly in its second-order version. The performance of this formalism is explored here in terms of computational speed, convergence over orders of multiple scattering, over orders of approximation, and over cluster size, by comparison with exact cluster-based formalisms. It is found that the second-order RA approximation [characterized by (6×6) scattering matrices] is adequate for many situations, particularly if the initial state from which photoemission occurs is of s or p type. For the most general and quantitative applications, higher-order versions of RA may become necessary for d initial states [third-order, i.e., (10×10) matrices] and f initial states [fourth-order, i.e., (15×15) matrices]. However, the required RA order decreases as an electron wave proceeds along a multiple-scattering path, and this can be exploited, together with the selective and automated cutoff of weakly contributing matrix elements and paths, to yield computer time savings of at least an order of magnitude with no significant loss of accuracy. Cluster sizes of up to approximately 100 atoms should be sufficient for most problems that require about 5% accuracy in diffracted intensities. Excellent sensitivity to structure is seen in comparisons of second-order theory with variable geometry to exact theory as a fictitious ``experiment.'' Our implementation of the Rehr-Albers formalism thus represents a versatile, quantitative, and efficient method for the accurate simulation of photoelectron diffraction.

  6. Photoelectron and Auger electron diffraction studies of a sulfur-terminated GaAs(001)-(2×6) surface

    NASA Astrophysics Data System (ADS)

    Shimoda, M.; Tsukamoto, S.; Koguchi, N.

    1998-01-01

    Core-level X-ray photoelectron diffraction (XPD) and Auger electron diffraction (AED) have been applied to investigate the sulfur-terminated GaAs(001)-(2×6) surface. No forward scattering peaks were found in the XPD pattern of S 2s emission, indicating that adsorbed S atoms form a single layer on the GaAs substrate. In accordance with the zincblende structure of GaAs, the AED patterns of Ga L 3M 45M 45 and As L 3M 45M 45 emission almost coincide with each other, if one of the emissions is rotated by 90° around the [001] direction. This fact suggests that the diffraction patterns mainly reflect the structure of the bulk GaAs crystal. In order to investigate the surface structure, AED patterns in large polar angles were analyzed with single scattering cluster (SSC) calculations. The best result was obtained with a model cluster where the S-S bond length was set at 0.28 nm, 30% shorter than the corresponding length of the ideal (1×1) structure, and the adsorption height was set at 0.12-0.13 nm, 10% shorter than the ideal interlayer distance of GaAs(001) planes. These values are in good agreement with the results of STM measurements. A modulation of the inter-dimer distance was also found, suggesting the existence of missing dimers.

  7. Elastic and inelastic contributions to the XPS photoelectron diffraction patterns of Ni(100) and NiO(100)

    NASA Astrophysics Data System (ADS)

    Steiner, P.; Straub, Th.; Reinert, Fr.; Zimmermann, R.; Hüfner, S.

    1993-07-01

    XPS spectra of Ni(100) and NiO(100) single crystals, measured as a function of the polar angle in the [100]-[010] emission plane, are successfully decomposed into their elastic (intrinsic spectrum) and inelastic contributions using the background subtraction procedure as proposed by Tougaard et al. [Phys. Rev. B 25 (1981) 4452; Surf. Interface Anal. 11 (1988) 453; J. Electron Spectrosc. Relat. Phenom. 52 (1990) 243], with an electron energy loss function deduced from experimental electron energy loss spectra. The inelastic background correction factor shows a diffraction pattern which anticorrelates nearly linearly to the photoelectron diffraction pattern of the intrinsic spectrum, that is its maxima and minima coincide with the minima and maxima of the latter. This behaviour can be described by a simple model, based on heuristic arguments on inelastic and elastic losses and "defocusing" due to multiple scattering along densely packed rows of atoms in the lattice. The consequence of different background subtraction procedures on the shape of the XPS diffraction pattern and for the quantification of XPS data is discussed.

  8. Fraunhofer-like diffracted lateral photoelectron momentum distributions of H2+ in charge-resonance-enhanced ionization in strong laser fields

    NASA Astrophysics Data System (ADS)

    Xin, Lin; Qin, Han-Cheng; Wu, Wan-Yang; He, Feng

    2015-12-01

    For H2+ at the critical internuclear distance where the charge-resonance-enhanced ionization is most prominent, the lateral photoelectron momentum distribution presents the Fraunhofer-like diffraction pattern: a central disk surrounded by one or more rings. We study this phenomenon by simulating the time-dependent Schrödinger equation and unveil the mechanism: the stretched molecule constructs an interatomic Coulomb potential, which works as a circular aperture and diffracts the electron when it travels between two nuclei. This distinct lateral photoelectron momentum distribution offers another perspective to look into molecular structures.

  9. Structural analysis of Pt(1 1 1)c(√3 × 5)rect. CO using photoelectron diffraction

    NASA Astrophysics Data System (ADS)

    Nisbet, G.; Lamont, C. L. A.; Polcik, M.; Terborg, R.; Sayago, D. I.; Hoeft, J. T.; Kittel, M.; Toomes, R. L.; Woodruff, D. P.

    2007-03-01

    Core level shift scanned-energy mode photoelectron diffraction using the two distinct components of the C 1s emission has been used to determine the structure of the Pt(1 1 1)c(√3 × 5)rect.-CO phase formed by 0.6 ML of adsorbed CO. The results confirm earlier assignments of these components to CO in atop and bridging sites, further confirm that the best structural model involves a 2:1 occupation ratio of these two sites, and provides quantitative structural parameter values. In particular the Pt-C chemisorption bondlengths for the atop and bridging sites are, respectively, 1.86 ± 0.02 Å and 2.02 ± 0.04 Å. These values are closely similar to those found in the 0.5 ML coverage c(4 × 2) phase, involving an atop:bridge occupation ratio of 1:1, obtained in earlier quantitative low energy electron diffraction studies. The results also indicate a clear tilt of the molecular axis of atop CO species in this compression phase, consistent with the finding of an earlier electron-stimulated desorption ion angular distribution investigation.

  10. Adsorption, X-ray Diffraction, Photoelectron, and Atomic Emission Spectroscopy Benchmark Studies for the Eighth Industrial Fluid Properties Simulation Challenge.

    PubMed

    Ross, Richard B; Aeschliman, David B; Ahmad, Riaz; Brennan, John K; Brostrom, Myles L; Frankel, Kevin A; Moore, Jonathan D; Moore, Joshua D; Mountain, Raymond D; Poirier, Derrick M; Thommes, Matthias; Shen, Vincent K; Schultz, Nathan E; Siderius, Daniel W; Smith, Kenneth D

    2016-02-01

    The primary goal of the eighth industrial fluid properties simulation challenge was to test the ability of molecular simulation methods to predict the adsorption of organic adsorbates in activated carbon materials. The challenge focused on the adsorption of perfluorohexane in the activated carbon standard BAM-P109 (Panne and Thünemann 2010). Entrants were challenged to predict the adsorption of perfluorohexane in the activated carbon at a temperature of 273 K and at relative pressures of 0.1, 0.3, and 0.6. The relative pressure (P/Po) is defined as that relative to the bulk saturation pressure predicted by the fluid model at a given temperature (273 K in this case). The predictions were judged by comparison to a set of experimentally determined values, which are published here for the first time and were not disclosed to the entrants prior to the challenge. Benchmark experimental studies, described herein, were also carried out and provided to entrants in order to aid in the development of new force fields and simulation methods to be employed in the challenge. These studies included argon, carbon dioxide, and water adsorption in the BAM-P109 activated carbon as well as X-ray diffraction, X-ray microtomography, photoelectron spectroscopy, and atomic emission spectroscopy studies of BAM-P109. Several concurrent studies were carried out for the BAM-P108 activated carbon (Panne and Thünemann 2010). These are included in the current manuscript for comparison.

  11. Adsorption, X-ray Diffraction, Photoelectron, and Atomic Emission Spectroscopy Benchmark Studies for the Eighth Industrial Fluid Properties Simulation Challenge*+

    PubMed Central

    Ross, Richard B.; Aeschliman, David B.; Ahmad, Riaz; Brennan, John K.; Brostrom, Myles L.; Frankel, Kevin A.; Moore, Jonathan D.; Moore, Joshua D.; Mountain, Raymond D.; Poirier, Derrick M.; Thommes, Matthias; Shen, Vincent K.; Schultz, Nathan E.; Siderius, Daniel W.; Smith, Kenneth D.

    2016-01-01

    The primary goal of the eighth industrial fluid properties simulation challenge was to test the ability of molecular simulation methods to predict the adsorption of organic adsorbates in activated carbon materials. The challenge focused on the adsorption of perfluorohexane in the activated carbon standard BAM-P109 (Panne and Thünemann 2010). Entrants were challenged to predict the adsorption of perfluorohexane in the activated carbon at a temperature of 273 K and at relative pressures of 0.1, 0.3, and 0.6. The relative pressure (P/Po) is defined as that relative to the bulk saturation pressure predicted by the fluid model at a given temperature (273 K in this case). The predictions were judged by comparison to a set of experimentally determined values, which are published here for the first time and were not disclosed to the entrants prior to the challenge. Benchmark experimental studies, described herein, were also carried out and provided to entrants in order to aid in the development of new force fields and simulation methods to be employed in the challenge. These studies included argon, carbon dioxide, and water adsorption in the BAM-P109 activated carbon as well as X-ray diffraction, X-ray microtomography, photoelectron spectroscopy, and atomic emission spectroscopy studies of BAM-P109. Several concurrent studies were carried out for the BAM-P108 activated carbon (Panne and Thünemann 2010). These are included in the current manuscript for comparison. PMID:27840543

  12. The local adsorption structure of benzene on Si(001)-(2 × 1): a photoelectron diffraction investigation

    NASA Astrophysics Data System (ADS)

    Nisbet, G.; Lamont, C. L. A.; Polcik, M.; Terborg, R.; Sayago, D. I.; Kittel, M.; Hoeft, J. T.; Toomes, R. L.; Woodruff, D. P.

    2008-07-01

    Scanned-energy mode C 1s photoelectron diffraction has been used to investigate the local adsorption geometry of benzene on Si(001) at saturation coverage and room temperature. The results show that two different local bonding geometries coexist, namely the 'standard butterfly' (SB) and 'tilted bridge' (TB) forms, with a composition of 58 ± 29% of the SB species. Detailed structural parameter values are presented for both species including Si-C bond lengths. On the basis of published measurements of the rate of conversion of the SB to the TB form on this surface, we estimate that the timescale of our experiment is sufficient for achieving equilibrium, and in this case our results indicate that the difference in the Gibbs free energy of adsorption, ΔG(TB)-ΔG(SB), is in the range -0.023 to +0.049 eV. We suggest, however, that the relative concentration of the two species may also be influenced by a combination of steric effects influencing the kinetics, and a sensitivity of the adsorption energies of the adsorbed SB and TB forms to the nature of the surrounding benzene molecules.

  13. Growth kinetics of CaF2/Si(111) heteroepitaxy: An x-ray photoelectron diffraction study

    NASA Astrophysics Data System (ADS)

    Denlinger, J. D.; Rotenberg, Eli; Hessinger, U.; Leskovar, M.; Olmstead, Marjorie A.

    1995-02-01

    Kinetic variations of the initial stages of CaF2 growth on Si(111) by molecular-beam epitaxy are studied with the in situ combination of x-ray photoelectron spectroscopy and diffraction. After the formation of a chemically reacted interface layer, the morphology of the subsequent bulk layers is found to be dependent on the substrate temperature and incident flux rate, as well as the initial interface structure. For substrate temperatures above ~600 °C, subsequent layers do not easily wet the interface layer, and a transition is observed from a three-dimensional island formation at low flux to a laminar growth following the coalescence of bilayer islands at higher flux. At lower substrate temperatures (~450 °C), a different stoichiometry and structure of the interface layer leads to laminar growth at all fluxes, but with a different bulk nucleation behavior. Crystalline heteroepitaxy is not observed when growth initiates at room temperature, but homoepitaxy does proceed at room temperature if the first few layers are deposited at a high temperature. The different growth regimes are discussed in terms of a kinetic model separating step and terrace nucleation where, contrary to homoepitaxy, step nucleation leads to islanded growth.

  14. Angle Resolved Photoelectron and Auger Electron Diffraction as a Structural Probe for Surfaces, Interfaces, and Epitaxial Films.

    NASA Astrophysics Data System (ADS)

    Li, Hong

    The recently developed techniques of angle-resolved photoelectron and Auger electron diffraction (ARXPD/AED) have shown promise in identifying the structures of epitaxial films. This is due to the realization that electrons scattered by other atoms are enhanced along the forward direction. In this dissertation research, we have further investigated the capabilities of the ARXPD/AED technique. First, the complete polar angle distribution of the Auger electron intensity from Cu(001) was measured from the (100) to the (110) azimuth. The presentation of the ARAED in the form of a contour map clearly shows the relationship of the constructive and destructive interference of electron scattering to the crystallographic index of the crystal. Secondly, the angular distributions of electron emissions with initial states of 3p, 3d, 4d, and the Auger emission with electron kinetic energies ranging from 348 eV to 1477 eV were measured for single crystal Ag(001). The results show that all of these electron emissions have similar electron forward scattering enhancements along the directions of nearest and next nearest neighbour atoms in the crystal. The forward scattering enhancements do not shift as the electron kinectic energy changes. The ARXPD/AED combined with low energy electron diffraction (LEED) has been demonstrated to be a very powerful technique in probing both the long range order and the short range order of the epitaxial films. The epitaxial films studied include Co on Cu(001), Fe on Ag(001), Co on Ag(001), and Co on an ultra-thin film of Fe(001), which was epitaxially grown on Ag(001). We find that up to 20 ML thickness of high quality metastable fcc Co can be stabilized on Cu(001) at room temperature. We have directly verified that the Fe on Ag(001) is bcc. The Co on Ag(001) is neither bcc nor fcc for coverages of less than 3 ML. Thick films of Co on Ag(001) are disordered, of which a very small portion has a local structure of bcc. The bcc Co phases has been

  15. The structure of formate on TiO{sub 2}(110) by scanned-energy and scanned-angle photoelectron diffraction

    SciTech Connect

    Thevuthasan, S.; Kim, Y.J.; Herman, G.S.

    1997-04-01

    There is a considerable interest in understanding the interaction of small organic molecules with oxide surfaces. The chemistry of formate interactions with TiO{sub 2}(110) has been investigated by several groups, but there is little information on the structure of the adsorbate/surface complex. Recently the authors combined high-energy x-ray photoelectron diffraction (XPD) measurements at PNNL with low-energy scanned-angle and scanned-energy photoelectron diffraction measurements at the ALS to investigate the structure of the formate ion on TiO{sub 2}(110) in detail. The high-energy XPD results reveal that formate binds through the oxygens in a bidentate fashion to Ti cation rows along the [001] direction with an O-C-O bond angle of about 126{degrees}. Low-energy photoelectron diffraction data, which is briefly described below, was used to identify the specific bonding geometry, including the bond length between the Ti cation and the oxygen in the formate.

  16. Polarity of semipolar wurtzite crystals: X-ray photoelectron diffraction from GaN(101⁻1) and GaN(202⁻1) surfaces

    SciTech Connect

    Romanyuk, O. Jiříček, P.; Bartoš, I.; Paskova, T.

    2014-09-14

    Polarity of semipolar GaN(101⁻1) (101⁻1⁻) and GaN(202⁻1) (202⁻1⁻) surfaces was determined with X-ray photoelectron diffraction (XPD) using a standard MgKα source. The photoelectron emission from N 1s core level measured in the a-plane of the crystals shows significant differences for the two crystal orientations within the polar angle range of 80–100° from the (0001) normal. It was demonstrated that XPD polar plots recorded in the a-plane are similar for each polarity of the GaN(101⁻1) and GaN(202⁻1) crystals if referred to (0001) crystal axes. For polarity determinations of all important GaN(h0h⁻l) semipolar surfaces, the above given polar angle range is suitable.

  17. Following the molecular motion of near-resonant excited CO on Pt(111): A simulated x-ray photoelectron diffraction study based on molecular dynamics calculations

    PubMed Central

    Greif, Michael; Nagy, Tibor; Soloviov, Maksym; Castiglioni, Luca; Hengsberger, Matthias; Meuwly, Markus; Osterwalder, Jürg

    2015-01-01

    A THz-pump and x-ray-probe experiment is simulated where x-ray photoelectron diffraction (XPD) patterns record the coherent vibrational motion of carbon monoxide molecules adsorbed on a Pt(111) surface. Using molecular dynamics simulations, the excitation of frustrated wagging-type motion of the CO molecules by a few-cycle pulse of 2 THz radiation is calculated. From the atomic coordinates, the time-resolved XPD patterns of the C 1s core level photoelectrons are generated. Due to the direct structural information in these data provided by the forward scattering maximum along the carbon-oxygen direction, the sequence of these patterns represents the equivalent of a molecular movie. PMID:26798798

  18. X-ray photoelectron spectroscopy and diffraction investigation of a metal-oxide-semiconductor heterostructure: Pt/Gd2O3/Si(111)

    NASA Astrophysics Data System (ADS)

    Ferrah, D.; El Kazzi, M.; Niu, G.; Botella, C.; Penuelas, J.; Robach, Y.; Louahadj, L.; Bachelet, R.; Largeau, L.; Saint-Girons, G.; Liu, Q.; Vilquin, B.; Grenet, G.

    2015-04-01

    Platinum thin films deposited by physical vapor deposition (PVD) on Gd2O3/Si(111) templates are investigated by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), and X-ray photoelectron diffraction (XPD). Both XRD and XPD give clear evidence that Gd2O3 grows (111)-oriented and single-domain on Si(111) with mirror epitaxial relationship viz., [1bar10] Gd2O3(111)//[11bar0] Si(111). On Gd2O3/Si(111), Pt is partially crystallized with (111) orientation. There are two epitaxial domains and a slightly visible (111) fiber texture. The in-plane relationships of these Pt(111) domains with Gd2O3(111) are a direct one: [11bar0] Pt(111)//[11bar0] Gd2O3(111) and a mirror one: [1bar10] Pt(111)//[11bar0] Gd2O3(111). XPS reveals that Pt4f exhibits a metallic behavior even for small amounts of Pt but very small chemical shifts suggest that Pt environment is different at the interface with Gd2O3. These XPS chemical shifts have been correlated with features in XPD azimuth curves, which could be related with the existence of hexagonal α-PtO2(0001)layer.

  19. Atomic-scale structure of the fivefold surface of an AlPdMn quasicrystal: A quantitative x-ray photoelectron diffraction analysis

    NASA Astrophysics Data System (ADS)

    Zheng, Jin-Cheng; Huan, C. H.; Wee, A. T.; van Hove, M. A.; Fadley, C. S.; Shi, F. J.; Rotenberg, E.; Barman, S. R.; Paggel, J. J.; Horn, K.; Ebert, Ph.; Urban, K.

    2004-04-01

    The atomic-scale structure of the fivefold symmetric surface of an AlPdMn quasicrystal is investigated quantitatively by comparing x-ray photoelectron diffraction simulations to experiment. The observed fivefold symmetry of the diffraction patterns indicates that the surface is quasicrystalline with no hint of a reconstruction from the bulk structure. In analyzing the experimental data, many possible bulk terminations have been tested. Those few that fit best to the data have in common that they contain an Al-rich surface layer followed by a dense mixed Al/Pd/Mn layer. These best terminations, while not identical to each other, are suggested to form terraces coexisting on a real surface. Structural relaxations of the quasicrystal surface are also analyzed: mixing several best-fit terminations gives average best-fit interlayer spacing changes of Δd12=-0.057 Å and Δd24=+0.159 Å. These results are in good agreement with a prior structure determination by low-energy electron diffraction on a sample that was prepared in a different manner.

  20. Near Edge X-Ray Absorption and X-Ray Photoelectron Diffraction Studies of the Structural Environment of Ge-Si Systems

    NASA Astrophysics Data System (ADS)

    Castrucci, P.; Gunnella, R.; Pinto, N.; Bernardini, R.; de Crescenzi, M.; Sacchi, M.

    Near edge X-ray absorption spectroscopy (XAS), X-ray photoelectron diffraction (XPD) and Auger electron diffraction (AED) are powerful techniques for the qualitative study of the structural and electronic properties of several systems. The recent development of a multiple scattering approach to simulating experimental spectra opened a friendly way to the study of structural environments of solids and surfaces. This article reviews recent X-ray absorption experiments using synchrotron radiation which were performed at Ge L edges and core level electron diffraction measurements obtained using a traditional X-ray source from Ge core levels for ultrathin Ge films deposited on silicon substrates. Thermodynamics and surface reconstruction have been found to play a crucial role in the first stages of Ge growth on Si(001) and Si(111) surfaces. Both techniques show the occurrence of intermixing processes even for room-temperature-grown Ge/Si(001) samples and give a straightforward measurement of the overlayer tetragonal distortion. The effects of Sb as a surfactant on the Ge/Si(001) interface have also been investigated. In this case, evidence of layer-by-layer growth of the fully strained Ge overlayer with a reduced intermixing is obtained when one monolayer of Sb is predeposited on the surface.

  1. High-resolution electron-energy-loss spectroscopy and photoelectron-diffraction studies of the geometric structure of adsorbates on single-crystal metal surfaces

    SciTech Connect

    Rosenblatt, D.H.

    1982-11-01

    Two techniques which have made important contributions to the understanding of surface phenomena are high resolution electron energy loss spectroscopy (EELS) and photoelectron diffraction (PD). EELS is capable of directly measuring the vibrational modes of clean and adsorbate covered metal surfaces. In this work, the design, construction, and performance of a new EELS spectrometer are described. These results are discussed in terms of possible structures of the O-Cu(001) system. Recommendations for improvements in this EELS spectrometer and guidelines for future spectrometers are given. PD experiments provide accurate quantitative information about the geometry of atoms and molecules adsorbed on metal surfaces. The technique has advantages when used to study disordered overlayers, molecular overlayers, multiple site systems, and adsorbates which are weak electron scatterers. Four experiments were carried out which exploit these advantages.

  2. Adsorption site of c(2×2) O on Ni(0001): An off-normal-direction energy-dependent photoelectron-diffraction study

    NASA Astrophysics Data System (ADS)

    Mei, W. N.; Tong, S. Y.

    1986-01-01

    We have used the technique of energy-dependent photoelectron diffraction (EDPD) to study the pseudo-bridge-site model proposed by Demuth et al. for the adsorption of c(2×2) O on Ni(001). Calculated EDPD curves at the normal exit direction for the pseudo-bridge site, averaged over four domains, were compared with those for the fourfold hollow site. We found no significant differences in the EDPD curves for the two different structural models. However, the calculated EDPD curves at off-normal directions, such as those along the [011] direction, or along the O-Ni bond directions, were qualitatively different for the two sites. We therefore conclude that off-normal-direction EDPD curves, when compared with measured data, can effectively determine the lateral coordinates of the oxygen overlayer on Ni(001).

  3. Tracking the amorphous to epitaxial transition in RF-sputtered cubic BFO-STO heterojunctions by means of X-ray photoelectron diffraction

    NASA Astrophysics Data System (ADS)

    Giampietri, Alessio; Drera, Giovanni; Píš, Igor; Magnano, Elena; Sangaletti, Luigi

    2016-09-01

    The epitaxial growth of cubic BiFeO3 ultrathin films on SrTiO3 (001) substrates by off-axis RF sputtering is demonstrated, suitable to X-ray spectroscopies interface investigation. X-ray photoelectron diffraction is used as a tool to probe the long-range crystal order and to track the transition from amorphous to epitaxial growth as a function of deposition parameters. Further spectroscopic measurements, in particular, X-ray linear dichroism on the Fe L 3 , 2 edge, confirm the heteroepitaxial growth of BiFeO3 and clearly indicate a 3+ valence state for the iron cation. Finally, XPS is used to reconstruct the band alignment diagram, which results in a staggered configuration with a remarkable energy shift of the SrTiO3 band edges which can ultimately favor the n-type doping of SrTiO3.

  4. The effect of Sr and Bi on the Si(100) surface oxidation - Auger electron spectroscopy, low energy electron diffraction, and X-ray photoelectron spectroscopy study

    NASA Technical Reports Server (NTRS)

    Fan, W. C.; Mesarwi, A.; Ignatiev, A.

    1990-01-01

    The effect of Sr and Bi on the oxidation of the Si(100) surface has been studied by Auger electron spectroscopy, low electron diffraction, and X-ray photoelectron spectroscopy. A dramatic enhancement, by a factor of 10, of the Si oxidation has been observed for Si(100) with a Sr overlayer. The SR-enhanced Si oxidation has been studied as a function of O2 exposure and Sr coverage. In contrast to the oxidation promotion of Sr on Si, it has been also observed that a Bi overlayer on Si(100) reduced Si oxidation significantly. Sr adsorption on the Si(100) with a Bi overlayer enhances Si oxidation only at Sr coverage of greater than 0.3 ML.

  5. Structure determination of molecules in an alignment laser field by femtosecond photoelectron diffraction using an X-ray free-electron laser

    PubMed Central

    Minemoto, Shinichirou; Teramoto, Takahiro; Akagi, Hiroshi; Fujikawa, Takashi; Majima, Takuya; Nakajima, Kyo; Niki, Kaori; Owada, Shigeki; Sakai, Hirofumi; Togashi, Tadashi; Tono, Kensuke; Tsuru, Shota; Wada, Ken; Yabashi, Makina; Yoshida, Shintaro; Yagishita, Akira

    2016-01-01

    We have successfully determined the internuclear distance of I2 molecules in an alignment laser field by applying our molecular structure determination methodology to an I 2p X-ray photoelectron diffraction profile observed with femtosecond X-ray free electron laser pulses. Using this methodology, we have found that the internuclear distance of the sample I2 molecules in an alignment Nd:YAG laser field of 6 × 1011 W/cm2 is elongated by from 0.18 to 0.30 Å “in average” relatively to the equilibrium internuclear distance of 2.666 Å. Thus, the present experiment constitutes a critical step towards the goal of femtosecond imaging of chemical reactions and opens a new direction for the study of ultrafast chemical reaction in the gas phase. PMID:27934891

  6. X-ray photoelectron-diffraction study of intermixing and morphology at the Ge/Si(001) and Ge/Sb/Si(001) interface

    NASA Astrophysics Data System (ADS)

    Gunnella, R.; Castrucci, P.; Pinto, N.; Davoli, I.; Sébilleau, D.; de Crescenzi, M.

    1996-09-01

    We used the XPD (x-ray photoelectron diffraction) and AED (Auger electron diffraction) from Ge core levels to probe the crystalline structure of 3 and 6 ML of Ge epitaxially grown by molecular-beam epitaxy on the Si(001) surface. In order to check the film tetragonal distortion and the pseudomorphic growth morphology, we used two different temperatures of the substrate during the deposition: room temperature and 400 °C. Evidence for an interfacial intermixing has been found by means of the observation of the angular behavior of the intensity of the emitted electrons. We also investigated the effects of Sb as a surfactant on such an interface. In this case indications of a laminar growth of strained Ge overlayer with reduced intermixing is obtained when 1 ML of Sb is predeposited on the substrate. Furthermore making use of a multiple-scattering approach to reproduce the experimental XPD patterns, a higher amount of accessible information on the morphology of the interface, beyond the determination of the strain content, is obtained.

  7. Atomic scale structure of the 5-fold surface of an AlPdMn quasicrystal: A quantitative X-Ray photoelectron diffraction analysis

    SciTech Connect

    Zheng, Jin-Cheng; Huan, C.H.A.; Wee, A.T.S.; Van Hove, M.A.; Fadley, C.S.; Shi, F.J.; Rotenberg, E.; Barman, S.R.; Paggel, J.J.; Horn, K.; Ebert, Ph.; Urban, K.

    2004-02-11

    The atomic scale structure of the 5-fold symmetric surface of an AlPdMn quasicrystal is investigated quantitatively by comparing x-ray photoelectron diffraction (XPD) simulations to experiment. The observed 5-fold symmetry of the diffraction patterns indicates that the surface is quasicrystalline with no hint of a reconstruction from the bulk structure. In analyzing the experimental data, many possible bulk terminations have been tested. Those few that fit best to the data have in common that they contain an Al-rich surface layer followed by a dense mixed Al/Pd/Mn layer. These best terminations, while not identical to each other, are suggested to form terraces coexisting on a real surface. Structural relaxations of the quasicrystal surface are also analyzed: mixing several best-fit terminations gives average best-fit interlayer spacing changes of Dd12 = -0.057 Angstrom, Dd24 = +0.159 Angstrom. These results are in good agreement with a prior structure determination by LEED on a sample that was prepared in a different manner.

  8. Epitaxial BaTiO3(100) films on Pt(100): a low-energy electron diffraction, scanning tunneling microscopy, and x-ray photoelectron spectroscopy study.

    PubMed

    Förster, Stefan; Huth, Michael; Schindler, Karl-Michael; Widdra, Wolf

    2011-09-14

    The growth of epitaxial ultrathin BaTiO(3) films on a Pt(100) substrate has been studied by scanning tunneling microscopy (STM), low-energy electron diffraction (LEED), and x-ray photoelectron spectroscopy (XPS). The films have been prepared by radio-frequency-assisted magnetron sputter deposition at room temperature and develop a long-range order upon annealing at 900 K in O(2). By adjusting the Ar and O(2) partial pressures of the sputter gas, the stoichiometry was tuned to match that of a BaTiO(3)(100) single crystal as determined by XPS. STM reveals the growth of continuous BaTiO(3) films with unit cell high islands on top. With LEED already for monolayer thicknesses, the formation of a BaTiO(3)(100)-(1 × 1) structure has been observed. Films of 2-3 unit cell thickness show a brilliant (1 × 1) LEED pattern for which an extended set of LEED I-V data has been acquired. At temperatures above 1050 K the BaTiO(3) thin film starts to decay by formation of vacancy islands. In addition (4 × 4) and (3 × 3) surface reconstructions develop upon prolonged heating.

  9. Structural origin of Si-2p core-level shifts from Si(100)-c[4x2] surface: A spectral x-ray photoelectron diffraction study

    SciTech Connect

    Chen, X.; Tonner, B.P.; Denlinger, J.

    1997-04-01

    The authors have performed angle-resolved x-ray photoelectron diffraction (XPD) from a Si(100)-c(4x2) surface to study the structural origin of Si-2p core-level shifts. In the experiment, the highly resolved surface Si-2p core-level spectra were measured as a fine grid of hemisphere and photon energies, using the SpectroMicroscopy Facility {open_quotes}ultraESCA{close_quotes} instrument. By carefully decomposing the spectra into several surface peaks, the authors are able to obtain surface-atom resolved XPD patterns. Using a multiple scattering analysis, they derived a detailed atomic model for the Si(100)-c(4x2) surface. In this model, the asymmetric dimers were found tilted by 11.5 plus/minus 2.0 degrees with bond length of 2.32 plus/minus 0.05{angstrom}. By matching model XPD patterns to experiment, the authors can identify which atoms in the reconstructed surface are responsible for specific photoemission lines in the 2p spectrum.

  10. Oxidation of UO 2 fuel pellets in air at 503 and 543 K studied using X-ray photoelectron spectroscopy and X-ray diffraction

    NASA Astrophysics Data System (ADS)

    Tempest, P. A.; Tucker, P. M.; Tyler, J. W.

    1988-02-01

    An understanding of the low temperature oxidation behaviour of UO 2 pellets in air is important in the unlikely event of gas ingress to a fuel can during handling or storage. The main parameter of concern is the production time of U 3O 8 particulate as a function of temperature. Factors which affect the UO2 → U3O8 transformation have been investigated by sequentially oxidising UO 2 fuel pellets in air at 503 and 543 K and monitoring the growth of U 3O and U 3O 7 using X-ray photoelectron spectroscopy, X-ray diffraction and scanning electron microscopy. Initially oxidation proceeded at a linear rate by the inward diffusion of oxygen to form a complete layer of substoichiometric U 3O 7. This phase was tetragonal with a {c}/{a} ratio of 1.015, significantly less than the value of 1.03 measured on UO 2 powder when oxidised under identical conditions. This difference and the preferred orientation exhibited by surface grains were caused by growth stresses induced in the pellet surface. Both intergranular and transgranular cracking occurred and became nucleation sites for the growth of U 3O 8. The linear oxidation period associated with U 3O 7 growth was much shorter at 543 than at 503 K and U 3O 8 nucleated earlier. Spallation and the production of particulate were only observed during the formation of U 3O 8 when a 30% increase in volume arose from the U3O7 → U3O8 phase change.

  11. Site-Specific Infrared Probes of Proteins

    PubMed Central

    Ma, Jianqiang; Pazos, Ileana M.; Zhang, Wenkai; Culik, Robert M.; Gai, Feng

    2015-01-01

    Infrared spectroscopy has played an instrumental role in studying a wide variety of biological questions. However, in many cases it is impossible or difficult to rely on the intrinsic vibrational modes of biological molecules of interest, such as proteins, to reveal structural and/or environmental information in a site-specific manner. To overcome this limitation, many recent efforts have been dedicated to the development and application of various extrinsic vibrational probes that can be incorporated into biological molecules and used to site-specifically interrogate their structural and/or environmental properties. In this Review, we highlight some recent advancements of this rapidly growing research area. PMID:25580624

  12. DOE site-specific threat assessment

    SciTech Connect

    West, D.J.; Al-Ayat, R.A.; Judd, B.R.

    1985-07-12

    A facility manager faced with the challenges of protecting a nuclear facility against potential threats must consider the likelihood and consequences of such threats, know the capabilities of the facility safeguards and security systems, and make informed decisions about the cost-effectivness of safeguards and security upgrades. To help meet these challenges, the San Francisco Operations Office of the Department of Energy, in conjunction with the Lawrence Livermore Laboratory, has developed a site-specific threat assessment approach and a quantitative model to improve the quality and consistency of site-specific threat assessment and resultant security upgrade decisions at sensitive Department of Energy facilities. 5 figs.

  13. Photoelectron Spectra

    ERIC Educational Resources Information Center

    Bock, Hans; Mollere, Phillip D.

    1974-01-01

    Presents an experimental approach to teaching molecular orbital models. Suggests utilizing photoelectron spectroscopy and molecular orbital theory as complementary approaches to teaching the qualitative concepts basic to molecular orbital theory. (SLH)

  14. Site-Specific Rules for Risk Assessment.

    ERIC Educational Resources Information Center

    Tucker, William; And Others

    1994-01-01

    This article examines the development of regulatory guidance upon which the technology of risk assessment has matured into a decision-making method of choice. It examines in particular the role of site-specific risk assessment at Superfund sites. (LZ)

  15. Nanoparticles for Site Specific Genome Editing

    NASA Astrophysics Data System (ADS)

    McNeer, Nicole Ali

    Triplex-forming peptide nucleic acids (PNAs) can be used to coordinate the recombination of short 50-60 by "donor DNA" fragments into genomic DNA, resulting in site-specific correction of genetic mutations or the introduction of advantageous genetic modifications. Site-specific gene editing in hematopoietic stem and progenitor cells (HSPCs) could result in treatment or cure of inherited disorders of the blood such as beta-thalassemia. Gene editing in HSPCs and differentiated T cells could help combat HIV/AIDs by modifying receptors, such as CCR5, necessary for R5-tropic HIV entry. However, translation of genome modification technologies to clinical practice is limited by challenges in intracellular delivery, especially in difficult-to-transfect hematolymphoid cells. In vivo gene editing could also provide novel treatment for systemic monogenic disorders such as cystic fibrosis, an autosomal recessive disorder caused by mutations in the cystic fibrosis transmembrane receptor. Here, we have engineered biodegradable nanoparticles to deliver oligonucleotides for site-specific genome editing of disease-relevant genes in human cells, with high efficiency, low toxicity, and editing of clinically relevant cell types. We designed nanoparticles to edit the human beta-globin and CCR5 genes in hematopoietic cells. We show that poly(lactic-co-glycolic acid) (PLGA) nanoparticles can delivery PNA and donor DNA for site-specific gene modification in human hematopoietic cells in vitro and in vivo in NOD-scid IL2rgammanull mice. Nanoparticles delivered by tail vein localized to hematopoietic compartments in the spleen and bone marrow of humanized mice, resulting in modification of the beta-globin and CCR5 genes. Modification frequencies ranged from 0.005 to 20% of cells depending on the organ and cell type, without detectable toxicity. This project developed highly versatile methods for delivery of therapeutics to hematolymphoid cells and hematopoietic stem cells, and will help to

  16. Site-specific non-LTR retrotransposons.

    PubMed

    Fujiwara, Haruhiko

    2015-04-01

    Although most of non-long terminal repeat (non-LTR) retrotransposons are incorporated in the host genome almost randomly, some non-LTR retrotransposons are incorporated into specific sequences within a target site. On the basis of structural and phylogenetic features, non-LTR retrotransposons are classified into two large groups, restriction enzyme-like endonuclease (RLE)-encoding elements and apurinic/apyrimidinic endonuclease (APE)-encoding elements. All clades of RLE-encoding non-LTR retrotransposons include site-specific elements. However, only two of more than 20 APE-encoding clades, Tx1 and R1, contain site-specific non-LTR elements. Site-specific non-LTR retrotransposons usually target within multi-copy RNA genes, such as rRNA gene (rDNA) clusters, or repetitive genomic sequences, such as telomeric repeats; this behavior may be a symbiotic strategy to reduce the damage to the host genome. Site- and sequence-specificity are variable even among closely related non-LTR elements and appeared to have changed during evolution. In the APE-encoding elements, the primary determinant of the sequence- specific integration is APE itself, which nicks one strand of the target DNA during the initiation of target primed reverse transcription (TPRT). However, other factors, such as interaction between mRNA and the target DNA, and access to the target region in the nuclei also affect the sequence-specificity. In contrast, in the RLE-encoding elements, DNA-binding motifs appear to affect their sequence-specificity, rather than the RLE domain itself. Highly specific integration properties of these site-specific non-LTR elements make them ideal alternative tools for sequence-specific gene delivery, particularly for therapeutic purposes in human diseases.

  17. Site-Specific PEGylation of Therapeutic Proteins

    PubMed Central

    Dozier, Jonathan K.; Distefano, Mark D.

    2015-01-01

    The use of proteins as therapeutics has a long history and is becoming ever more common in modern medicine. While the number of protein-based drugs is growing every year, significant problems still remain with their use. Among these problems are rapid degradation and excretion from patients, thus requiring frequent dosing, which in turn increases the chances for an immunological response as well as increasing the cost of therapy. One of the main strategies to alleviate these problems is to link a polyethylene glycol (PEG) group to the protein of interest. This process, called PEGylation, has grown dramatically in recent years resulting in several approved drugs. Installing a single PEG chain at a defined site in a protein is challenging. Recently, there is has been considerable research into various methods for the site-specific PEGylation of proteins. This review seeks to summarize that work and provide background and context for how site-specific PEGylation is performed. After introducing the topic of site-specific PEGylation, recent developments using chemical methods are described. That is followed by a more extensive discussion of bioorthogonal reactions and enzymatic labeling. PMID:26516849

  18. Site-Specific PEGylation of Therapeutic Proteins.

    PubMed

    Dozier, Jonathan K; Distefano, Mark D

    2015-10-28

    The use of proteins as therapeutics has a long history and is becoming ever more common in modern medicine. While the number of protein-based drugs is growing every year, significant problems still remain with their use. Among these problems are rapid degradation and excretion from patients, thus requiring frequent dosing, which in turn increases the chances for an immunological response as well as increasing the cost of therapy. One of the main strategies to alleviate these problems is to link a polyethylene glycol (PEG) group to the protein of interest. This process, called PEGylation, has grown dramatically in recent years resulting in several approved drugs. Installing a single PEG chain at a defined site in a protein is challenging. Recently, there is has been considerable research into various methods for the site-specific PEGylation of proteins. This review seeks to summarize that work and provide background and context for how site-specific PEGylation is performed. After introducing the topic of site-specific PEGylation, recent developments using chemical methods are described. That is followed by a more extensive discussion of bioorthogonal reactions and enzymatic labeling.

  19. Savannah River Site's Site Specific Plan

    SciTech Connect

    Not Available

    1991-08-01

    This Site Specific Plan (SSP) has been prepared by the Savannah River Site (SRS) in order to show the Environmental Restoration and Waste Management activities that were identified during the preparation of the Department of Energy-Headquarters (DOE-HQ) Environmental Restoration and Waste Management Five-Year Plan (FYP) for FY 1992--1996. The SSP has been prepared in accordance with guidance received from DOE-HQ. DOE-SR is accountable to DOE-HQ for the implementation of this plan. The purpose of the SSP is to develop a baseline for policy, budget, and schedules for the DOE Environmental Restoration and Waste Management activities. The plan explains accomplishments since the Fiscal Year (FY) 1990 plan, demonstrates how present and future activities are prioritized, identifies currently funded activities and activities that are planned to be funded in the upcoming fiscal year, and describes future activities that SRS is considering.

  20. Site-Specific Carbon Isotopes in Organics

    NASA Astrophysics Data System (ADS)

    Piasecki, A.; Eiler, J. M.

    2012-12-01

    Natural organic molecules exhibit a wide range of internal site-specific isotope variation (i.e., molecules with same isotopic substitution type but different site). Such variations are generally unconstrained by bulk isotopic measurements. If known, site-specific variations might constrain temperatures of equilibrium, mechanisms of formation or consumption reactions, and possibly other details. For example, lipids can exhibit carbon isotope differences of up to 30‰ between adjacent carbon sites as a result of fractionations arising during decarboxylation of pyruvate and other steps in lipid biosynthesis(1). We present a method for site-specific carbon isotope analysis of propane, based on high-resolution, multi-collector gas source mass spectrometry, using a novel prototype instrument - the Thermo MAT 253 Ultra. This machine has an inlet system and electron bombardment ion source resembling those in conventional stable isotope gas source mass spectrometers, and the energy filter, magnet, and detector array resembling those in multi-collector ICPMS and TIMS. The detector array has 7 detector positions, 6 of which are movable, and each of which can collect ions with either a faraday cup (read through amplifiers ranging from 107-1012 ohms) or an SEM. High mass resolving power (up to 27,000, MRP = M/dM definition) is achieved through a narrow entrance slit, adjustable from 250 to 5 μm. Such resolution can cleanly separate isobaric interferences between isotopologues of organic molecules having the same cardinal mass (e.g., 13CH3 and 12CH2D). We use this technology to analyze the isotopologues and fragments of propane, and use such data to solve for the site-specific carbon isotope fractionation. By measuring isotopologues of both the one-carbon (13CH3) and the two-carbon (13C12CH4) fragment ion, we can solve for both bulk δ13C and the difference in δ13C between the terminal and central carbon position. We tested this method by analyzing mixtures between natural

  1. Examining site-specific GPCR phosphorylation.

    PubMed

    Butcher, Adrian J; Tobin, Andrew B; Kong, Kok Choi

    2011-01-01

    Phosphorylation of G protein-coupled receptors (GPCRs) is one of the most prominent post-translation modifications mediated by agonist stimulation. This process has been shown to result not only in receptor desensitisation but also, via the recruitment of arrestin adaptor proteins, to promote receptor coupling to numerous signalling pathways. Furthermore, there is now a growing body of evidence suggesting that GPCRs may employ phosphorylation as a mechanism to regulate their cell-type-specific signalling, hence generating tissue-specific functions. These advances have resulted partly from improved methods used in the determination of phospho-acceptor sites on GPCRs and improved analysis of the consequences of phosphorylation. This chapter aims to describe the methods used in our laboratory for the investigation of site-specific phosphorylation of the M₃-muscarinic receptor. These methods could easily be applied in the study of other receptors.

