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Sample records for site-specific ion desorption

  1. 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

  2. Integrated field emission array for ion desorption

    DOEpatents

    Resnick, Paul J; Hertz, Kristin L; Holland, Christopher; Chichester, David; Schwoebel, Paul

    2013-09-17

    An integrated field emission array for ion desorption includes an electrically conductive substrate; a dielectric layer lying over the electrically conductive substrate comprising a plurality of laterally separated cavities extending through the dielectric layer; a like plurality of conically-shaped emitter tips on posts, each emitter tip/post disposed concentrically within a laterally separated cavity and electrically contacting the substrate; and a gate electrode structure lying over the dielectric layer, including a like plurality of circular gate apertures, each gate aperture disposed concentrically above an emitter tip/post to provide a like plurality of annular gate electrodes and wherein the lower edge of each annular gate electrode proximate the like emitter tip/post is rounded. Also disclosed herein are methods for fabricating an integrated field emission array.

  3. Integrated field emission array for ion desorption

    DOEpatents

    Resnick, Paul J; Hertz, Kristin L.; Holland, Christopher; Chichester, David

    2016-08-23

    An integrated field emission array for ion desorption includes an electrically conductive substrate; a dielectric layer lying over the electrically conductive substrate comprising a plurality of laterally separated cavities extending through the dielectric layer; a like plurality of conically-shaped emitter tips on posts, each emitter tip/post disposed concentrically within a laterally separated cavity and electrically contacting the substrate; and a gate electrode structure lying over the dielectric layer, including a like plurality of circular gate apertures, each gate aperture disposed concentrically above an emitter tip/post to provide a like plurality of annular gate electrodes and wherein the lower edge of each annular gate electrode proximate the like emitter tip/post is rounded. Also disclosed herein are methods for fabricating an integrated field emission array.

  4. Site-Specific Cryo-focused Ion Beam Sample Preparation Guided by 3D Correlative Microscopy

    PubMed Central

    Arnold, Jan; Mahamid, Julia; Lucic, Vladan; de Marco, Alex; Fernandez, Jose-Jesus; Laugks, Tim; Mayer, Tobias; Hyman, Anthony A.; Baumeister, Wolfgang; Plitzko, Jürgen M.

    2016-01-01

    The development of cryo-focused ion beam (cryo-FIB) for the thinning of frozen-hydrated biological specimens enabled cryo-electron tomography (cryo-ET) analysis in unperturbed cells and tissues. However, the volume represented within a typical FIB lamella constitutes a small fraction of the biological specimen. Retaining low-abundance and dynamic subcellular structures or macromolecular assemblies within such limited volumes requires precise targeting of the FIB milling process. In this study, we present the development of a cryo-stage allowing for spinning-disk confocal light microscopy at cryogenic temperatures and describe the incorporation of the new hardware into existing workflows for cellular sample preparation by cryo-FIB. Introduction of fiducial markers and subsequent computation of three-dimensional coordinate transformations provide correlation between light microscopy and scanning electron microscopy/FIB. The correlative approach is employed to guide the FIB milling process of vitrified cellular samples and to capture specific structures, namely fluorescently labeled lipid droplets, in lamellas that are 300 nm thick. The correlation procedure is then applied to localize the fluorescently labeled structures in the transmission electron microscopy image of the lamella. This approach can be employed to navigate the acquisition of cryo-ET data within FIB-lamellas at specific locations, unambiguously identified by fluorescence microscopy. PMID:26769364

  5. Modern Focused-Ion-Beam-Based Site-Specific Specimen Preparation for Atom Probe Tomography.

    PubMed

    Prosa, Ty J; Larson, David J

    2017-02-06

    Approximately 30 years after the first use of focused ion beam (FIB) instruments to prepare atom probe tomography specimens, this technique has grown to be used by hundreds of researchers around the world. This past decade has seen tremendous advances in atom probe applications, enabled by the continued development of FIB-based specimen preparation methodologies. In this work, we provide a short review of the origin of the FIB method and the standard methods used today for lift-out and sharpening, using the annular milling method as applied to atom probe tomography specimens. Key steps for enabling correlative analysis with transmission electron-beam backscatter diffraction, transmission electron microscopy, and atom probe tomography are presented, and strategies for preparing specimens for modern microelectronic device structures are reviewed and discussed in detail. Examples are used for discussion of the steps for each of these methods. We conclude with examples of the challenges presented by complex topologies such as nanowires, nanoparticles, and organic materials.