  2. The Connectivity Between Site-Specific Life Cycle Impact Assessment and Site-Specific Weighting

    EPA Science Inventory

    The goal of many LCIAs is to come to a single score with all of the impacts from a wide variety of impact assessments weighted to form this single score. My past experiences with developing site-specific impact assessment methodologies and how this can change the valuation porti...

  3. Statistical and Economic Techniques for Site-specific Nematode Management.

    PubMed

    Liu, Zheng; Griffin, Terry; Kirkpatrick, Terrence L

    2014-03-01

    Recent advances in precision agriculture technologies and spatial statistics allow realistic, site-specific estimation of nematode damage to field crops and provide a platform for the site-specific delivery of nematicides within individual fields. This paper reviews the spatial statistical techniques that model correlations among neighboring observations and develop a spatial economic analysis to determine the potential of site-specific nematicide application. The spatial econometric methodology applied in the context of site-specific crop yield response contributes to closing the gap between data analysis and realistic site-specific nematicide recommendations and helps to provide a practical method of site-specifically controlling nematodes.

  4. RESRAD. Site-Specific Residual Radioactivity

    SciTech Connect

    Yu, C.

    1989-06-01

    RESRAD is designed to derive site-specific guidelines for allowable residual concentrations of radionuclides in soil. A guideline is defined as a radionuclide concentration or a level of radiation or radioactivity that is acceptable if a site is to be used without radiological restrictions. Guidelines are expressed as (1) concentrations of residual radionuclides in soil, (2) concentrations of airborne radon decay products, (3) levels of external gamma radiation, (4) levels of radioactivity from surface contamination, and (5) concentrations of residual radionuclides in air and water. Soil is defined as unconsolidated earth material, including rubble and debris that may be present. The controlling principles of all guidelines are (1) the annual radiation dose received by a member of the critical population group from the residual radioactive material - predicted by a realistic but reasonably conservative analysis and averaged over a 50 year period - should not exceed 100 mrem/yr, and (2) doses should be kept as low as reasonably achievable. All significant exposure pathways for the critical population group are considered in deriving soil guidelines. These pathways include direct exposure to external radiation from the contaminated soil material; internal radiation from inhalation of airborne radionuclides; and internal radiation from ingestion of plant foods grown in the contaminated soil, meat and milk from livestock fed with contaminated fodder and water, drinking water from a contaminated well, and fish from a contaminated pond.

  5. Site-Specific, Climate-Friendly Farming

    NASA Astrophysics Data System (ADS)

    Brown, D. J.; Brooks, E. S.; Eitel, J.; Huggins, D. R.; Painter, K.; Rupp, R.; Smith, J. L.; Stockle, C.; Vierling, L. A.

    2011-12-01

    Of the four most important atmospheric greenhouse gasses (GHG) enriched through human activities, only nitrous oxide (N2O) emissions are due primarily to agriculture. However, reductions in the application of synthetic N fertilizers could have significant negative consequences for a growing world population given the crucial role that these fertilizers have played in cereal yield increases since WWII. Increasing N use efficiency (NUE) through precision management of agricultural N in space and time will therefore play a central role in the reduction of agricultural N2O emissions. Precision N management requires a greater understanding of the spatio-temporal variability of factors supporting N management decisions such as crop yield, water and N availability, utilization and losses. We present an overview of a large, collaborative, multi-disciplinary project designed to improve our basic understanding of nitrogen (N), carbon (C) and water (H2O) spatio-temporal dynamics for wheat-based cropping systems on complex landscapes, and develop management tools to optimize water- and nitrogen-use efficiency for these systems and landscapes. Major components of this project include: (a) cropping systems experiments addressing nitrogen application rate and seeding density for different landscape positions; (b) GHG flux experiments and monitoring; (c) soil microbial genetics and stable isotope analyses to elucidate biochemical pathways for N2O production; (d) proximal soil sensing for construction of detailed soil maps; (e) LiDAR and optical remote sensing for crop growth monitoring; (f) hydrologic experiments, monitoring, and modeling; (g) refining the CropSyst simulation model to estimate biophysical processes and GHG emissions under a variety of management and climatic scenarios; and (h) linking farm-scale enterprise budgets to simulation modeling in order to provide growers with economically viable site-specific climate-friendly farming guidance.

  6. X-ray diffraction and photoelectron spectroscopy studies of MoO 2 as catalyst for the partial oxidation of isooctane

    NASA Astrophysics Data System (ADS)

    Marin-Flores, Oscar; Scudiero, L.; Ha, Su

    2009-08-01

    X-ray diffraction (XRD), X-ray photoemission (XPS) as well as ultraviolet photoemission (UPS) spectroscopy experiments on MoO 2 powders were carried out to examine the bulk, the core level energies, and the electronic structure of MoO 2 samples that were employed as catalysts for the partial oxidation of isooctane. Five fresh 0.5-g MoO 2 samples were exposed for 0, 0.5, 9, 20, and 43 h to identical reforming environments and their spent samples were analyzed using the techniques mentioned above. Our results indicate the rapid appearance of an intermediate Mo phase with a binding energy of 228.5 eV and whose concentration progressively increases with time. The oxidation state for this new phase was graphically estimated to approximately +2.6 and assigned to the compound Mo 2O 3, which forms on the catalyst surface as a result of its exposure to the reforming environment. The electronic structure probed by UPS reveals two bands, one at 1.62 eV and another at 0.55 eV below the Fermi level, that decrease with the increasing time on stream. These results correlate very well with the drop in the catalytic performance of MoO 2 for the partial oxidation of isooctane and with the decline in the concentration of dioxide (Mo 4+) detected not only on the catalyst surface, but also in the bulk structure, as confirmed by our XRD analysis.

  7. Photoelectron Microscopy

    NASA Astrophysics Data System (ADS)

    King, Paul Lawrence

    1992-01-01

    This thesis describes the theory and first operations of a novel synchrotron-based imaging system allowing photoemission spectroscopy (XPS or ESCA) to be performed at lateral resolutions better than 10 microns. Originally developed in David Turner's group at Oxford, the MicroESCA^ {rm TM} relies on the diverging magnetic field from a 7 Tesla superconducting solenoid to project photoemitted electrons from a sample to an imaging detector located 1.5 meters away. The diverging magnetic field converts off-axis momentum to forward momentum and electrons form a magnified image at the detector while moving nearly parallel to one another. Because of this "parallelization", a planar gridded retarding field analyzer achieves excellent energy resolution with only minor impact on image quality. The thesis begins with an overview of the various techniques by which high lateral resolution photoelectron spectroscopy can be achieved. This is followed by a theoretical treatment of magnetic projection leading to predictions of lateral and energy resolution. Chapter 3 documents resolution tests and known deviations from ideality. Image forming capabilities and energy resolution of the retarding field analyzer are demonstrated at near-theoretical limits. Practical limitations of the microscope are recognized in the form of poor signal to noise ratios of core level images which originate from a combination of the narrow dynamic range of the imaging detector and the large backgrounds inherent in retarding field spectroscopy of solids. Chapter 4 describes an interactive image processing and interpretation scheme that relies on scatter plots and principal component analysis to reduce the dimensionality of retarding field image sets and improve image signal to noise. This procedure is generally applicable to all imaging spectroscopies and an example from SEM-based energy dispersive spectroscopy (EDS) is included. In a final results section, variations in the surface Fermi levels on cleaved

  8. SITE-SPECIFIC CHARACTERIZATION OF SOIL RADON POTENTIALS

    EPA Science Inventory

    The report presents a theoretical basis for measuring site-specific radon potentials. However, the empirical measurements suggest that the precision of such measurements is marginal, leaving an uncertainty of about a factor of 2 in site-specific estimates. Although this may be us...

  9. Double clicking for site-specific coupling of multiple enzymes.

    PubMed

    Lim, Sung In; Cho, Jinhwan; Kwon, Inchan

    2015-09-14

    A method to site-specifically couple multiple enzymes is reported. The approach is based on the site-specific incorporation of a clickable non-natural amino acid into enzymes and two compatible click reactions. The multi-enzyme reaction system exhibited enhanced catalytic efficiency over the respective free enzymes.

  10. Enhancing adoption of site-specific variable rate sprinkler systems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    More than twenty years of private and public research on site-specific variable-rate sprinkler irrigation (SS-VRI) has resulted in very limited commercial adoption of the technology. Documented and proven water conservation strategies using site-specific irrigation are quite limited, and its cost-ef...

  11. Site specific protein labeling by enzymatic posttranslational modification.

    PubMed

    Sunbul, Murat; Yin, Jun

    2009-09-07

    Site specific protein labeling plays a key role in elucidating the function of the proteins at the molecular level by revealing their locations in the cell, their interaction networks with other cellular components and the dynamic mechanisms of their bio-generation, trafficking and degradation in response to regulatory signals in a biological system. Site specific protein labeling is, in essence, artificial modification of proteins with new chemical entities at the posttranslational stage. Based on the analogy between protein labeling and protein posttranslational modification, enzymatic tools have been developed for site specific and efficient labeling of target proteins with chemical probes of diverse structures and functionalities. This perspective surveys a number of protein labeling methods based on the application of protein posttranslational modification enzymes.

  12. Utilization of Site-Specific Recombination in Biopharmaceutical Production.

    PubMed

    Ahmadi, Maryam; Damavandi, Narges; Akbari Eidgahi, Mohammad Reza; Davami, Fatemeh

    2016-01-01

    Mammalian expression systems, due to their capacity in post-translational modification, are preferred systems for biopharmaceutical protein production. Several recombinant protein systems have been introduced to the market, most of which are under clinical development. In spite of significant improvements such as cell line engineering, introducing novel expression methods, gene silencing and process development, expression level is unpredictable and unstable because of the random location of integration in the genome. Site-specific recombination techniques are capable of producing stable and high producer clonal cells; therefore, they are gaining more importance in the biopharmaceutical production. Site-specific recombination methods increase the recombinant protein production by specifically inserting a vector at a locus with specific expression trait. The present review focused on the latest developments in site-specific recombination techniques, their specific features and comparisons.

  13. Utilization of Site-Specific Recombination in Biopharmaceutical Production

    PubMed Central

    Ahmadi, Maryam; Damavandi, Narges; Akbari, Mohammad Reza; Davami, Fatemeh

    2016-01-01

    Mammalian expression systems, due to their capacity in post-translational modification, are preferred systems for biopharmaceutical protein production. Several recombinant protein systems have been introduced to the market, most of which are under clinical development. In spite of significant improvements such as cell line engineering, introducing novel expression methods, gene silencing and process development, expression level is unpredictable and unstable because of the random location of integration in the genome. Site-specific recombination techniques are capable of producing stable and high producer clonal cells; therefore, they are gaining more importance in the biopharmaceutical production. Site-specific recombination methods increase the recombinant protein production by specifically inserting a vector at a locus with specific expression trait. The present review focused on the latest developments in site-specific recombination techniques, their specific features and comparisons. PMID:26602035

  14. Evaluation of potential water conservation using site-specific irrigation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    With the advent of site-specific variable-rate irrigation (VRI) systems, irrigation can be spatially managed within sub-field-sized zones. Spatial irrigation management can optimize spatial water use efficiency and may conserve water. Spatial VRI systems are currently being managed by consultants ...

  15. Site-Specific Dance: Promoting Social Awareness in Choreography

    ERIC Educational Resources Information Center

    MacBean, Arianne

    2004-01-01

    Site-specific dance, which is often defined as dance that occurs outside of the conventional theater space, challenges choreographers to look at, listen to, feel, and think about the space in which the dance is performed. It also asks audiences to be active participants in the performance experience. The dances have to be informed by the space and…

  16. Uncertainty Analysis with Site Specific Groundwater Models: Experiences and Observations

    SciTech Connect

    Brewer, K.

    2003-07-15

    Groundwater flow and transport predictions are a major component of remedial action evaluations for contaminated groundwater at the Savannah River Site. Because all groundwater modeling results are subject to uncertainty from various causes; quantification of the level of uncertainty in the modeling predictions is beneficial to project decision makers. Complex site-specific models present formidable challenges for implementing an uncertainty analysis.

  17. Invasive Weed Management Is Site-Specific Weed Management.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Site-specific weed management in crops and invasive weed management in natural lands and rangelands appear to be unrelated research areas but there are many connections in the research problems, approaches and solutions. An obvious link is technology. The technology of precision agriculture - GPS, ...

  18. Wireless Site-specific Irrigation - The Future of Intelligent Agriculture

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A wireless site-specific irrigation system was developed with a distributed wireless sensor network. The system allows growers to remotely access field conditions and an irrigation operation at the home or office via wireless radio communication, directing individual sprinklers on how much water to ...

  19. Delineating site-specific management units with proximal sensors

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Conventional farming uniformly manages fields with no consideration for spatial variability. This causes reduced productivity, misuse of finite resources (e.g., water and fertilizer), and detriment impacts on the environment. Site-specific management units (SSMUs) have been proposed as a means of ...

  20. Site-specific nicking within the adenovirus inverted terminal repetition.

    PubMed Central

    Chow, K C; Pearson, G D

    1984-01-01

    Site-specific nicking occurs on the l-strand, but not on the r-strand, of the adenovirus left inverted terminal repeat. Nicks are presumably introduced into double- or single-stranded DNA by a cellular endonuclease in an ATP-independent reaction. The consensus nick site has the sequence: (sequence in text). Images PMID:6322107

  1. Development of site-specific locking plates for acetabular fractures.

    PubMed

    Xu, Meng; Zhang, Li-Hai; Zhang, Ying-Ze; He, Chun-Qing; Zhang, Li-Cheng; Wang, Yan; Tang, Pei-Fu

    2013-05-01

    Site-specific locking plates have gained popularity for the treatment of fractures. However, the clinical use of a site-specific locking plate for acetabular fractures remains untested due to production limits. To design a universal site-specific locking plate for acetabular fractures, the 3-dimensional (3D) photographic records of 171 pelvises were retrospectively studied to generate a universal posterior innominate bone surface. Using 3D photographical processing software, the 3D coordinate system was reset according to bony landmarks and was scaled based on the acetabular diameter to allow a direct comparison between surfaces. The measured surface was separated into measurement units. At each measurement unit, the authors calculated the average z-axis values in all samples and obtained the 3D coordinate values of the point cloud that could be reconstructed into the universal surface. A plate was subsequently designed in 3D photographical processing software, and the orientation and distribution of locking screws was included. To manufacture a plate, the data were entered into Unigraphics NX version 6.0 software (Siemens PLM Software, Co, Ltd, Plano, Texas) and a CNC digital milling machine (FANUC Co, Ltd, Yamanashi, Japan). The resulting locking plate fit excellently with the reduced bone surface intraoperatively. Plate contouring was avoided intraoperatively. Universal 3.5-mm locking screws locked successfully into the plate, and their orientations were consistent with the design. No screw yielded to acetabular penetration. This method of designing a site-specific acetabular locking plate is practical, and the plates are suitable for clinical use. These site-specific locking plates may be an option for the treatment of acetabular fractures, particularly in elderly patients.

  2. Marker-free site-specific gene integration in plants.

    PubMed

    Srivastava, Vibha; Ow, David W

    2004-12-01

    For nearly 15 years, the use of site-specific recombination systems in plants has focused on the deletion or integration of DNA. Each of these applications offers practical solutions to two problems in biotechnology: the presence of unneeded DNA in the transgene locus and variation in the locus structure among independent transgenic lines. Given that each of these separate applications is becoming more practical for commercial use, it is time to consider combining them into an integrated technology. Here we propose a strategy for a "combined step" method that makes use of two site-specific recombination systems: one for integrating the DNA and a second for removing sequences that are not needed after DNA transfer. This strategy is based on published data and exemplifies the use of the Cre-lox, FLP-FRT and R-RS inducible systems.

  3. A general approach to site-specific antibody drug conjugates

    PubMed Central

    Tian, Feng; Lu, Yingchun; Manibusan, Anthony; Sellers, Aaron; Tran, Hon; Sun, Ying; Phuong, Trung; Barnett, Richard; Hehli, Brad; Song, Frank; DeGuzman, Michael J.; Ensari, Semsi; Pinkstaff, Jason K.; Sullivan, Lorraine M.; Biroc, Sandra L.; Cho, Ho; Schultz, Peter G.; DiJoseph, John; Dougher, Maureen; Ma, Dangshe; Dushin, Russell; Leal, Mauricio; Tchistiakova, Lioudmila; Feyfant, Eric; Gerber, Hans-Peter; Sapra, Puja

    2014-01-01

    Using an expanded genetic code, antibodies with site-specifically incorporated nonnative amino acids were produced in stable cell lines derived from a CHO cell line with titers over 1 g/L. Using anti-5T4 and anti-Her2 antibodies as model systems, site-specific antibody drug conjugates (NDCs) were produced, via oxime bond formation between ketones on the side chain of the incorporated nonnative amino acid and hydroxylamine functionalized monomethyl auristatin D with either protease-cleavable or noncleavable linkers. When noncleavable linkers were used, these conjugates were highly stable and displayed improved in vitro efficacy as well as in vivo efficacy and pharmacokinetic stability in rodent models relative to conventional antibody drug conjugates conjugated through either engineered surface-exposed or reduced interchain disulfide bond cysteine residues. The advantages of the oxime-bonded, site-specific NDCs were even more apparent when low–antigen-expressing (2+) target cell lines were used in the comparative studies. NDCs generated with protease-cleavable linkers demonstrated that the site of conjugation had a significant impact on the stability of these rationally designed prodrug linkers. In a single-dose rat toxicology study, a site-specific anti-Her2 NDC was well tolerated at dose levels up to 90 mg/kg. These experiments support the notion that chemically defined antibody conjugates can be synthesized in commercially relevant yields and can lead to antibody drug conjugates with improved properties relative to the heterogeneous conjugates formed by nonspecific chemical modification. PMID:24443552

  4. Site-specific gene modification by PNAs conjugated to psoralen.

    PubMed

    Kim, Ki-Hyun; Nielsen, Peter E; Glazer, Peter M

    2006-01-10

    DNA-binding molecules, including triplex-forming oligonucleotides (TFOs) and peptide nucleic acids (PNAs), can be utilized to introduce site-specific mutations or to promote recombination at selected genomic sites. To further evaluate the utility of PNAs for site-specific gene modification, we tested dimeric bis-PNAs conjugated to psoralen. These PNAs are designed to form a triplex-invasion complex within the supF reporter gene in an episomal shuttle vector and to direct site-specific photoadduct formation by the conjugated psoralen. The psoralen-bis-PNA conjugate was found to direct photoadduct formation to the intended 5'-TpA base step next to the PNA-binding site, and the photoadduct formation efficiency displayed both concentration and UVA irradiation dependence. The effect of PNA-targeted photoadducts in a mammalian system was tested by SV40-based shuttle vector assay. After in vitro binding, we found that photoadducts directed by PNAs conjugated to psoralen-induced mutations at frequencies in the range of 0.46%, 6.5-fold above the background. In a protocol for intracellular gene targeting in the episomal shuttle vector, the psoralen-PNA-induced mutation frequency was 0.13%, 3.5-fold higher than the background. Most of the induced mutations were deletions and single-base-pair substitutions at or adjacent to the targeted PNA-binding and photoadduct-formation sites. When the results are taken together, they demonstrate the ability of bis-PNAs conjugated with psoralen to mediate site-specific gene modification, and they further support the development of PNAs as tools for gene-targeting applications.

  5. Pretargeted PET Imaging Using a Site-Specifically Labeled Immunoconjugate.

    PubMed

    Cook, Brendon E; Adumeau, Pierre; Membreno, Rosemery; Carnazza, Kathryn E; Brand, Christian; Reiner, Thomas; Agnew, Brian J; Lewis, Jason S; Zeglis, Brian M

    2016-08-17

    In recent years, both site-specific bioconjugation techniques and bioorthogonal pretargeting strategies have emerged as exciting technologies with the potential to improve the safety and efficacy of antibody-based nuclear imaging. In the work at hand, we have combined these two approaches to create a pretargeted PET imaging strategy based on the rapid and bioorthogonal inverse electron demand Diels-Alder reaction between a (64)Cu-labeled tetrazine radioligand ((64)Cu-Tz-SarAr) and a site-specifically modified huA33-trans-cyclooctene immunoconjugate ((ss)huA33-PEG12-TCO). A bioconjugation strategy that harnesses enzymatic transformations and strain-promoted azide-alkyne click chemistry was used to site-specifically append PEGylated TCO moieties to the heavy chain glycans of the colorectal cancer-targeting huA33 antibody. Preclinical in vivo validation studies were performed in athymic nude mice bearing A33 antigen-expressing SW1222 human colorectal carcinoma xenografts. To this end, mice were administered (ss)huA33-PEG12-TCO via tail vein injection and-following accumulation intervals of 24 or 48 h-(64)Cu-Tz-SarAr. PET imaging and biodistribution studies reveal that this strategy clearly delineates tumor tissue as early as 1 h post-injection (6.7 ± 1.7%ID/g at 1 h p.i.), producing images with excellent contrast and high tumor-to-background activity concentration ratios (tumor:muscle = 21.5 ± 5.6 at 24 h p.i.). Furthermore, dosimetric calculations illustrate that this pretargeting approach produces only a fraction of the overall effective dose (0.0214 mSv/MBq; 0.079 rem/mCi) of directly labeled radioimmunoconjugates. Ultimately, this method effectively facilitates the high contrast pretargeted PET imaging of colorectal carcinoma using a site-specifically modified immunoconjugate.

  6. Site specific atomic polarizabilities in endohedral fullerenes and carbon onions

    SciTech Connect

    Zope, Rajendra R. Baruah, Tunna; Bhusal, Shusil; Basurto, Luis; Jackson, Koblar

    2015-08-28

    We investigate the polarizability of trimetallic nitride endohedral fullerenes by partitioning the total polarizability into site specific components. This analysis indicates that the polarizability of the endohedral fullerene is essentially due to the outer fullerene cage and has insignificant contribution from the encapsulated unit. Thus, the outer fullerene cages effectively shield the encapsulated clusters and behave like Faraday cages. The polarizability of endohedral fullerenes is slightly smaller than the polarizability of the corresponding bare carbon fullerenes. The application of the site specific polarizabilities to C{sub 60}@C{sub 240} and C{sub 60}@C{sub 180} onions shows that, compared to the polarizability of isolated C{sub 60} fullerene, the encapsulation of the C{sub 60} in C{sub 240} and C{sub 180} fullerenes reduces its polarizability by 75% and 83%, respectively. The differences in the polarizability of C{sub 60} in the two onions is a result of differences in the bonding (intershell electron transfer), fullerene shell relaxations, and intershell separations. The site specific analysis further shows that the outer atoms in a fullerene shell contribute most to the fullerene polarizability.

  7. Site specific atomic polarizabilities in endohedral fullerenes and carbon onions

    NASA Astrophysics Data System (ADS)

    Zope, Rajendra R.; Bhusal, Shusil; Basurto, Luis; Baruah, Tunna; Jackson, Koblar

    2015-08-01

    We investigate the polarizability of trimetallic nitride endohedral fullerenes by partitioning the total polarizability into site specific components. This analysis indicates that the polarizability of the endohedral fullerene is essentially due to the outer fullerene cage and has insignificant contribution from the encapsulated unit. Thus, the outer fullerene cages effectively shield the encapsulated clusters and behave like Faraday cages. The polarizability of endohedral fullerenes is slightly smaller than the polarizability of the corresponding bare carbon fullerenes. The application of the site specific polarizabilities to C60@C240 and C60@C180 onions shows that, compared to the polarizability of isolated C60 fullerene, the encapsulation of the C60 in C240 and C180 fullerenes reduces its polarizability by 75% and 83%, respectively. The differences in the polarizability of C60 in the two onions is a result of differences in the bonding (intershell electron transfer), fullerene shell relaxations, and intershell separations. The site specific analysis further shows that the outer atoms in a fullerene shell contribute most to the fullerene polarizability.

  8. Site-specifically radioiodinated antibody for targeting tumors

    SciTech Connect

    Rea, D.W.; Ultee, M.E.; Belinka, B.A. Jr.; Coughlin, D.J.; Alvarez, V.L. )

    1990-02-01

    Labeling of an antibody site specifically through its carbohydrate regions preserves its antigen-binding activity. Previously site-specific labeling studies have conjugated antibodies with metallic radioisotopes or drugs. We now report site-specific labeling with a new radioiodinated compound, 2-hydroxy-5-iodo-3-methylbenzoyl hydrazide, whose synthesis we described earlier. The compound is reacted with aldehyde groups produced by specific oxidation of the carbohydrate portion of the antibody with sodium m-periodate. Optimized conjugation conditions give good recovery of active antibody containing 10 groups per molecule. The conjugate is stable in solution for at least several weeks at both 4 and -70 degrees C. When injected into nude mice bearing LS174T human cancer xenografts, the conjugate of B72.3 antibody localizes well to tumor tissue, with low uptake by other organs. This biodistribution is similar to that of conjugate prepared by using solid-phase chloramine-T (Iodohead). There are only two significant differences. First, the carbohydrate conjugate is much less susceptible to dehalogenation, and thus shows much less thyroid uptake. Secondly, the biological half-life of the carbohydrate conjugate was about half that of the chloramine-T one. This could be due primarily to lysis of the hydrazine bond through which the antibody is attached to the compound, which would then be excreted rapidly by itself. The new reagent will be especially useful for antibodies which either cannot be labeled by chloramine-T methods, or whose activity is impaired by them.

  9. Site specific atomic polarizabilities in endohedral fullerenes and carbon onions.

    PubMed

    Zope, Rajendra R; Bhusal, Shusil; Basurto, Luis; Baruah, Tunna; Jackson, Koblar

    2015-08-28

    We investigate the polarizability of trimetallic nitride endohedral fullerenes by partitioning the total polarizability into site specific components. This analysis indicates that the polarizability of the endohedral fullerene is essentially due to the outer fullerene cage and has insignificant contribution from the encapsulated unit. Thus, the outer fullerene cages effectively shield the encapsulated clusters and behave like Faraday cages. The polarizability of endohedral fullerenes is slightly smaller than the polarizability of the corresponding bare carbon fullerenes. The application of the site specific polarizabilities to C60@C240 and C60@C180 onions shows that, compared to the polarizability of isolated C60 fullerene, the encapsulation of the C60 in C240 and C180 fullerenes reduces its polarizability by 75% and 83%, respectively. The differences in the polarizability of C60 in the two onions is a result of differences in the bonding (intershell electron transfer), fullerene shell relaxations, and intershell separations. The site specific analysis further shows that the outer atoms in a fullerene shell contribute most to the fullerene polarizability.

  10. Optimization Under Uncertainty of Site-Specific Turbine Configurations

    NASA Astrophysics Data System (ADS)

    Quick, J.; Dykes, K.; Graf, P.; Zahle, F.

    2016-09-01

    Uncertainty affects many aspects of wind energy plant performance and cost. In this study, we explore opportunities for site-specific turbine configuration optimization that accounts for uncertainty in the wind resource. As a demonstration, a simple empirical model for wind plant cost of energy is used in an optimization under uncertainty to examine how different risk appetites affect the optimal selection of a turbine configuration for sites of different wind resource profiles. If there is unusually high uncertainty in the site wind resource, the optimal turbine configuration diverges from the deterministic case and a generally more conservative design is obtained with increasing risk aversion on the part of the designer.

  11. Site-specific labeling of proteins for electron microscopy

    PubMed Central

    Dambacher, Corey M.; Lander, Gabriel C.

    2015-01-01

    Electron microscopy is commonly employed to determine the subunit organization of large macromolecular assemblies. However, the field lacks a robust molecular labeling methodology for unambiguous identification of constituent subunits. We present a strategy that exploits the unique properties of an unnatural amino acid in order to enable site-specific attachment of a single, readily identifiable protein label at any solvent-exposed position on the macromolecular surface. Using this method, we show clear labeling of a subunit within the 19S proteasome lid subcomplex that has not been amenable to labeling by traditional approaches. PMID:26409249

  12. Site Specific Probable Maximum Precipitation Estimates and Professional Judgement

    NASA Astrophysics Data System (ADS)

    Hayes, B. D.; Kao, S. C.; Kanney, J. F.; Quinlan, K. R.; DeNeale, S. T.

    2015-12-01

    State and federal regulatory authorities currently rely upon the US National Weather Service Hydrometeorological Reports (HMRs) to determine probable maximum precipitation (PMP) estimates (i.e., rainfall depths and durations) for estimating flooding hazards for relatively broad regions in the US. PMP estimates for the contributing watersheds upstream of vulnerable facilities are used to estimate riverine flooding hazards while site-specific estimates for small water sheds are appropriate for individual facilities such as nuclear power plants. The HMRs are often criticized due to their limitations on basin size, questionable applicability in regions affected by orographic effects, their lack of consist methods, and generally by their age. HMR-51 for generalized PMP estimates for the United States east of the 105th meridian, was published in 1978 and is sometimes perceived as overly conservative. The US Nuclear Regulatory Commission (NRC), is currently reviewing several flood hazard evaluation reports that rely on site specific PMP estimates that have been commercially developed. As such, NRC has recently investigated key areas of expert judgement via a generic audit and one in-depth site specific review as they relate to identifying and quantifying actual and potential storm moisture sources, determining storm transposition limits, and adjusting available moisture during storm transposition. Though much of the approach reviewed was considered a logical extension of HMRs, two key points of expert judgement stood out for further in-depth review. The first relates primarily to small storms and the use of a heuristic for storm representative dew point adjustment developed for the Electric Power Research Institute by North American Weather Consultants in 1993 in order to harmonize historic storms for which only 12 hour dew point data was available with more recent storms in a single database. The second issue relates to the use of climatological averages for spatially

  13. Optimization Under Uncertainty of Site-Specific Turbine Configurations

    SciTech Connect

    Quick, J.; Dykes, K.; Graf, P.; Zahle, F.

    2016-10-03

    Uncertainty affects many aspects of wind energy plant performance and cost. In this study, we explore opportunities for site-specific turbine configuration optimization that accounts for uncertainty in the wind resource. As a demonstration, a simple empirical model for wind plant cost of energy is used in an optimization under uncertainty to examine how different risk appetites affect the optimal selection of a turbine configuration for sites of different wind resource profiles. Lastly, if there is unusually high uncertainty in the site wind resource, the optimal turbine configuration diverges from the deterministic case and a generally more conservative design is obtained with increasing risk aversion on the part of the designer.

  14. Optimization under Uncertainty of Site-Specific Turbine Configurations: Preprint

    SciTech Connect

    Quick, Julian; Dykes, Katherine; Graf, Peter; Zahle, Frederik

    2016-11-01

    Uncertainty affects many aspects of wind energy plant performance and cost. In this study, we explore opportunities for site-specific turbine configuration optimization that accounts for uncertainty in the wind resource. As a demonstration, a simple empirical model for wind plant cost of energy is used in an optimization under uncertainty to examine how different risk appetites affect the optimal selection of a turbine configuration for sites of different wind resource profiles. If there is unusually high uncertainty in the site wind resource, the optimal turbine configuration diverges from the deterministic case and a generally more conservative design is obtained with increasing risk aversion on the part of the designer.

  15. Site-Specific, Sustained Release of Drugs to the Brain

    NASA Astrophysics Data System (ADS)

    Bodor, Nicholas; Farag, Hassan H.; Brewster, Marcus E.

    1981-12-01

    A dihydropyridine-pyridinium salt type of redox system is used in a general and flexible method for site-specific or sustained delivery (or both) of drugs to the brain. A biologically active compound linked to a lipoidal dihydropyridine carrier easily penetrates the blood-brain barrier. Oxidation of the carrier part in vivo to the ionic pyridinium salt prevents its elimination from the brain, while elimination from the general circulation is accelerated. Subsequent cleavage of the quaternary carrier-drug species results in sustained delivery of the drug in the brain and facile elimination of the carrier part.

  16. Editing livestock genomes with site-specific nucleases.

    PubMed

    Carlson, Daniel F; Tan, Wenfang; Hackett, Perry B; Fahrenkrug, Scott C

    2013-01-01

    Over the past 5 years there has been a major transformation in our ability to precisely manipulate the genomes of animals. Efficiencies of introducing precise genetic alterations in large animal genomes have improved 100000-fold due to a succession of site-specific nucleases that introduce double-strand DNA breaks with a specificity of 10(-9). Herein we describe our applications of site-specific nucleases, especially transcription activator-like effector nucleases, to engineer specific alterations in the genomes of pigs and cows. We can introduce variable changes mediated by non-homologous end joining of DNA breaks to inactive genes. Alternatively, using homology-directed repair, we have introduced specific changes that support either precise alterations in a gene's encoded polypeptide, elimination of the gene or replacement by another unrelated DNA sequence. Depending on the gene and the mutation, we can achieve 10%-50% effective rates of precise mutations. Applications of the new precision genetics are extensive. Livestock now can be engineered with selected phenotypes that will augment their value and adaption to variable ecosystems. In addition, animals can be engineered to specifically mimic human diseases and disorders, which will accelerate the production of reliable drugs and devices. Moreover, animals can be engineered to become better providers of biomaterials used in the medical treatment of diseases and disorders.

  17. Site specific modification of the human plasma proteome by methylglyoxal.

    PubMed

    Kimzey, Michael J; Kinsky, Owen R; Yassine, Hussein N; Tsaprailis, George; Stump, Craig S; Monks, Terrence J; Lau, Serrine S

    2015-12-01

    Increasing evidence identifies dicarbonyl stress from reactive glucose metabolites, such as methylglyoxal (MG), as a major pathogenic link between hyperglycemia and complications of diabetes. MG covalently modifies arginine residues, yet the site specificity of this modification has not been thoroughly investigated. Sites of MG adduction in the plasma proteome were identified using LC-MS/MS analysis in vitro following incubation of plasma proteins with MG. Treatment of plasma proteins with MG yielded 14 putative MG hotspots from five plasma proteins (albumin [nine hotspots], serotransferrin, haptoglobin [2 hotspots], hemopexin, and Ig lambda-2 chain C regions). The search results revealed two versions of MG-arginine modification, dihydroxyimidazolidine (R+72) and hydroimidazolone (R+54) adducts. One of the sites identified was R257 in human serum albumin, which is a critical residue located in drug binding site I. This site was validated as a target for MG modification by a fluorescent probe displacement assay, which revealed significant drug dissociation at 300 μM MG from a prodan-HSA complex (75 μM). Moreover, twelve human plasma samples (six male, six female, with two type 2 diabetic subjects from both genders) were analyzed using multiple reaction monitoring (MRM) tandem mass spectrometry and revealed the presence of the MG-modified albumin R257 peptide. These data provide insights into the nature of the site-specificity of MG modification of arginine, which may be useful for therapeutic treatments that aim to prevent MG-mediated adverse responses in patients.

  18. Site-specific features influence sediment stability of intertidal flats

    NASA Astrophysics Data System (ADS)

    Defew, Emma C.; Tolhurst, Trevor J.; Paterson, David M.

    The factors that influence the sediment stability and the transport of estuarine mudflats are not yet fully understood but knowledge of them is essential in coastal engineering applications and pollution ecology studies. The suggestion that variation in predictive models of sediment stability might be due to site-specific characteristics is investigated using data from four estuarine mudflats (Eden Estuary, Scotland, the Biezelingsche Ham, Zandkreek, and Molenplaat mudflats in The Netherlands). These estuaries differ in their environmental conditions, macrofaunal species composition and local features (e.g. Enteromorpha mats, migratory biofilms). Stable and unstable sediments were compared, and mean chlorophyll-a concentrations and granulometry of the sediments were significantly different between the two groups. Step-wise multiple linear regressions were applied to the sediment stability data of all sites to establish the influences on erosion threshold of microphytobenthic biomass, water content, granulometry, organic carbon content and the abundance of dominant macrofaunal species. The stability of each site was influenced by different factors. Sediment stability of the Eden Estuary was affected by the Enteromorpha bloom; Biezelingsche Ham was influenced by the highly migratory nature of the diatom biofilms and the abundance of Corophium volutator; the polychaete worm Arenicola marina had a net negative effect on sediment stability of the Zandkreek; and the Molenplaat was influenced by microphytobenthic biomass. This research highlights the need for site-specific calibration of models and suggests that a universal proxy parameter for sediment stability is unlikely to be obtained.

  19. Site-specific tumor-targeted fluorescent contrast agents

    NASA Astrophysics Data System (ADS)

    Achilefu, Samuel I.; Bugaj, Joseph E.; Dorshow, Richard B.; Jimenez, Hermo N.; Rajagopalan, Raghavan; Wilhelm, R. Randy; Webb, Elizabeth G.; Erion, Jack L.

    2001-01-01

    Site-specific delivery of drugs and contrast agents to tumors protects normal tissues from the cytotoxic effect of drugs, and enhances the contrast between normal and diseased tissues. In optical medicine, biocompatible dyes can be used as photo therapeutics or as contrast agents. Previous studies have shown that the use of covalent or non-covalent dye conjugates of carries such as antibodies, liposomes, and polysaccharides improves the delivery of such molecules to tumors. However, large biomolecules can elicit adverse immunogenic reactions and also result in prolonged blood circulation times, delaying visualization of target tissues. A viable alternative to this strategy is to use small bioactive molecule-dye conjugates. These molecules have several advantages over large biomolecules, including ease of synthesis of a variety of high purity compounds for combinatorial screening of new targets, enhanced diffusivity to solid tumors, and the ability to affect the pharmocokinetics of the conjugates by minor structural changes. Thus, we conjugated a near IR light absorbing dye to bioactive peptides that specifically target over expressed tumor receptors in established rat tumor lines. High tumor uptake of the conjugates was obtained without loss of either the peptide receptor affinity or the dye fluorescence. These findings demonstrate the efficacy of a small peptide-dye conjugate strategy for in vivo tumor imaging. Site-specific delivery of photodynamic therapy agents may also benefit form this approach.

  20. Recent advances in covalent, site-specific protein immobilization

    PubMed Central

    Meldal, Morten; Schoffelen, Sanne

    2016-01-01

    The properties of biosensors, biomedical implants, and other materials based on immobilized proteins greatly depend on the method employed to couple the protein molecules to their solid support. Covalent, site-specific immobilization strategies are robust and can provide the level of control that is desired in this kind of application. Recent advances include the use of enzymes, such as sortase A, to couple proteins in a site-specific manner to materials such as microbeads, glass, and hydrogels. Also, self-labeling tags such as the SNAP-tag can be employed. Last but not least, chemical approaches based on bioorthogonal reactions, like the azide–alkyne cycloaddition, have proven to be powerful tools. The lack of comparative studies and quantitative analysis of these immobilization methods hampers the selection process of the optimal strategy for a given application. However, besides immobilization efficiency, the freedom in selecting the site of conjugation and the size of the conjugation tag and the researcher’s expertise regarding molecular biology and/or chemical techniques will be determining factors in this regard. PMID:27785356

  1. Site-specific analysis of dielectric properties of finite systems.

    SciTech Connect

    Jackson, K.; Yang, M.; Jellinek, J.; Chemistry; Central Michigan Univ.

    2007-12-06

    A new scheme for decomposing the total dipole moment and polarizability of a system into site-specific contributions is presented. The scheme is based on partitioning the system volume into cells associated with its atoms or groups of atoms. The site-specific dipole moments and polarizabilities are computed from the charge densities within the individual cells and the responses of these densities to an external electric field. These dipole moments and polarizabilities are further partitioned into local/dipole and charge-transfer components. The utility of the scheme is illustrated through analysis of the structure-/shape- and size-specific aspects of the dipole moments and polarizabilities of silicon clusters. It is shown that the polarizabilities associated with the individual constituent Si atoms vary considerably with the structure/shape of the cluster and the location of the atom or site within a given structure. Surface atoms, and especially those at edges, have larger polarizabilities than interior atoms. The overall contribution of the charge-transfer components to the total cluster polarizability increases with the cluster size. Finally, the anisotropy of the total polarizability correlates with the anisotropy of the cluster shape, and the charge-transfer component is the part dominantly responsible for the polarizability anisotropy.

  2. Temporally-controlled site-specific recombination in zebrafish.

    PubMed

    Hans, Stefan; Kaslin, Jan; Freudenreich, Dorian; Brand, Michael

    2009-01-01

    Conventional use of the site-specific recombinase Cre is a powerful technology in mouse, but almost absent in other vertebrate model organisms. In zebrafish, Cre-mediated recombination efficiency was previously very low. Here we show that using transposon-mediated transgenesis, Cre is in fact highly efficient in this organism. Furthermore, temporal control of recombination can be achieved by using the ligand-inducible CreER(T2). Site-specific recombination only occurs upon administration of the drug tamoxifen (TAM) or its active metabolite, 4-hydroxy-tamoxifen (4-OHT). Cre-mediated recombination is detectable already 4 or 2 hours after administration of TAM or 4-OHT, demonstrating fast recombination kinetics. In addition, low doses of TAM allow mosaic labeling of single cells. Combined, our results show that conditional Cre/lox will be a valuable tool for both, embryonic and adult zebrafish studies. Furthermore, single copy insertion transgenesis of Cre/lox constructs suggest a strategy suitable also for other organisms.

  3. Site-Specific Genome Engineering in Human Pluripotent Stem Cells

    PubMed Central

    Merkert, Sylvia; Martin, Ulrich

    2016-01-01

    The possibility to generate patient-specific induced pluripotent stem cells (iPSCs) offers an unprecedented potential of applications in clinical therapy and medical research. Human iPSCs and their differentiated derivatives are tools for diseases modelling, drug discovery, safety pharmacology, and toxicology. Moreover, they allow for the engineering of bioartificial tissue and are promising candidates for cellular therapies. For many of these applications, the ability to genetically modify pluripotent stem cells (PSCs) is indispensable, but efficient site-specific and safe technologies for genetic engineering of PSCs were developed only recently. By now, customized engineered nucleases provide excellent tools for targeted genome editing, opening new perspectives for biomedical research and cellular therapies. PMID:27347935

  4. Methods for generating phosphorylation site-specific immunological reagents

    DOEpatents

    Anderson, Carl W.; Appella, Ettore; Sakaguchi, Kazuyasu

    2001-01-01

    The present invention provides methods for generating phosphorylation site-specific immunological reagents. More specifically, a phosphopeptide mimetic is incorporated into a polypeptide in place of a phosphorylated amino acid. The polypeptide is used as antigen by standard methods to generate either monoclonal or polyclonal antibodies which cross-react with the naturally phosphorylated polypeptide. The phosphopeptide mimetic preferably contains a non-hydrolyzable linkage from the appropriate carbon atom of the amino acid residue to a phosphate group. A preferred linkage is a CF.sub.2 group. Such a linkage is used to generate the phosphoserine mimetic F.sub.2 Pab, which is incorporated into a polypeptide sequence derived from p53 to produce antibodies which recognize a specific phosphorylation state of p53. A CF.sub.2 group linkage is also used to produce the phosphothreonine mimetic F.sub.2 Pmb, and to produce the phosphotyrosine mimetic, F.sub.2 Pmp.

  5. Synthesis of Site-Specifically (13)C Labeled Linoleic Acids.

    PubMed

    Offenbacher, Adam R; Zhu, Hui; Klinman, Judith P

    2016-10-12

    Soybean lipoxygenase-1 (SLO-1) catalyzes the C-H abstraction from the reactive carbon (C-11) in linoleic acid as the first and rate-determining step in the formation of alkylhydroperoxides. While previous labeling strategies have focused on deuterium labeling to ascertain the primary and secondary kinetic isotope effects for this reaction, there is an emerging interest and need for selectively enriched (13)C isotopologues. In this report, we present synthetic strategies for site-specific (13)C labeled linoleic acid substrates. We take advantage of a Corey-Fuchs formyl to terminal (13)C-labeled alkyne conversion, using (13)CBr4 as the labeling source, to reduce the number of steps from a previous fatty acid (13)C synthetic labeling approach. The labeled linoleic acid substrates are useful as nuclear tunneling markers and for extracting active site geometries of the enzyme-substrate complex in lipoxygenase.

  6. Optimization Under Uncertainty of Site-Specific Turbine Configurations

    DOE PAGES

    Quick, J.; Dykes, K.; Graf, P.; ...

    2016-10-03

    Uncertainty affects many aspects of wind energy plant performance and cost. In this study, we explore opportunities for site-specific turbine configuration optimization that accounts for uncertainty in the wind resource. As a demonstration, a simple empirical model for wind plant cost of energy is used in an optimization under uncertainty to examine how different risk appetites affect the optimal selection of a turbine configuration for sites of different wind resource profiles. Lastly, if there is unusually high uncertainty in the site wind resource, the optimal turbine configuration diverges from the deterministic case and a generally more conservative design is obtainedmore » with increasing risk aversion on the part of the designer.« less

  7. Site-Specific Genome Engineering in Human Pluripotent Stem Cells.

    PubMed

    Merkert, Sylvia; Martin, Ulrich

    2016-06-24

    The possibility to generate patient-specific induced pluripotent stem cells (iPSCs) offers an unprecedented potential of applications in clinical therapy and medical research. Human iPSCs and their differentiated derivatives are tools for diseases modelling, drug discovery, safety pharmacology, and toxicology. Moreover, they allow for the engineering of bioartificial tissue and are promising candidates for cellular therapies. For many of these applications, the ability to genetically modify pluripotent stem cells (PSCs) is indispensable, but efficient site-specific and safe technologies for genetic engineering of PSCs were developed only recently. By now, customized engineered nucleases provide excellent tools for targeted genome editing, opening new perspectives for biomedical research and cellular therapies.

  8. Site-specific DNA Inversion by Serine Recombinases

    PubMed Central

    2015-01-01

    Reversible site-specific DNA inversion reactions are widely distributed in bacteria and their viruses. They control a range of biological reactions that most often involve alterations of molecules on the surface of cells or phage. These programmed DNA rearrangements usually occur at a low frequency, thereby preadapting a small subset of the population to a change in environmental conditions, or in the case of phages, an expanded host range. A dedicated recombinase, sometimes with the aid of additional regulatory or DNA architectural proteins, catalyzes the inversion of DNA. RecA or other components of the general recombination-repair machinery are not involved. This chapter discusses site-specific DNA inversion reactions mediated by the serine recombinase family of enzymes and focuses on the extensively studied serine DNA invertases that are stringently controlled by the Fis-bound enhancer regulatory system. The first section summarizes biological features and general properties of inversion reactions by the Fis/enhancer-dependent serine invertases and the recently described serine DNA invertases in Bacteroides. Mechanistic studies of reactions catalyzed by the Hin and Gin invertases are then discussed in more depth, particularly with regards to recent advances in our understanding of the function of the Fis/enhancer regulatory system, the assembly of the active recombination complex (invertasome) containing the Fis/enhancer, and the process of DNA strand exchange by rotation of synapsed subunit pairs within the invertasome. The role of DNA topological forces that function in concert with the Fis/enhancer controlling element in specifying the overwhelming bias for DNA inversion over deletion and intermolecular recombination is emphasized. PMID:25844275

  9. Performance of site-specific parameterizations of longwave radiation

    NASA Astrophysics Data System (ADS)

    Formetta, Giuseppe; Bancheri, Marialaura; David, Olaf; Rigon, Riccardo

    2016-11-01

    In this work 10 algorithms for estimating downwelling longwave atmospheric radiation (L↓) and 1 for upwelling longwave radiation (L) are integrated into the JGrass-NewAge modelling system. The algorithms are tested against energy flux measurements available for 24 sites in North America to assess their reliability. These new JGrass-NewAge model components are used (i) to evaluate the performances of simplified models (SMs) of L↓, as presented in literature formulations, and (ii) to determine by automatic calibration the site-specific parameter sets for L↓ in SMs. For locations where calibration is not possible because of a lack of measured data, we perform a multiple regression using on-site variables, i.e. mean annual air temperature, relative humidity, precipitation, and altitude. The regressions are verified through a leave-one-out cross validation, which also gathers information about the possible errors of estimation. Most of the SMs, when executed with parameters derived from the multiple regressions, give enhanced performances compared to the corresponding literature formulation. A sensitivity analysis is carried out for each SM to understand how small variations of a given parameter influence SM performance. Regarding the L↓ simulations, the Brunt (1932) and Idso (1981) SMs, in their literature formulations, provide the best performances in many of the sites. The site-specific parameter calibration improves SM performances compared to their literature formulations. Specifically, the root mean square error (RMSE) is almost halved and the Kling-Gupta efficiency is improved at all sites. Also in this case, Brunt (1932) and Idso (1981) SMs provided the best performances. The L SM is tested by using three different temperatures (surface soil temperature, air temperature at 2 m elevation, and soil temperature at 4 cm depth) and model performances are then assessed. Results show that the best performances are achieved using the

  10. Site Specific Analyses of a Spent Nuclear Fuel Transportation Accident

    SciTech Connect

    Biwer, B. M.; Chen, S. Y.

    2003-02-24

    The number of spent nuclear fuel (SNF) shipments is expected to increase significantly during the time period that the United States' inventory of SNF is sent to a final disposal site. Prior work estimated that the highest accident risks of a SNF shipping campaign to the proposed geologic repository at Yucca Mountain were in the corridor states, such as Illinois. The largest potential human health impacts would be expected to occur in areas with high population densities such as urban settings. Thus, our current study examined the human health impacts from the most plausible severe SNF transportation accidents in the Chicago metropolitan area. The RISKIND 2.0 program was used to model site-specific data for an area where the largest impacts might occur. The results have shown that the radiological human health consequences of a severe SNF rail transportation accident on average might be similar to one year of exposure to natural background radiation for those persons living a nd working in the most affected areas downwind of the actual accident location. For maximally exposed individuals, an exposure similar to about two years of exposure to natural background radiation was estimated. In addition to the accident probabilities being very low (approximately 1 chance in 10,000 or less during the entire shipping campaign), the actual human health impacts are expected to be lower if any of the accidents considered did occur, because the results are dependent on the specific location and weather conditions, such as wind speed and direction, that were selected to maximize the results. Also, comparison of the results of longer duration accident scenarios against U.S. Environmental Protection Agency guidelines was made to demonstrate the usefulness of this site-specific analysis for emergency planning purposes.

  11. Site-specific probing of charge transfer dynamics in organic photovoltaics

    SciTech Connect

    Arion, Tiberiu; Roth, Friedrich; Hussain, Zahid; Eberhardt, Wolfgang

    2015-03-23

    We report the site-specific probing of charge-transfer dynamics in a prototype system for organic photovoltaics (OPVs) by picosecond time-resolved X-ray photoelectron spectroscopy. A layered system consisting of approximately two monolayers of C{sub 60} deposited on top of a thin film of Copper-Phthalocyanine (CuPC) is excited by an optical pump pulse and the induced electronic dynamics are probed with 590 eV X-ray pulses. Charge transfer from the electron donor (CuPC) to the acceptor (C{sub 60}) and subsequent charge carrier dynamics are monitored by recording the time-dependent C 1s core level photoemission spectrum of the system. The arrival of electrons in the C{sub 60} layer is readily observed as a completely reversible, transient shift of the C{sub 60} associated C 1s core level, while the C 1s level of the CuPC remains unchanged. The capability to probe charge transfer and recombination dynamics in OPV assemblies directly in the time domain and from the perspective of well-defined domains is expected to open additional pathways to better understand and optimize the performance of this emerging technology.

  12. Compact, Integrated Photoelectron Linacs

    NASA Astrophysics Data System (ADS)

    Yu, David

    2000-12-01

    The innovative compact high energy iniector which has been developed by DULY Research Inc., will have wide scientific industrial and medical applications. The new photoelectron injector integrates the photocathode directly into a multicell linear accelerator with no drift space between the injector and the linac. By focusing the beam with solenoid or permanent magnets, and producing high current with low emittance, extremely high brightness is achieved. In addition to providing a small footprint and improved beam quality in an integrated structure, the compact system considerably simplifies external subsystems required to operate the photoelectron linac, including rf power transport, beam focusing, vacuum and cooling. The photoelectron linac employs an innovative Plane-Wave-Transformer (PWT) design, which provides strong cell-to-cell coupling, relaxes manufacturing tolerance and facilitates the attachment of external ports to the compact structure with minimal field interference. DULY Research Inc. under the support of the DOE Small Business Innovation Research (SBIR) program, has developed, constructed and installed a 20-MeV, S-band compact electron source at UCLA. DULY Research is also presently engaged in the development of an X-band photoelectron linear accelerator in another SBIR project. The higher frequency structure when completed will be approximately three times smaller, and capable of a beam brightness ten times higher than the S-band structure.

  13. Simultaneous Site-Specific Dual Protein Labeling Using Protein Prenyltransferases.

    PubMed

    Zhang, Yi; Blanden, Melanie J; Sudheer, Ch; Gangopadhyay, Soumyashree A; Rashidian, Mohammad; Hougland, James L; Distefano, Mark D

    2015-12-16

    Site-specific protein labeling is an important technique in protein chemistry and is used for diverse applications ranging from creating protein conjugates to protein immobilization. Enzymatic reactions, including protein prenylation, have been widely exploited as methods to accomplish site-specific labeling. Enzymatic prenylation is catalyzed by prenyltransferases, including protein farnesyltransferase (PFTase) and geranylgeranyltransferase type I (GGTase-I), both of which recognize C-terminal CaaX motifs with different specificities and transfer prenyl groups from isoprenoid diphosphates to their respective target proteins. A number of isoprenoid analogues containing bioorthogonal functional groups have been used to label proteins of interest via PFTase-catalyzed reaction. In this study, we sought to expand the scope of prenyltransferase-mediated protein labeling by exploring the utility of rat GGTase-I (rGGTase-I). First, the isoprenoid specificity of rGGTase-I was evaluated by screening eight different analogues and it was found that those with bulky moieties and longer backbone length were recognized by rGGTase-I more efficiently. Taking advantage of the different substrate specificities of rat PFTase (rPFTase) and rGGTase-I, we then developed a simultaneous dual labeling method to selectively label two different proteins by using isoprenoid analogue and CaaX substrate pairs that were specific to only one of the prenyltransferases. Using two model proteins, green fluorescent protein with a C-terminal CVLL sequence (GFP-CVLL) and red fluorescent protein with a C-terminal CVIA sequence (RFP-CVIA), we demonstrated that when incubated together with both prenyltransferases and the selected isoprenoid analogues, GFP-CVLL was specifically modified with a ketone-functionalized analogue by rGGTase-I and RFP-CVIA was selectively labeled with an alkyne-containing analogue by rPFTase. By switching the ketone-containing analogue to an azide-containing analogue, it was

  14. Bone site-specific delivery of siRNA

    PubMed Central

    Liu, Xinli

    2016-01-01

    Abstract Small interfering RNAs (siRNA) have enormous potential as therapeutics to target and treat various bone disorders such as osteoporosis and cancer bone metastases. However, effective and specific delivery of siRNA therapeutics to bone and bone-specific cells in vivo is very challenging. To realize the full therapeutic potential of siRNA in treating bone disorders, a safe and efficient, tissue- and cell-specific delivery system must be developed. This review focuses on recent advances in bone site-specific delivery of siRNA at the tissue or cellular level. Bone-targeted nanoparticulate siRNA carriers and various bone-targeted moieties such as bisphosphonates, oligopeptides (Asp)8 and (AspSerSer)6, and aptamers are highlighted. Incorporation of these bone-seeking targeting moieties into siRNA carriers allows for recognition of different sub-tissue functional domains of bone and also specific cell types residing in bone tissue. It also provides a means for bone-formation surface-, bone-resorption surface-, or osteoblast-specific targeting and transportation of siRNA therapeutics. The discussion mainly focuses on systemic and local bone-specific delivery of siRNA in osteoporosis and bone metastasis preclinical models. PMID:26642236

  15. Genetic fate mapping using site-specific recombinases.

    PubMed

    Legué, Emilie; Joyner, Alexandra L

    2010-01-01

    Understanding how cells are assembled in three dimensions to generate an organ, or a whole organism, is a pivotal question in developmental biology. Similarly, it is critical to understand how adult stem cells integrate into an existing organ during regeneration or in response to injury. Key to discovering the answers to these questions is being able to study the various behaviors of distinct cell types during development or regeneration. Fate mapping techniques are fundamental to studying cell behaviors such as proliferation, movement, and lineage segregation, as the techniques allow precursor cells to be marked and their descendants followed and characterized over time. The generation of transgenic mice, combined with the use of site-specific recombinases (SSR) in the mouse genome, has provided a means to develop powerful genetic fate mapping approaches. A key advantage of genetic fate mapping is that it allows cells to be genetically marked, and therefore the mark is transmitted to all the descendants of the initially marked cells. By making modifications to the SSRs that render their enzymatic activity inducible, and the development of an assortment of reporter alleles for marking cells, increasingly sophisticated genetic fate mapping studies can be performed. In this chapter, we review the four main genetic fate mapping methods that utilize intrachromosomal recombination to mark cells (cumulative, inducible, clonal, and intersectional) and one interchromosomal method, the tools required to carry out each approach, and the practical considerations that have to be taken into account before embarking on each type of genetic fate mapping study.

  16. An exactly solvable model of random site-specific recombinations

    PubMed Central

    Wei, Yi; Koulakov, Alexei A.

    2017-01-01

    Cre-lox and other systems are used as genetic tools to control site-specific recombination (SSR) events in genomic DNA. If multiple recombination sites are organized in a compact cluster within the same genome, a series of random recombination events may generate substantial cell specific genomic diversity. This diversity is used, for example, to distinguish neurons in the brain of the same multicellular mosaic organism, within the brainbow approach to neuronal connectome. In this paper we study an exactly solvable statistical model for SSR operating on a cluster of recombination sites. We consider two types of recombination events: inversions and excisions. Both of these events are available in the Cre-lox system. We derive three properties of the sequences generated by multiple recombination events. First, we describe the set of sequences that can in principle be generated by multiple inversions operating on the given initial sequence. We call this description the ergodicity theorem. On the basis of this description we calculate the number of sequences that can be generated from an initial sequence. This number of sequences is experimentally testable. Second, we demonstrate that after a large number of random inversions every sequence that can be generated is generated with equal probability. Lastly, we derive the equations for the probability to find a sequence as a function of time in the limit when excisions are much less frequent than inversions, such as in shufflon sequences. PMID:23151958

  17. Analysis of Chemokine Receptor Trafficking by Site-Specific Biotinylation

    PubMed Central

    Liebick, Marcel; Schläger, Christian; Oppermann, Martin

    2016-01-01

    Chemokine receptors undergo internalization and desensitization in response to ligand activation. Internalized receptors are either preferentially directed towards recycling pathways (e.g. CCR5) or sorted for proteasomal degradation (e.g. CXCR4). Here we describe a method for the analysis of receptor internalization and recycling based on specific Bir A-mediated biotinylation of an acceptor peptide coupled to the receptor, which allows a more detailed analysis of receptor trafficking compared to classical antibody-based detection methods. Studies on constitutive internalization of the chemokine receptors CXCR4 (12.1% ± 0.99% receptor internalization/h) and CCR5 (13.7% ± 0.68%/h) reveals modulation of these processes by inverse (TAK779; 10.9% ± 0.95%/h) or partial agonists (Met-CCL5; 15.6% ± 0.5%/h). These results suggest an actively driven internalization process. We also demonstrate the advantages of specific biotinylation compared to classical antibody detection during agonist-induced receptor internalization, which may be used for immunofluorescence analysis as well. Site-specific biotinylation may be applicable to studies on trafficking of transmembrane proteins, in general. PMID:27310579

  18. Site-specific PEGylation of lidamycin and its antitumor activity

    PubMed Central

    Li, Liang; Shang, Boyang; Hu, Lei; Shao, Rongguang; Zhen, Yongsu

    2015-01-01

    In this study, N-terminal site-specific mono-PEGylation of the recombinant lidamycin apoprotein (rLDP) of lidamycin (LDM) was prepared using a polyethyleneglycol (PEG) derivative (Mw 20 kDa) through a reactive terminal aldehyde group under weak acidic conditions (pH 5.5). The biochemical properties of mPEG-rLDP-AE, an enediyne-integrated conjugate, were analyzed by SDS-PAGE, RP-HPLC, SEC-HPLC and MALDI-TOF. Meanwhile, in vitro and in vivo antitumor activity of mPEG-rLDP-AE was evaluated by MTT assays and in xenograft model. The results indicated that mPEG-rLDP-AE showed significant antitumor activity both in vitro and in vivo. After PEGylation, mPEG-rLDP still retained the binding capability to the enediyne AE and presented the physicochemical characteristics similar to that of native LDP. It is of interest that the PEGylation did not diminish the antitumor efficacy of LDM, implying the possibility that this derivative may function as a payload to deliver novel tumor-targeted drugs. PMID:26579455

  19. Micro-tattoo guided OCT imaging of site specific inflammation

    NASA Astrophysics Data System (ADS)

    Phillips, Kevin G.; Choudhury, Niloy; Samatham, Ravikant V.; Singh, Harvinder; Jacques, Steven L.

    2010-02-01

    Epithelial biologists studying human skin diseases such as cancer formation and psoriasis commonly utilize mouse models to characterize the interplay among cells and intracellular signal transduction pathways that result in programmed changes in gene expression and cellular behaviors. The information obtained from animal models is useful only when phenotypic presentations of disease recapitulate those observed in humans. Excision of tissues followed by histochemical analysis is currently the primary means of establishing the morphological presentation. Non invasive imaging of animal models provides an alternate means to characterize tissue morphology associated with the disease of interest in vivo. While useful, the ability to perform in vivo imaging at different time points in the same tissue location has been a challenge. This information is key to understanding site specific changes as the imaged tissue can now be extracted and analyzed for mRNA expression. We present a method employing a micro-tattoo to guide optical coherence tomography (OCT) imaging of ultraviolet induced inflammation over time in the same tissue locations.

  20. Site-specific group selection drives locally adapted group compositions.

    PubMed

    Pruitt, Jonathan N; Goodnight, Charles J

    2014-10-16

    Group selection may be defined as selection caused by the differential extinction or proliferation of groups. The socially polymorphic spider Anelosimus studiosus exhibits a behavioural polymorphism in which females exhibit either a 'docile' or 'aggressive' behavioural phenotype. Natural colonies are composed of a mixture of related docile and aggressive individuals, and populations differ in colonies' characteristic docile:aggressive ratios. Using experimentally constructed colonies of known composition, here we demonstrate that population-level divergence in docile:aggressive ratios is driven by site-specific selection at the group level--certain ratios yield high survivorship at some sites but not others. Our data also indicate that colonies responded to the risk of extinction: perturbed colonies tended to adjust their composition over two generations to match the ratio characteristic of their native site, thus promoting their long-term survival in their natal habitat. However, colonies of displaced individuals continued to shift their compositions towards mixtures that would have promoted their survival had they remained at their home sites, regardless of their contemporary environment. Thus, the regulatory mechanisms that colonies use to adjust their composition appear to be locally adapted. Our data provide experimental evidence of group selection driving collective traits in wild populations.

  1. Site-specific protein glycosylation analysis with glycan isomer differentiation.

    PubMed

    Hua, Serenus; Nwosu, Charles C; Strum, John S; Seipert, Richard R; An, Hyun Joo; Zivkovic, Angela M; German, J Bruce; Lebrilla, Carlito B

    2012-05-01

    Glycosylation is one of the most common yet diverse post-translational modifications. Information on glycan heterogeneity and glycosite occupancy is increasingly recognized as crucial to understanding glycoprotein structure and function. Yet, no approach currently exists with which to holistically consider both the proteomic and glycomic aspects of a system. Here, we developed a novel method of comprehensive glycosite profiling using nanoflow liquid chromatography/mass spectrometry (nano-LC/MS) that shows glycan isomer-specific differentiation on specific sites. Glycoproteins were digested by controlled non-specific proteolysis in order to produce informative glycopeptides. High-resolution, isomer-sensitive chromatographic separation of the glycopeptides was achieved using microfluidic chip-based capillaries packed with graphitized carbon. Integrated LC/MS/MS not only confirmed glycopeptide composition but also differentiated glycan and peptide isomers and yielded structural information on both the glycan and peptide moieties. Our analysis identified at least 13 distinct glycans (including isomers) corresponding to five compositions at the single N-glycosylation site on bovine ribonuclease B, 59 distinct glycans at five N-glycosylation sites on bovine lactoferrin, 13 distinct glycans at one N-glycosylation site on four subclasses of human immunoglobulin G, and 20 distinct glycans at five O-glycosylation sites on bovine κ-casein. Porous graphitized carbon provided effective separation of glycopeptide isomers. The integration of nano-LC with MS and MS/MS of non-specifically cleaved glycopeptides allows quantitative, isomer-sensitive, and site-specific glycoprotein analysis.

  2. Site-specific hydrogen diffusion rates during clinopyroxene dehydration

    NASA Astrophysics Data System (ADS)

    Ferriss, Elizabeth; Plank, Terry; Walker, David

    2016-06-01

    The rate of hydrogen diffusion in clinopyroxene is relevant to interpreting hydrogen ("water") concentrations in xenoliths, phenocrysts, and clinopyroxene-hosted melt inclusions to provide insight into the deep-earth water cycle and volcanic explosivity. Here, we determine bulk and site-specific hydrogen diffusivities in two diopsides and an augite by heating initially homogeneous water-bearing samples in a 1-atm CO/CO2 gas-mixing furnace at 800-1000 °C and oxygen fugacity at the quartz-fayalite-magnetite buffer and observing H-loss profiles. The O-H stretching range between wavenumbers 3000 and 4000 cm-1 in FTIR spectra is resolved into 4-6 peaks, each of which is assumed to represent a distinct defect site for the hydrogen, to determine peak-specific diffusivities using our previously published whole-block method. For the diopside from the Kunlun Mts. in China, Arrhenius relations are reported for peaks at 3645, 3617, 3540, 3443, and 3355 cm-1 based on measurements at 816, 904, and 1000 °C. Bulk and site-specific diffusivities are determined for the same set of peaks at 904 °C for the second diopside (Jaipur). The augite (PMR-53) was a triangular thin slab, and hydrogen diffusivities were determined for bulk hydrogen and peaks at 3620, 3550, 3460, and 3355 cm-1 in the thickness direction at 800 °C. Bulk hydrogen diffusivity in the Jaipur diopside is consistent with previous work, and hydrogen diffusivity in augite PMR-53 is slightly lower than the fast direction diffusivities measured || [100] and [001]* in Jaipur diopside. Both diopsides show 1-2 orders of magnitude differences in the peaks-specific diffusivities, with the fastest diffusivities at 3450 cm-1 and the slowest at 3645 cm-1. However, the hydrogen diffusivities in Jaipur diopside are 2-4 orders of magnitude higher than those in Kunlun diopside for bulk hydrogen and all peaks. Thus, peak-specific differences cannot by themselves adequately explain the 5 orders of magnitude range in hydrogen

  3. Xer Site Specific Recombination: Double and Single Recombinase Systems

    PubMed Central

    Castillo, Fabio; Benmohamed, Amal; Szatmari, George

    2017-01-01

    The separation and segregation of newly replicated bacterial chromosomes can be constrained by the formation of circular chromosome dimers caused by crossing over during homologous recombination events. In Escherichia coli and most bacteria, dimers are resolved to monomers by site-specific recombination, a process performed by two Chromosomally Encoded tyrosine Recombinases (XerC and XerD). XerCD recombinases act at a 28 bp recombination site dif, which is located at the replication terminus region of the chromosome. The septal protein FtsK controls the initiation of the dimer resolution reaction, so that recombination occurs at the right time (immediately prior to cell division) and at the right place (cell division septum). XerCD and FtsK have been detected in nearly all sequenced eubacterial genomes including Proteobacteria, Archaea, and Firmicutes. However, in Streptococci and Lactococci, an alternative system has been found, composed of a single recombinase (XerS) genetically linked to an atypical 31 bp recombination site (difSL). A similar recombination system has also been found in 𝜀-proteobacteria such as Campylobacter and Helicobacter, where a single recombinase (XerH) acts at a resolution site called difH. Most Archaea contain a recombinase called XerA that acts on a highly conserved 28 bp sequence dif, which appears to act independently of FtsK. Additionally, several mobile elements have been found to exploit the dif/Xer system to integrate their genomes into the host chromosome in Vibrio cholerae, Neisseria gonorrhoeae, and Enterobacter cloacae. This review highlights the versatility of dif/Xer recombinase systems in prokaryotes and summarizes our current understanding of homologs of dif/Xer machineries. PMID:28373867

  4. Site-Specific Seismic Site Response Model for the Waste Treatment Plant, Hanford, Washington

    SciTech Connect

    Rohay, Alan C.; Reidel, Steve P.

    2005-02-24

    This interim report documents the collection of site-specific geologic and geophysical data characterizing the Waste Treatment Plant site and the modeling of the site-specific structure response to earthquake ground motions.

  5. Improving Site-Specific Radiological Performance Assessments - 13431

    SciTech Connect

    Tauxe, John; Black, Paul; Catlett, Kate; Lee, Robert; Perona, Ralph; Stockton, Tom; Sully, Mike

    2013-07-01

    An improved approach is presented for conducting complete and defensible radiological site-specific performance assessments (PAs) to support radioactive waste disposal decisions. The basic tenets of PA were initiated some thirty years ago, focusing on geologic disposals and evaluating compliance with regulations. Some of these regulations were inherently probabilistic (i.e., addressing uncertainty in a quantitative fashion), such as the containment requirements of the U.S. Environmental Protection Agency's (EPA's) 40 CFR 191, Environmental Radiation Protection Standards for Management and Disposal of Spent Nuclear Fuel, High-Level and Transuranic Radioactive Wastes, Chap. 191.13 [1]. Methods of analysis were developed to meet those requirements, but at their core early PAs used 'conservative' parameter values and modeling approaches. This limited the utility of such PAs to compliance evaluation, and did little to inform decisions about optimizing disposal, closure and long-term monitoring and maintenance, or, in general, maintaining doses 'as low as reasonably achievable' (ALARA). This basic approach to PA development in the United States was employed essentially unchanged through the end of the 20. century, principally by the U.S. Department of Energy (DOE). Performance assessments developed in support of private radioactive waste disposal operations, regulated by the U.S. Nuclear Regulatory Commission (NRC) and its agreement states, were typically not as sophisticated. Discussion of new approaches to PA is timely, since at the time of this writing, the DOE is in the midst of revising its Order 435.1, Radioactive Waste Management [2], and the NRC is revising 10 CFR 61, Licensing Requirements for Land Disposal of Radioactive Waste [3]. Over the previous decade, theoretical developments and improved computational technology have provided the foundation for integrating decision analysis (DA) concepts and objective-focused thinking, plus a Bayesian approach to

  6. Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases.

    PubMed Central

    McClelland, M; Nelson, M; Raschke, E

    1994-01-01

    Restriction endonucleases have site-specific interactions with DNA that can often be inhibited by site-specific DNA methylation and other site-specific DNA modifications. However, such inhibition cannot generally be predicted. The empirically acquired data on these effects are tabulated for over 320 restriction endonucleases. In addition, a table of known site-specific DNA modification methyltransferases and their specificities is presented along with EMBL database accession numbers for cloned genes. PMID:7937074

  7. 40 CFR 258.42 - Approval of site-specific flexibility requests in Indian country.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 25 2014-07-01 2014-07-01 false Approval of site-specific flexibility... site-specific flexibility requests in Indian country. (a) Salt River Pima-Maricopa Indian Community... flexibility provided through this site-specific rule. (9) In seeking any renewal of the authority...

  8. Site-specific retention of colloids at rough rock surfaces.

    PubMed

    Darbha, Gopala Krishna; Fischer, Cornelius; Luetzenkirchen, Johannes; Schäfer, Thorsten

    2012-09-04

    The spatial deposition of polystyrene latex colloids (d = 1 μm) at rough mineral and rock surfaces was investigated quantitatively as a function of Eu(III) concentration. Granodiorite samples from Grimsel test site (GTS), Switzerland, were used as collector surfaces for sorption experiments. At a scan area of 300 × 300 μm(2), the surface roughness (rms roughness, Rq) range was 100-2000 nm, including roughness contribution from asperities of several tens of nanometers in height to the sample topography. Although, an increase in both roughness and [Eu(III)] resulted in enhanced colloid deposition on granodiorite surfaces, surface roughness governs colloid deposition mainly at low Eu(III) concentrations (≤5 × 10(-7) M). Highest deposition efficiency on granodiorite has been found at walls of intergranular pores at surface sections with roughness Rq = 500-2000 nm. An about 2 orders of magnitude lower colloid deposition has been observed at granodiorite sections with low surface roughness (Rq < 500 nm), such as large and smooth feldspar or quartz crystal surface sections as well as intragranular pores. The site-specific deposition of colloids at intergranular pores is induced by small scale protrusions (mean height = 0.5 ± 0.3 μm). These protrusions diminish locally the overall DLVO interaction energy at the interface. The protrusions prevent further rolling over the surface by increasing the hydrodynamic drag required for detachment. Moreover, colloid sorption is favored at surface sections with high density of small protrusions (density (D) = 2.6 ± 0.55 μm(-1), asperity diameter (φ) = 0.6 ± 0.2 μm, height (h) = 0.4 ± 0.1 μm) in contrast to surface sections with larger asperities and lower asperity density (D = 1.2 ± 0.6 μm(-1), φ = 1.4 ± 0.4 μm, h = 0.6 ± 0.2 μm). The study elucidates the importance to include surface roughness parameters into predictive colloid-borne contaminant migration calculations.

  9. Photoelectronic characterization of heterointerfaces.

    SciTech Connect

    Brumbach, Michael Todd

    2012-02-01

    In many devices such as solar cells, light emitting diodes, transistors, etc., the performance relies on the electronic structure at interfaces between materials within the device. The objective of this work was to perform robust characterization of hybrid (organic/inorganic) interfaces by tailoring the interfacial region for photoelectron spectroscopy. Self-assembled monolayers (SAM) were utilized to induce dipoles of various magnitudes at the interface. Additionally, SAMs of molecules with varying dipolar characteristics were mixed into spatially organized structures to systematically vary the apparent work function. Polymer thin films were characterized by depositing films of varying thicknesses on numerous substrates with and without interfacial modifications. Hard X-ray photoelectron spectroscopy (HAXPES) was performed to evaluate a buried interface between indium tin oxide (ITO), treated under various conditions, and poly(3-hexylthiophene) (P3HT). Conducting polymer films were found to be sufficiently conducting such that no significant charge redistribution in the polymer films was observed. Consequently, a further departure from uniform substrates was taken whereby electrically disconnected regions of the substrate presented ideally insulating interfacial contacts. In order to accomplish this novel strategy, interdigitated electrodes were used as the substrate. Conducting fingers of one half of the electrodes were electrically grounded while the other set of electrodes were electronically floating. This allowed for the evaluation of substrate charging on photoelectron spectra (SCOPES) in the presence of overlying semiconducting thin films. Such an experiment has never before been reported. This concept was developed out of the previous experiments on interfacial modification and thin film depositions and presents new opportunities for understanding chemical and electronic changes in a multitude of materials and interfaces.

  10. Vector potential photoelectron microscopy.

    PubMed

    Browning, R

    2011-10-01

    A new class of electron microscope has been developed for the chemical microanalysis of a wide range of real world samples using photoelectron spectroscopy. Highly structured, three-dimensional samples, such as fiber mats and fracture surfaces can be imaged, as well as insulators and magnetic materials. The new microscope uses the vector potential field from a solenoid magnet as a spatial reference for imaging. A prototype instrument has demonstrated imaging of uncoated silk, magnetic steel wool, and micron-sized single strand tungsten wires.

  11. 76 FR 10018 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-23

    ... Environmental Management Site-Specific Advisory Board, Idaho National Laboratory AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Idaho National Laboratory. The Federal Advisory Committee Act... Public Participation: The EM SSAB, Idaho National Laboratory, welcomes the attendance of the public...

  12. 75 FR 39008 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-07

    ... Environmental Management Site-Specific Advisory Board, Idaho National Laboratory AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Idaho National Laboratory. The Federal Advisory Committee Act... Laboratory, welcomes the attendance of the public at its advisory committee meetings and will make...

  13. 76 FR 66917 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-28

    ... Environmental Management Site-Specific Advisory Board, Idaho National Laboratory AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Idaho National Laboratory. The Federal Advisory Committee Act... Environmental Assessment Public Participation: The EM SSAB, Idaho National Laboratory, welcomes the...

  14. 78 FR 12747 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-25

    ... Environmental Management Site-Specific Advisory Board, Idaho National Laboratory AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Idaho National Laboratory. The Federal Advisory Committee Act... Participation: The EM SSAB, Idaho National Laboratory, welcomes the attendance of the public at its...

  15. 77 FR 53192 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-31

    ... Environmental Management Site-Specific Advisory Board, Idaho National Laboratory AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Idaho National Laboratory. The Federal Advisory Committee Act... Closeout Process Public Participation: The EM SSAB, Idaho National Laboratory, welcomes the attendance...

  16. 76 FR 25682 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-05

    ... Environmental Management Site-Specific Advisory Board, Idaho National Laboratory AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Idaho National ] Laboratory. The Federal Advisory Committee Act... National Laboratory, welcomes the attendance of the public at its advisory committee meetings and will...

  17. 76 FR 63613 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-13

    ...] [FR Doc No: 2011-26475] DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board... meeting of the Environmental Management Site-Specific Advisory Board (EM SSAB), Hanford. The Federal... is to make recommendations to DOE-EM and site management in the areas of environmental...

  18. 76 FR 80355 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-23

    ...] [FR Doc No: 2011-32913] DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board... a meeting of the Environmental Management Site-Specific Advisory Board (EM SSAB), Paducah. The... environmental restoration, waste management, and related activities. Tentative Agenda Call to...

  19. 77 FR 4027 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-26

    ... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... and site management in the areas of environmental restoration, waste management, and...

  20. 78 FR 20311 - Environmental Management Site-Specific Advisory Board Chairs

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-04

    ... Environmental Management Site-Specific Advisory Board Chairs AGENCY: Department of Energy. ACTION: Notice of Open Webinar. SUMMARY: This notice announces a webinar of the Environmental Management Site-Specific... recommendations to DOE-EM and site management in the areas of environmental restoration, waste management,...

  1. 78 FR 53135 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-28

    ... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... recommendations to DOE-EM and site management in the areas of environmental restoration, waste management,...

  2. 76 FR 80354 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-23

    ...] [FR Doc No: 2011-32910] DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board... meeting of the Environmental Management Site-Specific Advisory Board (EM SSAB), Nevada. The Federal... environmental restoration, waste management, and related activities. Tentative Agenda: Fiscal Year...

  3. 76 FR 20651 - Environmental Management Site-Specific Advisory Board Chairs

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-13

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board Chairs AGENCY: Department of Energy. ACTION: Notice of... Environmental Management Site-Specific Advisory Board Chairs (76 FR 17118). This notice announces...

  4. 78 FR 49737 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-15

    ... Environmental Management Site-Specific Advisory Board, Northern New Mexico AGENCY: Department of Energy. ACTION... Committee of the Environmental Management Site-Specific Advisory Board (EM SSAB), Northern New Mexico (known locally as the Northern New Mexico Citizens' Advisory Board ). The Federal Advisory Committee Act (Pub....

  5. 76 FR 38143 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-29

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy, DOE... Site-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L.... ADDRESSES: Savannah Rapids Pavilion, 3300 Evans to Locks Road, Martinez, GA 30907. FOR FURTHER...

  6. 77 FR 76475 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-28

    ...] [FR Doc No: 2012-31173] DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board... notice announces a meeting of the Environmental Management Site-Specific Advisory Board (EM SSAB), Idaho... the Board is to make recommendations to DOE-EM and site management in the areas of...

  7. 75 FR 2859 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-19

    ... Environmental Management Site-Specific Advisory Board, Hanford AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... management in the areas of environmental restoration, waste management, and related activities....

  8. FLP recombinase-mediated site-specific recombination in silkworm, Bombyx mori

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A comprehensive understanding of gene function and the production of site-specific genetically modified mutants are two major goals of genetic engineering in the post-genomic era. Although site-specific recombination systems have been powerful tools for genome manipulation of many organisms, they h...

  9. 78 FR 17648 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-22

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub..., Office of Science and Technical Information, 1 Science.gov Way, Oak Ridge, Tennessee 37830. FOR...

  10. 75 FR 7576 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-22

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, March 10, 2010, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak...

  11. 78 FR 75552 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-12

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub..., Office of Science and Technical Information, 1 ] Science.gov Way, Oak Ridge, Tennessee 37830. FOR...

  12. 76 FR 22388 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-21

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, May 11, 2011; 6 p.m. ADDRESSES: DOE Information Center, 475 Oak Ridge...

  13. 77 FR 23470 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-19

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Science.gov Way, Oak Ridge, Tennessee 37830. FOR FURTHER INFORMATION CONTACT: Melyssa P. Noe,...

  14. 75 FR 65466 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-25

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, November 10, 2010, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak...

  15. 77 FR 29996 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-21

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Science.gov Way, Oak Ridge, Tennessee 37830. FOR FURTHER INFORMATION CONTACT: Melyssa P. Noe,...

  16. 76 FR 36101 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-21

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, July 13, 2011 at 6 p.m. ADDRESSES: DOE Information Center, 475 Oak...

  17. 78 FR 12746 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-25

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub..., Office of Science and Technical Information, 1 Science.gov Way, Oak Ridge, Tennessee 37830. FOR...

  18. 76 FR 59393 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-26

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, October 12, 2011; 6 p.m. ADDRESSES: DOE Information Center, 475 Oak...

  19. 75 FR 13268 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-19

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, April 14, 2010, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak...

  20. 75 FR 71424 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-23

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, December 8, 2010, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak...

  1. 78 FR 44942 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-25

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Coordinator, Department of Energy Oak Ridge Operations Office, P.O. Box 2001, EM-90, Oak Ridge, TN...

  2. 75 FR 3455 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-21

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, February 10, 2010, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak...

  3. 77 FR 45345 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-31

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Oak Ridge Operations Office, P.O. Box 2001, EM-90, Oak Ridge, TN 37831. Phone (865) 241-3315; Fax...

  4. 77 FR 64494 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-22

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub..., Office of Science and Technical Information, 1 Science.gov Way, Oak Ridge, Tennessee 37830. FOR...

  5. 76 FR 1415 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-10

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... January 12, 2011, ] meeting of the Environmental Management Site-Specific Advisory Board (EM SSAB), Oak... Coordinator, Department of Energy Oak Ridge Operations Office, P.O. Box 2001, EM-90, Oak Ridge, TN...

  6. 76 FR 28759 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-18

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Thursday, May 26, 2011, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak Ridge...

  7. 75 FR 57462 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-21

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, October 13, 2010, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak...

  8. 77 FR 74836 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-18

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub..., Office of Science and Technical Information, 1 Science.gov Way, Oak Ridge, Tennessee 37830. FOR...

  9. 75 FR 43518 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-26

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub..., Department of Energy Oak Ridge Operations Office, P.O. Box 2001, EM-90, Oak Ridge, TN 37831. Phone (865)...

  10. 77 FR 38275 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-27

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy, DoE... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Science.gov Way, Oak Ridge, Tennessee 37830. FOR FURTHER INFORMATION CONTACT: Melyssa P. Noe,...

  11. 75 FR 27998 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-19

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, June 9, 2010, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak Ridge...

  12. 78 FR 3890 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-17

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub..., Office of Science and Technical Information, 1 Science.gov Way, Oak Ridge, Tennessee 37830. FOR...

  13. 78 FR 58292 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-23

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub..., Office of Science and Technical Information, 1 Science.gov Way, Oak Ridge, Tennessee 37830. FOR...

  14. 75 FR 51027 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-18

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, September 8, 2010, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak...

  15. 78 FR 49738 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-15

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Center, Office of Science and Technical Information, 1 Science.gov Way, Oak Ridge, Tennessee 37830....

  16. 76 FR 78908 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-20

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, January 11, 2012; 6 p.m. ADDRESSES: DOE Information Center, 475 Oak...

  17. 77 FR 2714 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-19

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, February 8, 2012; 6 p.m. ADDRESSES: DOE Information Center, 475 Oak...

  18. 78 FR 23241 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-18

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub..., Office of Science and Technical Information, 1 Science.gov Way, Oak Ridge, Tennessee 37830. FOR...

  19. 76 FR 17637 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-30

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, April 13, 2011, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak...

  20. 76 FR 9572 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-18

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, March 9, 2011, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak Ridge...

  1. 75 FR 24685 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-05

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, May 12, 2010, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak Ridge...

  2. 76 FR 52944 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-24

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, September 14, 2011, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak...

  3. 77 FR 58364 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-20

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub..., Office of Science and Technical Information, 1 Science.gov Way, Oak Ridge, Tennessee 37830. FOR...

  4. 78 FR 30911 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-23

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub..., Office of Science and Technical Information, 1 Science.gov Way, Oak Ridge, Tennessee 37830. FOR...

  5. 77 FR 49442 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-16

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Center, Office of Science and Technical Information, 1 Science.gov Way, Oak Ridge, Tennessee 37830....

  6. 76 FR 4644 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-26

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, February 9, 2011, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak...

  7. 77 FR 18243 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-27

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Science.gov Way, Oak Ridge, Tennessee 37830. FOR FURTHER INFORMATION CONTACT: Melyssa P. Noe,...

  8. 76 FR 65190 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-20

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, November 9, 2011, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak...

  9. 78 FR 63171 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation; Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-23

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation; Meeting AGENCY: Department of... Management Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act..., Office of Science and Technical Information, 1 Science.gov Way, Oak Ridge, Tennessee 37830. FOR...

  10. 77 FR 9219 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-16

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy, DoE... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Information, 1 Science.gov Way, Oak Ridge, Tennessee 37830. FOR FURTHER INFORMATION CONTACT: Melyssa P....

  11. 76 FR 29732 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-23

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, June 8, 2011, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak Ridge...

  12. 75 FR 35447 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-22

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, July 14, 2010, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak Ridge...

  13. 29 CFR 1926.752 - Site layout, site-specific erection plan and construction sequence.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 29 Labor 8 2010-07-01 2010-07-01 false Site layout, site-specific erection plan and construction... Steel Erection § 1926.752 Site layout, site-specific erection plan and construction sequence. (a... intended minimum compressive design strength or sufficient strength to support the loads imposed...

  14. 29 CFR 1926.752 - Site layout, site-specific erection plan and construction sequence.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 29 Labor 8 2011-07-01 2011-07-01 false Site layout, site-specific erection plan and construction... Steel Erection § 1926.752 Site layout, site-specific erection plan and construction sequence. (a... intended minimum compressive design strength or sufficient strength to support the loads imposed...

  15. 76 FR 52944 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-24

    ... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of... (EIS) Committee of the Environmental Management Site- Specific Advisory Board (EM SSAB), Nevada. The... be announced in the Federal Register. DATES: Wednesday, September 7, 2011; 2 p.m. ADDRESSES:...

  16. 76 FR 50204 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-12

    ... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of... (EIS) Committee of the Environmental Management Site- Specific Advisory Board (EM SSAB), Nevada. The... be announced in the Federal Register. DATES: Wednesday, August 17, 2011, 2 p.m. ADDRESSES:...

  17. 76 FR 55370 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-07

    ... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of... (EIS) Committee of the Environmental Management Site- Specific Advisory Board (EM SSAB), Nevada. The... be announced in the Federal Register. DATES: Tuesday, October 4, 2011; 2 p.m. ADDRESSES: Nevada...