  6. Increasing ion sorption and desorption rates of conductive electrodes

    DOEpatents

    DePaoli, David William; Kiggans, Jr., James O; Tsouris, Costas; Bourcier, William; Campbell, Robert; Mayes, Richard T

    2014-12-30

    An electrolyte system includes a reactor having a pair of electrodes that may sorb ions from an electrolyte. The electrolyte system also includes at least one power supply in electrical communication with the reactor. The at least one power supply may supply a DC signal and an AC signal to the pair of electrodes during sorption of the ions. In addition, the power supply may supply only the AC signal to the pair of electrodes during desorption of the ions.

  7. Site-specific DNA damage induced by sulfite in the presence of cobalt(II) ion. Role of sulfate radical.

    PubMed

    Kawanishi, S; Yamamoto, K; Inoue, S

    1989-10-15

    The reactivities of sulfite (SO23-) with DNA in the presence of metal ions were investigated by a DNA sequencing technique using 32P-labeled DNA fragments obtained from human c-Ha-ras-1 protooncogene. Sulfite caused DNA damage in the presence of Co2+, Cu2+ and Mn2+, although sulfite alone or metal ion alone did not. The order of inducing effect on sulfite-dependent DNA damage (Co2+ much greater than Cu2+ greater than Mn2+ Fe3+) was consistent with that of accelerating effect on the initial oxygen consumption rate of sulfite autoxidation. The DNA damage induced by sulfite plus Co2+ was inhibited by 3,5-dibromo-4-nitrobenzenesulfonate, primary and secondary alchols, whereas it was not inhibited by SOD, catalase and tert-butyl alcohol. Incubation of DNA with sulfite plus Co2+ followed by the piperidine treatment led to the predominant cleavage at the positions of guanine especially located 5' to guanine. Sulfite plus Cu2+ gave a DNA cleavage pattern different from that induced by sulfite plus Co2+. The photolysis of peroxydisulfate (S2O28-), which is known to produce SO-4 radicals, gave a DNA cleavage pattern similar to that induced by sulfite plus Co2+. ESR studies using spin-trapping reagent revealed the production of spin adduct possibly of SO-3 radical in a solution of sulfite plus Cu2+, whereas much less spin adduct was produced by sulfite plus Co2+. The results suggest that sulfite is rapidly autoxidized in the presence of Co2+ to produce SO4- radical causing site-specific DNA damage.

  8. Laser desorption lamp ionization source for ion trap mass spectrometry.

    PubMed

    Wu, Qinghao; Zare, Richard N

    2015-01-01

    A two-step laser desorption lamp ionization source coupled to an ion trap mass spectrometer (LDLI-ITMS) has been constructed and characterized. The pulsed infrared (IR) output of an Nd:YAG laser (1064 nm) is directed to a target inside a chamber evacuated to ~15 Pa causing desorption of molecules from the target's surface. The desorbed molecules are ionized by a vacuum ultraviolet (VUV) lamp (filled with xenon, major wavelength at 148 nm). The resulting ions are stored and detected in a three-dimensional quadrupole ion trap modified from a Finnigan Mat LCQ mass spectrometer operated at a pressure of ≥ 0.004 Pa. The limit of detection for desorbed coronene molecules is 1.5 pmol, which is about two orders of magnitude more sensitive than laser desorption laser ionization mass spectrometry using a fluorine excimer laser (157 nm) as the ionization source. The mass spectrum of four standard aromatic compounds (pyrene, coronene, rubrene and 1,4,8,11,15,18,22,25-octabutoxy-29H,31H-phthalocyanine (OPC)) shows that parent ions dominate. By increasing the infrared laser power, this instrument is capable of detecting inorganic compounds.

  9. Prompt Gas Desorption Due to Ion Impact on Accelerator Structures

    NASA Astrophysics Data System (ADS)

    Vijay, Sagar; Seidl, Peter A.; Faltens, Andy; Lidia, Steven M.