  18. Ligand binding and proton exchange dynamics in site-specific mutants of human myoglobin

    SciTech Connect

    Lambright, D.G.

    1992-01-01

    Site specific mutagenesis was used to make substitutions of four residues in the distal heme pocket of human myoglobin: Val68, His64, Lys45, and Asp60. Strongly diffracting crystals of the conservative mutation K45R in the met aquo form were grown in the trigonal space group P3[sub 2]21 and the X-ray crystal structure determined at 1.6 [angstrom] resolution. The overall structure is similar to that of sperm whale met aquo myoglobin. Several of the mutant proteins were characterized by 2-D NMR spectroscopy. The NMR data suggest the structural changes are localized to the region of the mutation. The dynamics of ligand binding to myoglobin mutants were studied by transient absorption spectroscopy following photolysis of the CO complexes. Transient absorption kinetics and spectra on the ns to ms timescale were measured in aqueous solution from 280 K to 310 K and in 75% glycerol: water from 250 K to 310 K. Two significant basis spectra were obtained from singular value decomposition of the matrix of time dependent spectra. The information was used to obtain approximations for the extent of ligand rebinding and the kinetics of conformational relaxation. Except for K45R, substitutions at Lys45 or Asp60 produce changes in the kinetics for ligand rebinding. Replacement of Lys45 with Arg increases the rate of ligand rebinding from the protein matrix by a factor of 2, but does not alter the rates for ligand escape or entry into the protein or the dynamics of the conformational relaxation. Substitutions at His64 and Val68 influence the kinetics of ligand rebinding and the dynamics of conformational relaxation. The results do not support the hypothesis that ligand migration between the heme pocket and solvent is determined solely by fluctuations of Arg45 and His64 between open and closed conformations of the heme pocket but can be rationalized if ligand diffusion through the protein matrix involves multiple competing pathways.

  19. FLP recombinase-mediated site-specific recombination in silkworm, Bombyx mori.

    PubMed

    Long, Ding-Pei; Zhao, Ai-Chun; Chen, Xue-Jiao; Zhang, Yang; Lu, Wei-Jian; Guo, Qing; Handler, Alfred M; Xiang, Zhong-Huai

    2012-01-01

    A comprehensive understanding of gene function and the production of site-specific genetically modified mutants are two major goals of genetic engineering in the post-genomic era. Although site-specific recombination systems have been powerful tools for genome manipulation of many organisms, they have not yet been established for use in the manipulation of the silkworm Bombyx mori genome. In this study, we achieved site-specific excision of a target gene at predefined chromosomal sites in the silkworm using a FLP/FRT site-specific recombination system. We first constructed two stable transgenic target silkworm strains that both contain a single copy of the transgene construct comprising a target gene expression cassette flanked by FRT sites. Using pre-blastoderm microinjection of a FLP recombinase helper expression vector, 32 G3 site-specific recombinant transgenic individuals were isolated from five of 143 broods. The average frequency of FLP recombinase-mediated site-specific excision in the two target strains genome was approximately 3.5%. This study shows that it is feasible to achieve site-specific recombination in silkworms using the FLP/FRT system. We conclude that the FLP/FRT system is a useful tool for genome manipulation in the silkworm. Furthermore, this is the first reported use of the FLP/FRT system for the genetic manipulation of a lepidopteran genome and thus provides a useful reference for the establishment of genome manipulation technologies in other lepidopteran species.

  20. Development of site-specific earthquake response spectra for eastern US sites

    SciTech Connect

    Beavers, J.E.; Brock, W.R.; Hunt, R.J.; Shaffer, K.E.

    1993-08-01

    Site-specific earthquake, uniform-hazard response spectra have been defined for the Department of Energy Oak Ridge, Tennessee, and Portsmouth, Ohio, sites for use in evaluating existing facilities and designing new facilities. The site-specific response spectra were defined from probabilistic and deterministic seismic hazard studies following the requirements in DOE-STD-1024-92, ``Guidelines for Probabilistic Seismic Hazard Curves at DOE Sites.` For these two sites, the results show that site-specific uniform-hazard response spectra are slightly higher in the high-frequency range and considerably lower in the low-frequency range compared with response spectra defined for these sites in the past.

  1. A METHOD FOR THE MEASUREMENT OF SITE-SPECIFIC TAUTOMERIC AND ZWITTERIONIC MICROSPECIES EQUILIBRIUM CONSTANTS

    EPA Science Inventory

    We describe a method for the individual measurement of simultaneously occurring, unimolecular, site-specific "microequilibrium" constants as in, for example, prototropic tautomerism and zwitterionic equilibria. Our method represents an elaboration of that of Nygren et al. (Anal. ...

  2. 78 FR 38969 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-28

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION... FURTHER INFORMATION CONTACT: Rachel Blumenfeld, Deputy Designated Federal Officer, Department of...

  3. 77 FR 4799 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-31

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION... FURTHER INFORMATION CONTACT: Reinhard Knerr, Deputy Designated Federal Officer, Department of...

  4. 78 FR 16260 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-14

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION... FURTHER INFORMATION CONTACT: Rachel Blumenfeld, Deputy Designated Federal Officer, Department of...

  5. 78 FR 73519 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-06

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE) ACTION: Notice... FURTHER INFORMATION CONTACT: Rachel Blumenfeld, Deputy Designated Federal Officer, Department of...

  6. 77 FR 11516 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-27

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION... FURTHER INFORMATION CONTACT: Reinhard Knerr, Deputy Designated Federal Officer, Department of...

  7. 78 FR 25064 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-29

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION... FURTHER INFORMATION CONTACT: Rachel Blumenfeld, Deputy Designated Federal Officer, Department of...

  8. 78 FR 45518 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-29

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION... FURTHER INFORMATION CONTACT: Rachel Blumenfeld, Deputy Designated Federal Officer, Department of...

  9. 76 FR 19003 - Land Disposal Restrictions: Nevada and California; Site Specific Treatment Variances for...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-06

    ... From the Federal Register Online via the Government Publishing Office ENVIRONMENTAL PROTECTION AGENCY 40 CFR Part 268 Land Disposal Restrictions: Nevada and California; Site Specific Treatment Variances for Hazardous Selenium Bearing Waste AGENCY: Environmental Protection Agency (EPA)....

  10. 76 FR 78909 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-20

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of Open Meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... environmental restoration, waste management, and related activities. Tentative Agenda Call to...

  11. METHOD FOR THE MEASUREMENT OF SITE-SPECIFIC TAUTOMERIC AND ZWITTERIONIC MICROSPECIES EQUILIBRIUM CONSTANTS

    EPA Science Inventory

    We describe a method for the individual measurement of simultaneously occurring, unimolecular, site-specific “microequilibrium” constants as in, for example, prototropic tautomerism and zwitterionic equilibria. Our method represents an elaboration of that of Nygren et al. (Anal. ...

  12. SUPPORTING THE REDEVELOPMENT OF BROWNFIELD SITES USING SITE-SPECIFIC MANAGEMENT APPROACHES AND REDEVELOPMENT TOOLS (SMART)

    EPA Science Inventory

    The Site-Specific Management Approaches and Redevelopment Tools (SMART) provides potential solutions for facilitating the redevelopment of brownfield sites. The term "brownfield site" refers to previously developed property whose reuse may be complicated by the presence of hazar...

  13. 75 FR 17701 - Environmental Management Site-Specific Advisory Board Chairs

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-07

    ... 28, 2010 EM Program Update, Priorities, and American Recovery and Reinvestment Act Discussion EM SSAB Chairs' Round Robin: Top Three Site-Specific Issues, EM SSAB Accomplishments, and Major Board...

  14. Photoelectron angular distributions of ultrathin Ni/Cu(001) films

    SciTech Connect

    Mankey, G.J.; Subramanian, K.; Stockbauer, R.L.; Kurtz, R.L.

    1996-12-31

    The authors present measurements of the evolution with film thickness of the 3d electronic states at the Fermi energy of ultrathin Ni films. The morphology and thickness of the films is determined from x-ray photoelectron spectroscopy, x-ray photoelectron diffraction and x-ray magnetic linear dichroism using synchrotron radiation. Photoelectron angular distributions were measured using an ellipsoidal mirror analyzer. Even at submonolayer Ni coverages, the 3d electronic states exhibit bulk-like properties. This is attributed to the short screening length of electrons in metals, the localization of the 3d electrons, the similarity of the Ni and Cu ion cores, and finally the interaction with the underlying fcc periodic potential.

  15. pH-sensitive nanocargo based on smart polymer functionalized graphene oxide for site-specific drug delivery.

    PubMed

    Kavitha, Thangavelu; Abdi, Syed Izhar Haider; Park, Soo-Young

    2013-04-14

    Graphene oxide (GO) was functionalized covalently with pH-sensitive poly(2-(diethylamino) ethyl methacrylate) (PDEA) by surface-initiated in situ atom transfer radical polymerization. The structure of the PDEA-grafted GO (GO-PDEA) were examined by Fourier-transform infrared spectroscopy, proton nuclear magnetic resonance spectroscopy, X-ray photoelectron spectroscopy, thermogravimetric analysis and atomic force microscopy. The grafted PDEA endowed the GO sheets with good solubility and stability in physiological solutions. Simple physisorption by π-π stacking and hydrophobic interactions on GO-PDEA can be used to load camptothecin (CPT), a widely used water-insoluble cancer drug. The loaded CPT was released only at the lower (acidic) pH normally found in a tumor environment but not in basic and neutral pH. GO-PDEA did not show practical toxicity to N2a cancer cells but the GO-PDEA-CPT complex exhibited high potency in killing N2a cancer cells in vitro. These results suggest that the GO-PDEA nanocargo carrier might be a promising material for site-specific anticancer drug delivery and controlled release.

  16. Photoelectron circular dichroism of isopropanolamine

    NASA Astrophysics Data System (ADS)

    Catone, D.; Turchini, S.; Contini, G.; Prosperi, T.; Stener, M.; Decleva, P.; Zema, N.

    2017-01-01

    Spectroscopies based on circular polarized light are sensitive to the electronic and structural properties of chiral molecules. Photoelectron circular dichroism (PECD) is a powerful technique that combines the chiral sensitivity of the circular polarized light and the electronic information obtained by photoelectron spectroscopy. An experimental and theoretical PECD study of the outer valence and C 1s core states of 1-amino-2-propanol in the gas phase is presented. The experimental dichroic dispersions in the photoelectron kinetic energy are compared with theoretical calculations employing a multicentric basis set of B-spline functions and a Kohn-Sham Hamiltonian. In order to understand analogies and differences in the dichroism of structural isomers bearing the same functional groups, a comparison with previous PECD study of valence band of 2-amino-1-propanol is carried out.

  17. Photoelectron backscattering in vacuum phototubes

    NASA Astrophysics Data System (ADS)

    Lubsandorzhiev, B. K.; Vasiliev, R. V.; Vyatchin, Y. E.; Shaibonov, B. A. J.

    2006-11-01

    In this article we describe results of studies of a photoelectron backscattering effect in vacuum phototubes: classical photomultipliers (PMT) and hybrid phototubes (PH). Late pulses occurring in PMTs are attributed to the photoelectron backscattering and distinguished from pulses due to an anode glow effect. The late pulses are measured in a number of PMTs and HPs with various photocathode sizes covering 1 50 cm range and different types of the first dynode materials and construction designs. It is shown that the late pulses are a generic feature of all vacuum photodetectors—PMTs and PHs—and they do not deteriorate dramatically amplitude and timing responses of vacuum phototubes.

  18. Photoelectron photoion molecular beam spectroscopy

    SciTech Connect

    Trevor, D.J.

    1980-12-01

    The use of supersonic molecular beams in photoionization mass spectroscopy and photoelectron spectroscopy to assist in the understanding of photoexcitation in the vacuum ultraviolet is described. Rotational relaxation and condensation due to supersonic expansion were shown to offer new possibilities for molecular photoionization studies. Molecular beam photoionization mass spectroscopy has been extended above 21 eV photon energy by the use of Stanford Synchrotron Radiation Laboratory (SSRL) facilities. Design considerations are discussed that have advanced the state-of-the-art in high resolution vuv photoelectron spectroscopy. To extend gas-phase studies to 160 eV photon energy, a windowless vuv-xuv beam line design is proposed.

  19. In vivo and in vitro characterization of site-specific recombination of actinophage R4 integrase.

    PubMed

    Miura, Takamasa; Hosaka, Yayoi; Yan-Zhuo, Yang; Nishizawa, Tomoyasu; Asayama, Munehiko; Takahashi, Hideo; Shirai, Makoto

    2011-01-01

    The site-specific integrase of actinophage R4 belongs to the serine recombinase family. During the lysogenization process, it catalyzes site-specific recombination between the phage genome and the chromosome of Streptomyces parvulus 2297. An in vivo assay using Escherichia coli cells revealed that the minimum lengths of the recombination sites attB and attP are 50-bp and 49-bp, respectively, for efficient intramolecular recombination. The in vitro assay using overproduced R4 integrases as a hexahistidine (His(6))-glutathione-S-transferase (GST)-R4 integrase fusion protein, showed that the purified protein preparation retains the site-specific recombination activity which catalyzes the site-specific recombination between attP and attB in the intermolecular reaction. It also revealed that the inverted repeat within attP is essential for efficient in vitro intermolecular recombination. In addition, a gel shift assay showed that His(6)-GST-R4 integrase bound to the 50-bp attB and 49-bp attP specifically. Moreover, based on a detailed comparison analysis of amino acid sequences of serine integrases, we found the DNA binding region that is conserved in the serine recombinase containing the large C-terminal domain. Based on the results presented on this report, attachment sites needed in vitro and in vivo for site-specific recombination by the R4 integrase have been defined more precisely. This knowledge is useful for developing new genetic manipulation tools in the future.

  20. A study to control chemical reactions using Si:2p core ionization: site-specific fragmentation.

    PubMed

    Nagaoka, Shin-ichi; Fukuzawa, Hironobu; Prümper, Georg; Takemoto, Mai; Takahashi, Osamu; Yamaguchi, Katsuhiro; Kakiuchi, Takuhiro; Tabayashi, Kiyohiko; Suzuki, Isao H; Harries, James R; Tamenori, Yusuke; Ueda, Kiyoshi

    2011-08-18

    In an aim to create a "sharp" molecular knife, we have studied site-specific fragmentation caused by Si:2p core photoionization of bridged trihalosilyltrimethylsilyl molecules in the vapor phase. Highly site-specific bond dissociation has been found to occur around the core-ionized Si site in some of the molecules studied. The site specificity in fragmentation and the 2p binding energy difference between the two Si sites depend in similar ways on the intersite bridge and the electronegativities of the included halogen atoms. The present experimental and computational results show that for efficient "cutting" the following conditions for the two atomic sites to be separated by the knife should be satisfied. First, the sites should be located far from each other and connected by a chain of saturated bonds so that intersite electron migration can be reduced. Second, the chemical environments of the atomic sites should be as different as possible.

  1. Bifunctional chelating agent for the design and development of site specific radiopharmaceuticals and biomolecule conjugation strategy

    DOEpatents

    Katti, Kattesh V.; Prabhu, Kandikere R.; Gali, Hariprasad; Pillarsetty, Nagavara Kishore; Volkert, Wynn A.

    2003-10-21

    There is provided a method of labeling a biomolecule with a transition metal or radiometal in a site specific manner to produce a diagnostic or therapeutic pharmaceutical compound by synthesizing a P.sub.2 N.sub.2 -bifunctional chelating agent intermediate, complexing the intermediate with a radio metal or a transition metal, and covalently linking the resulting metal-complexed bifunctional chelating agent with a biomolecule in a site specific manner. Also provided is a method of synthesizing the --PR.sub.2 containing biomolecules by synthesizing a P.sub.2 N.sub.2 -bifunctional chelating agent intermediate, complexing the intermediate with a radiometal or a transition metal, and covalently linking the resulting radio metal-complexed bifunctional chelating agent with a biomolecule in a site specific manner. There is provided a therapeutic or diagnostic agent comprising a --PR.sub.2 containing biomolecule.

  2. 76 FR 30027 - Land Disposal Restrictions: Site-Specific Treatment Variance for Hazardous Selenium-Bearing Waste...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-24

    ... Selenium-Bearing Waste Treated by U.S. Ecology Nevada in Beatty, NV and Withdrawal of Site-Specific... site-specific treatment variance to U.S. Ecology Nevada in Beatty, Nevada and withdrew an existing site... variance to U.S. Ecology Nevada in Beatty, Nevada and withdrawing an existing site-specific...

  3. 75 FR 11872 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-12

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Idaho National Laboratory AGENCY: Department of Energy..., Idaho National Laboratory to be held on March 16, 2010 75 FR 9590. In that notice, the meeting...

  4. 76 FR 24831 - Site-Specific Analyses for Demonstrating Compliance With Subpart C Performance Objectives

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-03

    ... proposing to amend its regulations to require low-level radioactive waste disposal facilities to conduct... safe disposal of low-level radioactive waste. The NRC is proposing additional changes to the... regulations to require low-level radioactive waste disposal facilities to conduct site-specific analyses...

  5. 75 FR 65466 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-25

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... Double Tree Hotel, 2651 Perimeter Parkway, Augusta, GA 30909. FOR FURTHER INFORMATION CONTACT:...

  6. Hellsgate Big Game Winter Range Wildlife Mitigation Site Specific Management Plan for the Hellsgate Project.

    SciTech Connect

    Berger, Matthew T.; Judd, Steven L.

    1999-01-01

    This report contains a detailed site-specific management plan for the Hellsgate Winter Range Wildlife Mitigation Project. The report provides background information about the mitigation process, the review process, mitigation acquisitions, Habitat Evaluation Procedures (HEP) and mitigation crediting, current habitat conditions, desired future habitat conditions, restoration/enhancements efforts and maps.

  7. Site-specific risk factors for ray blight in Tasmanian pyrethrum fields

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ray blight of pyrethrum, caused by Phoma ligulicola var. inoxydablis can cause significant reductions in crop growth and pyrethrin yield. Weather and site-specific disease risk factors for ray blight have not been identified or quantified in terms of relative risk, which has limited the efficiency ...

  8. Evaluation of closed-loop site-specific irrigation with wireless sensor network

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Automated site-specific sprinkler irrigation system can save water and maximize productivity, but implementing automated irrigation is challenging in system integration and decision making. A controllable irrigation system was integrated into a closed-loop control with a distributed wireless in-fiel...

  9. Software Design for Wireless Sensor-based Site-specific Irrigation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In-field sensor-based site-specific irrigation management is of benefit to producers for efficient water management. Integration of the decision making process with the controls is a viable option for determining when and where to irrigate, and how much water to apply. This research presents the des...

  10. 77 FR 2282 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-17

    ... Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy. ACTION: Notice of... of open meeting announcing a meeting on January 19, 2012, of the Environmental Management Site... being cancelled because the board will not have a quorum due to scheduling conflicts by members....

  11. Design, development and evaluation of a tree planting-site-specific fumigant applicator

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The goal of this research was to use recent advances in the global positioning system (GPS) and computer technology to apply just the right amount of fumigant where it is most needed (i.e., tree-planting-site-specific application) to decrease the incidence of replant disease, and achieve the environ...

  12. 77 FR 43583 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-25

    ... Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... management in the areas of environmental restoration, waste management and related activities....

  13. 78 FR 78952 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-27

    ... Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... management in the areas of environmental restoration, waste management and related activities....

  14. 76 FR 36100 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-21

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy. DOE. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... Board is to make recommendations to DOE-EM and site management in the areas of environmental...

  15. 75 FR 20832 - Environmental Management Site-Specific Advisory Board, Nevada Test Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-21

    ...This notice announces a meeting of the Environmental Management Site-Specific Advisory Board (EM SSAB), Nevada Test Site. The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat. 770) requires that public notice of this meeting be announced in the Federal...

  16. 76 FR 30695 - Environmental Management Site-Specific Advisory Board Chairs

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-26

    ... restoration, waste management, and related activities. Tentative Agenda Topics Wednesday, June 15, 2011 EM Program Update, EM SSAB Chairs' Round Robin: Top Three Site-Specific Topics and Achievements, EM... will make every effort to accommodate persons with physical disabilities or special needs. If...

  17. Germinal transmission of site-specific excised genomic DNA by the bacterial ParA resolvase

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genome engineering is an essential tool in research and product development. Behind some of the recent advances in plant gene transfer is the development of site-specific recombination systems that enable the precise manipulation of DNA, e.g. the deletion, integration or translocation of DNA. DNA ...

  18. 77 FR 10485 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-22

    ... Environmental Management Site-Specific Advisory Board, Idaho National Laboratory AGENCY: Department of Energy. ACTION: Notice of Open Meeting. SUMMARY: This notice announces a meeting of the Environmental Management... of the Board: The purpose of the Board is to make recommendations to DOE-EM and site management...

  19. Site-specific ionisation edge fine-structure of Rutile in the electron microscope.

    PubMed

    Hetaba, Walid; Löffler, Stefan; Willinger, Marc-Georg; Schuster, Manfred Erwin; Schlögl, Robert; Schattschneider, Peter

    2014-08-01

    Combined Bloch-wave and density functional theory simulations are performed to investigate the effects of different channelling conditions on the fine-structure of electron energy-loss spectra. The simulated spectra compare well with experiments. Furthermore, we demonstrate that using this technique, the site-specific investigation of atomic orbitals is possible. This opens new possibilities for chemical analyses.

  20. 78 FR 10612 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-14

    ... Environmental Management Site-Specific Advisory Board, Northern New Mexico AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Northern New Mexico (known locally as the Northern New Mexico Citizens... INFORMATION CONTACT: Menice Santistevan, Northern New Mexico Citizens' Advisory Board, 94 Cities of Gold...

  1. 76 FR 11772 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-03

    ... Environmental Management Site-Specific Advisory Board, Northern New Mexico AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Northern New Mexico (known locally as the Northern New Mexico Citizens... Norte, Espanola, New Mexico 87532. FOR FURTHER INFORMATION CONTACT: Menice Santistevan, Northern...

  2. 76 FR 18540 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-04

    ... Environmental Management Site-Specific Advisory Board, Northern New Mexico AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Northern New Mexico (known locally as the Northern New Mexico Citizens....m.-4 p.m. ADDRESSES: Holiday Inn Express and Suites, 60 Entrada Drive, Los Alamos, New Mexico...

  3. 76 FR 11773 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-03

    ... Environmental Management Site-Specific Advisory Board, Northern New Mexico AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Northern New Mexico. The Federal Advisory Committee Act (Pub. L. 92-463..., Santa Fe, New Mexico 87507. FOR FURTHER INFORMATION CONTACT: Menice Santistevan, Northern New...

  4. 78 FR 49739 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-15

    ... Environmental Management Site-Specific Advisory Board, Northern New Mexico AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Northern New Mexico. The Federal Advisory Committee Act (Pub. L. 92-463... Pueblo Sur, Taos, New Mexico 87571. FOR FURTHER INFORMATION CONTACT: Menice Santistevan, Northern...

  5. 77 FR 24695 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-25

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. . 92... Hilton Savannah DeSoto, 15 East Liberty Street Savannah, GA 31401. FOR FURTHER INFORMATION CONTACT:...

  6. 75 FR 24684 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-05

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463..., 601 East Bay Street, Savannah, Georgia 31401. FOR FURTHER INFORMATION CONTACT: Gerri Flemming,...

  7. 76 FR 25682 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-05

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463... Savannah, Two West Bay Street, Savannah, GA 31402. FOR FURTHER INFORMATION CONTACT: Gerri Flemming,...

  8. 77 FR 53193 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-31

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463... CONTACT: Gerri Flemming, Office of External Affairs, Department of Energy, Savannah River...

  9. 77 FR 13104 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-05

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463... of External Affairs, Department of Energy, Savannah River Operations Office, P.O. Box A, Aiken,...

  10. 78 FR 26005 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-03

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463...: Gerri Flemming, Office of External Affairs, Department of Energy, Savannah River Operations Office,...

  11. 78 FR 14088 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-04

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act requires that....m.-5:30 p.m.; Tuesday, March 26, 2013, 8:00 a.m.-4:30 p.m. ADDRESSES: Westin Savannah Harbor,...

  12. 76 FR 55369 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-07

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463... Flemming, Office of External Affairs, Department of Energy, Savannah River Operations Office, P.O. Box...

  13. 76 FR 65706 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-24

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463... Flemming, Office of External Affairs, Department of Energy, Savannah River Operations Office, P.O. Box...

  14. 78 FR 716 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-04

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463..., Office of External Affairs, Department of Energy, Savannah River Operations Office, P.O. Box A, Aiken,...

  15. 75 FR 39007 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-07

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463...: Gerri Flemming, Office of External Affairs, Department of Energy, Savannah River Operations Office,...

  16. 75 FR 82001 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-29

    ..., Savannah River Site AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific Advisory Board (EM SSAB), Savannah River... FURTHER INFORMATION CONTACT: Gerri Flemming, Office of External Affairs, Department of Energy,...

  17. 78 FR 65979 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-04

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463..., Office of External Affairs, Department of Energy, Savannah River Operations Office, P.O. Box A, Aiken,...

  18. 75 FR 57462 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-21

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. No. 92...: Gerri Flemming, Office of External Affairs, Department of Energy, Savannah River Operations Office,...

  19. 76 FR 11772 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-03

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463... of External Affairs, Department of Energy, Savannah River Operations Office, P.O. Box A, Aiken,...

  20. 78 FR 16260 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-14

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board, Savannah River Site (78 FR 14088). This document makes a correction to that notice..., Savannah River Operations Office, P.O. ] Box A, Aiken, SC 29802; Phone: (803) 952-7886. Corrections In...

  1. 77 FR 60688 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-04

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463... Flemming, Office of External Affairs, Department of Energy, Savannah River Operations Office, P.O. Box...

  2. 78 FR 54461 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-04

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463.... ADDRESSES: Embassy Suites-Savannah, 145 Mulberry Boulevard, Savannah, GA 31322. FOR FURTHER...

  3. 77 FR 39235 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-02

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463...: Gerri Flemming, Office of External Affairs, Department of Energy, Savannah River Operations Office,...

  4. 78 FR 40130 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-03

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. No. 92... CONTACT: Gerri Flemming, Office of External Affairs, Department of Energy, Savannah River...

  5. 75 FR 9885 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-04

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463... External Affairs, Department of Energy, Savannah River Operations Office, P.O. Box A, Aiken, SC...

  6. 30 CFR 46.11 - Site-specific hazard awareness training.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 30 Mineral Resources 1 2013-07-01 2013-07-01 false Site-specific hazard awareness training. 46.11 Section 46.11 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR EDUCATION AND TRAINING TRAINING AND RETRAINING OF MINERS ENGAGED IN SHELL DREDGING OR EMPLOYED AT SAND, GRAVEL,...

  7. 30 CFR 46.11 - Site-specific hazard awareness training.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Site-specific hazard awareness training. 46.11 Section 46.11 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR EDUCATION AND TRAINING TRAINING AND RETRAINING OF MINERS ENGAGED IN SHELL DREDGING OR EMPLOYED AT SAND, GRAVEL,...

  8. 30 CFR 46.11 - Site-specific hazard awareness training.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Site-specific hazard awareness training. 46.11 Section 46.11 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR EDUCATION AND TRAINING TRAINING AND RETRAINING OF MINERS ENGAGED IN SHELL DREDGING OR EMPLOYED AT SAND, GRAVEL,...

  9. 30 CFR 46.11 - Site-specific hazard awareness training.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 30 Mineral Resources 1 2014-07-01 2014-07-01 false Site-specific hazard awareness training. 46.11 Section 46.11 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR EDUCATION AND TRAINING TRAINING AND RETRAINING OF MINERS ENGAGED IN SHELL DREDGING OR EMPLOYED AT SAND, GRAVEL,...

  10. 30 CFR 46.11 - Site-specific hazard awareness training.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 30 Mineral Resources 1 2012-07-01 2012-07-01 false Site-specific hazard awareness training. 46.11 Section 46.11 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR EDUCATION AND TRAINING TRAINING AND RETRAINING OF MINERS ENGAGED IN SHELL DREDGING OR EMPLOYED AT SAND, GRAVEL,...

  11. 78 FR 63172 - Environmental Management Site-Specific Advisory Board, Paducah; Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-23

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Paducah; Meeting AGENCY: Department of Energy (DOE... of Energy Paducah Site Office, Post Office Box 1410, MS-103, Paducah, Kentucky 42001, (270)...

  12. 76 FR 18921 - Land Disposal Restrictions: Nevada and California; Site Specific Treatment Variances for...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-06

    ... Variances for Hazardous Selenium Bearing Waste AGENCY: Environmental Protection Agency (EPA). ACTION: Direct...-Bearing Waste II. Basis for This Determination III. Development of This Variance A. U.S. Ecology Nevada... from 0.16 mg/L to 5.7 mg/L TCLP. C. Site-Specific Treatment Variance for Selenium-Bearing Waste On...

  13. 76 FR 57981 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-19

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... Board is to make recommendations to DOE-EM and site management in the areas of environmental...

  14. 77 FR 59598 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-28

    ... Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... management in the areas of environmental restoration, waste management and related activities....

  15. 78 FR 32640 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-31

    ... Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION: Notice of Open Meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... management in the areas of environmental restoration, waste management and related activities....

  16. 77 FR 29997 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-21

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... Board is to make recommendations to DOE-EM and site management in the areas of environmental...

  17. Site-specific mouth rinsing can improve oral odor by altering bacterial counts

    PubMed Central

    Alqumber, Mohammed A.; Arafa, Khaled A.

    2014-01-01

    Objectives: To determine whether site-specific mouth rinsing with oral disinfectants can improve oral odor beyond the traditional panoral mouth disinfection with mouth rinses by targeting specifically oral malodor implicated anaerobic bacteria Methods: Twenty healthy fasting subjects volunteered for a blinded prospective, descriptive correlational crossover cross-section clinical trial conducted during the month of Ramadan between July and August 2013 in Albaha province in Saudi Arabia involving the application of Listerine® Cool Mint® mouth rinse by either the traditional panoral rinsing method, or a site-specific disinfection method targeting the subgingival and supragingival plaque and the posterior third of the tongue dorsum, while avoiding the remaining locations within the oral cavity. The viable anaerobic and aerobic bacterial counts, volatile sulfur compounds (VSCs) levels, organoleptic assessment of oral odor, and the tongue-coating index were compared at baseline, one, 5, and 9 hours after the treatment. Results: The site-specific disinfection method reduced the VSCs and anaerobic bacterial loads while keeping the aerobic bacterial numbers higher than the traditional panoral rinsing method. Conclusion: Site-specific disinfection can more effectively maintain a healthy oral cavity by predominantly disinfecting the niches of anaerobic bacteria within the oral cavity. PMID:25399224

  18. Automated measurement of site-specific N-glycosylation occupancy with SWATH-MS.

    PubMed

    Xu, Ying; Bailey, Ulla-Maja; Schulz, Benjamin L

    2015-07-01

    Asparagine-linked glycosylation is a common post-translational modification of proteins catalyzed by oligosaccharyltransferase that is important in regulating many aspects of protein function. Analysis of protein glycosylation, including glycoproteomic measurement of the site-specific extent of glycosylation, remains challenging. Here, we developed methods combining enzymatic deglycosylation and protease digestion with SWATH-MS to enable automated measurement of site-specific occupancy at many glycosylation sites. Deglycosylation with peptide-endoglycosidase H, leaving a remnant N-acetylglucosamine on asparagines previously carrying high-mannose glycans, followed by trypsin digestion allowed robust automated measurement of occupancy at many sites. Combining deglycosylation with the more general peptide-N-glycosidase F enzyme with AspN protease digest allowed robust automated differentiation of nonglycosylated and deglycosylated forms of a given glycosylation site. Ratiometric analysis of deglycosylated peptides and the total intensities of all peptides from the corresponding proteins allowed relative quantification of site-specific glycosylation occupancy between yeast strains with various isoforms of oligosaccharyltransferase. This approach also allowed robust measurement of glycosylation sites in human salivary glycoproteins. This method for automated relative quantification of site-specific glycosylation occupancy will be a useful tool for research with model systems and clinical samples.

  19. 78 FR 30910 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-23

    ... Environmental Management Site-Specific Advisory Board, Idaho National Laboratory AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management... the Board is to make recommendations to DOE-EM and site management in the areas of...

  20. 75 FR 24685 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-05

    ... Environmental Management Site-Specific Advisory Board, Idaho National Laboratory AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management... Board: The purpose of the Board is to make recommendations to DOE-EM and site management in the areas...

  1. SITE-SPECIFIC PROTOCOL FOR MEASURING SOIL RADON POTENTIALS FOR FLORIDA HOUSES

    EPA Science Inventory

    The report describes a protocol for site-specific measurement of radon potentials for Florida houses that is consistent with existing residential radon protection maps. The protocol gives further guidance on the possible need for radon-protective house construction features. In a...

  2. 78 FR 38305 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-26

    ... Environmental Management Site-Specific Advisory Board, Northern New Mexico AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Northern New Mexico. The Federal Advisory Committee Act (Pub. L. 92-463... 87544. ] FOR FURTHER INFORMATION CONTACT: Menice Santistevan, Northern New Mexico Citizens'...

  3. 77 FR 47047 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-07

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Northern New Mexico AGENCY: Department of Energy. ACTION... Why? Database Guided Tour Data Input and Validation and Verification Process 4:45 p.m. Wrap-up...

  4. Site-specific management of soil pH and nutrients in blueberry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Site-specific management of soil pH and fertilizers is one of the most promising strategies in precision agriculture and is potentially applicable to many horticultural crops, including blueberry. Unlike most fruit crops, blueberry is adapted to low soil pH conditions in the range of 4-5.5 and has ...

  5. Evaluation of water-effect ratio methodology for establishing site-specific water quality criteria

    SciTech Connect

    Welsh, P.G.; Lipton, J.; Chapman, G.A.

    2000-06-01

    One approach outlined by the US Environmental Protection Agency (US EPA) for derivation of site-specific water quality criteria for metals in natural surface waters involves the development of water-effect ratios (WERs). This approach entails multiplying national water quality criteria by an experimentally derived WER, where the WER is defined as the ratio of the toxicity of the metal in the site water to the toxicity of the same metal in standard laboratory water. The authors discuss technical issues associated with test methods described in the US EPA WER guidance documents that may lead to inappropriate WERs. Critical issues include accounting for differences in calcium and magnesium concentrations (Ca:Mg ratios), alkalinity, and pH between site and laboratory waters; ensuring appropriate fish acclimation; and accounting for interspecies variability, multiple metals interactions, end-point variability, and temporal and spatial variability in the derivation of the WER. Failure to address these issues may have the unintended effect of deriving site-specific water quality criteria that are underprotective of aquatic life. The authors recommend that WER testing and future regulatory guidance for derivation of site-specific water quality criteria incorporate consideration of these potential confounding variables so that site-specific criteria can be established with greater confidence.

  6. Summary of some feasibility studies for site-specific solar industrial process heat

    SciTech Connect

    1982-01-01

    Some feasibility studies for several different site specific solar industrial process heat applications are summarized. The followng applications are examined. Leather Tanning; Concrete Production: Lumber and Paper Processing; Milk Processing; Molding, Curing or Drying; Automobile Manufacture; and Food Processing and Preparation. For each application, site and process data, system design, and performance and cost estimates are summarized.

  7. CAN SITE-SPECIFIC TRENDS BE EXTRAPOLATED TO A REGION? AN ACIDIFICATION EXAMPLE FOR THE NORTHEAST

    EPA Science Inventory

    In the absence of true regional data on changes in the acid/base status of lakes in the northeastern United States, we explore the possibility of using site-specific trends information from a judgment sample of lakes to assess the efficacy of the Clean Air Act Amendments. A meta-...

  8. Derivation of site-specific skeletal masses within the current ICRP age series.

    PubMed

    Watchman, Christopher J; Hasenauer, Deanna; Bolch, Wesley E

    2007-06-07

    The calculation of absorbed dose to the radiosensitive tissues of the skeleton is routinely performed using reference masses provided in publications from the International Commission on Radiological Protection (ICRP). These values typically include total skeleton tissue masses by reference subject age, but not by individual bone site at a given age. Site-specific variations in absorbed fractions are known to occur for internal alpha-particle and beta-particle emitters, and in certain medical dose reconstructions, site-specific estimates of marrow dose may be desirable. Furthermore, bone-site-specific tissue masses are required to properly estimate skeletal-averaged absorbed fractions and, more importantly, specific absorbed fractions for internalized radionuclides and radiopharmaceuticals. Reference masses by skeletal site are also needed in the development of ICRP compliant tomographic phantoms, as this organ system is initially segmented from medical images only as a homogeneous tissue region. ICRP reference skeletal masses are assigned based upon several independent data sources, many of which may not be entirely consistent with one another. In this study, a methodology is presented, using data from the various ICRP publications, to derive site-specific skeletal tissue masses for each member of the ICRP age series. Active marrow masses are calculated and differences are shown with respect to ICRP Publications 70 and 89 values. New data for a revised surrogate tissue region for the osteoprogenitor cells within bone marrow is presented with estimates of its total mass throughout the skeleton and for different subject ages.

  9. 36 CFR 219.33 - Appeals of site-specific decisions.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 36 Parks, Forests, and Public Property 2 2010-07-01 2010-07-01 false Appeals of site-specific decisions. 219.33 Section 219.33 Parks, Forests, and Public Property FOREST SERVICE, DEPARTMENT OF AGRICULTURE PLANNING National Forest System Land and Resource Management Planning Objections and Appeals §...

  10. 78 FR 61348 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-03

    ...On September 16, 2013, in FR Doc. 2013-22453, on page 56871, the Department of Energy (DOE) published a notice of open meeting announcing a meeting on October 2, 2013 of the Environmental Management Site-Specific Advisory Board, Portsmouth (78 FR 56871). This notice announces the cancellation of this...

  11. The Bxb1 recombination system demonstrates heritable transmission of site-specific excision in Arabidopsis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: The mycobacteriophage large serine recombinase Bxb1 catalyzes site-specific recombination between its corresponding attP and attB recognition sites. Previously, we and others have shown that Bxb1 has catalytic activity in various eukaryotic species including Nicotiana tabacum, Schizosacc...

  12. The parA resolvase performs site-specific genomic excision in Arabidopsis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have designed a site-specific excision detection system in Arabidopsis to study the in planta activity of the small serine recombinase ParA. Using a transient expression assay as well as stable transgenic plant lines, we show that the ParA recombinase is catalytically active and capable of perfo...

  13. Site-specific Topguard application based on aerial imagery for effective management of cotton root rot

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cotton root rot is a century-old cotton disease that can be controlled with Topguard Fungicide recently. As this disease tends to occur in the same general areas within fields in recurring years, site-specific application of the fungicide only to the infected areas can be more effective and economic...

  14. Development of Unmanned Aerial Vehicles for Site-Specific Crop Production Management

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Unmanned Aerial Vehicles (UAV) have been developed and applied to support the practice of precision agriculture. Compared to piloted aircrafts, an Unmanned Aerial Vehicle can focus on much smaller crop fields with much lower flight altitude than regular airplanes to perform site-specific management ...

  15. Integration of aerial imaging and variable-rate technology for site-specific aerial herbicide application

    Technology Transfer Automated Retrieval System (TEKTRAN)

    As remote sensing and variable rate technology are becoming more available for aerial applicators, practical methodologies on effective integration of these technologies are needed for site-specific aerial applications of crop production and protection materials. The objectives of this study were to...

  16. 77 FR 2713 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-19

    ... open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... open to the public. The EM SSAB, Hanford, welcomes the attendance of the public at its advisory... above. Minutes will also be available at the following Web site:...

  17. 75 FR 64718 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-20

    ... open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific.... Open Government Plan. Public Participation: The meeting is open to the public. The EM SSAB, Hanford....hanford.gov/page.cfm/hab . Issued at Washington, DC, on October 14, 2010. Rachel Samuel, Deputy...

  18. 78 FR 4139 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-18

    ... open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... Advisory Board (HAB) advice on the TC&WMFEIS. Status from Executive Issues Committee issues managers regarding HAB draft recommendations for Board diversity and other Board effectiveness issues....

  19. 77 FR 64112 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-18

    ... Committee Reports Board Business--Selection of new HAB Chair Public Participation: The meeting is open to... open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... Protection Agency Draft White Paper on Hanford Advisory Board (HAB) Values Draft Letter/Advice--Other...

  20. 75 FR 6018 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-05

    ... open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... Discussion of HAB member comments on the TC and WM EIS Development of HAB advice principles Adjourn Public Participation: The meeting is open to the public. The EM SSAB, Hanford, welcomes the attendance of the public...

  1. 75 FR 8050 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-23

    ... open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... Environmental Impact Statement. Board Business. Public Participation: The meeting is open to the public. The EM.../page.cfm/hab . Issued at Washington, DC, on February 18, 2010. Rachel Samuel, Deputy...

  2. 77 FR 48131 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-13

    ... open meeting. SUMMARY: This notice announces a meeting of the Environmental ] Management Site-Specific... Board (HAB) Values White Paper Fiscal Year 2012 Board Accomplishments 2013 Tri-Party Agreement Priorities and HAB Work Plan Priorities 2013 HAB Meeting Calendar Board Business HAB Budget...

  3. 76 FR 14386 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-16

    ... open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific...: The meeting is open to the public. The EM SSAB, Hanford, welcomes the attendance of the public at its... site: http://www.hanford.gov/page.cfm/hab . Issued at Washington, DC, on March 11, 2011. LaTanya...

  4. 76 FR 28218 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-16

    ... open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... Discussions: Issue Managers. Advice Development. Public Participation: The meeting is open to the public. The... the following Web site: http://www.hanford.gov/page.cfm/hab . ] Issued at Washington, DC on May...

  5. 75 FR 13269 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-19

    ... Open Meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... meeting is open to the public. The EM SSAB, Hanford, welcomes the attendance of the public at its advisory.... Minutes will also be available at the following website: http://www.hanford.gov/page.cfm/hab . Issued...

  6. 75 FR 27999 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-19

    ... open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific..., M-91) 2012 Budget Request Board Business Public Participation: The meeting is open to the public... also be available at the following Web site: http://www.hanford.gov/page.cfm/hab . Issued at...

  7. Appreciating "Thirdspace": An Alternative Way of Viewing and Valuing Site-Specific Dance Performance

    ERIC Educational Resources Information Center

    Munjee, Tara

    2014-01-01

    Site-specific dance performance involves the presentation of choreography in connection with a site. The context of the site combined with a viewer's personal history, beliefs, and identity impact the reading and appreciation of the performance. Although both stage and site dance performance valuing elicit multiple interpretations of artistic…

  8. 75 FR 82001 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-29

    ... Board, Oak Ridge Reservation AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific Advisory Board (EM SSAB), Oak... Center, 475 Oak Ridge Turnpike, Oak Ridge, Tennessee 37830. FOR FURTHER INFORMATION CONTACT: Patricia...

  9. Site-specific management of pH-induced iron chlorosis of maize

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A study was conducted over nine site/years in Nebraska, USA between 2004 and 2005 to evaluate the potential to predict chlorosis-prone areas within fields which are relatively stable in space and time. The study also investigated the potential benefits of site-specific cultivar management according ...

  10. Use of GIS-based Site-specific Nitrogen Management for Improving Energy Efficiency

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To our knowledge, geographical information system (GIS)-based site-specific nitrogen management (SSNM) techniques have not been used to assess agricultural energy costs and efficiency. This chapter uses SSNM case studies for corn (Zea mays L.) grown in Missouri and cotton (Gossypium hirsutum L.) gro...

  11. Design, synthesis, and characterization of nucleosomes containing site-specific DNA damage.

    PubMed

    Taylor, John-Stephen

    2015-12-01

    How DNA damaged is formed, recognized, and repaired in chromatin is an area of intense study. To better understand the structure activity relationships of damaged chromatin, mono and dinucleosomes containing site-specific damage have been prepared and studied. This review will focus on the design, synthesis, and characterization of model systems of damaged chromatin for structural, physical, and enzymatic studies.

  12. 40 CFR 170.232 - Knowledge of labeling and site-specific information.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Knowledge of labeling and site... (CONTINUED) PESTICIDE PROGRAMS WORKER PROTECTION STANDARD Standard for Pesticide Handlers § 170.232 Knowledge of labeling and site-specific information. (a) Knowledge of labeling information. (1) The...

  13. Stoichiometry of site-specific lysine acetylation in an entire proteome.

    PubMed

    Baeza, Josue; Dowell, James A; Smallegan, Michael J; Fan, Jing; Amador-Noguez, Daniel; Khan, Zia; Denu, John M

    2014-08-01

    Acetylation of lysine ϵ-amino groups influences many cellular processes and has been mapped to thousands of sites across many organisms. Stoichiometric information of acetylation is essential to accurately interpret biological significance. Here, we developed and employed a novel method for directly quantifying stoichiometry of site-specific acetylation in the entire proteome of Escherichia coli. By coupling isotopic labeling and a novel pairing algorithm, our approach performs an in silico enrichment of acetyl peptides, circumventing the need for immunoenrichment. We investigated the function of the sole NAD(+)-dependent protein deacetylase, CobB, on both site-specific and global acetylation. We quantified 2206 peptides from 899 proteins and observed a wide distribution of acetyl stoichiometry, ranging from less than 1% up to 98%. Bioinformatic analysis revealed that metabolic enzymes, which either utilize or generate acetyl-CoA, and proteins involved in transcriptional and translational processes displayed the highest degree of acetylation. Loss of CobB led to increased global acetylation at low stoichiometry sites and induced site-specific changes at high stoichiometry sites, and biochemical analysis revealed altered acetyl-CoA metabolism. Thus, this study demonstrates that sirtuin deacetylase deficiency leads to both site-specific and global changes in protein acetylation stoichiometry, affecting central metabolism.

  14. 78 FR 64932 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-30

    ..., November 20, 2013, 5:00 p.m. ADDRESSES: National Atomic Testing Museum, 755 E. Flamingo Road, Las Vegas... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of... Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat....

  15. 78 FR 17192 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-20

    ... 17, 2013 5:00 p.m. ADDRESSES: National Atomic Testing Museum, 755 E. Flamingo Road, Las Vegas, Nevada... Underground Testing Area Activity Public Participation: The EM SSAB, Nevada, welcomes the attendance of the... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice...

  16. 77 FR 75627 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-21

    ... 16, 2013, 5:00 p.m. ADDRESSES: National Atomic Testing Museum, 755 E. Flamingo Road, Las Vegas... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of... Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat....

  17. 75 FR 48662 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-11

    ...: Wednesday, September 1, 2010, 4 p.m. ADDRESSES: Atomic Testing Museum, 755 East Flamingo Road, Las Vegas... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of... Advisory Board (EM SSAB), Nevada Test Site. The Federal Advisory Committee Act (Pub. L. 92-463, 86...

  18. 76 FR 21878 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-19

    ..., 2011, 5 p.m. ADDRESSES: Atomic Testing Museum, 755 East Flamingo Road, Las Vegas, Nevada 89119. FOR... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of... Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat....

  19. 77 FR 49442 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-16

    ..., September 12, 2012, 4:00 p.m. ADDRESSES: Atomic Testing Museum, 755 E. Flamingo Road, Las Vegas, Nevada... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of... Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub. L. No. 92-463, 86 Stat....

  20. 78 FR 23760 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-22

    ..., 2013, 5:00 p.m. ADDRESSES: National Atomic Testing Museum, 755 E. Flamingo Road, Las Vegas, Nevada... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of... Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat....

  1. 76 FR 10343 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-24

    ..., 2011, 5 p.m. ADDRESSES: Atomic Testing Museum, 755 East Flamingo Road, Las Vegas, Nevada 89119. FOR... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of... Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat....

  2. 76 FR 51362 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-18

    ..., September 14, 2011, 4 p.m. ADDRESSES: Atomic Testing Museum, 755 East Flamingo Road, Las Vegas, Nevada 89119... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of... Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat....

  3. 77 FR 24694 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-25

    ..., 2012, 5 p.m. ADDRESSES: Atomic Testing Museum, 755 East Flamingo Road, Las Vegas, Nevada 89119. FOR... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of... Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat....

  4. 77 FR 66962 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-08

    ..., November 28, 2012, 5:00 p.m. ADDRESSES: National Atomic Testing Museum, 755 E. Flamingo Road, Las Vegas... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of... Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat....

  5. 40 CFR 60.3019 - What site-specific documentation is required?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 6 2010-07-01 2010-07-01 false What site-specific documentation is required? 60.3019 Section 60.3019 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR... operators that addresses the nine topics described in paragraphs (a)(1) through (9) of this section....

  6. 40 CFR 60.2910 - What site-specific documentation is required?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 6 2010-07-01 2010-07-01 false What site-specific documentation is required? 60.2910 Section 60.2910 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR... facility and readily accessible for all OSWI unit operators that addresses the nine topics described...

  7. 40 CFR 60.2095 - What site-specific documentation is required?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 6 2010-07-01 2010-07-01 false What site-specific documentation is required? 60.2095 Section 60.2095 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR... ten topics described in paragraphs (a)(1) through (10) of this section. You must maintain...

  8. 40 CFR 60.2660 - What site-specific documentation is required?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 6 2010-07-01 2010-07-01 false What site-specific documentation is required? 60.2660 Section 60.2660 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR... accessible for all CISWI unit operators that addresses the ten topics described in paragraphs (a)(1)...

  9. 40 CFR 60.2095 - What site-specific documentation is required?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 7 2013-07-01 2013-07-01 false What site-specific documentation is required? 60.2095 Section 60.2095 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR... readily accessible for all CISWI unit operators that addresses the ten topics described in paragraphs...

  10. Site-specific management of cotton root rot using airborne and satellite imagery

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cotton root rot is a serious cotton disease that can now be effectively controlled with Topguard Terra Fungicide. The objectives of this research were to demonstrate how site-specific fungicide application could be implemented based on historical remote sensing imagery and variable rate technology. ...

  11. 77 FR 2283 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-17

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site..., Department of Energy Portsmouth/Paducah Project Office, Post Office Box 700, Piketon, Ohio 45661, (740)...

  12. 77 FR 6790 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-09

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site..., Department of Energy Portsmouth/Paducah Project Office, Post Office Box 700, Piketon, Ohio 45661, (740)...

  13. Use of GIS-based site-specific nitrogen management for improving energy efficiency

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Nitrogen (N) is a significant energy component of in support of crop production but it can be highly variable within fields. To our knowledge, no efforts have been made to employ GIS-based site-specific N management (SSNM) to assess and improve energy costs and efficiency. We examine recent SSNM ca...

  14. 78 FR 75552 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-12

    ...This notice announces a combined meeting of the Environmental Monitoring and Remediation Committee and Waste Management Committee of the Environmental Management Site-Specific Advisory Board (EM SSAB), Northern New Mexico (known locally as the Northern New Mexico Citizens' Advisory Board [NNMCAB]). The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat. 770) requires that public notice of......

  15. 77 FR 16021 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-19

    ... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of... Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat. 770... Street, Pahrump, Nevada 89048. FOR FURTHER INFORMATION CONTACT: Denise Rupp, Board Administrator,...

  16. 75 FR 6370 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-09

    ... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of... Advisory Board (EM SSAB), Nevada Test Site. The Federal Advisory Committee Act (Pub. L. No. 92-463, 86 Stat..., Nevada 89131. FOR FURTHER INFORMATION CONTACT: Denise Rupp, Board Administrator, 232 Energy Way, M/S...

  17. 77 FR 39234 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-02

    ... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of... Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat. 770..., 2012, 5 p.m. ADDRESSES: Bob Ruud Community Center, 150 North Highway 160, Pahrump, Nevada 89060....

  18. 76 FR 12349 - Environmental Management Site-Specific Advisory Board, Nevada; Correction

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-07

    ... Environmental Management Site-Specific Advisory Board, Nevada; Correction AGENCY: Department of Energy. ACTION..., Nevada to be held on March 9, 2011 (76 FR 10343). This document makes several corrections to that notice... Vegas, Nevada 89030. Phone: (702) 657- 9088; Fax (702) 295-5300 or E-mail:...

  19. 76 FR 59393 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-26

    ... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of... Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat. 770... 12, 2011, 5 p.m. ADDRESSES: Las Vegas Country Club, 3000 Joe W. Brown Boulevard, Las Vegas,...

  20. 78 FR 46330 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-31

    ... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ] ACTION: Notice of... Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat. 770... 21, 2013 5:00 p.m. ADDRESSES: Bob Ruud Community Center, 150 N. Highway 160, Pahrump, Nevada...

  1. 77 FR 12044 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-28

    ... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of... Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat. 770... Vegas, Nevada 89135. FOR FURTHER INFORMATION CONTACT: Denise Rupp, Board Administrator, 232 Energy...

  2. Photoelectron spectroscopy of molecular clusters

    NASA Astrophysics Data System (ADS)

    Zhang, Xu; Pitts, Jonathan; Zheng, Chaowen; Knee, Joseph L.

    1995-09-01

    High resolution photoelectron spectroscopy is applied to the study of molecular clusters. The primary species studied are fluorene-Arn complexes. Spectroscopy of the neutral S1 state has been performed on clusters as large as n equals 30. In order to study the photoelectron spectra of the clusters size selectively mass analyzed threshold ionization (MATI) is used which is a mass resolved version of the ZEKE technique. MATI spectroscopy has been applied to clusters up to n equals 5. The spectral shifts in the S1 origin and ion threshold are used as a measure of the relative stability of the different clusters. Using previous experimental and theoretical work on related clusters the structures of the clusters are inferred from the observed spectral shifts. In some cases multiple conformations of a particular cluster size are identified.

  3. Combining site-specific mutagenesis and seeding as a strategy to crystallize ‘difficult’ proteins: the case of Staphylococcus aureus thioredoxin

    SciTech Connect

    Roos, Goedele; Brosens, Elke; Wahni, Khadija; Desmyter, Aline; Spinelli, Silvia; Wyns, Lode; Messens, Joris; Loris, Remy

    2006-12-01

    S. aureus thioredoxin was crystallized using a combination of seeding and site-specific mutagenesis. The P31T mutant of Staphylococcus aureus thioredoxin crystallizes spontaneously in space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 41.7, b = 49.5, c = 55.6 Å. The crystals diffract to 2.2 Å resolution. Isomorphous crystals of wild-type thioredoxin as well as of other point mutants only grow when seeded with the P31T mutant. These results suggest seeding as a valuable tool complementing surface engineering for proteins that are hard to crystallize.

  4. Insect pest densities across site-specific management zones of irrigated corn in northeastern Colorado.

    PubMed

    Davidson, Silas A; Peairs, Frank B; Khosla, Rajiv

    2007-06-01

    The ability to manage insect pests in a site-specific manner is hindered by the costs and time required to describe pest densities and distributions. The purpose of this study was to determine whether insect pest distributions are related to site-specific management zones (SSMZs). Site-specific management zones, as described in this study, delineate fields into three zones of similar yield potential: high, medium, and low productivity. If insect densities vary across SSMZs, it is possible that management decisions could be made at the SSMZ level instead of treating the whole field. This research was conducted during summers 2001 and 2002 on cooperators' farms in northeastern Colorado. Surveys were conducted within corn, Zea mays L., fields, so that densities of three common insect pests of Colorado corn could be compared across SSMZ. The three insect pests were western corn rootworm, Diabrotica virgifera virgifera LeConte; European corn borer, Ostrinia nubilalis (HiAbner); and western bean cutworm, Richia albicosta (Smith). D. v. virgifera larvae and adults were most common in the high-productivity SSMZ. O. nubilalis larval abundance was similar at three fields, whereas in a fourth field the larvae were most common in the high-productivity SSMZ. In one field that contained substantial numbers of R. albicosta, egg abundance was similar across SSMZs, whereas larvae were most common in the high-productivity SSMZ. Site-specific management zones seemed to correlate well with the abundance of some insect pests and might prove useful for managing insects in a site-specific manner.

  5. Site-Specific Tandem Knoevenagel Condensation-Michael Addition To Generate Antibody-Drug Conjugates.

    PubMed

    Kudirka, Romas A; Barfield, Robyn M; McFarland, Jesse M; Drake, Penelope M; Carlson, Adam; Bañas, Stefanie; Zmolek, Wes; Garofalo, Albert W; Rabuka, David

    2016-11-10

    Expanded ligation techniques are sorely needed to generate unique linkages for the growing field of functionally enhanced proteins. To address this need, we present a unique chemical ligation that involves the double addition of a pyrazolone moiety with an aldehyde-labeled protein. This ligation occurs via a tandem Knoevenagel condensation-Michael addition. A pyrazolone reacts with an aldehyde to generate an enone, which undergoes subsequent attack by a second pyrazolone to generate a bis-pyrazolone species. This rapid and facile ligation technique is performed under mild conditions in the absence of catalyst to generate new architectures that were previously inaccessible via conventional ligation reactions. Using this unique ligation, we generated three site-specifically labeled antibody-drug conjugates (ADCs) with an average of four drugs to one antibody. The in vitro and in vivo efficacies along with pharmacokinetic data of the site-specific ADCs are reported.

  6. Generating site-specifically modified proteins via a versatile and stable nucleophilic carbon ligation.

    PubMed

    Kudirka, Romas; Barfield, Robyn M; McFarland, Jesse; Albers, Aaron E; de Hart, Gregory W; Drake, Penelope M; Holder, Patrick G; Banas, Stefanie; Jones, Lesley C; Garofalo, Albert W; Rabuka, David

    2015-02-19

    There is a need for facile chemistries that allow for chemo- and regioselectivity in bioconjugation reactions. To address this need, we are pioneering site-specific bioconjugation methods that use formylglycine as a bioorthogonal handle on a protein surface. Here we introduce aldehyde-specific bioconjugation chemistry, the trapped-Knoevenagel ligation. The speed and stability of the trapped-Knoevenagel ligation further advances the repertoire of aldehyde-based bioconjugations and expands the toolbox for site-specific protein modifications. The trapped-Knoevenagel ligation reaction can be run at near neutral pH in the absence of catalysts to produce conjugates that are stable under physiological conditions. Using this new ligation, we generated an antibody-drug conjugate that demonstrates excellent efficacy in vitro and in vivo.

  7. Recent Advances in Site Specific Conjugations of Antibody Drug Conjugates (ADCs).

    PubMed

    Gao, Wenlong; Zhang, Jingxin; Xiang, Jun; Zhang, Lei; Wu, Chengbin; Dhal, Pradeep K; Chen, Bo

    2016-01-01

    Antibody-drug conjugates (ADCs) take the advantage of antigen specificity of monoclonal antibodies to deliver highly potent cytotoxic drugs selectively to antigen-expressing tumor cells. The recent approval of Adcetris™ and Kadcyla™ as well as emerging data from numerous ongoing clinical trials underscore the role of ADCs as a new therapeutic option for cancer patients. However, conventional conjugation methods generally result in a heterogeneous mixture of ADCs, which can result in significant therapeutic liabilities and can lead to complicated manufacturing processes. The increased understanding from the clinical investigation of current ADCs and site-specific bioconjugation technologies has enabled scientists to accelerate the discovery and development of the next generation ADCs with defined and homogeneous composition. The present manuscript reviews the recent advances and trends in the research and development of novel ADCs obtained by site-specific conjugation method.

  8. Recent Developments in the Site-Specific Immobilization of Proteins onto Solid Supports

    SciTech Connect

    Camarero, J A

    2007-02-21

    Immobilization of proteins onto surfaces is of great importance in numerous applications, including protein analysis, drug screening, and medical diagnostics, among others. The success of all these technologies relies on the immobilization technique employed to attach a protein to the corresponding surface. Non-specific physical adsorption or chemical cross-linking with appropriate surfaces results in the immobilization of the protein in random orientations. Site-specific covalent attachment, on the other hand, leads to molecules being arranged in a definite, orderly fashion and allows the use of spacers and linkers to help minimize steric hindrances between the protein and the surface. The present work reviews the latest chemical and biochemical developments for the site-specific covalent attachment of proteins onto solid supports.

  9. Site-Specific Integration of Exogenous Genes Using Genome Editing Technologies in Zebrafish.

    PubMed

    Kawahara, Atsuo; Hisano, Yu; Ota, Satoshi; Taimatsu, Kiyohito

    2016-05-13

    The zebrafish (Danio rerio) is an ideal vertebrate model to investigate the developmental molecular mechanism of organogenesis and regeneration. Recent innovation in genome editing technologies, such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) system, have allowed researchers to generate diverse genomic modifications in whole animals and in cultured cells. The CRISPR/Cas9 and TALEN techniques frequently induce DNA double-strand breaks (DSBs) at the targeted gene, resulting in frameshift-mediated gene disruption. As a useful application of genome editing technology, several groups have recently reported efficient site-specific integration of exogenous genes into targeted genomic loci. In this review, we provide an overview of TALEN- and CRISPR/Cas9-mediated site-specific integration of exogenous genes in zebrafish.

  10. Site-Specific Integration of Exogenous Genes Using Genome Editing Technologies in Zebrafish

    PubMed Central

    Kawahara, Atsuo; Hisano, Yu; Ota, Satoshi; Taimatsu, Kiyohito

    2016-01-01

    The zebrafish (Danio rerio) is an ideal vertebrate model to investigate the developmental molecular mechanism of organogenesis and regeneration. Recent innovation in genome editing technologies, such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) system, have allowed researchers to generate diverse genomic modifications in whole animals and in cultured cells. The CRISPR/Cas9 and TALEN techniques frequently induce DNA double-strand breaks (DSBs) at the targeted gene, resulting in frameshift-mediated gene disruption. As a useful application of genome editing technology, several groups have recently reported efficient site-specific integration of exogenous genes into targeted genomic loci. In this review, we provide an overview of TALEN- and CRISPR/Cas9-mediated site-specific integration of exogenous genes in zebrafish. PMID:27187373

  11. Site-specific photobiotinylation of antibodies, light chains, and immunoglobulin fragments.

    PubMed

    Pavlinkova, G; Lou, D; Kohler, H

    2000-09-01

    The high affinity of biotin for avidin has been exploited for many antibody-based assays. This requires that biotin is covalently conjugated to the antibody molecule. Several chemically reactive biotinylation reagents are commercially available. Except for the attachment via sulfhydryl groups in the immunoglobulin (Ig) molecule, these reagents attach biotin randomly to various amino acid side chains. Although non-site-specific modification of antibodies does not interfere in most immunoassays, specific application and sensitive antibodies would benefit from site-specific biotinylation. Here we describe an affinity biotinylation technique based on a photoreactive biotin reagent. The design of this reaction was possible from the discovery of a conserved binding site in the variable Ig domain for nucleotides and nucleosides. The described photoaffinity biotinylation offers the advantages of ease, convenience, and production of a reproducible and defined biotinylated antibody preparation.

  12. Comparative fitness assessment of Anopheles stephensi transgenic lines receptive to site-specific integration.

    PubMed

    Amenya, D A; Bonizzoni, M; Isaacs, A T; Jasinskiene, N; Chen, H; Marinotti, O; Yan, G; James, A A

    2010-04-01

    Genetically modified mosquitoes that are unable to transmit pathogens offer opportunities for controlling vector-borne diseases such as malaria and dengue. Site-specific gene recombination technologies are advantageous in the development of these insects because antipathogen effector genes can be inserted at integration sites in the genome that cause the least alteration in mosquito fitness. Here we describe Anopheles stephensi transgenic lines containing phi C31 attP'docking' sites linked to a fluorescent marker gene. Chromosomal insertion sites were determined and life-table parameters were assessed for transgenic mosquitoes of each line. No significant differences in fitness between the transgenic and nontransgenic mosquitoes were detected in this study. These transgenic lines are suitable for future site-specific integrations of antiparasite transgenes into the attP sites.

  13. Site-specific immobilization and micrometer and nanometer scale photopatterning of yellow fluorescent protein on glass surfaces.

    PubMed

    Reynolds, Nicholas P; Tucker, Jaimey D; Davison, Paul A; Timney, John A; Hunter, C Neil; Leggett, Graham J

    2009-01-28

    A simple method is described for the site-specific attachment of yellow fluorescent protein (YFP) to glass surfaces on length scales ranging from tens of micrometers to ca. 200 nm. 3-Mercaptopropyl(triethoxy silane) is adsorbed onto a glass substrate and subsequently derivatized using a maleimide-functionalized oligomer of ethylene glycol. The resulting protein-resistant surface is patterned by exposure to UV light, causing photochemical degradation of the oligo(ethylene glycol) units to yield aldehyde groups in exposed regions. These are covalently bound to N-(5-amino-1-carboxypentyl)iminoacetic acid, yielding a nitrilotriacetic acid (NTA)-functionalized surface, which following complexation with Ni(2+), is coupled to His-tagged YFP. Using scanning near-field photolithography, in which a UV laser coupled to a scanning near-field optical microscope is utilized as the light source for photolithography, it is possible to fabricate lines of protein smaller than 200 nm, in which the biomolecules remain strongly optically active, facilitating the acquisition of diffraction-limited fluorescence images by confocal microscopy.

  14. Effects of Tributyltin Antifouling Paint Leachates on Pearl Harbor Organisms. Site-Specific Flowthrough Bioassay Tests.

    DTIC Science & Technology

    1985-12-01

    Organotin paint leachate. antifoulitip coa~tings. marine n~ii r, isms.A.benthicFIEL GRUP SB GOUP organisms. harbor pollutani fributt Iti omplx cmmuitie...of organotins should be closely monitored for ossible shifts in dominance of specific organisms- ~ 20 DISTRIBUJTION, AVAILABIUITY OF ABSTRACT 21...d* J 77. EXECUTIVE SUMMARY Site-specific bioassay tests were performed to determine the effects of organotin paint leachate on complex communities of

  15. Regulation of BRCA1 Function by DNA Damage-Induced Site-Specific Phosphorylation

    DTIC Science & Technology

    2005-06-01

    Rad51p proteins, the lat - end-joining. BRCA-2 complexed with machinery. ter a member of the RAD-52 epi- RAD-51 is active in strand exchange BRCA- 1 has...AD Award Number: DAMD17-02- 1 -0584 TITLE: Regulation of BRCAl Function by DNA Damage-Induced Site- Specific Phosphorylation PRINCIPAL INVESTIGATOR...ApprovedREPORT DOCUMENTATION PAGE OMB No. 0704-0188 Public reporting burden for this collection of Information Is estimated to average 1 hour per

  16. Complete Genome Sequence of Streptomyces parvulus 2297, Integrating Site-Specifically with Actinophage R4

    PubMed Central

    Miura, Takamasa; Harada, Chizuko; Guo, Yong; Narisawa, Kazuhiko; Ohta, Hiroyuki; Takahashi, Hideo; Shirai, Makoto

    2016-01-01

    Streptomyces parvulus 2297, which is a host for site-specific recombination according to actinophage R4, is derived from the type strain ATCC 12434. Species of S. parvulus are known as producers of polypeptide antibiotic actinomycins and have been considered for industrial applications. We herein report for the first time the complete genome sequence of S. parvulus 2297. PMID:27563047

  17. Site-specific investigations and preliminary design for the Gorleben repository

    SciTech Connect

    Brennecke, P.; Kranz, H.; Schneider, H. )

    1992-01-01

    In the Federal Republic of Germany, the disposal of radioactive waste is being planned for deep geologic formations only. A repository will be constructed in the Gorleben salt dome for all kinds of radioactive waste, in particular, heat-generating waste from reprocessing and spent fuel. Pusuant to German safety criteria, a detailed site characterization program including above-ground and underground investigations must be performed to provide all necessary data for the site-specific safety assessment.

  18. Intruder scenarios for site-specific low-level radioactive waste classification

    SciTech Connect

    Kennedy, W.E. Jr.; Peloquin, R.A.

    1988-09-01

    The US Department of Energy (DOE) has revised its low-level radioactive waste (LLW) management requirements and guidelines for waste generated at its facilities supporting defense missions. Specifically, draft DOE Order 5820.2A, Chapter 3 describes the purpose, policy, and requirements necessary for the management of defense LLW. The draft DOE policy calls for LLW operations to be managed to protect the health and safety of the public, preserve the environment, and ensure that no remedial action will be necessary after termination of operations. The basic approach used by DOE is to establish overall performance objectives, in terms of groundwater protection and public radiation dose limits, and to require site-specific performance assessments to determine compliance. As a result of these performance assessments, each site will develop waste acceptance criteria that define the allowable quantities and concentrations of specific radioisotopes. Additional limitations on waste disposal design, waste form, and waste treatment will also be developed on a site-specific basis. As a key step in the site-specific performance assessments, an evaluation must be conducted of potential radiation doses to intruders who may inadvertently move onto a closed DOE LLW disposal site after loss of institutional controls. This report (1) describes the types of intruder scenarios that should be considered when performing this step of the site-specific performance assessment, (2) provides the results of generic calculations performed using unit concentrations of various radionuclides as a comparison of the magnitude of importance of the various intruder scenarios, and (3) shows the relationship between the generic doses and waste classification limits for defense wastes.

  19. Site-Specific Differentiation of Fibroblasts in Normal and Scleroderma Skin

    DTIC Science & Technology

    2010-06-01

    expression of one HOX lncRNA, termed nc-HOXC10, is correlated with fibrotic gene expression in fibroblasts. In our initial study, we found nc-HOXC10...anatomic expression pattern of Hox genes from embryonic development through adulthood. The ongoing Hox expression endowed fibroblasts with site...specific inductive activities that control the homeostasis and regeneration of epithelia throughout the body. The epigenetic memory of Hox genes depend on

  20. Site-specific functionalization of proteins and their applications to therapeutic antibodies

    PubMed Central

    van Vught, Remko; Pieters, Roland J; Breukink, Eefjan

    2014-01-01

    Protein modifications are often required to study structure and function relationships. Instead of the random labeling of lysine residues, methods have been developed to (sequence) specific label proteins. Next to chemical modifications, tools to integrate new chemical groups for bioorthogonal reactions have been applied. Alternatively, proteins can also be selectively modified by enzymes. Herein we review the methods available for site-specific modification of proteins and their applications for therapeutic antibodies. PMID:24757499

  1. Site-specific fatty acid-conjugation to prolong protein half-life in vivo

    PubMed Central

    Lim, Sung In; Mizuta, Yukina; Takasu, Akinori; Hahn, Young S.; Kim, Yong Hwan; Kwon, Inchan

    2015-01-01

    Therapeutic proteins are indispensable in treating numerous human diseases. However, therapeutic proteins often suffer short serum half-life. In order to extend the serum half-life, a natural albumin ligand (a fatty acid) has been conjugated to small therapeutic peptides resulting in a prolonged serum half-life via binding to patients' serum albumin in vivo. However, fatty acid-conjugation has limited applicability due to lack of site-specificity resulting in the heterogeneity of conjugated proteins and a significant loss in pharmaceutical activity. In order to address these issues, we exploited the site-specific fatty acid-conjugation to a permissive site of a protein, using copper-catalyzed alkyne-azide cycloaddition, by linking a fatty acid derivative to p-ethynylphenylalanine incorporated into a protein using an engineered pair of yeast tRNA/aminoacyl tRNA synthetase. As a proof-of-concept, we show that single palmitic acid conjugated to superfolder green fluorescent protein (sfGFP) in a site-specific manner enhanced a protein's albumin-binding in vitro about 20 times and the serum half-life in vivo 5 times when compared to those of the unmodified sfGFP. Furthermore, the fatty acid conjugation did not cause a significant reduction in the fluorescence of sfGFP. Therefore, these results clearly indicate that the site-specific fatty acid-conjugation is a very promising strategy to prolong protein serum half-life in vivo without compromising its folded structure and activity. PMID:23735573

  2. Use of a water effect ratio to develop an estuarine copper site-specific standard

    SciTech Connect

    Brosnan, T.

    1995-12-31

    Development of a copper site-specific standard in New York Harbor involved several steps: (1) EPA`s Indicator Species Procedure was used to develop a Water Effect Ratio (WER), which produces a biologically-based adjustment to the existing criteria. Samples from seven stations were collected during high and low river-flow conditions in 1992--93. Toxicity testing included embryo-larval development tests on two bivalves, an urchin, and a shrimp. A red algae was used for a sexual reproduction test. This testing yielded WER`s of 1.33 2.1 7, with an average of 1.49. When multiplied by the existing EPA criteria of 2.9 ug/L (total recoverable), this yielded a preliminary acute site specific standard of 4.3 ug/L (total recoverable); (2) Further analysis of these data, combined with a literature search of similar data, resulted in a recalculation of the original national acute criteria value, from 2.9 ug/L (total recoverable) to 5.3 ug/L (dissolved). Multiplying the WER by the recalculated national criteria yielded a final acute site, specific criteria of 7.9 ug/L (dissolved); (3) Finally, EPA`s original criteria indicated that achieving the acute criterion would be protective of chronic effects (i.e. the acute:chronic ratio (ACR) was 2). However, EPA, recently decided that an ACR of 2 was no longer valid, and decided to use the freshwater ACR of 2.8. This resulted in a recalculation of the national chronic criteria to 3.75 ug/L (dissolved). Combined with the WER of 1.49, this yielded a final chronic site specific standard of 5.6 ug/L. The new standard eliminated ambient violations in most of the harbor, and removed the need for wasteload allocations at 12 of NYC`s 14 sewage treatment plants.

  3. Generic guidelines versus site-specific assessments: Does marriage make sense?

    SciTech Connect

    Gaudet, C.L.; Keenleyside, K.A.; Smith, S.L.; Kent, R.A.; Wong, M.P.

    1995-12-31

    The maintenance, protection and restoration of a high level of environmental quality requires the availability of practical scientific tools. Environmental quality guidelines (also called criteria) are one such scientific tool that help measure progress towards these goals. These guidelines provide scientific benchmarks that can offer consistency and clarity in defining scientific measures for environmental quality that are easily understood, communicated, and implemented as the basis for management decisions. At the same time, debate exists over the use of generic guidelines versus site-specific risk assessments. It is the contention that generic and site-specific approaches are not mutually exclusive, but complementary decision-support tools and that any apparent controversy stems from an incomplete understanding of the nature and intent of generic environmental quality guidelines or from the use of guidelines in the absence of a coherent framework. The authors advocate an approach that marries the strengths of the generic and site-specific approaches and promotes consistent, scientifically-defensible decisions that support broad societal goals for environmental protection. Using Canadian environmental quality guidelines as an example, they provide an overview of the role of environmental quality guidelines in decision-making, with concrete examples of their implementation in addressing specific environmental quality issues.

  4. Site-Specific N-Glycosylation of Endothelial Cell Receptor Tyrosine Kinase VEGFR-2.

    PubMed

    Chandler, Kevin Brown; Leon, Deborah R; Meyer, Rosana D; Rahimi, Nader; Costello, Catherine E

    2017-02-03

    Vascular endothelial growth factor receptor-2 (VEGFR-2) is an important receptor tyrosine kinase (RTK) that plays critical roles in both physiologic and pathologic angiogenesis. The extracellular domain of VEGFR-2 is composed of seven immunoglobulin-like domains, each with multiple potential N-glycosylation sites (sequons). N-glycosylation plays a central role in RTK ligand binding, trafficking, and stability. However, despite its importance, the functional role of N-glycosylation of VEGFR-2 remains poorly understood. The objectives of the present study were to characterize N-glycosylation sites in VEGFR-2 via enzymatic release of the glycans and concomitant incorporation of (18)O into formerly N-glycosylated sites followed by tandem mass spectrometry (MS/MS) analysis to determine N-glycosylation site occupancy and the site-specific N-glycan heterogeneity of VEGFR-2 glycopeptides. The data demonstrated that all seven VEGFR-2 immunoglobulin-like domains have at least one occupied N-glycosylation site. MS/MS analyses of glycopeptides and deamidated, deglycosylated (PNGase F-treated) peptides from ectopically expressed VEGFR-2 in porcine aortic endothelial (PAE) cells identified N-glycans at the majority of the 17 potential N-glycosylation sites on VEGFR-2 in a site-specific manner. The data presented here provide direct evidence for site-specific, heterogeneous N-glycosylation and N-glycosylation site occupancy on VEGFR-2. The study has important implications for the therapeutic targeting of VEGFR-2, ligand binding, trafficking, and signaling.

  5. Comparisons of CAP88PC version 2.0 default parameters to site specific inputs

    SciTech Connect

    Lehto, M. A.; Courtney, J. C.; Charter, N.; Egan, T.

    2000-03-02

    The effects of varying the input for the CAP88PC Version 2.0 program on the total effective dose equivalents (TEDEs) were determined for hypothetical releases from the Hot Fuel Examination Facility (HFEF) located at the Argonne National Laboratory site on the Idaho National Engineering and Environmental Laboratory (INEEL). Values for site specific meteorological conditions and agricultural production parameters were determined for the 80 km radius surrounding the HFEF. Four nuclides, {sup 3}H, {sup 85}Kr, {sup 129}I, and {sup 137}Cs (with its short lived progeny, {sup 137m}Ba) were selected for this study; these are the radioactive materials most likely to be released from HFEF under normal or abnormal operating conditions. Use of site specific meteorological parameters of annual precipitation, average temperature, and the height of the inversion layer decreased the TEDE from {sup 137}Cs-{sup 137m}Ba up to 36%; reductions for other nuclides were less than 3%. Use of the site specific agricultural parameters reduced TEDE values between 7% and 49%, depending on the nuclide. Reductions are associated with decreased committed effective dose equivalents (CEDEs) from the ingestion pathway. This is not surprising since the HFEF is located well within the INEEL exclusion area, and the surrounding area closest to the release point is a high desert with limited agricultural diversity. Livestock and milk production are important in some counties at distances greater than 30 km from the HFEF.

  6. Generation of site-specific mutant mice using the CRISPR/Cas9 system.

    PubMed

    Min, Bai; Qi, Li; Yanjiao, Shao; Yuanhua, Huang; Dali, Li; Yanlin, Ma

    2015-10-01

    The CRISPR/Cas9 system is a recently developed important technology for genome editing in cellular and animal models. Here we established a CRISPR/Cas9-based system of generating site-specific mutant mice using DNA double-strand breaks (DSBs) induced homologous recombination (HR)-dependent or independent repair mechanism. Through co-microinjection of Cas9 mRNA and single-guide RNA (sgRNA) targeting genomic DNA sequence corresponding to enzyme activity of lysine (K)-specific demethylase 2b (Kdm2b), both a frame-shifted Kdm2b null mutant and a Kdm2b enzyme activity disrupted mouse strain were obtained simultaneously. Moreover, sgRNA targeting flavin containing monooxygenases3 (Fmo3) gene and the corresponding single strand oligonucleotides (ssODN) donor template with point mutation were co-injected into the male pronucleus of one-cell mouse embryos stimulated HR-mediated repair mechanism. Genomic sequence analysis of F0 mice showed that frame-shifted Fmo3 knockout mouse and site-specific Fmo3 knock-in mouse with single base substitution were successfully generated, and these mutations could be stably transmitted to the next generation. Therefore, we successfully generated mouse strains containing site-specific mutations through HR-dependent and -independent DSB repair using the CRISPR/Cas9 system.

  7. Cancer registries in Japan: National Clinical Database and site-specific cancer registries.

    PubMed

    Anazawa, Takayuki; Miyata, Hiroaki; Gotoh, Mitsukazu

    2015-02-01

    The cancer registry is an essential part of any rational program of evidence-based cancer control. The cancer control program is required to strategize in a systematic and impartial manner and efficiently utilize limited resources. In Japan, the National Clinical Database (NCD) was launched in 2010. It is a nationwide prospective registry linked to various types of board certification systems regarding surgery. The NCD is a nationally validated database using web-based data collection software; it is risk adjusted and outcome based to improve the quality of surgical care. The NCD generalizes site-specific cancer registries by taking advantage of their excellent organizing ability. Some site-specific cancer registries, including pancreatic, breast, and liver cancer registries have already been combined with the NCD. Cooperation between the NCD and site-specific cancer registries can establish a valuable platform to develop a cancer care plan in Japan. Furthermore, the prognosis information of cancer patients arranged using population-based and hospital-based cancer registries can help in efficient data accumulation on the NCD. International collaboration between Japan and the USA has recently started and is expected to provide global benchmarking and to allow a valuable comparison of cancer treatment practices between countries using nationwide cancer registries in the future. Clinical research and evidence-based policy recommendation based on accurate data from the nationwide database may positively impact the public.

  8. Hypoxia drives transient site-specific copy gain and drug-resistant gene expression

    PubMed Central

    Black, Joshua C.; Atabakhsh, Elnaz; Kim, Jaegil; Biette, Kelly M.; Van Rechem, Capucine; Ladd, Brendon; Burrowes, Paul d.; Donado, Carlos; Mattoo, Hamid; Kleinstiver, Benjamin P.; Song, Bing; Andriani, Grasiella; Joung, J. Keith; Iliopoulos, Othon; Montagna, Cristina; Pillai, Shiv; Getz, Gad

    2015-01-01

    Copy number heterogeneity is a prominent feature within tumors. The molecular basis for this heterogeneity remains poorly characterized. Here, we demonstrate that hypoxia induces transient site-specific copy gains (TSSGs) in primary, nontransformed, and transformed human cells. Hypoxia-driven copy gains are not dependent on HIF1α or HIF2α; however, they are dependent on the KDM4A histone demethylase and are blocked by inhibition of KDM4A with a small molecule or the natural metabolite succinate. Furthermore, this response is conserved at a syntenic region in zebrafish cells. Regions with site-specific copy gain are also enriched for amplifications in hypoxic primary tumors. These tumors exhibited amplification and overexpression of the drug resistance gene CKS1B, which we recapitulated in hypoxic breast cancer cells. Our results demonstrate that hypoxia provides a biological stimulus to create transient site-specific copy alterations that could result in heterogeneity within tumors and cell populations. These findings have major implications in our understanding of copy number heterogeneity and the emergence of drug resistance genes in cancer. PMID:25995187

  9. Characterizing site specific considerations for protecting aircraft during LGS operations at W. M. Keck Observatory

    NASA Astrophysics Data System (ADS)

    Stomski, Paul J., Jr.; Campbell, Randy; McCann, Kevin; Shimko, Steve

    2010-07-01

    W. M. Keck Observatory (WMKO) routinely operates laser guide star (LGS) Adaptive Optics (AO) systems at the telescope facility on the Big Island of Hawaii. One of the operational requirements for the LGS system is that a safety system to prevent nearby aircraft from being adversely affected by the laser must be provided. We will support operations in the near term with human aircraft spotters until we can successfully develop and get the appropriate approvals needed for an Automated, Integrated and Reliable System for an Aircraft Friendly Environment (AIRSAFE). This report describes some of the preliminary requirements development work at WMKO in support of the future development of AIRSAFE. We discuss the results of recent work to characterize site specific considerations that impact requirements development. The site specific considerations include the proximity of WMKO laser operations to nearby commercial airports, the implications of military operations in the area and the character of the air traffic volume and flight patterns over the telescope facility. Finally, we discuss how the design and implementation of AIRSAFE will be impacted by these site specific considerations.

  10. Multiple DNA binding activities of the novel site-specific recombinase, Piv, from Moraxella lacunata.

    PubMed

    Tobiason, D M; Lenich, A G; Glasgow, A C

    1999-04-02

    The recombinase, Piv, is essential for site-specific DNA inversion of the type IV pilin DNA segment in Moraxella lacunata and Moraxella bovis. Piv shows significant homology with the transposases of the IS110/IS492 family of insertion elements, but, surprisingly, Piv contains none of the conserved amino acid motifs of the lambda Int or Hin/Res families of site-specific recombinases. Therefore, Piv may mediate site-specific recombination by a novel mechanism. To begin to determine how Piv may assemble a synaptic nucleoprotein structure for DNA cleavage and strand exchange, we have characterized the interaction of Piv with the DNA inversion region of M. lacunata. Gel shift and nuclease/chemical protection assays, competition and dissociation rate analyses, and cooperativity studies indicate that Piv binds two distinct recognition sequences. One recognition sequence, found at multiple sites within and outside of the invertible segment, is bound by Piv protomers with high affinity. The second recognition sequence is located at the recombination cross-over sites at the ends of the invertible element; Piv interacts with this sequence as an oligomer with apparent low affinity. A model is proposed for the role of the different Piv binding sites of the M. lacunata inversion region in the formation of an active synaptosome.

  11. Synthesis of DNA Oligodeoxynucleotides Containing Site-Specific 1,3-Butadiene- Deoxyadenosine Lesions

    PubMed Central

    Wickramaratne, Susith; Seiler, Christopher L.

    2016-01-01

    Post-oligomerization synthesis is a useful technique for preparing site-specifically modified DNA oligomers. This approach involves site-specific incorporation of inherently reactive halogenated nucleobases into DNA strands using standard solid phase synthesis, followed by post-oligomerization nucleophilic aromatic substitution (SNAr) reactions with carcinogen-derived synthons. In these reactions, the inherent reactivities of DNA and carcinogen-derived species are reversed: the modified DNA nucleobase acts as an electrophile, while the carcinogen-derived species acts as a nucleophile. In the present protocol, we describe the use of the post-oligomerization approach to prepare DNA strands containing site- and stereospecific N6-adenine and N1, N6-adenine adducts induced by epoxide metabolites of the known human and animal carcinogen, 1,3-butadiene (BD). The resulting oligomers containing site specific, structurally defined DNA adducts can be used in structural and biological studies to reveal the roles of specific BD adducts in carcinogenesis and mutagenesis. PMID:26344227

  12. Site-specific protein labeling with PRIME and chelation-assisted Click chemistry

    PubMed Central

    Uttamapinant, Chayasith; Sanchez, Mateo I.; Liu, Daniel S.; Yao, Jennifer Z.; White, Katharine A.; Grecian, Scott; Clarke, Scott; Gee, Kyle R.; Ting, Alice Y.

    2016-01-01

    This protocol describes an efficient method to site-specifically label cell-surface or purified proteins with chemical probes in two steps: PRobe Incorporation Mediated by Enzymes (PRIME) followed by chelation-assisted copper-catalyzed azide-alkyne cycloaddition (CuAAC). In the PRIME step, Escherichia coli lipoic acid ligase site-specifically attaches a picolyl azide derivative to a 13-amino acid recognition sequence that has been genetically fused onto the protein of interest. Proteins bearing picolyl azide are chemoselectively derivatized with an alkyne-probe conjugate by chelation-assisted CuAAC in the second step. We describe herein the optimized protocols to synthesize picolyl azide, perform PRIME labeling, and achieve CuAAC derivatization of picolyl azide on live cells, fixed cells, and purified proteins. Reagent preparations, including synthesis of picolyl azide probes and expression of lipoic acid ligase, take 12 d, while the procedure to perform site-specific picolyl azide ligation and CuAAC on cells or on purified proteins takes 40 min-3 h. PMID:23887180

  13. Site-specific gene integration in rice genome mediated by the FLP-FRT recombination system.

    PubMed

    Nandy, Soumen; Srivastava, Vibha

    2011-08-01

    Plant transformation based on random integration of foreign DNA often generates complex integration structures. Precision in the integration process is necessary to ensure the formation of full-length, single-copy integration. Site-specific recombination systems are versatile tools for precise genomic manipulations such as DNA excision, inversion or integration. The yeast FLP-FRT recombination system has been widely used for DNA excision in higher plants. Here, we report the use of FLP-FRT system for efficient targeting of foreign gene into the engineered genomic site in rice. The transgene vector containing a pair of directly oriented FRT sites was introduced by particle bombardment into the cells containing the target locus. FLP activity generated by the co-bombarded FLP gene efficiently separated the transgene construct from the vector-backbone and integrated the backbone-free construct into the target site. Strong FLP activity, derived from the enhanced FLP protein, FLPe, was important for the successful site-specific integration (SSI). The majority of the transgenic events contained a precise integration and expressed the transgene. Interestingly, each transgenic event lacked the co-bombarded FLPe gene, suggesting reversion of the integration structure in the presence of the constitutive FLPe expression. Progeny of the precise transgenic lines inherited the stable SSI locus and expressed the transgene. This work demonstrates the application of FLP-FRT system for site-specific gene integration in plants using rice as a model.