    2011-10-01

    The repetition rate and peak current of high intensity ion accelerators for inertial fusion or other applications may be limited under certain conditions by the desorption of gas molecules and atoms due to stray ions striking the accelerator structure. We have measured the prompt yield of atoms in close proximity to the point of impact of the ions on a surface. Using the 300-keV, K+ ion beam of the Neutralized Drift Compression Experiment (NDCX-I), ions strike a metal target in a 5-10 microsecond bunch. The collector of a Bayert-Alpert style ionization gauge is used to detect the local pressure burst several centimeters away. Pressure transients are observed on a micro-second time scale due to the initial burst of desorbed gas, and on a much longer (~1 second) timescale, corresponding to the equilibration of the pressure after many ``bounces'' of atoms in the vacuum chamber. We report on these time dependent pressure measurements, modeling of the pressure transient, and implications for high-intensity ion accelerators. Work performed under auspices of U.S. DOE by LBNL under Contract DE-AC02-05CH1123.

  10. Site specific isolated nanostructure array formation on a large area by broad ion beam without any mask and resist

    SciTech Connect

    Karmakar, Prasanta

    2014-06-09

    We report the formation of isolated nanostructure arrays on a large area via broad ion beam implantation without the aid of any mask or resist. Desired ions have been implanted at specific locations of the prefabricated silicon ripple or triangular structures by exploiting the variation of local ion impact angles. We have shown that the implantation of Fe ions on an O{sup +} ions induced pre fabricated triangular shaped patterned Si surface results in a self-organized periodic array of striped magnetic nanostructures having several micron length and about 50 nm width arranged with a spacial separation of ∼200 nm. The morphology, composition, crystalline structure, and magnetic property of these nanopatterns have been analyzed using high-resolution cross-sectional transmission electron microscopy and atomic force microscopy. A geometrical model has been proposed to explain the fundamental features of such ion-induced nanopattern structures.

  11. Carbon dioxide ion dissociations after inner shell excitation and ionization: The origin of site-specific effects

    SciTech Connect

    Eland, J. H. D.; Zagorodskikh, S.; Mucke, M.; Squibb, R. J.; Feifel, R.; Sorensen, S. L.

    2014-05-14

    Multi-coincidence experiments with detection of both electrons and ions from decay of core-excited and core-ionized states of CO{sub 2} confirm that O{sub 2}{sup +} is formed specifically in Auger decay from the C1s-π* and O1s-π* resonances. Molecular rearrangement occurs by bending in the resonant states, and O{sub 2}{sup +} is produced by both single and double Auger decay. It is suggested that electron capture by C{sup +} after partial dissociation in the doubly ionized core of excited CO{sub 2}{sup +}, formed by shake-up in spectator resonant Auger decay, accounts for high kinetic energy and high internal energy in some C + O{sub 2}{sup +} fragments.

  12. Cytoxicity of vitamin C and metal ions: a site-specific Fenton mechanism. Progress report, July 1981-June 1982

    SciTech Connect

    Samuni, A.; Aronovitch, J.; Godinger, D.; Chevion, M.; Czapski, G.

    1982-01-01

    The toxicity of ascorbate toward phages T2 through T7 has been investigated. The T-odd bacteriophages are highly susceptible to ascorbate-induced damage, whereas the t-even phages are practically resistant. The toxicity of ascorbate is dependent on the presence of copper (or iron) ions and on oxygen. The dependence on oxygen does not exist in the presence of hydrogen perioxide. Hydrogen peroxide enhances the damage and is essential for the ascorbate induced biological damage, as catalase fully protects the phages. Chelating agents such as salicylate or 1,10-phenanthroline do not prevent the damage, though they reduce the rate of phage inactivation roughly 5-fold. By contrast, EDTA or histidine fully protect the phages. OH-scavengers such as sucrose, formate, mannitol, t-BuOH or polyethylene glycol do not protect. Experiments with isotopically labeled DNA indicate that both phage adsorption to the host and the injection of its DNA are impaired as a result of the exposure to ascorbate and copper. It is also possible that some failure to express the viral genetic information contributes towards the loss of phage PFA.

  13. Laser desorption studies of high mass biomolecules in Fourier-transform ion cyclotron resonance mass spectrometry.

    PubMed Central

    Solouki, T; Russell, D H

    1992-01-01

    Matrix-assisted laser desorption ionization is used to obtain Fourier-transform ion cyclotron resonance mass spectra of model peptides (e.g., gramicidin S, angiotensin I, renin substrate, melittin, and bovine insulin). Matrix-assisted laser desorption ionization yields ions having appreciable kinetic energies. Two methods for trapping the high kinetic energy ions are described: (i) the ion signal for [M+H]+ ions is shown to increase with increasing trapping voltages, and (ii) collisional relaxation is used for the detection of [M+H]+ ions of bovine insulin. Images PMID:1378614