  14. Biologically Derived Nanoparticle Arrays via a Site-Specific Reconstitution of Ferritin and their Electrochemistry

    NASA Technical Reports Server (NTRS)

    Kim, Jae-Woo; Choi, Sang H.; Lillehei, Peter T.; King, Glen C.; Elliott, James R.; Chu, Sang-Hyon; Park, Yeonjoon; Watt, Gerald D.

    2004-01-01

    Nanoparticle arrays biologically derived from an electrochemically-controlled site-specific biomineralization were fabricated on a gold substrate through the immobilization process of biomolecules. The work reported herein includes the immobilization of ferritin with various surface modifications, the electrochemical biomineralization of ferritins with different inorganic cores, the fabrication of self-assembled arrays with the immobilized ferritin, and the electrochemical characterization of various core materials. Protein immobilization on the substrate is achieved by anchoring ferritins with dithiobis-N-succinimidyl propionate (DTSP). A reconstitution process of electrochemical site-specific biomineralization with a protein cage loads ferritins with different core materials such as Pt, Co, Mn, and Ni. The ferritin acts as a nano-scale template, a biocompatible cage, and a separator between the nanoparticles. The nano-sized metalcored ferritins on a gold substrate displayed a good electrochemical activity for the electron transport and storage, which is suitable for bioelectronics applications such as biofuel cell, bionanobattery, biosensors, etc. Keywords: Ferritin, immobilization, site-specific reconstitution, biomineralization, and bioelectronics

  15. Confident assignment of site-specific glycosylation in complex glycoproteins in a single step.

    PubMed

    Khatri, Kshitij; Staples, Gregory O; Leymarie, Nancy; Leon, Deborah R; Turiák, Lilla; Huang, Yu; Yip, Shun; Hu, Han; Heckendorf, Christian F; Zaia, Joseph

    2014-10-03

    A glycoprotein may contain several sites of glycosylation, each of which is heterogeneous. As a consequence of glycoform diversity and signal suppression from nonglycosylated peptides that ionize more efficiently, typical reversed-phase LC-MS and bottom-up proteomics database searching workflows do not perform well for identification of site-specific glycosylation for complex glycoproteins. We present an LC-MS system for enrichment, separation, and analysis of glycopeptides from complex glycoproteins (>4 N-glycosylation sequons) in a single step. This system uses an online HILIC enrichment trap prior to reversed-phase C18-MS analysis. We demonstrated the effectiveness of the system using a set of glycoproteins including human transferrin (2 sequons), human alpha-1-acid glycoprotein (5 sequons), and influenza A virus hemagglutinin (9 sequons). The online enrichment renders glycopeptides the most abundant ions detected, thereby facilitating the generation of high-quality data-dependent tandem mass spectra. The tandem mass spectra exhibited product ions from both glycan and peptide backbone dissociation for a majority of the glycopeptides tested using collisionally activated dissociation that served to confidently assign site-specific glycosylation. We demonstrated the value of our system to define site-specific glycosylation using a hemagglutinin containing 9 N-glycosylation sequons from a single HILIC-C18-MS acquisition.

  16. Attosecond photoelectron microscopy of H2+

    NASA Astrophysics Data System (ADS)

    Hu, S. X.; Collins, L. A.; Schneider, B. I.

    2009-08-01

    We present a numerical study of the ultrafast ionization dynamics of H2+ exposed to attosecond extreme ultraviolet (xuv) pulses that goes beyond the Born-Openheimer approximation. The four-dimensional, time-dependent Schrödinger equation was solved using a generalization of the finite-element discrete-variable-representation/real-space-product technique used in our previous calculations to include the dynamical motion of the nuclei. This has enabled us to expose the target to any polarized light at arbitrary angles with respect to the molecular axis. Calculations have been performed at different angles and photon energies ( ℏω=50eV up to 630 eV) to investigate the energy and orientation dependence of the photoionization probability. A strong orientation dependence of the photoionization probability of H2+ was found at a photon energy of ℏω=50eV . At this energy, we found that the ionization probability is three times larger in the perpendicular polarization than in the parallel case. These observations are explained by the different geometric “cross sections” seen by the photoejected electron as it leaves the molecule. This ionization anisotropy vanishes at the higher-photon energy of ℏω≥170eV . When these higher-energy xuv pulses are polarized perpendicular to the internuclear axis, a “double-slit-like” interference pattern is observed. However, we find that the diffraction angle only approaches the classical formula ϕn=sin-1(nλe/R0) , where n is the diffraction order, λe is the released electron wavelength, and R0 is the internuclear distance, when nλe becomes less than 65% of R0 . These results illustrate the possibility of employing attosecond pulses to perform photoelectron microscopy of molecules.

  17. Site-Specific Analyses for Demonstrating Compliance with 10 CFR 61 Performance Objectives - 12179

    SciTech Connect

    Grossman, C.J.; Esh, D.W.; Yadav, P.; Carrera, A.G.

    2012-07-01

    The U.S. Nuclear Regulatory Commission (NRC) is proposing to amend its regulations at 10 CFR Part 61 to require low-level radioactive waste disposal facilities to conduct site-specific analyses to demonstrate compliance with the performance objectives in Subpart C. The amendments would require licensees to conduct site-specific analyses for protection of the public and inadvertent intruders as well as analyses for long-lived waste. The amendments would ensure protection of public health and safety, while providing flexibility to demonstrate compliance with the performance objectives, for current and potential future waste streams. NRC staff intends to submit proposed rule language and associated regulatory basis to the Commission for its approval in early 2012. The NRC staff also intends to develop associated guidance to accompany any proposed amendments. The guidance is intended to supplement existing low-level radioactive waste guidance on issues pertinent to conducting site-specific analyses to demonstrate compliance with the performance objectives. The guidance will facilitate implementation of the proposed amendments by licensees and assist competent regulatory authorities in reviewing the site-specific analyses. Specifically, the guidance provides staff recommendations on general considerations for the site-specific analyses, modeling issues for assessments to demonstrate compliance with the performance objectives including the performance assessment, intruder assessment, stability assessment, and analyses for long-lived waste. This paper describes the technical basis for changes to the rule language and the proposed guidance associated with implementation of the rule language. The NRC staff, per Commission direction, intends to propose amendments to 10 CFR Part 61 to require licensees to conduct site-specific analyses to demonstrate compliance with performance objectives for the protection of public health and the environment. The amendments would require a

  18. Risks of all-cause and site-specific fractures among hospitalized patients with COPD

    PubMed Central

    Liao, Kuang-Ming; Liang, Fu-Wen; Li, Chung-Yi

    2016-01-01

    Abstract Patients with chronic obstructive pulmonary disease (COPD) have a high prevalence of osteoporosis. The clinical sequel of osteoporosis is fracture. Patients with COPD who experience a fracture also have increased morbidity and mortality. Currently, the types of all-cause and site-specific fracture among patients with COPD are unknown. Thus, we elucidated the all-cause and site-specific fractures among patients with COPD. A retrospective, population-based, cohort study was conducted utilizing the Taiwan Longitudinal Health Insurance Database. Patients with COPD were defined as those who were hospitalized with an International Classification of Diseases, Ninth Revision, Clinical Modification code of 490 to 492 or 496 between 2001 and 2011. The index date was set as the date of discharge. The study patients were followed from the index date to the date when they sought care for any type of fracture, date of death, date of health insurance policy termination, or the last day of 2013. The types of fracture analyzed in this study included vertebral, rib, humeral, radial and ulnar/wrist, pelvic, femoral, and tibial and fibular fractures. The cohort consisted of 11,312 patients with COPD. Among these patients, 1944 experienced fractures. The most common site-specific fractures were vertebral, femoral, rib, and forearm fractures (radius, ulna, and wrist) at 32.4%, 31%, 12%, and 11.8%, respectively. The adjusted hazard ratios of fracture were 1.71 [95% confidence interval (95% CI) = 1.56–1.87] for female patient with COPD and 1.50 (95% CI = 1.39–1.52) for patients with osteoporosis after covariate adjustment. Vertebral and hip fractures are common among patients with COPD, especially among males with COPD. Many comorbidities contribute to the high risk of fracture among patients with COPD. PMID:27749576

  19. Site-specific modification of ED-B-targeting antibody using intein-fusion technology

    PubMed Central

    2011-01-01

    Background A promising new approach in cancer therapy is the use of tumor specific antibodies coupled to cytotoxic agents. Currently these immunoconjugates are prepared by rather unspecific coupling chemistries, resulting in heterogeneous products. As the drug load is a key parameter for the antitumor activity, site-specific strategies are desired. Expressed protein ligation (EPL) and protein trans-splicing (PTS) are methods for the specific C-terminal modification of a target protein. Both include the expression as an intein fusion protein, followed by the exchange of the intein for a functionalized moiety. Results A full-length IgG specific for fibronectin ED-B was expressed as fusion protein with an intein (Mxe GyrA or Npu DnaE) attached to each heavy chain. In vitro protocols were established to site-specifically modify the antibodies in high yields by EPL or PTS, respectively. Although reducing conditions had to be employed during the process, the integrity or affinity of the antibody was not affected. The protocols were used to prepare immunoconjugates containing two biotin molecules per antibody, attached to the C-termini of the heavy chains. Conclusion Full-length antibodies can be efficiently and site-specifically modified at the C-termini of their heavy chains by intein-fusion technologies. The described protocols can be used to prepare immunoconjugates of high homogeneity and with a defined drug load of two. The attachment to the C-termini is expected to retain the affinity and effector functions of the antibodies. PMID:21777442

  20. Spatial Distribution and Site-Specific Spraying of Main Sucking Pests of Elm Trees.

    PubMed

    Karimzadeh, R; Iranipour, S

    2016-11-09

    Elm trees are important landscape trees and sucking insects weaken the elm trees and produce large amounts of honeydew. The main objectives of this study were to identify main honeydew-producing pests of elm trees and do site-specific spraying against these pests. To map the spatial distribution of the sucking pests in the large scale, the study area was divided into 40 × 40 m grids and one tree was chosen randomly from each grid (a total of 55 trees). These trees were sampled twice a year in 2011 and 2012. Each sample was a 30-cm branch terminal. Eight samples were taken from each tree in four cardinal directions and two canopy levels. The number of sucking insects and leaves of each sample were counted and recorded. Spatial analysis of the data was carried out using geostatistics. Kriging was used for producing prediction maps. Insecticide application was restricted to the regions with populations higher than threshold. To identify within-tree distribution of the honeydew-producing pests, six and four elm trees were chosen in 2011 and 2012 respectively, and sampled weekly. These trees were sampled as described previously. European elm scale (EES), Gossyparia spuria (Modeer) and two species of aphids were the dominant honeydew-producing pests. The results revealed that the effects of direction, canopy level and their interactions on insect populations were not statistically significant (P < 0.05). Site-specific spraying decreased the amount of insecticides used by ca. 20%, while satisfactory control of the sucking pests and honeydew excretion was obtained. Considering the environmental and economic benefits of site-specific spraying, it is worth doing more complementary works in this area.

  1. Site-specific methylated reporter constructs for functional analysis of DNA methylation.

    PubMed

    Han, Weiguo; Shi, Miao; Spivack, Simon D

    2013-11-01

    Methods to experimentally alter and functionally evaluate cytosine methylation in a site-specific manner have proven elusive. We describe a site-specific DNA methylation method, using synthetically methylated primers and high fidelity PCR coupled with ligation of reporter constructs. We applied this method to introduce methylated cytosines into fragments of the respective DAPK and RASSF1A promoters that had been cloned into luciferase reporters. We found that methylation of 3-7 residue CpG clusters that were 5' adjacent to the transcription start site (TSS) of the DAPK gene produced up to a 54% decrease in promoter activity (p<0.01). Similarly, for RASSF1A promoter reporter constructs, the methylation of either of two clusters of four CpGs each, but not an intervening cluster, produced a 63% decrease in promoter activity (p<0.01), suggesting that precise mCpG position is crucial, and factors other than simple proximity to the TSS are at play. Chromatin immunoprecipitation analysis of these reporter constructs demonstrated that transcription factor Oct-1 and Sp1 preferentially bound the unmethylated vs. methylated DAPK or RASSF1A promoter reporter constructs at the functional CpG sites. Histone H1, hnRNP1, and MeCP2 showed preferential binding to methylated sequence at functional sites in these reporter constructs, as well as highly preferential (> 8-80-fold) binding to native methylated vs. unmethylated chromatin. These results suggest that: (1) site-specific, precision DNA methylation of a reporter construct can be used for functional analysis of commonly observed gene promoter methylation patterns; (2) the reporter system contains key elements of the endogenous chromatin machinery.

  2. Femtosecond photoelectron point projection microscope

    SciTech Connect

    Quinonez, Erik; Handali, Jonathan; Barwick, Brett

    2013-10-15

    By utilizing a nanometer ultrafast electron source in a point projection microscope we demonstrate that images of nanoparticles with spatial resolutions of the order of 100 nanometers can be obtained. The duration of the emission process of the photoemitted electrons used to make images is shown to be of the order of 100 fs using an autocorrelation technique. The compact geometry of this photoelectron point projection microscope does not preclude its use as a simple ultrafast electron microscope, and we use simple analytic models to estimate temporal resolutions that can be expected when using it as a pump-probe ultrafast electron microscope. These models show a significant increase in temporal resolution when comparing to ultrafast electron microscopes based on conventional designs. We also model the microscopes spectroscopic abilities to capture ultrafast phenomena such as the photon induced near field effect.

  3. Enhanced Aqueous Suzuki–Miyaura Coupling Allows Site-Specific Polypeptide 18F-Labeling

    PubMed Central

    2013-01-01

    The excesses of reagents used in protein chemistry are often incompatible with the reduced or even inverse stoichiometries used for efficient radiolabeling. Analysis and screening of aqueous Pd(0) ligand systems has revealed the importance of a guanidine core and the discovery of 1,1-dimethylguanidine as an enhanced ligand for aqueous Suzuki–Miyaura cross-coupling. This novel Pd catalyst system has now allowed the labeling of small molecules, peptides, and proteins with the fluorine-18 prosthetic [18F]4-fluorophenylboronic acid. These findings now enable site-specific protein 18F-labeling under biologically compatible conditions using a metal-triggered reaction. PMID:23991754

  4. Analysis of site-specific N-glycan remodeling in the endoplasmic reticulum and the Golgi

    PubMed Central

    Hang, Ivan; Lin, Chia-wei; Grant, Oliver C; Fleurkens, Susanna; Villiger, Thomas K; Soos, Miroslav; Morbidelli, Massimo; Woods, Robert J; Gauss, Robert; Aebi, Markus

    2015-01-01

    The hallmark of N-linked protein glycosylation is the generation of diverse glycan structures in the secretory pathway. Dynamic, non-template-driven processes of N-glycan remodeling in the endoplasmic reticulum and the Golgi provide the cellular setting for structural diversity. We applied newly developed mass spectrometry-based analytics to quantify site-specific N-glycan remodeling of the model protein Pdi1p expressed in insect cells. Molecular dynamics simulation, mutational analysis, kinetic studies of in vitro processing events and glycan flux analysis supported the defining role of the protein in N-glycan processing. PMID:26240167

  5. Site specific chemoselective labelling of proteins with robust and highly sensitive Ru(II) bathophenanthroline complexes.

    PubMed

    Uzagare, Matthew C; Claussnitzer, Iris; Gerrits, Michael; Bannwarth, Willi

    2012-03-21

    The bioorthogonal and chemoselective fluorescence labelling of several cell-free synthesized proteins containing a site-specifically incorporated azido amino acid was possible using different alkyne-functionalized Ru(II) bathophenanthroline complexes. We were able to achieve a selective labelling even in complex mixtures of proteins despite the fact that ruthenium dyes normally show a high tendency for unspecific interactions with proteins and are commonly used for total staining of proteins. Since the employed Ru complexes are extremely robust, photo-stable and highly sensitive, the approach should be applicable to the production of labelled proteins for single molecule spectroscopy and fluorescence-based interaction studies.

  6. The species- and site-specific acid-base properties of penicillamine and its homodisulfide

    NASA Astrophysics Data System (ADS)

    Mirzahosseini, Arash; Szilvay, András; Noszál, Béla

    2014-08-01

    Penicillamine, penicillamine disulfide and 4 related compounds were studied by 1H NMR-pH titrations and case-tailored evaluation methods. The resulting acid-base properties are quantified in terms of 14 macroscopic and 28 microscopic protonation constants and the concomitant 7 interactivity parameters. The species- and site-specific basicities are interpreted by means of inductive and shielding effects through various intra- and intermolecular comparisons. The thiolate basicities determined this way are key parameters and exclusive means for the prediction of thiolate oxidizabilities and chelate forming properties in order to understand and influence chelation therapy and oxidative stress at the molecular level.

  7. Site-Specific Labeling of scVEGF with Fluorine-18 for Positron Emission Tomography Imaging

    PubMed Central

    Wang, Hui; Gao, Haokao; Guo, Ning; Niu, Gang; Ma, Ying; Kiesewetter, Dale O.; Chen, Xiaoyuan

    2012-01-01

    Vascular endothelial growth factor (VEGF) is one of the most important mediators of angiogenesis. Single-chain (sc)-VEGF protein containing an N-terminal Cys-tag has been designed for site-specific modification with a variety of imaging and therapeutic moieties. Site-specific labeling of scVEGF with thiol-reactive prosthetic group, N-[2-(4-18F-fluorobenzamido) ethyl] maleimide ([18F]FBEM) for positron emission tomography (PET) imaging of VEFGR may provide a new tracer which has great potential for clinical translation. Methods: [18F]FBEM-scVEGF was synthesized by site-specific conjugation of 18F-FBEM to a thiol group in Cys-tag of scVEGF at room temperature. The functional activity after labeling was tested by immunofluorescence staining, cellular uptake and efflux. The tumor targeting and in vivo properties were evaluated by biodistribution and microPET studies in tumor-bearing mice. Results: The radiolabeling yield and specific activity of [18F]FBEM-scVEGF were 20.6 ± 15.1% (based on starting [18F]FBEM, uncorrected, n = 5) and 58.8 ± 12.4 GBq/µmol, respectively. Noninvasive microPET and direct tissue sampling experiments demonstrated that [18F]FBEM-scVEGF had VEGFR specific tumor uptake in MDA-MB-435, U87MG and 4T1 xenograft models. The optimal tumor uptake was achieved at 2 h p.i., which can be partially, but significantly blocked by co-injection of non-labeled scVEGF protein. Overall, [18F]FBEM-scVEGF showed VEGFR specific tumor uptake. Conclusion: The scVEGF was site-specifically labeled with 18F via [18F]FBEM prosthetic group and the tracer [18F]FBEM-scVEGF exhibited high receptor binding affinity and tumor targeting efficacy. Further study of [18F] FBEM-scVEGF to evaluate angiogenesis in cancer and other disease types is warranted. PMID:22768028

  8. Site Specific Incorporation of Amino Acid Analogues into Proteins In Vivo

    DTIC Science & Technology

    2010-08-11

    Positions in CCR5 ( ) and rhodopsin ( ) subjected to site-specific incorporation of unnatural amino acids are indicated. Figure 15. Expression...of functional CCR5 mutants containing Acp or Bzp at positions 28, 96, or 260. HEK293T cells were transfected with plasmids carrying the genes for... CCR5 -wt or CCR5 mutant with an amber mutation at position I28, F96, or F260. Plasmids encoding Bst-Yam and E. coli TyrRS (AcpRS or BzpRS) were co

  9. Site-specific Chemical Modification of a Glycoprotein Fragment Expressed in Yeast

    PubMed Central

    Xiao, Junpeng; Tolbert, Thomas J.

    2011-01-01

    Site-specific modification of glycoproteins has wide application in both biochemical and biophysical studies. This method describes the conjugation of synthetic molecules to the N-terminus of a glycoprotein fragment: immunoglobulin G subclass 1 fragment crystallizable (IgG1 Fc) by native chemical ligation. The glycosylated IgG1 Fc is expressed in a glycosylation deficient yeast strain. The N-terminal cysteine is generated by the endogenous yeast protease Kex2 in the yeast secretory pathway. The N-terminal cysteine is then conjugated with a biotin thioester to produce a biotinylated, glycosylated IgG1 Fc using native chemical ligation. PMID:21674341

  10. Site-specific DNA-antibody conjugates for specific and sensitive immuno-PCR

    PubMed Central

    Kazane, Stephanie A.; Sok, Devin; Cho, Edward H.; Uson, Maria Loressa; Kuhn, Peter; Schultz, Peter G.; Smider, Vaughn V.

    2012-01-01

    Antibody conjugates are widely used as diagnostics and imaging reagents. However, many such conjugates suffer losses in sensitivity and specificity due to nonspecific labeling techniques. We have developed methodology to site-specifically conjugate oligonucleotides to antibodies containing a genetically encoded unnatural amino acid with orthogonal chemical reactivity. These oligobody molecules were used in immuno-PCR assays to detect Her2+ cells with greater sensitivity and specificity than nonspecifically coupled fragments, and can detect extremely rare Her2+ cells in a complex cellular environment. Such designed antibody-oligonucleotide conjugates should provide sensitive and specific reagents for diagnostics, as well as enable other unique applications based on oligobody building blocks. PMID:22345566

  11. Coverage intervals for trace elements in human scalp hair are site specific.

    PubMed

    Tamburo, E; Varrica, D; Dongarrà, G

    2015-01-01

    Coverage intervals for trace elements in human scalp hair commonly provide the basis for interpreting laboratory results and also in comparative decision-making processes regarding exposure risk assessment. This short communication documents, by some examples, that those computed for human hair are to be considered site specific, as they reflect local environmental conditions; also each geographic area has a typical profile of hair elemental composition of its inhabitants. Therefore, the levels of trace elements in hair are not strictly comparable between different areas of the world. This issue is particularly relevant when identification of anomalous environmental exposures are requested or even in detecting physiological disorders.

  12. Environmental restoration and waste management Site-Specific Plan for the Oak Ridge Reservation. FY 1993

    SciTech Connect

    Not Available

    1993-01-15

    The United States Department of Energy (DOE) is committed to achieving and maintaining environmental regulatory compliance while responding to public concerns and emphasizing waste minimization. DOE publishes the Environmental Restoration and Waste Management Five-Year Plan (FYP) annually to document its progress towards these goals. The purpose of this Site-Specific Plan (SSP) is to describe the activities undertaken to implement the FYP goals at the DOE Oak Ridge Field Office (DOE/OR) installations and programs specifically for the Oak Ridge Reservation (ORR) and surrounding areas. This SSP addresses activities and goals to be accomplished during FY93 even through the FYP focuses on FY94.

  13. Site specific incorporation of heavy atom-containing unnatural amino acids into proteins for structure determination

    DOEpatents

    Xie, Jianming; Wang, Lei; Wu, Ning; Schultz, Peter G.

    2008-07-15

    Translation systems and other compositions including orthogonal aminoacyl tRNA-synthetases that preferentially charge an orthogonal tRNA with an iodinated or brominated amino acid are provided. Nucleic acids encoding such synthetases are also described, as are methods and kits for producing proteins including heavy atom-containing amino acids, e.g., brominated or iodinated amino acids. Methods of determining the structure of a protein, e.g., a protein into which a heavy atom has been site-specifically incorporated through use of an orthogonal tRNA/aminoacyl tRNA-synthetase pair, are also described.

  14. Influence of Optical Properties on the Spin Polarization of Cu3P Photoelectrons

    NASA Astrophysics Data System (ADS)

    Chassé, A.; Niebergall, L.

    We have investigated the influence of optical properties of Cu(001) on the spin polarization in Cu3p photoelectron diffraction patterns. The refraction and absorption of light have been taken into account in the calculation of the dipole transition matrix element. Therefore, a general polarization vector of light is defined within a macroscopic theory of electromagnetic fields. Results are shown and discussed for Cu3p photoelectrons excited by linearly or circularly polarized light, respectively. It is shown that the optical behavior of crystals may cause a symmetry breaking in the angular dependence of the photoelectron intensity. Besides, there are strong quantitative changes in the related spin polarization of Cu3p photoelectrons.

  15. Effective and site-specific phosphoramidation reaction for universally labeling nucleic acids.

    PubMed

    Su, Yu-Chih; Chen, Hsing-Yin; Ko, Ni Chien; Hwang, Chi-Ching; Wu, Min Hui; Wang, Li-Fang; Wang, Yun-Ming; Chang, Sheng-Nan; Wang, Eng-Chi; Wang, Tzu-Pin

    2014-03-15

    Here we report efficient and selective postsynthesis labeling strategies, based on an advanced phosphoramidation reaction, for nucleic acids of either synthetic or enzyme-catalyzed origin. The reactions provided phosphorimidazolide intermediates of DNA or RNA which, whether reacted in one pot (one-step) or purified (two-step), were directly or indirectly phosphoramidated with label molecules. The acquired fluorophore-labeled nucleic acids, prepared from the phosphoramidation reactions, demonstrated labeling efficacy by their F/N ratio values (number of fluorophores per molecule of nucleic acid) of 0.02-1.2 which are comparable or better than conventional postsynthesis fluorescent labeling methods for DNA and RNA. Yet, PCR and UV melting studies of the one-step phosphoramidation-prepared FITC-labeled DNA indicated that the reaction might facilitate nonspecific hybridization in nucleic acids. Intrinsic hybridization specificity of nucleic acids was, however, conserved in the two-step phosphoramidation reaction. The reaction of site-specific labeling nucleic acids at the 5'-end was supported by fluorescence quenching and UV melting studies of fluorophore-labeled DNA. The two-step phosphoramidation-based, effective, and site-specific labeling method has the potential to expedite critical research including visualization, quantification, structural determination, localization, and distribution of nucleic acids in vivo and in vitro.

  16. Cre recombinase-mediated site-specific recombination between plant chromosomes.

    PubMed Central

    Qin, M; Bayley, C; Stockton, T; Ow, D W

    1994-01-01

    We report the use of the bacteriophage P1 Cre-lox system for generating conservative site-specific recombination between tobacco chromosomes. Two constructs, one containing a promoterless hygromycin-resistance gene preceded by a lox site (lox-hpt) and the other containing a cauliflower mosaic virus 35S promoter linked to a lox sequence and the cre coding region (35S-lox-cre), were introduced separately into tobacco plants. Crosses between plants harboring either construct produced plants with the two constructs situated on different chromosomes. Plants with recombination events were identified by selecting for hygromycin resistance, a phenotype expressed upon recombination. Molecular analysis showed that these recombination events occurred specifically at the lox sites and resulted in the reciprocal exchange of flanking host DNA. Progenies of these plants showed 67-100% cotransmission of the new transgenes, 35S-lox-hpt and lox-cre, consistent with the preferential cosegregation of translocated chromosomes. These results illustrate that site-specific recombination systems can be useful tools for the large-scale manipulation of eukaryotic chromosomes in vivo. Images PMID:8127869

  17. The Skeletal Site-Specific Role of Connective Tissue Growth Factor in Prenatal Osteogenesis

    PubMed Central

    Lambi, Alex G.; Pankratz, Talia L.; Mundy, Christina; Gannon, Maureen; Barbe, Mary F.; Richtsmeier, Joan T.; Popoff, Steven N.

    2013-01-01

    Background Connective tissue growth factor (CTGF/CCN2) is a matricellular protein that is highly expressed during bone development. Mice with global CTGF ablation (knockout, KO) have multiple skeletal dysmorphisms and perinatal lethality. A quantitative analysis of the bone phenotype has not been conducted. Results We demonstrated skeletal site-specific changes in growth plate organization, bone microarchitecture, and shape and gene expression levels in CTGF KO compared with wild-type mice. Growth plate malformations included reduced proliferation zone and increased hypertrophic zone lengths. Appendicular skeletal sites demonstrated decreased metaphyseal trabecular bone, while having increased mid-diaphyseal bone and osteogenic expression markers. Axial skeletal analysis showed decreased bone in caudal vertebral bodies, mandibles, and parietal bones in CTGF KO mice, with decreased expression of osteogenic markers. Analysis of skull phenotypes demonstrated global and regional differences in CTGF KO skull shape resulting from allometric (size-based) and nonallometric shape changes. Localized differences in skull morphology included increased skull width and decreased skull length. Dysregulation of the transforming growth factor-β-CTGF axis coupled with unique morphologic traits provides a potential mechanistic explanation for the skull phenotype. Conclusions We present novel data on a skeletal phenotype in CTGF KO mice, in which ablation of CTGF causes site-specific aberrations in bone formation. PMID:23073844

  18. Coulomb nanoradiator-mediated, site-specific thrombolytic proton treatment with a traversing pristine Bragg peak

    NASA Astrophysics Data System (ADS)

    Jeon, Jae-Kun; Han, Sung-Mi; Min, Soon-Ki; Seo, Seung-Jun; Ihm, Kyuwook; Chang, Won-Seok; Kim, Jong-Ki

    2016-11-01

    Traversing proton beam-irradiated, mid/high-Z nanoparticles produce site-specific enhancement of X-ray photon-electron emission via the Coulomb nanoradiator (CNR) effect, resulting in a nano- to micro-scale therapeutic effect at the nanoparticle-uptake target site. Here, we demonstrate the uptake of iron oxide nanoparticles (IONs) and nanoradiator-mediated, site-specific thrombolysis without damaging the vascular endothelium in an arterial thrombosis mouse model. The enhancement of low-energy electron (LEE) emission and reactive oxygen species (ROS) production from traversing proton beam-irradiated IONs was examined. Flow recovery was only observed in CNR-treated mice, and greater than 50% removal of the thrombus was achieved. A 2.5-fold greater reduction in the thrombus-enabled flow recovery was observed in the CNR group compared with that observed in the untreated ION-only and proton-only control groups (p < 0.01). Enhancement of the X-ray photon-electron emission was evident from both the pronounced Shirley background in the electron yield and the 1.2- to 2.5-fold enhanced production of ROS by the proton-irradiated IONs, which suggests chemical degradation of the thrombus without potent emboli.

  19. Hybrid TiO II nanoparticles: an approach for developing site specific DNA cleavage

    NASA Astrophysics Data System (ADS)

    Liu, J.; Saponjic, Z.; Dimitrijevic, N. M.; Luo, S.; Preuss, D.; Rajh, T.

    2006-02-01

    We have developed hybrid light responsive TiO II nanoparticles electronically linked to PNA oligonucleotides that site specifically bind to double stranded target DNA. This opens a new opportunity for the development of a highly efficient "artificial restriction enzyme" whose activity can be controlled by using light. The work focuses on the use of TiO II nanocomposites as analogs of restriction enzymes with unique specificity that does not exist in current biological approaches. TiO II nanoparticles electronically linked to DNA or PNA adapters have been site-specifically attached along double stranded λ DNA vectors. Illumination of this assembly results in selective oxidation of DNA at the deepest "thermodynamic traps" located closest to the nanoparticle surface, causing DNA cleavage. We investigate the effect of the sequence and length of DNA and PNA adapters on the specificity of DNA cleavage. Related to this issue, the potential use of TiO II/DNA nanocomposites as "rare cutters" that cleave DNA in the places not achieved with existing protein-based enzymes is investigated.

  20. Site specific rates of mitochondrial genomes and the phylogeny of eutheria

    PubMed Central

    Kjer, Karl M; Honeycutt, Rodney L

    2007-01-01

    Background Traditionally, most studies employing data from whole mitochondrial genomes to diagnose relationships among the major lineages of mammals have attempted to exclude regions that potentially complicate phylogenetic analysis. Components generally excluded are 3rd codon positions of protein-encoding genes, the control region, rRNAs, tRNAs, and the ND6 gene (encoded on the opposite strand). We present an approach that includes all the data, with the exception of the control region. This approach is based on a site-specific rate model that accommodates excessive homoplasy and that utilizes secondary structure as a reference for proper alignment of rRNAs and tRNAs. Results Mitochondrial genomic data for 78 eutherian mammals, 8 metatherians, and 3 monotremes were analyzed with a Bayesian analysis and our site specific rate model. The resultant phylogeny revealed strong support for most nodes and was highly congruent with more recent phylogenies based on nuclear DNA sequences. In addition, many of the conflicting relationships observed by earlier mitochondrial-based analyses were resolved without need for the exclusion of large subsets of the data. Conclusion Rather than exclusion of data to minimize presumed noise associated with non-protein encoding genes in the mitochondrial genome, our results indicate that selection of an appropriate model that accommodates rate heterogeneity across data partitions and proper treatment of RNA genes can result in a mitochondrial genome-based phylogeny of eutherian mammals that is reasonably congruent with recent phylogenies derived from nuclear genes. PMID:17254354

  1. Synthesis of Site-Specific DNA–Protein Conjugates and Their Effects on DNA Replication

    PubMed Central

    2015-01-01

    DNA–protein cross-links (DPCs) are bulky, helix-distorting DNA lesions that form in the genome upon exposure to common antitumor drugs, environmental/occupational toxins, ionizing radiation, and endogenous free-radical-generating systems. As a result of their considerable size and their pronounced effects on DNA–protein interactions, DPCs can interfere with DNA replication, transcription, and repair, potentially leading to mutagenesis, genotoxicity, and cytotoxicity. However, the biological consequences of these ubiquitous lesions are not fully understood due to the difficulty of generating DNA substrates containing structurally defined, site-specific DPCs. In the present study, site-specific cross-links between the two biomolecules were generated by copper-catalyzed [3 + 2] Huisgen cycloaddition (click reaction) between an alkyne group from 5-(octa-1,7-diynyl)-uracil in DNA and an azide group within engineered proteins/polypeptides. The resulting DPC substrates were subjected to in vitro primer extension in the presence of human lesion bypass DNA polymerases η, κ, ν, and ι. We found that DPC lesions to the green fluorescent protein and a 23-mer peptide completely blocked DNA replication, while the cross-link to a 10-mer peptide was bypassed. These results indicate that the polymerases cannot read through the larger DPC lesions and further suggest that proteolytic degradation may be required to remove the replication block imposed by bulky DPC adducts. PMID:24918113

  2. Generation of Food-Grade Recombinant Lactic Acid Bacterium Strains by Site-Specific Recombination

    PubMed Central

    Martín, M. Cruz; Alonso, Juan C.; Suárez, Juan E.; Alvarez, Miguel A.

    2000-01-01

    The construction of a delivery and clearing system for the generation of food-grade recombinant lactic acid bacterium strains, based on the use of an integrase (Int) and a resolvo-invertase (β-recombinase) and their respective target sites (attP-attB and six, respectively) is reported. The delivery system contains a heterologous replication origin and antibiotic resistance markers surrounded by two directly oriented six sites, a multiple cloning site where passenger DNA could be inserted (e.g., the cI gene of bacteriophage A2), the int gene, and the attP site of phage A2. The clearing system provides a plasmid-borne gene encoding β-recombinase. The nonreplicative vector-borne delivery system was transformed into Lactobacillus casei ATCC 393 and, by site-specific recombination, integrated as a single copy in an orientation- and Int-dependent manner into the attB site present in the genome of the host strain. The transfer of the clearing system into this strain, with the subsequent expression of the β-recombinase, led to site-specific DNA resolution of the non-food-grade DNA. These methods were validated by the construction of a stable food-grade L. casei ATCC 393-derived strain completely immune to phage A2 infection during milk fermentation. PMID:10831443

  3. Site-specific emergency response concept plans for the Chemical Stockpile Disposal Program

    SciTech Connect

    Carnes, S.A.

    1989-12-01

    Site-specific emergency response concept plans were developed to help initiate enhanced emergency preparedness for continued storage of the stockpile and the Chemical Stockpile Disposal Program (CSDP) at the eight army installations storing the unitary chemical stockpile -- Aberdeen Proving Ground, Anniston Army Depot, Lexington-Blue Grass Army Depot, Newport Army Ammunition Plant, Pine Bluff Arsenal, Pueblo Depot Activity, Tooele Army Depot, and Umatilla Depot Activity. This document summarizes the emergency response plans for all the sites and highlights similarities and differences among them. Section 2 summarizes site-specific differences in stockpile hazard and risk by showing differences in planning-basis accident categories and distributions of topographical features, meteorological conditions, and populations at risk. Section 3 presents a summary of the methodology used to identify the emergency planning zones for each site and the actual recommended boundaries of those zones for the eight sites. Section 4 identifies feasible and recommended protective actions for the sites and explains reasons for differences in them. Finally, Section 5 notes the dependence of protective action effectiveness on the development and implementation of command and control and warning systems that can be implemented in a timely manner, it also identifies the differences in recommended lead times (i.e., from the onset of an accidental release) needed at the sites for effective implementation of protective actions. 17 refs., 11 figs. , 12 tabs.

  4. Coulomb nanoradiator-mediated, site-specific thrombolytic proton treatment with a traversing pristine Bragg peak

    PubMed Central

    Jeon, Jae-Kun; Han, Sung-Mi; Min, Soon-Ki; Seo, Seung-Jun; Ihm, Kyuwook; Chang, Won-Seok; Kim, Jong-Ki

    2016-01-01

    Traversing proton beam-irradiated, mid/high-Z nanoparticles produce site-specific enhancement of X-ray photon-electron emission via the Coulomb nanoradiator (CNR) effect, resulting in a nano- to micro-scale therapeutic effect at the nanoparticle-uptake target site. Here, we demonstrate the uptake of iron oxide nanoparticles (IONs) and nanoradiator-mediated, site-specific thrombolysis without damaging the vascular endothelium in an arterial thrombosis mouse model. The enhancement of low-energy electron (LEE) emission and reactive oxygen species (ROS) production from traversing proton beam-irradiated IONs was examined. Flow recovery was only observed in CNR-treated mice, and greater than 50% removal of the thrombus was achieved. A 2.5-fold greater reduction in the thrombus-enabled flow recovery was observed in the CNR group compared with that observed in the untreated ION-only and proton-only control groups (p < 0.01). Enhancement of the X-ray photon-electron emission was evident from both the pronounced Shirley background in the electron yield and the 1.2- to 2.5-fold enhanced production of ROS by the proton-irradiated IONs, which suggests chemical degradation of the thrombus without potent emboli. PMID:27897205

  5. Site-specific fluorescent labeling to visualize membrane translocation of a myristoyl switch protein

    PubMed Central

    Yang, Sung-Tae; Lim, Sung In; Kiessling, Volker; Kwon, Inchan; Tamm, Lukas K.

    2016-01-01

    Fluorescence approaches have been widely used for elucidating the dynamics of protein-membrane interactions in cells and model systems. However, non-specific multi-site fluorescent labeling often results in a loss of native structure and function, and single cysteine labeling is not feasible when native cysteines are required to support a protein’s folding or catalytic activity. Here, we develop a method using genetic incorporation of non-natural amino acids and bio-orthogonal chemistry to site-specifically label with a single fluorescent small molecule or protein the myristoyl-switch protein recoverin, which is involved in rhodopsin-mediated signaling in mammalian visual sensory neurons. We demonstrate reversible Ca2+-responsive translocation of labeled recoverin to membranes and show that recoverin favors membranes with negative curvature and high lipid fluidity in complex heterogeneous membranes, which confers spatio-temporal control over down-stream signaling events. The site-specific orthogonal labeling technique is promising for structural, dynamical, and functional studies of many lipid-anchored membrane protein switches. PMID:27605302

  6. High throughput peptide mapping method for analysis of site specific monoclonal antibody oxidation.

    PubMed

    Li, Xiaojuan; Xu, Wei; Wang, Yi; Zhao, Jia; Liu, Yan-Hui; Richardson, Daisy; Li, Huijuan; Shameem, Mohammed; Yang, Xiaoyu

    2016-08-19

    Oxidation of therapeutic monoclonal antibodies (mAbs) often occurs on surface exposed methionine and tryptophan residues during their production in cell culture, purification, and storage, and can potentially impact the binding to their targets. Characterization of site specific oxidation is critical for antibody quality control. Antibody oxidation is commonly determined by peptide mapping/LC-MS methods, which normally require a long (up to 24h) digestion step. The prolonged sample preparation procedure could result in oxidation artifacts of susceptible methionine and tryptophan residues. In this paper, we developed a rapid and simple UV based peptide mapping method that incorporates an 8-min trypsin in-solution digestion protocol for analysis of oxidation. This method is able to determine oxidation levels at specific residues of a mAb based on the peptide UV traces within <1h, from either TBHP treated or UV light stressed samples. This is the simplest and fastest method reported thus far for site specific oxidation analysis, and can be applied for routine or high throughput analysis of mAb oxidation during various stability and degradation studies. By using the UV trace, the method allows more accurate measurement than mass spectrometry and can be potentially implemented as a release assay. It has been successfully used to monitor antibody oxidation in real time stability studies.

  7. Development of a site-specific marine water quality standard for cyanide

    SciTech Connect

    Arredondo, L.A.; Brix, K.V.; Cardwell, R.D.; Marsden, A.

    1995-12-31

    A study was conducted to develop a site-specific marine standard for cyanide. The generic cyanide standard of 1 {micro}g/L is ``driven`` by toxicity data for eastern rock crab (Cancer irroratus) zoeae. The reported LC50 for C. irroratus is 4.9 {micro}g/L cyanide and is six times more sensitive that any other marine species tested. In order to develop a site-specific standard for Washington state, cyanide toxicity tests were conducted using the first stage zoeae of Cancer magister and Cancer oregonensis, two Cancer resident to Puget Sound, in accordance with standard ASTM test methods. Testing with C. magister and C. oregonensis resulted in Species Mean Acute Values (SMAVS) of 68 and 131 {micro}g/L cyanide based on measured test concentrations. This is considerably higher than that reported for C. irroratus, is more consistent with cyanide toxicity values for other species tested, and results in a water quality criterion of 9.85 {micro}g/L cyanide with inclusion of these values in the data set. This paper presents the test methods used and the potential effects the test results may have on the marine water quality criterion for cyanide.

  8. New developments for the site-specific attachment of protein to surfaces

    SciTech Connect

    Camarero, J A

    2005-05-12

    Protein immobilization on surfaces is of great importance in numerous applications in biology and biophysics. The key for the success of all these applications relies on the immobilization technique employed to attach the protein to the corresponding surface. Protein immobilization can be based on covalent or noncovalent interaction of the molecule with the surface. Noncovalent interactions include hydrophobic interactions, hydrogen bonding, van der Waals forces, electrostatic forces, or physical adsorption. However, since these interactions are weak, the molecules can get denatured or dislodged, thus causing loss of signal. They also result in random attachment of the protein to the surface. Site-specific covalent attachment of proteins onto surfaces, on the other hand, leads to molecules being arranged in a definite, orderly fashion and uses spacers and linkers to help minimize steric hindrances between the protein surface. This work reviews in detail some of the methods most commonly used as well as the latest developments for the site-specific covalent attachment of protein to solid surfaces.