  14. Gas Desorption and Electron Emission from 1 MeV Potassium Ion Bombardment of Stainless Steel

    SciTech Connect

    Molvik, A W; Covo, M K; Bieniosek, F M; Prost, L; Seidl, P A; Baca, D; Coorey, A; Sakumi, A

    2004-07-19

    Gas desorption and electron emission coefficients were measured for 1 MeV potassium ions incident on stainless steel at grazing angles (between 80 and 88 from normal incidence) using a new gas-electron source diagnostic (GESD). Issues addressed in design and commissioning of the GESD include effects from backscattering of ions at the surface, space-charge limited emission current, and reproducibility of desorption measurements. We find that electron emission coefficients {gamma}{sub e} scale as 1/cos({theta}) up to angles of 86, where {gamma}{sub e} = 90. Nearer grazing incidence, {gamma}{sub e} is reduced below the 1/cos({theta}) scaling by nuclear scattering of ions through large angles, reaching {gamma}{sub e} = 135 at 88. Electrons were emitted with a measured temperature of {approx}30 eV. Gas desorption coefficients {gamma}{sub sigma} were much larger, of order {gamma}{sub sigma} = 104. They also varied with angle, but much more slowly than 1/cos({theta}). From this we conclude that the desorption was not entirely from adsorbed layers of gas on the surface. Two mitigation techniques were investigated: rough surfaces reduced electron emission by a factor of ten and gas desorption by a factor of two; a mild bake to 230 had no effect on electron emission, but decreased gas desorption by 15% near grazing incidence. We propose that gas desorption is due to electronic sputtering.

  15. Particle reflection and ion-induced desorption from tungsten surfaces with chemisorbed nitrogen

    NASA Astrophysics Data System (ADS)

    Yamamura, Y.; Kimura, H.

    1987-06-01

    Using the Monte Carlo simulation program ACAT, ion-induced desorption yields of nitrogen chemisorbed on tungsten surfaces and the associated particle reflection coefficients have been calculated for low-energy helium-ions. It is found that both the particle reflection coefficients and the energy distributions of the reflected particles depend strongly on the thickness of the adsorbate layer on the surface if the ion energy is in the threshold regime and that the collision sequence of the near-threshold mechanism includes at least two adsorbate atoms. The ACAT desorption yields are found to be in good agreement with experimental yields.

  16. Particle reflection and ion-induced desorption from tungsten surfaces with chemisorbed nitrogen

    NASA Astrophysics Data System (ADS)

    Yamamura, Y.; Kimura, H.

    Using the Monte Carlo simulation program ACAT, ion-induced desorption yields of nitrogen chemisorbed on tungsten surfaces and the associated particle reflection coefficients have been calculated for low-energy helium-ions. It is found that both the particle reflection coefficients and the energy distributions of the reflected particles depend strongly on the thickness of the adsorbate layer on the surface if the ion energy is in the threshold regime and that the collision sequence of the near-threshold mechanism includes at least two adsorbate atoms. The ACAT desorption yields are found to be in good agreement with experimental yields.

  17. Polarization dependent fragmentation of ions produced by laser desorption from nanopost arrays.

    PubMed

    Stolee, Jessica A; Vertes, Akos

    2011-05-28

    Tailored silicon nanopost arrays (NAPA) enable controlled and resonant ion production in laser desorption ionization experiments and have been termed nanophotonic ion sources (Walker et al., J. Phys. Chem. C, 2010, 114, 4835-4840). As the post dimensions are comparable to or smaller than the laser wavelength, near-field effects and localized electromagnetic fields are present in their vicinity. In this contribution, we explore the desorption and ionization mechanism by studying how surface derivatization affects ion yields and fragmentation. We demonstrate that by increasing the laser fluence on derivatized NAPA with less polar surfaces that have decreased interaction energy between the structured silicon substrate and the adsorbate, the spectrum changes from exhibiting primarily molecular ions to showing a growing variety and abundance of fragments. The polarization angle of the laser beam had been shown to dramatically affect the ion yields of adsorbates. For the first time, we report that by rotating the plane of polarization of the desorption laser, the internal energy of the adsorbate can also be modulated resulting in polarization dependent fragmentation. This polarization effect also resulted in selective fragmentation of vitamin B(12). To explore the internal energy of NAPA generated ions, the effect of the post aspect ratios on the laser desorption thresholds and on the internal energy of a preformed ion was studied. Elevated surface temperatures and enhanced near fields in the vicinity of high aspect ratio posts are thought to contribute to desorption and ionization from NAPA. Comparison of the fluence dependence of the internal energies of ions produced from nanoporous silicon and NAPA substrates indicates that surface restructuring or transient melting by the desorption laser is a prerequisite for the former but not for the latter.