  9. Photoaffinity site-specific covalent labeling of human corticosteroid-binding globulin.

    PubMed Central

    Marver, D; Chiu, W; Wolff, M E; Edelman, I S

    1976-01-01

    A method was developed for the synthesis of high-specific-activity 21-diazo-21-[6,7-(3)H]deoxycorticosterone, an analog of corticosterone. This analog was used as a photoaffinity label of a high affinity steroid-binding protein, human corticosteroid-binding globulin. Based on direct binding studies and crosscompetition experiments, this diazo derivative exhibited the requisite affinity (within a factor of 1.5 times that of corticosterone) and site specificity to qualify as an affinity labeling legand. Irradiation of corticosteroid-binding globulin with the 21-diazo derivative resulted in irreversible binding to corticosteroid-binding globulin, identified by polyacrylamide gel electrophoresis. Specificity of covalent binding to corticosteroid-binding globulin was established by competition analysis with various steroids. Irreversibility of photodependent binding was shown by persistence of the complex on electrophoresis (in contrast to the noncovalently linked complex), and resistance to exchange with corticosterone or pregnanediol and to solvent extraction. Site specificity of covalent binding was inferred from the effects of a scavenger, Tris-HC1, and fluorescence quenching of a neighboring tryptophan. PMID:1069998

  10. Applying nitrogen site-specifically using soil electrical conductivity maps and precision agriculture technology.

    PubMed

    Lund, E D; Wolcott, M C; Hanson, G P

    2001-10-16

    Soil texture varies significantly within many agricultural fields. The physical properties of soil, such as soil texture, have a direct effect on water holding capacity, cation exchange capacity, crop yield, production capability, and nitrogen (N) loss variations within a field. In short, mobile nutrients are used, lost, and stored differently as soil textures vary. A uniform application of N to varying soils results in a wide range of N availability to the crop. N applied in excess of crop usage results in a waste of the grower"s input expense, a potential negative effect on the environment, and in some crops a reduction of crop quality, yield, and harvestability. Inadequate N levels represent a lost opportunity for crop yield and profit. The global positioning system (GPS)-referenced mapping of bulk soil electrical conductivity (EC) has been shown to serve as an effective proxy for soil texture and other soil properties. Soils with a high clay content conduct more electricity than coarser textured soils, which results in higher EC values. This paper will describe the EC mapping process and provide case studies of site-specific N applications based on EC maps. Results of these case studies suggest that N can be managed site-specifically using a variety of management practices, including soil sampling, variable yield goals, and cropping history.

  11. Site specific passive acoustic detection and densities of humpback whale calls off the coast of California

    NASA Astrophysics Data System (ADS)

    Helble, Tyler Adam

    Passive acoustic monitoring of marine mammal calls is an increasingly important method for assessing population numbers, distribution, and behavior. Automated methods are needed to aid in the analyses of the recorded data. When a mammal vocalizes in the marine environment, the received signal is a filtered version of the original waveform emitted by the marine mammal. The waveform is reduced in amplitude and distorted due to propagation effects that are influenced by the bathymetry and environment. It is important to account for these effects to determine a site-specific probability of detection for marine mammal calls in a given study area. A knowledge of that probability function over a range of environmental and ocean noise conditions allows vocalization statistics from recordings of single, fixed, omnidirectional sensors to be compared across sensors and at the same sensor over time with less bias and uncertainty in the results than direct comparison of the raw statistics. This dissertation focuses on both the development of new tools needed to automatically detect humpback whale vocalizations from single-fixed omnidirectional sensors as well as the determination of the site-specific probability of detection for monitoring sites off the coast of California. Using these tools, detected humpback calls are "calibrated" for environmental properties using the site-specific probability of detection values, and presented as call densities (calls per square kilometer per time). A two-year monitoring effort using these calibrated call densities reveals important biological and ecological information on migrating humpback whales off the coast of California. Call density trends are compared between the monitoring sites and at the same monitoring site over time. Call densities also are compared to several natural and human-influenced variables including season, time of day, lunar illumination, and ocean noise. The results reveal substantial differences in call densities

  12. Development of remote sensing based site specific weed management for Midwest mint production

    NASA Astrophysics Data System (ADS)

    Gumz, Mary Saumur Paulson

    Peppermint and spearmint are high value essential oil crops in Indiana, Michigan, and Wisconsin. Although the mints are profitable alternatives to corn and soybeans, mint production efficiency must improve in order to allow industry survival against foreign produced oils and synthetic flavorings. Weed control is the major input cost in mint production and tools to increase efficiency are necessary. Remote sensing-based site-specific weed management offers potential for decreasing weed control costs through simplified weed detection and control from accurate site specific weed and herbicide application maps. This research showed the practicability of remote sensing for weed detection in the mints. Research was designed to compare spectral response curves of field grown mint and weeds, and to use these data to develop spectral vegetation indices for automated weed detection. Viability of remote sensing in mint production was established using unsupervised classification, supervised classification, handheld spectroradiometer readings and spectral vegetation indices (SVIs). Unsupervised classification of multispectral images of peppermint production fields generated crop health maps with 92 and 67% accuracy in meadow and row peppermint, respectively. Supervised classification of multispectral images identified weed infestations with 97% and 85% accuracy for meadow and row peppermint, respectively. Supervised classification showed that peppermint was spectrally distinct from weeds, but the accuracy of these measures was dependent on extensive ground referencing which is impractical and too costly for on-farm use. Handheld spectroradiometer measurements of peppermint, spearmint, and several weeds and crop and weed mixtures were taken over three years from greenhouse grown plants, replicated field plots, and production peppermint and spearmint fields. Results showed that mints have greater near infrared (NIR) and lower green reflectance and a steeper red edge slope than

  13. Site-specific range uncertainties caused by dose calculation algorithms for proton therapy

    NASA Astrophysics Data System (ADS)

    Schuemann, J.; Dowdell, S.; Grassberger, C.; Min, C. H.; Paganetti, H.

    2014-08-01

    The purpose of this study was to assess the possibility of introducing site-specific range margins to replace current generic margins in proton therapy. Further, the goal was to study the potential of reducing margins with current analytical dose calculations methods. For this purpose we investigate the impact of complex patient geometries on the capability of analytical dose calculation algorithms to accurately predict the range of proton fields. Dose distributions predicted by an analytical pencil-beam algorithm were compared with those obtained using Monte Carlo (MC) simulations (TOPAS). A total of 508 passively scattered treatment fields were analyzed for seven disease sites (liver, prostate, breast, medulloblastoma-spine, medulloblastoma-whole brain, lung and head and neck). Voxel-by-voxel comparisons were performed on two-dimensional distal dose surfaces calculated by pencil-beam and MC algorithms to obtain the average range differences and root mean square deviation for each field for the distal position of the 90% dose level (R90) and the 50% dose level (R50). The average dose degradation of the distal falloff region, defined as the distance between the distal position of the 80% and 20% dose levels (R80-R20), was also analyzed. All ranges were calculated in water-equivalent distances. Considering total range uncertainties and uncertainties from dose calculation alone, we were able to deduce site-specific estimations. For liver, prostate and whole brain fields our results demonstrate that a reduction of currently used uncertainty margins is feasible even without introducing MC dose calculations. We recommend range margins of 2.8% + 1.2 mm for liver and prostate treatments and 3.1% + 1.2 mm for whole brain treatments, respectively. On the other hand, current margins seem to be insufficient for some breast, lung and head and neck patients, at least if used generically. If no case specific adjustments are applied, a generic margin of 6.3% + 1.2 mm would be

  14. Polymerase-Mediated Site-Specific Incorporation of a Synthetic Fluorescent Isomorphic G Surrogate into RNA.

    PubMed

    Li, Yao; Fin, Andrea; McCoy, Lisa; Tor, Yitzhak

    2017-01-24

    An enzyme-mediated approach for the assembly of singly modified RNA constructs in which specific G residues are replaced with (th) G, an emissive isomorphic G surrogate, is reported. Transcription in the presence of (th) G and native nucleoside triphosphates enforces initiation with the unnatural analogue, yielding 5'-end modified transcripts that can be mono-phosphorylated and ligated to provide longer site-specifically modified RNA constructs. The scope of this unprecedented enzymatic approach to non-canonical purine-containing RNAs is explored via the assembly of several altered hammerhead (HH) ribozymes and a singly modified HH substrate. By strategically modifying key positions, a mechanistic insight into the ribozyme-mediated cleavage is gained. Additionally, the emissive features of the modified nucleoside and its responsiveness to environmental changes can be used to monitor cleavage in real time by steady state fluorescence spectroscopy.

  15. Tyrosinase-catalyzed site-specific immobilization of engineered C-phycocyanin to surface.

    PubMed

    Faccio, Greta; Kämpf, Michael M; Piatti, Chiara; Thöny-Meyer, Linda; Richter, Michael

    2014-06-20

    Enzymatic crosslinking of proteins is often limited by the steric availability of the target residues, as of tyrosyl side chains in the case of tyrosinase. Carrying an N-terminal peptide-tag containing two tyrosine residues, the fluorescent protein C-phycocyanin HisCPC from Synechocystis sp. PCC6803 was crosslinked to fluorescent high-molecular weight forms with tyrosinase. Crosslinking with tyrosinase in the presence of L-tyrosine produced non fluorescent high-molecular weight products. Incubated in the presence of tyrosinase, HisCPC could also be immobilized to amino-modified polystyrene beads thus conferring a blue fluorescence. Crosslinking and immobilization were site-specific as both processes required the presence of the N-terminal peptide in HisCPC.

  16. Tyrosinase-catalyzed site-specific immobilization of engineered C-phycocyanin to surface

    NASA Astrophysics Data System (ADS)

    Faccio, Greta; Kämpf, Michael M.; Piatti, Chiara; Thöny-Meyer, Linda; Richter, Michael

    2014-06-01

    Enzymatic crosslinking of proteins is often limited by the steric availability of the target residues, as of tyrosyl side chains in the case of tyrosinase. Carrying an N-terminal peptide-tag containing two tyrosine residues, the fluorescent protein C-phycocyanin HisCPC from Synechocystis sp. PCC6803 was crosslinked to fluorescent high-molecular weight forms with tyrosinase. Crosslinking with tyrosinase in the presence of L-tyrosine produced non fluorescent high-molecular weight products. Incubated in the presence of tyrosinase, HisCPC could also be immobilized to amino-modified polystyrene beads thus conferring a blue fluorescence. Crosslinking and immobilization were site-specific as both processes required the presence of the N-terminal peptide in HisCPC.

  17. Magnetically Controllable Polymer Nanotubes from a Cyclized Crosslinker for Site-Specific Delivery of Doxorubicin

    NASA Astrophysics Data System (ADS)

    Newland, Ben; Leupelt, Daniel; Zheng, Yu; Thomas, Laurent S. V.; Werner, Carsten; Steinhart, Martin; Wang, Wenxin

    2015-12-01

    Externally controlled site specific drug delivery could potentially provide a means of reducing drug related side effects whilst maintaining, or perhaps increasing therapeutic efficiency. The aim of this work was to develop a nanoscale drug carrier, which could be loaded with an anti-cancer drug and be directed by an external magnetic field. Using a single, commercially available monomer and a simple one-pot reaction process, a polymer was synthesized and crosslinked within the pores of an anodized aluminum oxide template. These polymer nanotubes (PNT) could be functionalized with iron oxide nanoparticles for magnetic manipulation, without affecting the large internal pore, or inherent low toxicity. Using an external magnetic field the nanotubes could be regionally concentrated, leaving areas devoid of nanotubes. Lastly, doxorubicin could be loaded to the PNTs, causing increased toxicity towards neuroblastoma cells, rendering a platform technology now ready for adaptation with different nanoparticles, degradable pre-polymers, and various therapeutics.

  18. Site-specific labeling of proteins via sortase: protocols for the molecular biologist.

    PubMed

    Popp, Maximilian Wei-Lin

    2015-01-01

    Creation of site-specifically labeled protein bioconjugates is an important tool for the molecular biologist and cell biologist. Chemical labeling methods, while versatile with respect to the types of moieties that can be attached, suffer from lack of specificity, often targeting multiple positions within a protein. Here we describe protocols for the chemoenzymatic labeling of proteins at the C-terminus using the bacterial transpeptidase, sortase A. We detail a protocol for the purification of an improved pentamutant variant of the Staphylococcus aureus enzyme (SrtA 5(o)) that exhibits vastly improved kinetics relative to the wild-type enzyme. Importantly, a protocol for the construction of peptide probes compatible with sortase labeling using techniques that can be adapted to any cellular/molecular biology lab with no existing infrastructure for synthetic chemistry is described. Finally, we provide an example of how to optimize the labeling reaction using the improved SrtA 5(o) variant.

  19. Crystal structure of the site-specific recombinase, XerD.

    PubMed Central

    Subramanya, H S; Arciszewska, L K; Baker, R A; Bird, L E; Sherratt, D J; Wigley, D B

    1997-01-01

    The structure of the site-specific recombinase, XerD, that functions in circular chromosome separation, has been solved at 2.5 A resolution and reveals that the protein comprises two domains. The C-terminal domain contains two conserved sequence motifs that are located in similar positions in the structures of XerD, lambda and HP1 integrases. However, the extreme C-terminal regions of the three proteins, containing the active site tyrosine, are very different. In XerD, the arrangement of active site residues supports a cis cleavage mechanism. Biochemical evidence for DNA bending is encompassed in a model that accommodates extensive biochemical and genetic data, and in which the DNA is wrapped around an alpha-helix in a manner similar to that observed for CAP complexed with DNA. PMID:9311978

  20. Site-specific structural constraints on protein sequence evolutionary divergence: local packing density versus solvent exposure.

    PubMed

    Yeh, So-Wei; Liu, Jen-Wei; Yu, Sung-Huan; Shih, Chien-Hua; Hwang, Jenn-Kang; Echave, Julian

    2014-01-01

    Protein sequences evolve under selection pressures imposed by functional and biophysical requirements, resulting in site-dependent rates of amino acid substitution. Relative solvent accessibility (RSA) and local packing density (LPD) have emerged as the best candidates to quantify structural constraint. Recent research assumes that RSA is the main determinant of sequence divergence. However, it is not yet clear which is the best predictor of substitution rates. To address this issue, we compared RSA and LPD with site-specific rates of evolution for a diverse data set of enzymes. In contrast with recent studies, we found that LPD measures correlate better than RSA with evolutionary rate. Moreover, the independent contribution of RSA is minor. Taking into account that LPD is related to backbone flexibility, we put forward the possibility that the rate of evolution of a site is determined by the ease with which the backbone deforms to accommodate mutations.

  1. The design of a Phase I non site-specific Centralized Interim Storage Facility

    SciTech Connect

    Stringer, J.; Kane, D.

    1997-10-28

    The Department of Energy (DOE), Office of Civilian Radioactive Waste Management (OCRWM) recently completed a Topical Safety Analysis Report (TSAR) for a Phase 1 non site specific Centralized Interim Storage Facility (CISF). The TSAR will be used in licensing the CISF when and if a site is designated. The combined Phase 1 and Phase 2 CISF will provide federal storage capability for 40,000 metric tons of uranium (MTU) Spent Nuclear Fuel (SNF) under the oversight of the DOE. The Phase 1 TSAR was submitted to the NRC on May 1, 1997 and is currently under review having been docketed on June 10, 1997. This paper generally describes the Phase 1 CISF design and its operations as presented in the CISF TSAR.

  2. Savannah River Site`s Site Specific Plan. Environmental restoration and waste management, fiscal year 1992

    SciTech Connect

    Not Available

    1991-08-01

    This Site Specific Plan (SSP) has been prepared by the Savannah River Site (SRS) in order to show the Environmental Restoration and Waste Management activities that were identified during the preparation of the Department of Energy-Headquarters (DOE-HQ) Environmental Restoration and Waste Management Five-Year Plan (FYP) for FY 1992--1996. The SSP has been prepared in accordance with guidance received from DOE-HQ. DOE-SR is accountable to DOE-HQ for the implementation of this plan. The purpose of the SSP is to develop a baseline for policy, budget, and schedules for the DOE Environmental Restoration and Waste Management activities. The plan explains accomplishments since the Fiscal Year (FY) 1990 plan, demonstrates how present and future activities are prioritized, identifies currently funded activities and activities that are planned to be funded in the upcoming fiscal year, and describes future activities that SRS is considering.

  3. Access to site-specific Fc-cRGD peptide conjugates through streamlined expressed protein ligation.

    PubMed

    Frutos, S; Jordan, J B; Bio, M M; Muir, T W; Thiel, O R; Vila-Perelló, M

    2016-10-12

    An ideal drug should be highly effective, non-toxic and be delivered by a convenient and painless single dose. We are still far from such optimal treatment but peptides, with their high target selectivity and low toxicity profiles, provide a very attractive platform from which to strive towards it. One of the major limitations of peptide drugs is their high clearance rates, which limit dosage regimen options. Conjugation to antibody Fc domains is a viable strategy to improve peptide stability by increasing their hydrodynamic radius and hijacking the Fc recycling pathway. We report the use of a split-intein based semi-synthetic approach to site-specifically conjugate a synthetic integrin binding peptide to an Fc domain. The strategy described here allows conjugating synthetic peptides to Fc domains, which is not possible via genetic methods, fully maintaining the ability of both the Fc domain and the bioactive peptide to interact with their binding partners.

  4. Site-specific seasonal models of carbon fluxes in terrestrial biomes

    SciTech Connect

    King, A.W.; DeAngelis, D.L.

    1986-01-01

    A set of site-specific computer simulation models of seasonal terrestrial carbon exchange has been assembled from open-literature sources. This collection is designed to facilitate the development of biome-level models for each of the principal terrestrial vegetation biomes on earth, for their integration into a global model of seasonal CO/sub 2/ variation in the atmosphere. The models are described in sufficient detail that their underlying assumptions can be compared. Descriptions include the following aspects of each model: (1) the compartments; (2) the carbon fluxes between compartments; and (3) the climatic variables that drive the carbon fluxes. In particular, the functional forms of the dependencies of respiration and photosynthesis on the driving variables are described. The methods by which these models will be extrapolated to biome-level models are also discussed.

  5. Generalized theory on the mechanism of site-specific DNA-protein interactions

    NASA Astrophysics Data System (ADS)

    Niranjani, G.; Murugan, R.

    2016-05-01

    We develop a generalized theoretical framework on the binding of transcription factor proteins (TFs) with specific sites on DNA that takes into account the interplay of various factors regarding overall electrostatic potential at the DNA-protein interface, occurrence of kinetic traps along the DNA sequence, presence of other roadblock protein molecules along DNA and crowded environment, conformational fluctuations in the DNA binding domains (DBDs) of TFs, and the conformational state of the DNA. Starting from a Smolochowski type theoretical framework on site-specific binding of TFs we logically build our model by adding the effects of these factors one by one. Our generalized two-step model suggests that the electrostatic attractive forces present inbetween the positively charged DBDs of TFs and the negatively charged phosphate backbone of DNA, along with the counteracting shielding effects of solvent ions, is the core factor that creates a fluidic type environment at the DNA-protein interface. This in turn facilitates various one-dimensional diffusion (1Dd) processes such as sliding, hopping and intersegmental transfers. These facilitating processes as well as flipping dynamics of conformational states of DBDs of TFs between stationary and mobile states can enhance the 1Dd coefficient on a par with three-dimensional diffusion (3Dd). The random coil conformation of DNA also plays critical roles in enhancing the site-specific association rate. The extent of enhancement over the 3Dd controlled rate seems to be directly proportional to the maximum possible 1Dd length. We show that the overall site-specific binding rate scales with the length of DNA in an asymptotic way. For relaxed DNA, the specific binding rate will be independent of the length of DNA as length increases towards infinity. For condensed DNA as in in vivo conditions, the specific binding rate depends on the length of DNA in a turnover way with a maximum. This maximum rate seems to scale with the

  6. Hetero-site-specific X-ray pump-probe spectroscopy for femtosecond intramolecular dynamics

    PubMed Central

    Picón, A.; Lehmann, C. S.; Bostedt, C.; Rudenko, A.; Marinelli, A.; Osipov, T.; Rolles, D.; Berrah, N.; Bomme, C.; Bucher, M.; Doumy, G.; Erk, B.; Ferguson, K. R.; Gorkhover, T.; Ho, P. J.; Kanter, E. P.; Krässig, B.; Krzywinski, J.; Lutman, A. A.; March, A. M.; Moonshiram, D.; Ray, D.; Young, L.; Pratt, S. T.; Southworth, S. H.

    2016-01-01

    New capabilities at X-ray free-electron laser facilities allow the generation of two-colour femtosecond X-ray pulses, opening the possibility of performing ultrafast studies of X-ray-induced phenomena. Particularly, the experimental realization of hetero-site-specific X-ray-pump/X-ray-probe spectroscopy is of special interest, in which an X-ray pump pulse is absorbed at one site within a molecule and an X-ray probe pulse follows the X-ray-induced dynamics at another site within the same molecule. Here we show experimental evidence of a hetero-site pump-probe signal. By using two-colour 10-fs X-ray pulses, we are able to observe the femtosecond time dependence for the formation of F ions during the fragmentation of XeF2 molecules following X-ray absorption at the Xe site. PMID:27212390

  7. Site-Specific N-Terminal Labeling of Peptides and Proteins using Butelase 1 and Thiodepsipeptide.

    PubMed

    Nguyen, Giang K T; Cao, Yuan; Wang, Wei; Liu, Chuan Fa; Tam, James P

    2015-12-21

    An efficient ligase with exquisite site-specificity is highly desirable for protein modification. Recently, we discovered the fastest known ligase called butelase 1 from Clitoria ternatea for intramolecular cyclization. For intermolecular ligation, butelase 1 requires an excess amount of a substrate to suppress the reverse reaction, a feature similar to other ligases. Herein, we describe the use of thiodepsipeptide substrates with a thiol as a leaving group and an unacceptable nucleophile to render the butelase-mediated ligation reactions irreversible and in high yields. Butelase 1 also accepted depsipeptides as substrates, but unlike a thiodesipeptide, the desipeptide ligation was partially reversible as butelase 1 can tolerate an alcohol group as a poor nucleophile. The thiodesipeptide method was successfully applied in N-terminal labeling of ubiquitin and green fluorescent protein using substrates with or without a biotin group in high yields.

  8. Hetero-site-specific X-ray pump-probe spectroscopy for femtosecond intramolecular dynamics

    SciTech Connect

    Picón, A.; Lehmann, C. S.; Bostedt, C.; Rudenko, A.; Marinelli, A.; Osipov, T.; Rolles, D.; Berrah, N.; Bomme, C.; Bucher, M.; Doumy, G.; Erk, B.; Ferguson, K. R.; Gorkhover, T.; Ho, P. J.; Kanter, E. P.; Krässig, B.; Krzywinski, J.; Lutman, A. A.; March, A. M.; Moonshiram, D.; Ray, D.; Young, L.; Pratt, S. T.; Southworth, S. H.

    2016-05-23

    New capabilities at X-ray free-electron laser facilities allow the generation of two-colour femtosecond X-ray pulses, opening the possibility of performing ultrafast studies of X-ray-induced phenomena. Specifically, the experimental realization of hetero-site-specific X-ray-pump/X-ray-probe spectroscopy is of special interest, in which an X-ray pump pulse is absorbed at one site within a molecule and an X-ray probe pulse follows the X-ray-induced dynamics at another site within the same molecule. In this paper, we show experimental evidence of a hetero-site pump-probe signal. By using two-colour 10-fs X-ray pulses, we are able to observe the femtosecond time dependence for the formation of F ions during the fragmentation of XeF2 molecules following X-ray absorption at the Xe site.

  9. Delivery methods for site-specific nucleases: Achieving the full potential of therapeutic gene editing.

    PubMed

    Liu, Jia; Shui, Sai-Lan

    2016-12-28

    The advent of site-specific nucleases, particularly CRISPR/Cas9, provides researchers with the unprecedented ability to manipulate genomic sequences. These nucleases are used to create model cell lines, engineer metabolic pathways, produce transgenic animals and plants, perform genome-wide functional screen and, most importantly, treat human diseases that are difficult to tackle by traditional medications. Considerable efforts have been devoted to improving the efficiency and specificity of nucleases for clinical applications. However, safe and efficient delivery methods remain the major obstacle for therapeutic gene editing. In this review, we summarize the recent progress on nuclease delivery methods, highlight their impact on the outcomes of gene editing and discuss the potential of different delivery approaches for therapeutic gene editing.

  10. Y-12 site-specific earthquake response analysis and soil liquefaction assessment

    SciTech Connect

    Ahmed, S.B.; Hunt, R.J.; Manrod, W.E. III

    1995-09-29

    A site-specific earthquake response analysis and soil liquefaction assessment were performed for the Oak Ridge Y-12 Plant. The main purpose of these studies was to use the results of the analyses for evaluating the safety of the performance category -1, -2, and -3 facilities against the natural phenomena seismic hazards. Earthquake response was determined for seven (7), one dimensional soil columns (Fig. 12) using two horizontal components of the PC-3 design basis 2000-year seismic event. The computer program SHAKE 91 (Ref. 7) was used to calculate the absolute response accelerations on top of ground (soil/weathered shale) and rock outcrop. The SHAKE program has been validated for horizontal response calculations at periods less than 2.0 second at several sites and consequently is widely accepted in the geotechnical earthquake engineering area for site response analysis.

  11. Hetero-site-specific X-ray pump-probe spectroscopy for femtosecond intramolecular dynamics.

    PubMed

    Picón, A; Lehmann, C S; Bostedt, C; Rudenko, A; Marinelli, A; Osipov, T; Rolles, D; Berrah, N; Bomme, C; Bucher, M; Doumy, G; Erk, B; Ferguson, K R; Gorkhover, T; Ho, P J; Kanter, E P; Krässig, B; Krzywinski, J; Lutman, A A; March, A M; Moonshiram, D; Ray, D; Young, L; Pratt, S T; Southworth, S H

    2016-05-23

    New capabilities at X-ray free-electron laser facilities allow the generation of two-colour femtosecond X-ray pulses, opening the possibility of performing ultrafast studies of X-ray-induced phenomena. Particularly, the experimental realization of hetero-site-specific X-ray-pump/X-ray-probe spectroscopy is of special interest, in which an X-ray pump pulse is absorbed at one site within a molecule and an X-ray probe pulse follows the X-ray-induced dynamics at another site within the same molecule. Here we show experimental evidence of a hetero-site pump-probe signal. By using two-colour 10-fs X-ray pulses, we are able to observe the femtosecond time dependence for the formation of F ions during the fragmentation of XeF2 molecules following X-ray absorption at the Xe site.

  12. End-to-End Network Simulation Using a Site-Specific Radio Wave Propagation Model

    SciTech Connect

    Djouadi, Seddik M; Kuruganti, Phani Teja; Nutaro, James J

    2013-01-01

    The performance of systems that rely on a wireless network depends on the propagation environment in which that network operates. To predict how these systems and their supporting networks will perform, simulations must take into consideration the propagation environment and how this effects the performance of the wireless network. Network simulators typically use empirical models of the propagation environment. However, these models are not intended for, and cannot be used, to predict a wireless system will perform in a specific location, e.g., in the center of a particular city or the interior of a specific manufacturing facility. In this paper, we demonstrate how a site-specific propagation model and the NS3 simulator can be used to predict the end-to-end performance of a wireless network.

  13. Magnetically Controllable Polymer Nanotubes from a Cyclized Crosslinker for Site-Specific Delivery of Doxorubicin

    PubMed Central

    Newland, Ben; Leupelt, Daniel; Zheng, Yu; Thomas, Laurent S. V.; Werner, Carsten; Steinhart, Martin; Wang, Wenxin

    2015-01-01

    Externally controlled site specific drug delivery could potentially provide a means of reducing drug related side effects whilst maintaining, or perhaps increasing therapeutic efficiency. The aim of this work was to develop a nanoscale drug carrier, which could be loaded with an anti-cancer drug and be directed by an external magnetic field. Using a single, commercially available monomer and a simple one-pot reaction process, a polymer was synthesized and crosslinked within the pores of an anodized aluminum oxide template. These polymer nanotubes (PNT) could be functionalized with iron oxide nanoparticles for magnetic manipulation, without affecting the large internal pore, or inherent low toxicity. Using an external magnetic field the nanotubes could be regionally concentrated, leaving areas devoid of nanotubes. Lastly, doxorubicin could be loaded to the PNTs, causing increased toxicity towards neuroblastoma cells, rendering a platform technology now ready for adaptation with different nanoparticles, degradable pre-polymers, and various therapeutics. PMID:26619814

  14. Site-specific mutagenesis of the calcium-binding photoprotein aequorin

    PubMed Central

    Tsuji, Frederick I.; Inouye, Satoshi; Goto, Toshio; Sakaki, Yoshiyuki

    1986-01-01

    The luminescent protein aequorin from the jellyfish Aequoria victoria emits light by an intramolecular reaction in the presence of a trace amount of Ca2+. In order to understand the mechanism of the reaction, a study of structure-function relationships was undertaken with respect to modifying certain of its amino acid residues. This was done by carrying out oligonucleotide-directed site-specific mutagenesis of apoaequorin cDNA and expressing the mutagenized cDNA in Escherichia coli. Amino acid substitutions were made at the three Ca2+-binding sites, the three cysteines, and a histidine in one of the hydrophobic regions. Subsequent assay of the modified aequorin showed that the Ca2+-binding sites, the cysteines, and probably the histidine all play a role in the bioluminescence reaction of aequorin. PMID:16593774

  15. Site-Specific Cassette Exchange Systems in the Aedes aegypti Mosquito and the Plutella xylostella Moth

    PubMed Central

    Haghighat-Khah, Roya Elaine; Scaife, Sarah; Martins, Sara; St John, Oliver; Matzen, Kelly Jean; Morrison, Neil; Alphey, Luke

    2015-01-01

    Genetically engineered insects are being evaluated as potential tools to decrease the economic and public health burden of mosquitoes and agricultural pest insects. Here we describe a new tool for the reliable and targeted genome manipulation of pest insects for research and field release using recombinase mediated cassette exchange (RMCE) mechanisms. We successfully demonstrated the established ΦC31-RMCE method in the yellow fever mosquito, Aedes aegypti, which is the first report of RMCE in mosquitoes. A new variant of this RMCE system, called iRMCE, combines the ΦC31-att integration system and Cre or FLP-mediated excision to remove extraneous sequences introduced as part of the site-specific integration process. Complete iRMCE was achieved in two important insect pests, Aedes aegypti and the diamondback moth, Plutella xylostella, demonstrating the transferability of the system across a wide phylogenetic range of insect pests. PMID:25830287

  16. Proteomic Approaches for Site-specific O-GlcNAcylation Analysis

    SciTech Connect

    Wang, Sheng; Yang, Feng; Camp, David G.; Rodland, Karin D.; Qian, Weijun; Liu, Tao; Smith, Richard D.

    2014-10-01

    O-GlcNAcylation is a dynamic protein post-translational modification of serine or threonine residues by an O-linked monosaccharide N-acetylglucosamine (O-GlcNAc). O-GlcNAcylation was discovered three decades ago, and it has been shown to contribute to various disease states, such as metabolic diseases, cancer and neurological diseases. Yet it remains technically difficult to characterize comprehensively and quantitatively, due to its exceptionally low abundance and extremely labile nature under conventional tandem mass spectrometry conditions. Herein, we review the recent efforts for tackling these challenges in developing proteomic approaches for site-specific O-GlcNAcylation analysis, such as specific enrichment of O-GlcNAc peptides/proteins, unambiguous site-determination of O-GlcNAc modification, and quantitative analysis of O-GlcNAcylation.

  17. Introduction of Site-Specific Mutations Into the Genome of Influenza Virus

    NASA Astrophysics Data System (ADS)

    Enami, Masayoshi; Luytjes, Willem; Krystal, Mark; Palese, Peter

    1990-05-01

    We succeeded in rescuing infectious influenza virus by transfecting cells with RNAs derived from specific recombinant DNAs. RNA corresponding to the neuraminidase (NA) gene of influenza A/WSN/33 (WSN) virus was transcribed in vitro from plasmid DNA and, following the addition of purified influenza virus RNA polymerase complex, was transfected into MDBK cells. Superinfection with helper virus lacking the WSN NA gene resulted in the release of virus containing the WSN NA gene. We then introduced five point mutations into the WSN NA gene by cassette mutagenesis of the plasmid DNA. Sequence analysis of the rescued virus revealed that the genome contained all five mutations present in the mutated plasmid. The ability to create viruses with site-specific mutations will allow the engineering of influenza viruses with defined biological properties.

  18. Carbohydrates on Proteins: Site-Specific Glycosylation Analysis by Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Zhu, Zhikai; Desaire, Heather

    2015-07-01

    Glycosylation on proteins adds complexity and versatility to these biologically vital macromolecules. To unveil the structure-function relationship of glycoproteins, glycopeptide-centric analysis using mass spectrometry (MS) has become a method of choice because the glycan is preserved on the glycosylation site and site-specific glycosylation profiles of proteins can be readily determined. However, glycopeptide analysis is still challenging given that glycopeptides are usually low in abundance and relatively difficult to detect and the resulting data require expertise to analyze. Viewing the urgent need to address these challenges, emerging methods and techniques are being developed with the goal of analyzing glycopeptides in a sensitive, comprehensive, and high-throughput manner. In this review, we discuss recent advances in glycoprotein and glycopeptide analysis, with topics covering sample preparation, analytical separation, MS and tandem MS techniques, as well as data interpretation and automation.

  19. Carbohydrates on Proteins: Site-Specific Glycosylation Analysis by Mass Spectrometry.

    PubMed

    Zhu, Zhikai; Desaire, Heather

    2015-01-01

    Glycosylation on proteins adds complexity and versatility to these biologically vital macromolecules. To unveil the structure-function relationship of glycoproteins, glycopeptide-centric analysis using mass spectrometry (MS) has become a method of choice because the glycan is preserved on the glycosylation site and site-specific glycosylation profiles of proteins can be readily determined. However, glycopeptide analysis is still challenging given that glycopeptides are usually low in abundance and relatively difficult to detect and the resulting data require expertise to analyze. Viewing the urgent need to address these challenges, emerging methods and techniques are being developed with the goal of analyzing glycopeptides in a sensitive, comprehensive, and high-throughput manner. In this review, we discuss recent advances in glycoprotein and glycopeptide analysis, with topics covering sample preparation, analytical separation, MS and tandem MS techniques, as well as data interpretation and automation.

  20. Uncovering Global SUMOylation Signaling Networks in a Site-Specific Manner

    PubMed Central

    Hendriks, Ivo A.; D’Souza, Rochelle C.J.; Yang, Bing; Verlaan-de Vries, Matty; Mann, Matthias; Vertegaal, Alfred C.O.

    2014-01-01

    SUMOylation is a reversible post-translational modification essential for genome stability. Using high-resolution mass spectrometry, we have studied global SUMOylation in human cells and in a site-specific manner, identifying a total of over 4,300 SUMOylation sites in over 1,600 proteins. Moreover, for the first time in excess of 1,000 SUMOylation sites were identified under standard growth conditions. SUMOylation dynamics were quantitatively studied in response to SUMO protease inhibition, proteasome inhibition and heat shock. A considerable amount of SUMOylated lysines have previously been reported to be ubiquitylated, acetylated or methylated, indicating crosstalk between SUMO and other post-translational modifications. We identified 70 phosphorylation and 4 acetylation events in close proximity to SUMOylation sites, and provide evidence for acetylation-dependent SUMOylation of endogenous histone H3. SUMOylation regulates target proteins involved in all nuclear processes including transcription, DNA repair, chromatin remodeling, pre-mRNA splicing and ribosome assembly. PMID:25218447

  1. Magnetically Controllable Polymer Nanotubes from a Cyclized Crosslinker for Site-Specific Delivery of Doxorubicin.

    PubMed

    Newland, Ben; Leupelt, Daniel; Zheng, Yu; Thomas, Laurent S V; Werner, Carsten; Steinhart, Martin; Wang, Wenxin

    2015-12-01

    Externally controlled site specific drug delivery could potentially provide a means of reducing drug related side effects whilst maintaining, or perhaps increasing therapeutic efficiency. The aim of this work was to develop a nanoscale drug carrier, which could be loaded with an anti-cancer drug and be directed by an external magnetic field. Using a single, commercially available monomer and a simple one-pot reaction process, a polymer was synthesized and crosslinked within the pores of an anodized aluminum oxide template. These polymer nanotubes (PNT) could be functionalized with iron oxide nanoparticles for magnetic manipulation, without affecting the large internal pore, or inherent low toxicity. Using an external magnetic field the nanotubes could be regionally concentrated, leaving areas devoid of nanotubes. Lastly, doxorubicin could be loaded to the PNTs, causing increased toxicity towards neuroblastoma cells, rendering a platform technology now ready for adaptation with different nanoparticles, degradable pre-polymers, and various therapeutics.

  2. Computational design of a red fluorophore ligase for site-specific protein labeling in living cells

    SciTech Connect

    Liu, Daniel S.; Nivon, Lucas G.; Richter, Florian; Goldman, Peter J.; Deerinck, Thomas J.; Yao, Jennifer Z.; Richardson, Douglas; Phipps, William S.; Ye, Anne Z.; Ellisman, Mark H.; Drennan, Catherine L.; Baker, David; Ting, Alice Y.

    2014-10-13

    In this study, chemical fluorophores offer tremendous size and photophysical advantages over fluorescent proteins but are much more challenging to target to specific cellular proteins. Here, we used Rosetta-based computation to design a fluorophore ligase that accepts the red dye resorufin, starting from Escherichia coli lipoic acid ligase. X-ray crystallography showed that the design closely matched the experimental structure. Resorufin ligase catalyzed the site-specific and covalent attachment of resorufin to various cellular proteins genetically fused to a 13-aa recognition peptide in multiple mammalian cell lines and in primary cultured neurons. We used resorufin ligase to perform superresolution imaging of the intermediate filament protein vimentin by stimulated emission depletion and electron microscopies. This work illustrates the power of Rosetta for major redesign of enzyme specificity and introduces a tool for minimally invasive, highly specific imaging of cellular proteins by both conventional and superresolution microscopies.

  3. Computational design of a red fluorophore ligase for site-specific protein labeling in living cells

    DOE PAGES

    Liu, Daniel S.; Nivon, Lucas G.; Richter, Florian; ...

    2014-10-13

    In this study, chemical fluorophores offer tremendous size and photophysical advantages over fluorescent proteins but are much more challenging to target to specific cellular proteins. Here, we used Rosetta-based computation to design a fluorophore ligase that accepts the red dye resorufin, starting from Escherichia coli lipoic acid ligase. X-ray crystallography showed that the design closely matched the experimental structure. Resorufin ligase catalyzed the site-specific and covalent attachment of resorufin to various cellular proteins genetically fused to a 13-aa recognition peptide in multiple mammalian cell lines and in primary cultured neurons. We used resorufin ligase to perform superresolution imaging of themore » intermediate filament protein vimentin by stimulated emission depletion and electron microscopies. This work illustrates the power of Rosetta for major redesign of enzyme specificity and introduces a tool for minimally invasive, highly specific imaging of cellular proteins by both conventional and superresolution microscopies.« less

  4. Tyrosinase-catalyzed site-specific immobilization of engineered C-phycocyanin to surface

    PubMed Central

    Faccio, Greta; Kämpf, Michael M.; Piatti, Chiara; Thöny-Meyer, Linda; Richter, Michael

    2014-01-01

    Enzymatic crosslinking of proteins is often limited by the steric availability of the target residues, as of tyrosyl side chains in the case of tyrosinase. Carrying an N-terminal peptide-tag containing two tyrosine residues, the fluorescent protein C-phycocyanin HisCPC from Synechocystis sp. PCC6803 was crosslinked to fluorescent high-molecular weight forms with tyrosinase. Crosslinking with tyrosinase in the presence of L-tyrosine produced non fluorescent high-molecular weight products. Incubated in the presence of tyrosinase, HisCPC could also be immobilized to amino-modified polystyrene beads thus conferring a blue fluorescence. Crosslinking and immobilization were site-specific as both processes required the presence of the N-terminal peptide in HisCPC. PMID:24947668

  5. Site-Specific Pyrolysis Induced Cleavage at Aspartic Acid Residue in Peptides and Proteins

    PubMed Central

    Zhang, Shaofeng; Basile, Franco

    2011-01-01

    A simple and site-specific non-enzymatic method based on pyrolysis has been developed to cleave peptides and proteins. Pyrolytic cleavage was found to be specific and rapid as it induced a cleavage at the C-terminal side of aspartic acid in the temperature range of 220–250 °C in 10 seconds. Electrospray Ionization (ESI) mass spectrometry (MS) and tandem-MS (MS/MS) were used to characterize and identify pyrolysis cleavage products, confirming that sequence information is conserved after the pyrolysis process in both peptides and protein tested. This suggests that pyrolysis-induced cleavage at aspartyl residues can be used as a rapid protein digestion procedure for the generation of sequence specific protein biomarkers. PMID:17388620

  6. The unfolded protein response triggers site-specific regulatory ubiquitylation of 40S ribosomal proteins

    PubMed Central

    Rising, Lisa; Mak, Raymond; Webb, Kristofor; Kaiser, Stephen E.; Zuzow, Nathan; Riviere, Paul; Yang, Bing; Fenech, Emma; Tang, Xin; Lindsay, Scott A.; Christianson, John C.; Hampton, Randolph Y.; Wasserman, Steven A.; Bennett, Eric J.

    2015-01-01

    Summary Insults to endoplasmic reticulum (ER) homeostasis activate the unfolded protein response (UPR), which elevates protein folding and degradation capacity and attenuates protein synthesis. While a role for ubiquitin in regulating the degradation of misfolded ER-resident proteins is well described, ubiquitin-dependent regulation of translational reprogramming during the UPR remains uncharacterized. Using global quantitative ubiquitin proteomics, we identify evolutionarily conserved, site-specific regulatory ubiquitylation of 40S ribosomal proteins. We demonstrate that these events occur on assembled cytoplasmic ribosomes and are stimulated by both UPR activation and translation inhibition. We further show that ER stress-stimulated regulatory 40S ribosomal ubiquitylation occurs on a timescale similar to eIF2α phosphorylation, is dependent upon PERK signaling, and is required for optimal cell survival during chronic UPR activation. In total, these results reveal regulatory 40S ribosomal ubiquitylation as a previously uncharacterized and important facet of eukaryotic translational control. PMID:26051182

  7. Hetero-site-specific X-ray pump-probe spectroscopy for femtosecond intramolecular dynamics

    DOE PAGES

    Picón, A.; Lehmann, C. S.; Bostedt, C.; ...

    2016-05-23

    New capabilities at X-ray free-electron laser facilities allow the generation of two-colour femtosecond X-ray pulses, opening the possibility of performing ultrafast studies of X-ray-induced phenomena. Specifically, the experimental realization of hetero-site-specific X-ray-pump/X-ray-probe spectroscopy is of special interest, in which an X-ray pump pulse is absorbed at one site within a molecule and an X-ray probe pulse follows the X-ray-induced dynamics at another site within the same molecule. In this paper, we show experimental evidence of a hetero-site pump-probe signal. By using two-colour 10-fs X-ray pulses, we are able to observe the femtosecond time dependence for the formation of F ionsmore » during the fragmentation of XeF2 molecules following X-ray absorption at the Xe site.« less

  8. A second site specific endonuclease from Thermus thermophilus 111, Tth111II.

    PubMed Central

    Shinomiya, T; Kobayashi, M; Sato, S

    1980-01-01

    A second site specific endonuclease with novel specificity has been purified from Thermus thermophilus strain 111 and named Tth111II. The enzyme is active at temperature up to 80 degrees C and requires Mg2+ or Mn2+ for endonuclease activity. Tth111II cleaves phi X174RFDNA into 11 fragments and lambda NA into more than 25 fragments. From the 5'-terminal sequences of TthlllII fragments of phi X174RFDNA determined by the two dimensional homochromatography and the survey on nucleotide sequence of phi X174RFDNA, it was concluded that Tth111II recognizes the DNA sequence (see former index) and cleaves the sites as indicated by the arrows. Images PMID:6255411

  9. Mapping shallow underground features that influence site-specific agricultural production

    NASA Astrophysics Data System (ADS)

    Freeland, Robert S.; Yoder, Ronald E.; Ammons, John T.

    1998-10-01

    Modern agricultural production practices are rapidly evolving in the United States of America (USA). These new production practices present significant applications for nonintrusive subsurface imaging. One such imaging technology is GPR, and it is now being incorporated within site-specific agriculture in the detection of soil horizons, perched water (episaturation), fragipans, hydrological preferential flow paths, and soil compaction. These features traditionally have been mapped by soil scientists using intrusive measurements (e.g., soil augers, soil pits, coring tools). Rather than developing a tool for soil mapping, our studies are targeting the identification, dimensioning, and position of subsurface features that directly influence agricultural productivity. It is foreseen that this information will allow for an increase in agricultural efficiency through infield machinery automation, and it will also greatly enhance development of highly efficient crop production strategies. The field sensing methodologies that we have developed using existing geophysical technologies are highly dependent upon both the soil and site characteristics due to seasonal variations. The GPR applications presented herein were conducted primarily in a region of loess soil that extends east of the Mississippi River into western Tennessee. GPR studies were also conducted in central Tennessee on the Cumberland Plateau within a region of shallow, sandy loam soils. Additional studies were conducted on the karst area of central Kentucky. Although targeting site-specific agriculture, our results and procedures may benefit the traditional users of GPR technology. We suggest that large-scale agricultural applications of the technology would be enhanced by integrating global positioning (GPS) technology in future hardware and software products.

  10. Dynamics of RNA modification by a multi-site-specific tRNA methyltransferase

    PubMed Central

    Hamdane, Djemel; Guelorget, Amandine; Guérineau, Vincent; Golinelli-Pimpaneau, Béatrice

    2014-01-01

    In most organisms, the widely conserved 1-methyl-adenosine58 (m1A58) tRNA modification is catalyzed by an S-adenosyl-L-methionine (SAM)-dependent, site-specific enzyme TrmI. In archaea, TrmI also methylates the adjacent adenine 57, m1A57 being an obligatory intermediate of 1-methyl-inosine57 formation. To study this multi-site specificity, we used three oligoribonucleotide substrates of Pyrococcus abyssi TrmI (PabTrmI) containing a fluorescent 2-aminopurine (2-AP) at the two target positions and followed the RNA binding kinetics and methylation reactions by stopped-flow and mass spectrometry. PabTrmI did not modify 2-AP but methylated the adjacent target adenine. 2-AP seriously impaired the methylation of A57 but not A58, confirming that PabTrmI methylates efficiently the first adenine of the A57A58A59 sequence. PabTrmI binding provoked a rapid increase of fluorescence, attributed to base unstacking in the environment of 2-AP. Then, a slow decrease was observed only with 2-AP at position 57 and SAM, suggesting that m1A58 formation triggers RNA release. A model of the protein–tRNA complex shows both target adenines in proximity of SAM and emphasizes no major tRNA conformational change except base flipping during the reaction. The solvent accessibility of the SAM pocket is not affected by the tRNA, thereby enabling S-adenosyl-L-homocysteine to be replaced by SAM without prior release of monomethylated tRNA. PMID:25217588

  11. Site-specific conditions influence plant naturalization: The case of alien Proteaceae in South Africa

    NASA Astrophysics Data System (ADS)

    Moodley, Desika; Geerts, Sjirk; Rebelo, Tony; Richardson, David M.; Wilson, John R. U.

    2014-08-01

    The outcome of plant introductions is often considered in binary terms (invasive or non-invasive). However, most species experience a time lag before naturalization occurs, and many species become naturalized at some sites but not at others. It is therefore important to understand the site-specific mechanisms underlying naturalization. Proteaceae is an interesting case as some species are widespread invaders, while others, despite a long history of cultivation, show no signs of naturalization. At least 26 non-native Proteaceae species have been introduced to, and are cultivated in, South Africa. We mapped populations and examined differences between naturalized and non-naturalized populations (e.g. propagule pressure, land use and bioclimatic suitability). Of the 15 species surveyed, 6 were naturalized at one or more sites. Of these, Hakea salicifolia is most widely cultivated, but is only naturalizing in some areas (32 naturalized populations out of 62 populations that were surveyed). We found propagule pressure to be the most important determinant of naturalization for H. salicifolia. However, in suboptimal climatic conditions, naturalization only occurred if micro-site conditions were suitable, i.e. there was some disturbance and water available. For the other naturalized species there were few sites to compare, but we came to similar conclusions - Banksia integrifolia only naturalized at the site where it was planted the longest; Banksia serrata only naturalized at a site influenced by fire regimes; while Banksia formosa naturalized at sites with high propagule pressure, absence of fires and where there is no active clearing of the plants. Naturalization of Proteaceae in South Africa appears to be strongly mediated by site-specific anthropogenic activities (e.g. many planted individuals and water availability). More broadly, we argue that invasion biology needs to focus more closely on the mechanisms by which species and pathways interact to determine the

  12. Characterization of the Class 3 Integron and the Site-Specific Recombination System It Determines

    PubMed Central

    Collis, Christina M.; Kim, Mi-Jurng; Partridge, Sally R.; Stokes, H. W.; Hall, Ruth M.

    2002-01-01

    Integrons capture gene cassettes by using a site-specific recombination mechanism. As only one class of integron and integron-determined site-specific recombination system has been studied in detail, the properties of a second class, the only known class 3 integron, were examined. The configuration of the three potentially definitive features of integrons, the intI3 gene, the adjacent attI3 recombination site, and the Pc promoter that directs transcription of the cassettes, was similar to that found in the corresponding region (5′ conserved segment) of class 1 integrons. The integron features are flanked by a copy of the terminal inverted repeat, IRi, from class 1 integrons on one side and a resolvase-encoding tniR gene on the other, suggesting that they are part of a transposable element related to Tn402 but with the integron module in the opposite orientation. The IntI3 integrase was active and able to recognize and recombine both known types of IntI-specific recombination sites, the attI3 site in the integron, and different cassette-associated 59-be (59-base element) sites. Both integration of circularized cassettes into the attI3 site and excision of integrated cassettes were also catalyzed by IntI3. The attI3 site was localized to a short region adjacent to the intI3 gene. Recombination between a 59-be and secondary sites was also catalyzed by IntI3, but at frequencies significantly lower than observed with IntI1, the class 1 integron integrase. PMID:12003943

  13. Region and site specific design guidelines for the northeastern Venezuela development

    SciTech Connect

    Gajardo, E.; Paga, M.; Sully, J.P.

    1996-12-31

    Several site specific studies were performed for the northeastern Venezuelan offshore development in order to determine the environmental parameters for the engineering design. The geotechnical parameters were obtained from the analysis of the soil borings, in situ tests and the high resolution seismic surveys. An evaluation of the seismic hazard was done, based on a detailed neotectonic study, the compilation of historical and instrumental seismological information, and an attenuation relationship developed for the studied area. Seismic response analyses were performed using the seismic parameters and dynamic characteristics obtained form the soil borings and in situ tests of shear waves. The met-ocean design loads of the local conditions were obtained from mathematical modeling based on in situ and regional measurements. This study defines the platforms design conditions based on a probabilistic reliability approach and it has been used, among others, as a basis for the earthquake design guidelines proposed by the International Standards Organization. A sensitivity analysis was performed starting from the uncertainties of all the input parameters, in order to obtain the best estimate average design spectrum and associated coefficient of variability. The specific approach was to maintain the same safety index adopted by API RP2A code, with a bias modification factor that relates the site nominal spectra with the spectral acceleration that would be used in order to satisfy the API requirements. The results of this approach make possible the use of site specific detailed environmental data and the proven standard procedures established on the API RP2 codes, with significant cost reduction in terms of both platform and foundation design. The considerable amount of tectonic, seismological, and geotechnical information was the principal factor allowing the above methodology.

  14. Site-Specific Characterization of d-Amino Acid Containing Peptide Epimers by Ion Mobility Spectrometry

    PubMed Central

    2013-01-01

    Traditionally, the d-amino acid containing peptide (DAACP) candidate can be discovered by observing the differences of biological activity and chromatographic retention time between the synthetic peptides and naturally occurring peptides. However, it is difficult to determine the exact position of d-amino acid in the DAACP candidates. Herein, we developed a novel site-specific strategy to rapidly and precisely localize d-amino acids in peptides by ion mobility spectrometry (IMS) analysis of mass spectrometry (MS)-generated epimeric fragment ions. Briefly, the d/l-peptide epimers were separated by online reversed-phase liquid chromatography and fragmented by collision-induced dissociation (CID), followed by IMS analysis. The epimeric fragment ions resulting from d/l-peptide epimers exhibit conformational differences, thus showing different mobilities in IMS. The arrival time shift between the epimeric fragment ions was used as criteria to localize the d-amino acid substitution. The utility of this strategy was demonstrated by analysis of peptide epimers with different molecular sizes, [d-Trp]-melanocyte-stimulating hormone, [d-Ala]-deltorphin, [d-Phe]-achatin-I, and their counterparts that contain all-l amino acids. Furthermore, the crustacean hyperglycemia hormones (CHHs, 8.5 kDa) were isolated from the American lobster Homarus americanus and identified by integration of MS-based bottom-up and top-down sequencing approaches. The IMS data acquired using our novel site-specific strategy localized the site of isomerization of l- to d-Phe at the third residue of the CHHs from the N-terminus. Collectively, this study demonstrates a new method for discovery of DAACPs using IMS technique with the ability to localize d-amino acid residues. PMID:24328107

  15. Site-Specific Difference of Bone Geometry Indices in Hypoparathyroid Patients

    PubMed Central

    Park, Hye-Sun; Seo, Da Hea; Rhee, Yumie

    2017-01-01

    Background Hypoparathyroid patients often have a higher bone mineral density (BMD) than the general population. However, an increase in BMD does not necessarily correlate with a solid bone microstructure. This study aimed to evaluate the bone microstructure of hypoparathyroid patients by using hip structure analysis (HSA). Methods Ninety-five hypoparathyroid patients >20 years old were enrolled and 31 of them had eligible data for analyzing bone geometry parameters using HSA. And among the control data, we extracted sex-, age-, and body mass index-matched three control subjects to each patient. The BMD data were reviewed retrospectively and the bone geometry parameters of the patients were analyzed by HSA. Results The mean Z-scores of hypoparathyroid patients at the lumbar spine, femoral neck, and total hip were above zero (0.63±1.17, 0.48±1.13, and 0.62±1.10, respectively). The differences in bone geometric parameters were site specific. At the femoral neck and intertrochanter, the cross-sectional area (CSA) and cortical thickness (C.th) were higher, whereas the buckling ratio (BR) was lower than in controls. However, those trends were opposite at the femoral shaft; that is, the CSA and C.th were low and the BR was high. Conclusion Our study shows the site-specific effects of hypoparathyroidism on the bone. Differences in bone components, marrow composition, or modeling based bone formation may explain these findings. However, further studies are warranted to investigate the mechanism, and its relation to fracture risk. PMID:28181426

  16. Site-specific time heterogeneity of the substitution process and its impact on phylogenetic inference

    PubMed Central

    2011-01-01

    Background Model violations constitute the major limitation in inferring accurate phylogenies. Characterizing properties of the data that are not being correctly handled by current models is therefore of prime importance. One of the properties of protein evolution is the variation of the relative rate of substitutions across sites and over time, the latter is the phenomenon called heterotachy. Its effect on phylogenetic inference has recently obtained considerable attention, which led to the development of new models of sequence evolution. However, thus far focus has been on the quantitative heterogeneity of the evolutionary process, thereby overlooking more qualitative variations. Results We studied the importance of variation of the site-specific amino-acid substitution process over time and its possible impact on phylogenetic inference. We used the CAT model to define an infinite mixture of substitution processes characterized by equilibrium frequencies over the twenty amino acids, a useful proxy for qualitatively estimating the evolutionary process. Using two large datasets, we show that qualitative changes in site-specific substitution properties over time occurred significantly. To test whether this unaccounted qualitative variation can lead to an erroneous phylogenetic tree, we analyzed a concatenation of mitochondrial proteins in which Cnidaria and Porifera were erroneously grouped. The progressive removal of the sites with the most heterogeneous CAT profiles across clades led to the recovery of the monophyly of Eumetazoa (Cnidaria+Bilateria), suggesting that this heterogeneity can negatively influence phylogenetic inference. Conclusion The time-heterogeneity of the amino-acid replacement process is therefore an important evolutionary aspect that should be incorporated in future models of sequence change. PMID:21235782

  17. phiC31 Integrase-Mediated Site-Specific Recombination in Barley

    PubMed Central

    Rubtsova, Myroslava; Kumlehn, Jochen; Gils, Mario

    2012-01-01

    The Streptomyces phage phiC31 integrase was tested for its feasibility in excising transgenes from the barley genome through site-specific recombination. We produced transgenic barley plants expressing an active phiC31 integrase and crossed them with transgenic barley plants carrying a target locus for recombination. The target sequence involves a reporter gene encoding green fluorescent protein (GFP), which is flanked by the attB and attP recognition sites for the phiC31 integrase. This sequence disruptively separates a gusA coding sequence from an upstream rice actin promoter. We succeeded in producing site-specific recombination events in the hybrid progeny of 11 independent barley plants carrying the above target sequence after crossing with plants carrying a phiC31 expression cassette. Some of the hybrids displayed fully executed recombination. Excision of the GFP gene fostered activation of the gusA gene, as visualized in tissue of hybrid plants by histochemical staining. The recombinant loci were detected in progeny of selfed F1, even in individuals lacking the phiC31 transgene, which provides evidence of stability and generative transmission of the recombination events. In several plants that displayed incomplete recombination, extrachromosomal excision circles were identified. Besides the technical advance achieved in this study, the generated phiC31 integrase-expressing barley plants provide foundational stock material for use in future approaches to barley genetic improvement, such as the production of marker-free transgenic plants or switching transgene activity. PMID:23024817

  18. Site-specific fab fragment biotinylation at the conserved nucleotide binding site for enhanced Ebola detection.

    PubMed

    Mustafaoglu, Nur; Alves, Nathan J; Bilgicer, Basar

    2015-07-01

    The nucleotide binding site (NBS) is a highly conserved region between the variable light and heavy chains at the Fab domains of all antibodies, and a small molecule that we identified, indole-3-butyric acid (IBA), binds specifically to this site. Fab fragment, with its small size and simple production methods compared to intact antibody, is good candidate for use in miniaturized diagnostic devices and targeted therapeutic applications. However, commonly used modification techniques are not well suited for Fab fragments as they are often more delicate than intact antibodies. Fab fragments are of particular interest for sensor surface functionalization but immobilization results in damage to the antigen binding site and greatly reduced activity due to their truncated size that allows only a small area that can bind to surfaces without impeding antigen binding. In this study, we describe an NBS-UV photocrosslinking functionalization method (UV-NBS(Biotin) in which a Fab fragment is site-specifically biotinylated with an IBA-EG11-Biotin linker via UV energy exposure (1 J/cm(2)) without affecting its antigen binding activity. This study demonstrates successful immobilization of biotinylated Ebola detecting Fab fragment (KZ52 Fab fragment) via the UV-NBS(Biotin) method yielding 1031-fold and 2-fold better antigen detection sensitivity compared to commonly used immobilization methods: direct physical adsorption and NHS-Biotin functionalization, respectively. Utilization of the UV-NBS(Biotin) method for site-specific conjugation to Fab fragment represents a proof of concept use of Fab fragment for various diagnostic and therapeutic applications with numerous fluorescent probes, affinity molecules and peptides.

  19. Digital lock-in detection of site-specific magnetism in magnetic materials

    DOEpatents

    Haskel, Daniel; Lang, Jonathan C.; Srajer, George

    2008-07-22

    The polarization and diffraction characteristics of x-rays incident upon a magnetic material are manipulated to provide a desired magnetic sensitivity in the material. The contrast in diffracted intensity of opposite helicities of circularly polarized x-rays is measured to permit separation of magnetic signals by element type and by atomic environment. This allows for the direct probing of magnetic signals from elements of the same species in nonequivalent atomic environments to better understand the behavior and characteristics of permanent magnetic materials. By using known crystallographic information together with manipulation of the polarization of x-rays having energies tuned near element-specific electronic excitations and by detecting and comparing the incident and diffracted photons at the same frequency, more accurate magnetic measurements can be made over shorter observation periods.

  20. Mechanisms of site-specific photochemistry following core-shell ionization of chemically inequivalent carbon atoms in acetaldehyde (ethanal)

    NASA Astrophysics Data System (ADS)

    Zagorodskikh, Sergey; Eland, John H. D.; Zhaunerchyk, Vitali; Mucke, Melanie; Squibb, Richard J.; Linusson, Per; Feifel, Raimund

    2016-09-01

    Site-specific fragmentation upon 1s photoionisation of acetaldehyde has been studied using synchrotron radiation and a multi-electron-ion coincidence technique based on a magnetic bottle. Experimental evidence is presented that bond rupture occurs with highest probability in the vicinity of the initial charge localisation and possible mechanisms are discussed. We find that a significant contribution to site-specific photochemistry is made by different fragmentation patterns of individual quantum states populated at identical ionisation energies.

  1. Mechanisms of site-specific photochemistry following core-shell ionization of chemically inequivalent carbon atoms in acetaldehyde (ethanal).

    PubMed

    Zagorodskikh, Sergey; Eland, John H D; Zhaunerchyk, Vitali; Mucke, Melanie; Squibb, Richard J; Linusson, Per; Feifel, Raimund

    2016-09-28

    Site-specific fragmentation upon 1s photoionisation of acetaldehyde has been studied using synchrotron radiation and a multi-electron-ion coincidence technique based on a magnetic bottle. Experimental evidence is presented that bond rupture occurs with highest probability in the vicinity of the initial charge localisation and possible mechanisms are discussed. We find that a significant contribution to site-specific photochemistry is made by different fragmentation patterns of individual quantum states populated at identical ionisation energies.

  2. Photon diffraction

    NASA Astrophysics Data System (ADS)

    Hodge, John

    2009-11-01

    In current light models, a particle-like model of light is inconsistent with diffraction observations. A model of light is proposed wherein photon inferences are combined with the cosmological scalar potential model (SPM). That the photon is a surface with zero surface area in the travel direction is inferred from the Michelson-Morley experiment. That the photons in slits are mathematically treated as a linear antenna array (LAA) is inferred from the comparison of the transmission grating interference pattern and the single slit diffraction pattern. That photons induce a LAA wave into the plenum is inferred from the fractal model. Similarly, the component of the photon (the hod) is treated as a single antenna radiating a potential wave into the plenum. That photons are guided by action on the surface of the hod is inferred from the SPM. The plenum potential waves are a real field (not complex) that forms valleys, consistent with the pilot waves of the Bohm interpretation of quantum mechanics. Therefore, the Afshar experiment result is explained, supports Bohm, and falsifies Copenhagen. The papers may be viewed at http://web.citcom.net/˜scjh/.

  3. Fabrication of Nanometer- and Micrometer-Scale Protein Structures by Site-Specific Immobilization of Histidine-Tagged Proteins to Aminosiloxane Films with Photoremovable Protein-Resistant Protecting Groups

    PubMed Central

    2016-01-01

    The site-specific immobilization of histidine-tagged proteins to patterns formed by far-field and near-field exposure of films of aminosilanes with protein-resistant photolabile protecting groups is demonstrated. After deprotection of the aminosilane, either through a mask or using a scanning near-field optical microscope, the amine terminal groups are derivatized first with glutaraldehyde and then with N-(5-amino-1-carboxypentyl)iminodiacetic acid to yield a nitrilo-triacetic-acid-terminated surface. After complexation with Ni2+, this surface binds histidine-tagged GFP and CpcA-PEB in a site-specific fashion. The chemistry is simple and reliable and leads to extensive surface functionalization. Bright fluorescence is observed in fluorescence microscopy images of micrometer- and nanometer-scale patterns. X-ray photoelectron spectroscopy is used to study quantitatively the efficiency of photodeprotection and the reactivity of the modified surfaces. The efficiency of the protein binding process is investigated quantitatively by ellipsometry and by fluorescence microscopy. We find that regions of the surface not exposed to UV light bind negligible amounts of His-tagged proteins, indicating that the oligo(ethylene glycol) adduct on the nitrophenyl protecting group confers excellent protein resistance; in contrast, exposed regions bind His-GFP very effectively, yielding strong fluorescence that is almost completely removed on treatment of the surface with imidazole, confirming a degree of site-specific binding in excess of 90%. This simple strategy offers a versatile generic route to the spatially selective site-specific immobilization of proteins at surfaces. PMID:26820378

  4. Evolution of I-SceI homing endonucleases with increased DNA recognition site specificity

    PubMed Central

    Joshi, Rakesh; Ho, Kwok Ki; Tenney, Kristen; Chen, Jui-Hui; Golden, Barbara L.; Gimble, Frederick S.

    2010-01-01

    Summary Elucidating how homing endonucleases undergo changes in recognition site specificity will facilitate efforts to engineer proteins for gene therapy applications. I-SceI is a monomeric homing endonuclease that recognizes and cleaves within an 18-base-pair (bp) target. It tolerates limited degeneracy in its target sequence, including substitution of a C/G+4 base-pair for the wild-type A/T+4 base-pair. Libraries encoding randomized amino acids at I-SceI residue positions that contact or are proximal to A/T+4 were used in conjunction with a bacterial one-hybrid system to select I-SceI derivatives that bind to recognition sites containing either the A/T+4 or C/G+4 base-pairs. As expected, isolates encoding wild-type residues at the randomized positions were selected using either target sequence. All I-SceI proteins isolated using the C/G+4 recognition site included small side chain substitutions at G100, and either contained (K86R/G100T, K86R/G100S and K86R/G100C) or lacked (G100A, G100T) a K86R substitution. Interestingly, the binding affinities of the selected variants for the wild-type A/T+4 target are 4–11-fold lower than that of wild-type I-SceI, whereas those for the C/G+4 target are similar. The increased specificity of the mutant proteins is also evident in binding experiments in vivo. These differences in binding affinities account for the observed ~36-fold difference in target preference between the K86R/G100T and wild-type proteins in DNA cleavage assays. An X-ray crystal structure of the K86R/G100T mutant protein bound to a DNA duplex containing the C/G+4 substitution suggests how sequence specificity of a homing enzyme can increase. This biochemical and structural analysis defines one pathway by which site specificity is augmented for a homing endonuclease. PMID:21029741

  5. Site Specific Nematode Management—Development and Success in Cotton Production in the United States

    PubMed Central

    Overstreet, C.; McGawley, E. C.; Khalilian, A.; Kirkpatrick, T. L.; Monfort, W. S.; Henderson, W.; Mueller, J. D.

    2014-01-01

    Variability in edaphic factors such as clay content, organic matter, and nutrient availability within individual fields is a major obstacle confronting cotton producers. Adaptation of geospatial technologies such global positioning systems (GPS), yield monitors, autosteering, and the automated on-and-off technology required for site-specific nematicide application has provided growers with additional tools for managing nematodes. Multiple trials in several states were conducted to evaluate this technology in cotton. In a field infested with Meloidogyne spp., both shallow (0 to 0.3 m) and deep (0 to 0.91 m) apparent electrical conductivity (ECa) readings were highly correlated with sand content. Populations of Meloidogyne spp. were present when shallow and deep EC values were less than 30 and 90 mS/m, respectively. Across three years of trials in production fields in which verification strips (adjacent nematicide treated and untreated rows across all soil zones) were established to evaluate crop response to nematicide application, deep EC values from 27.4-m wide transects of verification strips were more predictive of yield response to application of 1,3-dichloropropene than were shallow EC values in one location and both ECa values equally effective at predicting responses at the second location. In 2006, yields from entire verification strips across three soil zones in four production fields showed that nematicide response was greatest in areas with the lowest EC values indicating highest content of sand. In 2008 in Ashley and Mississippi Counties, AR, nematicide treatment by soil zone resulted in 36% and 42% reductions in the amount of nematicide applied relative to whole-field application. In 2007 in Bamberg County, SC, there was a strong positive correlation between increasing population densities of Meloidogyne incognita and increasing sand content. Trials conducted during 2007 and 2009 in South Carolina against Hoplolaimus columbus showed a stepwise response

  6. Evolution of I-SceI Homing Endonucleases with Increased DNA Recognition Site Specificity

    SciTech Connect

    Joshi, Rakesh; Ho, Kwok Ki; Tenney, Kristen; Chen, Jui-Hui; Golden, Barbara L.; Gimble, Frederick S.

    2013-09-18

    Elucidating how homing endonucleases undergo changes in recognition site specificity will facilitate efforts to engineer proteins for gene therapy applications. I-SceI is a monomeric homing endonuclease that recognizes and cleaves within an 18-bp target. It tolerates limited degeneracy in its target sequence, including substitution of a C:G{sub +4} base pair for the wild-type A:T{sub +4} base pair. Libraries encoding randomized amino acids at I-SceI residue positions that contact or are proximal to A:T{sub +4} were used in conjunction with a bacterial one-hybrid system to select I-SceI derivatives that bind to recognition sites containing either the A:T{sub +4} or the C:G{sub +4} base pairs. As expected, isolates encoding wild-type residues at the randomized positions were selected using either target sequence. All I-SceI proteins isolated using the C:G{sub +4} recognition site included small side-chain substitutions at G100 and either contained (K86R/G100T, K86R/G100S and K86R/G100C) or lacked (G100A, G100T) a K86R substitution. Interestingly, the binding affinities of the selected variants for the wild-type A:T{sub +4} target are 4- to 11-fold lower than that of wild-type I-SceI, whereas those for the C:G{sub +4} target are similar. The increased specificity of the mutant proteins is also evident in binding experiments in vivo. These differences in binding affinities account for the observed -36-fold difference in target preference between the K86R/G100T and wild-type proteins in DNA cleavage assays. An X-ray crystal structure of the K86R/G100T mutant protein bound to a DNA duplex containing the C:G{sub +4} substitution suggests how sequence specificity of a homing enzyme can increase. This biochemical and structural analysis defines one pathway by which site specificity is augmented for a homing endonuclease.

  7. Site-specific O-Glycosylation Analysis of Human Blood Plasma Proteins.

    PubMed

    Hoffmann, Marcus; Marx, Kristina; Reichl, Udo; Wuhrer, Manfred; Rapp, Erdmann

    2016-02-01

    Site-specific glycosylation analysis is key to investigate structure-function relationships of glycoproteins, e.g. in the context of antigenicity and disease progression. The analysis, though, is quite challenging and time consuming, in particular for O-glycosylated proteins. In consequence, despite their clinical and biopharmaceutical importance, many human blood plasma glycoproteins have not been characterized comprehensively with respect to their O-glycosylation. Here, we report on the site-specific O-glycosylation analysis of human blood plasma glycoproteins. To this end pooled human blood plasma of healthy donors was proteolytically digested using a broad-specific enzyme (Proteinase K), followed by a precipitation step, as well as a glycopeptide enrichment and fractionation step via hydrophilic interaction liquid chromatography, the latter being optimized for intact O-glycopeptides carrying short mucin-type core-1 and -2 O-glycans, which represent the vast majority of O-glycans on human blood plasma proteins. Enriched O-glycopeptide fractions were subjected to mass spectrometric analysis using reversed-phase liquid chromatography coupled online to an ion trap mass spectrometer operated in positive-ion mode. Peptide identity and glycan composition were derived from low-energy collision-induced dissociation fragment spectra acquired in multistage mode. To pinpoint the O-glycosylation sites glycopeptides were fragmented using electron transfer dissociation. Spectra were annotated by database searches as well as manually. Overall, 31 O-glycosylation sites and regions belonging to 22 proteins were identified, the majority being acute-phase proteins. Strikingly, also 11 novel O-glycosylation sites and regions were identified. In total 23 O-glycosylation sites could be pinpointed. Interestingly, the use of Proteinase K proved to be particularly beneficial in this context. The identified O-glycan compositions most probably correspond to mono- and disialylated core-1

  8. Structural analysis of loci involved in pSAM2 site-specific integration in Streptomyces.

    PubMed

    Boccard, F; Smokvina, T; Pernodet, J L; Friedmann, A; Guérineau, M

    1989-01-01

    pSAM2 is an 11-kb plasmid integrated in the Streptomyces ambofaciens ATCC23877 and ATCC15154 genomes and found additionally as a free replicon in an uv derivative. After transfer into S. ambofaciens DSM40697 (devoid of pSAM2) or into Streptomyces lividans, specific integration of pSAM2 occurred very efficiently. A 58-bp sequence (att) present in both pSAM2 (attP) and S. ambofaciens strain DSM40697 (attB) attachment regions is found at the boundaries (attL and attR) of integrated pSAM2 in S. ambofaciens strain ATCC23877. The S. lividans chromosomal integration zone contained an imperfectly conserved att sequence (attB), and the integration event of pSAM2 was located within a 49-bp sequence of attB. Only one primary functional attB sequence was present in the S. lividans or S. ambofaciens DSM40697 total DNA. The integration zone of S. lividans hybridized with the integration zone of S. ambofaciens DSM40697. The two integration zones were homologous only to the right side of the att sequence. The conserved region contained an open reading frame (ORF A) with a stop codon located 99 bp from the attB sequence in both strains. S. ambofaciens DSM40697 contained DNA sequences related to pSAM2 on the left side of the att site. The att sequence was included in a region conserved in Streptomyces antibioticus, Streptomyces actuosus, Streptomyces bikiniensis, Streptomyces coelicolor, Streptomyces glaucescens, and Streptomyces parvulus. Site-specific integration of a pSAM2 derivative was characterized in another unrelated strain, Streptomyces griseofuscus. This strain contained an imperfectly conserved 58-bp attB sequence, and the integration event took place within a 45-bp sequence of attB. Site-specific integration of pSAM2 in three nonrelated Streptomyces strains suggests the wide host range of pSAM2 integration in Streptomyces.

  9. Environmental Management Waste Management Facility (EMWMF) Site-Specific Health and Safety Plan, Oak Ridge, Tennessee

    SciTech Connect

    Flynn, N.C. Bechtel Jacobs

    2008-04-21

    The Bechtel Jacobs Company LLC (BJC) policy is to provide a safe and healthy workplace for all employees and subcontractors. The implementation of this policy requires that operations of the Environmental Management Waste Management Facility (EMWMF), located one-half mile west of the U.S. Department of Energy (DOE) Y-12 National Security Complex, be guided by an overall plan and consistent proactive approach to environment, safety and health (ES&H) issues. The BJC governing document for worker safety and health, BJC/OR-1745, 'Worker Safety and Health Program', describes the key elements of the BJC Safety and Industrial Hygiene (IH) programs, which includes the requirement for development and implementation of a site-specific Health and Safety Plan (HASP) where required by regulation (refer also to BJC-EH-1012, 'Development and Approval of Safety and Health Plans'). BJC/OR-1745, 'Worker Safety and Health Program', implements the requirements for worker protection contained in Title 10 Code of Federal Regulations (CFR) Part 851. The EMWMF site-specific HASP requirements identifies safe operating procedures, work controls, personal protective equipment, roles and responsibilities, potential site hazards and control measures, site access requirements, frequency and types of monitoring, site work areas, decontamination procedures, and outlines emergency response actions. This HASP will be available on site for use by all workers, management and supervisors, oversight personnel and visitors. All EMWMF assigned personnel will be briefed on the contents of this HASP and will be required to follow the procedures and protocols as specified. The policies and procedures referenced in this HASP apply to all EMWMF operations activities. In addition the HASP establishes ES&H criteria for the day-to-day activities to prevent or minimize any adverse effect on the environment and personnel safety and health and to meet standards that define acceptable waste management practices. The

  10. Characterization of Photoelectron Emission for SGEMP Analysis.

    DTIC Science & Technology

    1980-05-01

    solar-cell cover glass 17 Normalized photoelectron spectral data from Mylar, 44 Teflon and two thicknesses of Kapton 18 Photoelectron signals from flat...silver, glass, copper, 63 Teflon /Thick Kapton and Mylar/Thin Mylar irradiated by OWL II aluminum-wire spectrum. Uncertainties are discussed in text 27...experiments; these included gold, silver, anodized aluminum, thick Kapton, thick Teflon , white thermal paint and solar cell covers. The other samples were

  11. Forward-backward asymmetries of atomic photoelectrons.

    SciTech Connect

    Biheux, J. C.; Dunford, R. W.; Gemmell, D. S.; Hasegawa, S.; Kanter, E. P.; Krassig, B.; Southworth, S. H.; Young, L.

    1999-01-19

    When atomic photoionization is treated beyond the dipole approximation, photoelectron angular distributions are asymmetric forward and backward with respect to the direction of the photon beam. We have measured forward-backward asymmetries of Ar 1s and Kr 1s and 2s photoelectrons using 2-19 keV x-rays. The measured asymmetries compare well with calculations which include interference between electric-dipole and electric-quadrupole amplitudes within the nonrelativistic, independent-particle approximations.

  12. Near threshold studies of photoelectron satellites

    SciTech Connect

    Heimann, P.A.

    1986-11-01

    Photoelectron spectroscopy and synchrotron radiation have been used to study correlation effects in the rare gases: He, Ne, Ar, Kr, and Xe. Two kinds of time-of-flight electron analyzers were employed to examine photoionization very close to threshold and at higher kinetic energies. Partial cross sections and angular distributions have been measured for a number of photoelectron satellites. The shake-off probability has been determined at some inner-shell resonances. 121 refs., 28 figs., 13 tabs.

  13. Site-specific investigations on aquifer thermal energy storage for space and process cooling

    NASA Astrophysics Data System (ADS)

    Brown, D. R.

    1991-08-01

    The Pacific Northwest Laboratory (PNL) has completed three preliminary site-specific feasibility studies that investigated aquifer thermal energy storage (ATES) for reducing space and process cooling costs. Chilled water stored in an ATES system could be used to meet all or part of the process and/or space cooling loads at the three facilities investigated. Seasonal or diurnal chill ATES systems could be significantly less expensive than a conventional electrically-driven, load-following chiller system at one of the three sites, depending on the cooling water loop return temperature and presumed future electricity escalation rate. For the other two sites investigated, a chill ATES system would be economically competitive with conventional chillers if onsite aquifer characteristics were improved. Well flow rates at one of the sites were adequate, but the expected thermal recovery efficiency was too low. The reverse of this situation was found at the other site, where the thermal recovery efficiency was expected to be adequate, but well flow rates were too low.

  14. Embracing the Emerging Precision Agriculture Technologies for Site-Specific Management of Yield-Limiting Factors

    PubMed Central

    Melakeberhan, H.

    2002-01-01

    Precision agriculture (PA) is providing an information revolution using Global Positioning (GPS) and Geographic Information (GIS) systems and Remote Sensing (RS). These technologies allow better decision making in the management of crop yield-limiting biotic and abiotic factors and their interactions on a site-specific (SSM) basis in a wide range of production systems. Characterizing the nature of the problem(s) and public education are among the challenges that scientists, producers, and industry face when adapting PA technologies. To apply SSM, spatio-temporal characteristics of the problem(s) need to be determined and variations within a field demonstrated. Spatio-temporal characteristics of a given pathogen or pest problem may be known but may not be the only or primary cause of the problem. Hence, exact cause-and-effect relationships need to be established by incorporating GIS, GPS, and RS-generated data as well as possible interactions. Exploiting the potential of PA technologies in sustainable ways depends on whether or not we first ask ''Are we doing the right thing?'' (strategic) as opposed to ''Are we doing it right?'' (tactical). PMID:19265931

  15. Osterix regulates tooth root formation in a site-specific manner.

    PubMed

    Kim, T H; Bae, C H; Lee, J C; Kim, J E; Yang, X; de Crombrugghe, B; Cho, E S

    2015-03-01

    Bone and dentin share similar biochemical compositions and physiological properties. Dentin, a major tooth component, is formed by odontoblasts; in contrast, bone is produced by osteoblasts. Osterix (Osx), a zinc finger-containing transcription factor, has been identified as an essential regulator of osteoblast differentiation and bone formation. However, it has been difficult to establish whether Osx functions in odontoblast differentiation and dentin formation. To understand the role of Osx in dentin formation, we analyzed mice in which Osx was subjected to tissue-specific ablation under the control of either the Col1a1 or the OC promoter. Two independent Osx conditional knockout mice exhibited similar molar abnormalities. Although no phenotype was found in the crowns of these teeth, both mutant lines exhibited short molar roots due to impaired root elongation. Furthermore, the interradicular dentin in these mice showed severe hypoplastic features, which were likely caused by disruptions in odontoblast differentiation and dentin formation. These phenotypes were closely related to the temporospatial expression pattern of Osx during tooth development. These findings indicate that Osx is required for root formation by regulating odontoblast differentiation, maturation, and root elongation. Cumulatively, our data strongly indicate that Osx is a site-specific regulator in tooth root formation.

  16. Site-specific function and regulation of Osterix in tooth root formation.

    PubMed

    He, Y D; Sui, B D; Li, M; Huang, J; Chen, S; Wu, L A

    2016-12-01

    Congenital diseases of tooth roots, in terms of developmental abnormalities of short and thin root phenotypes, can lead to loss of teeth. A more complete understanding of the genetic molecular pathways and biological processes controlling tooth root formation is required. Recent studies have revealed that Osterix (Osx), a key mesenchymal transcriptional factor participating in both the processes of osteogenesis and odontogenesis, plays a vital role underlying the mechanisms of developmental differences between root and crown. During tooth development, Osx expression has been identified from late embryonic to postnatal stages when the tooth root develops, particularly in odontoblasts and cementoblasts to promote their differentiation and mineralization. Furthermore, the site-specific function of Osx in tooth root formation has been confirmed, because odontoblastic Osx-conditional knockout mice demonstrate primarily short and thin root phenotypes with no apparent abnormalities in the crown (Journal of Bone and Mineral Research 30, 2014 and 742, Journal of Dental Research 94, 2015 and 430). These findings suggest that Osx functions to promote odontoblast and cementoblast differentiation and root elongation only in root, but not in crown formation. Mechanistic research shows regulatory networks of Osx expression, which can be controlled through manipulating the epithelial BMP signalling, mesenchymal Runx2 expression and cellular phosphorylation levels, indicating feasible routes of promoting Osx expression postnatally (Journal of Cellular Biochemistry 114, 2013 and 975). In this regard, a promising approach might be available to regenerate the congenitally diseased root and that regenerative therapy would be the best choice for patients with developmental tooth diseases.

  17. Site-specific function and regulation of Osterix in tooth root formation

    PubMed Central

    He, Y. D.; Sui, B. D.; Li, M.; Huang, J.; Chen, S.; Wu, L. A.

    2016-01-01

    Congenital diseases of tooth roots, in terms of developmental abnormalities of short and thin root phenotypes, can lead to loss of teeth. A more complete understanding of the genetic molecular pathways and biological processes controlling tooth root formation is required. Recent studies have revealed that Osterix (Osx), a key mesenchymal transcriptional factor participating in both the processes of osteogenesis and odontogenesis, plays a vital role underlying the mechanisms of developmental differences between root and crown. During tooth development, Osx expression has been identified from late embryonic to postnatal stages when the tooth root develops, particularly in odontoblasts and cementoblasts to promote their differentiation and mineralization. Furthermore, the site-specific function of Osx in tooth root formation has been confirmed, because odontoblastic Osx-conditional knockout mice demonstrate primarily short and thin root phenotypes with no apparent abnormalities in the crown (Journal of Bone and Mineral Research 30, 2014 and 742, Journal of Dental Research 94, 2015 and 430). These findings suggest that Osx functions to promote odontoblast and cementoblast differentiation and root elongation only in root, but not in crown formation. Mechanistic research shows regulatory networks of Osx expression, which can be controlled through manipulating the epithelial BMP signalling, mesenchymal Runx2 expression and cellular phosphorylation levels, indicating feasible routes of promoting Osx expression postnatally (Journal of Cellular Biochemistry 114, 2013 and 975). In this regard, a promising approach might be available to regenerate the congenitally diseased root and that regenerative therapy would be the best choice for patients with developmental tooth diseases. PMID:26599722

  18. Data-independent-acquisition mass spectrometry for identification of targeted-peptide site-specific modifications.

    PubMed

    Porter, Caleb J; Bereman, Michael S

    2015-09-01

    We present a novel strategy based on data-independent acquisition coupled to targeted data extraction for the detection and identification of site-specific modifications of targeted peptides in a completely unbiased manner. This method requires prior knowledge of the site of the modification along the peptide backbone from the protein of interest, but not the mass of the modification. The procedure, named multiplex adduct peptide profiling (MAPP), consists of three steps: 1) A fragment-ion tag is extracted from the data, consisting of the b-type and y-type ion series from the N and C-terminus, respectively, up to the amino-acid position that is believed to be modified; 2) MS1 features are matched to the fragment-ion tag in retention-time space, using the isolation window as a pre-filter to enable calculation of the mass of the modification; and 3) modified fragment ions are overlaid with the unmodified fragment ions to verify the mass calculated in step 2. We discuss the development, applications, and limitations of this new method for detection of unknown peptide modifications. We present an application of the method in profiling adducted peptides derived from abundant proteins in biological fluids with the ultimate objective of detecting biomarkers of exposure to reactive species.

  19. Assessing an unknown evolutionary process: effect of increasing site-specific knowledge through taxon addition.

    PubMed

    Pollock, D D; Bruno, W J

    2000-12-01

    Assessment of the evolutionary process is crucial for understanding the effect of protein structure and function on sequence evolution and for many other analyses in molecular evolution. Here, we used simulations to study how taxon sampling affects accuracy of parameter estimation and topological inference in the absence of branch length asymmetry. With maximum-likelihood analysis, we find that adding taxa dramatically improves both support for the evolutionary model and accurate assessment of its parameters when compared with increasing the sequence length. Using a method we call "doppelgänger trees," we distinguish the contributions of two sources of improved topological inference: greater knowledge about internal nodes and greater knowledge of site-specific rate parameters. Surprisingly, highly significant support for the correct general model does not lead directly to improved topological inference. Instead, substantial improvement occurs only with accurate assessment of the evolutionary process at individual sites. Although these results are based on a simplified model of the evolutionary process, they indicate that in general, assuming processes are not independent and identically distributed among sites, more extensive sampling of taxonomic biodiversity will greatly improve analytical results in many current sequence data sets with moderate sequence lengths.

  20. Site-specific gene transfer into the rat spinal cord by photomechanical waves

    NASA Astrophysics Data System (ADS)

    Ando, Takahiro; Sato, Shunichi; Toyooka, Terushige; Uozumi, Yoichi; Nawashiro, Hiroshi; Ashida, Hiroshi; Obara, Minoru

    2011-10-01

    Nonviral, site-specific gene delivery to deep tissue is required for gene therapy of a spinal cord injury. However, an efficient method satisfying these requirements has not been established. This study demonstrates efficient and targeted gene transfer into the spinal cord by using photomechanical waves (PMWs), which were generated by irradiating a black laser absorbing rubber with 532-nm nanosecond Nd:YAG laser pulses. After a solution of plasmid DNA coding for enhanced green fluorescent protein (EGFP) or luciferase was intraparenchymally injected into the spinal cord, PMWs were applied to the target site. In the PMW application group, we observed significant EGFP gene expression in the white matter and remarkably high luciferase activity only in the spinal cord segment exposed to the PMWs. We also assessed hind limb movements 24 h after the application of PMWs based on the Basso-Beattie-Bresnahan (BBB) score to evaluate the noninvasiveness of this method. Locomotor evaluation showed no significant decrease in BBB score under optimum laser irradiation conditions. These findings demonstrated that exogenous genes can be efficiently and site-selectively delivered into the spinal cord by applying PMWs without significant locomotive damage.