  18. Molecular recognition by thrombin. Role of the slow-->fast transition, site-specific ion binding energetics and thermodynamic mapping of structural components.

    PubMed

    Ayala, Y; Di Cera, E

    1994-01-14

    The interaction of thrombin with the potent natural inhibitor hirudin is controlled in a complex fashion by the binding of Na+ and Cl- to the enzyme and allosteric transitions. Binding of hirudin is positively linked to Na+ binding, but is opposed in a competitive fashion by the binding of Cl-. Since Na+ binding induces the slow-->fast transition of thrombin, it follows from linkage principles that hirudin binds to the fast form with higher affinity. Hence, the slow-->fast transition is a key component of molecular recognition of hirudin by thrombin. We propose a three-step mechanism for molecular recognition of hirudin by thrombin, which is also relevant for recognition of fibrinogen and possibly the platelet receptor and thrombomodulin. First, the C-terminal acidic tail of hirudin binds to the fibrinogen recognition site of thrombin displacing one Cl ion from the thrombin surface. Then, the enzyme undergoes a conformational transition that gives rise to increased accessibility of the catalytic pocket to small synthetic substrates through movement of the Trp148 loop. The changes in the catalytic moiety triggered allosterically by binding to the fibrinogen recognition site are linked to the uptake of Na+ and are similar to, if not identical with, those observed in the Na(+)-induced slow-->fast transition. Finally, the compact N-terminal domain is accommodated in the region surrounding the catalytic pocket. Hirudin binding is also used as a probe of site-specific ion-binding interactions of Na+ and Cl- with the enzyme, characterized by cooperativity between the Na+ and Cl- binding domains. The structural components directly involved or linked to Na+ and Cl- binding have been explored in terms of free energy perturbations of the binding of hirudin and a number of ligands. The fibrinogen recognition site stores most of the free energy of coupling with Cl- binding, while regions surrounding the access to the catalytic pocket provide most of the free energy of coupling

  19. Dynamic and static adsorption and desorption of Hg(II) ions on chitosan membranes and spheres.

    PubMed

    Vieira, Rodrigo S; Beppu, Marisa M

    2006-05-01

    The adsorption and desorption of Hg(II) ions was studied using static and dynamic methods, employing membranes and spheres of chitosan as the adsorbent. The quantity of adsorption was influenced by chitosan crosslinking and by the adsorbent shape. The Langmuir model was applied to fit the experimental equilibrium data. Glutaraldehyde-crosslinked membranes presented a lower desorption capacity, when compared to natural membranes, but could be regenerated for use in successive cycles. Dynamic adsorption experiments suggested that the adsorption capacity depended mainly on adsorbent geometry, due to differences between surface area to mass ratio and initial concentration of Hg(II) ions. The adsorption capacity determined by the dynamic method was 65% and 77% for membranes and spheres, respectively of the value obtained static method results. A process combining dynamic adsorption and static desorption can be used to concentrate the Hg(II) ions by a factor of nearly seven (7x), when compared to the initially treated volume.

  20. Remote mass spectrometric sampling of electrospray- and desorption electrospray-generated ions using an air ejector.

    PubMed

    Dixon, R Brent; Bereman, Michael S; Muddiman, David C; Hawkridge, Adam M

    2007-10-01

    A commercial air ejector was coupled to an electrospray ionization linear ion trap mass spectrometer (LTQ) to transport remotely generated ions from both electrospray (ESI) and desorption electrospray ionization (DESI) sources. We demonstrate the remote analysis of a series of analyte ions that range from small molecules and polymers to polypeptides using the AE-LTQ interface. The details of the ESI-AE-LTQ and DESI-AE-LTQ experimental configurations are described and preliminary mass spectrometric data are presented.

  1. Multicharged Ion Promoted Desorption (MIPD) of Reaction Co-Products

    DTIC Science & Technology

    2015-02-13

    HOPG), nanodiamond (ND) and polycarbonate (PC). Beams of oxygen (Q=3+ and 5+) and argon (Q=1+, 4+, and 8+) ions were focused at normal incidence...pyrolytic graphite (HOPG), nanodiamond (ND) and polycarbonate (PC). Beams of oxygen (Q=3+ and 5+) and argon (Q=1+, 4+, and 8+) ions were focused at...HOPG materials, the irradiations were carried out using beams of Carbon and Argon ions with nominal kinetic energies of 1.0 keV. All sample

  2. Effect of the surface on charge reduction and desorption kinetics of soft landed peptide ions.

    PubMed

    Hadjar, Omar; Wang, Peng; Futrell, Jean H; Laskin, Julia

    2009-06-01

    Charge reduction and desorption kinetics of ions and neutral molecules produced by soft-landing of mass-selected singly and doubly protonated Gramicidin S (GS) on different surfaces was studied using time dependant in situ secondary ion mass spectrometry (SIMS) integrated in a specially designed Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) research instrument. Soft-landing targets utilized in this study included inert self-assembled monolayers (SAMs) of 1-dodecane thiol (HSAM) and its fluorinated analog (FSAM) on gold and hydrophilic carboxyl-terminated (COOH-SAM) and amine-terminated (NH(2)-SAM) surfaces. We observed efficient neutralization of soft-landed ions on the COOH-SAM surface, partial retention of only one proton on the HSAM surface, and efficient retention of two protons on the FSAM surface. Slow desorption rates measured experimentally indicate fairly strong binding between peptide molecules and SAM surfaces with the binding energy of 20-25 kcal/mol.

  3. Defect mediated desorption of the KBr(001) surface induced by single highly charged ion impact.

    PubMed

    Heller, R; Facsko, S; Wilhelm, R A; Möller, W

    2008-08-29

    The individual impacts of slow (300 eV/amu) highly charged Xe ions induce nanometer sized pitlike structures on the KBr (001) surface. The volume of these structures shows a strong dependence on the ions potential energy. Total potential sputter yields from atomically flat (001) terraces are determined by imaging single ion impact sites. The dependence of the sputter yield on the ions initial charge state combined with structure formation at low and high-fluence irradiations indicates that agglomeration of defects into complex centers plays a major role in the desorption process induced by the potential energy.

  4. Liquid Beam Ion Desorption Mass Spectrometry for Evaluating CASSINI Data

    NASA Astrophysics Data System (ADS)

    Stolz, Ferdinand; Reviol, Rene; Srama, Ralf; Trieloff, Mario; Postberg, Frank; Abel, Bernd

    2013-04-01

    Saturn's moon Enceladus emits plumes of ice particles from an area near its south pole which are detected and chemically analyzed by the Cosmic Dust Analyzer (CDA) on board the CASSINI spacecraft. Studying these ice particles provides unique insights into Enceladus geological properties. Technically the CDA is a time-of-flight mass spectrometer which delivers mass spectra of the particles and their fragments. Since interpretation of the available CDA data is particularly challenging we employ a laboratory experiment to imitate experimental conditions in space. Key part of our experimental setup is a micron-sized water beam in high vacuum. This beam is rapidly heated up by an infrared laser pulse, which is tuned to excite the OH-stretch vibration of water molecules. This causes the water beam to dissipate into small droplets, some of which carry a net charge even though the laser energy is well below the molecular ionisation energy. The charged droplets are then analyzed in a time-of-flight mass spectrometer. With this experimental setup we successfully simulated the space born ice particles measured at Enceladus. By varying the laser intensity in our experiments, we can vary the amount of energy deposited in the liquid beam, and thus model different particle velocities. Also, variation of solute concentration in the water beam provides valuable information about ice particle composition. Some examples for anorganic solutes studied so far are sodium chloride, ammonia and hydrogen sulfite. A special feature of our experimental technique is that desorption of particles from the liquid beam is particularly soft. This is explained by the fact that all laser energy is absorbed by the water molecules. In this way molecular bonds of solutes stay intact and molecular solutes are transferred into the droplet phase without getting destroyed. This is particularly interesting in the context of analyzing organic compounds - some of which have been detected at Enceladus. Using

  5. Brominated Tyrosine and Polyelectrolyte Multilayer Analysis by Laser Desorption VUV Postionization and Secondary Ion Mass Spectrometry

    SciTech Connect

    University of Illinois at Chicago; Blaze, Melvin M. T.; Takahashi, Lynelle; Zhou, Jia; Ahmed, Musahid; Gasper, Gerald; Pleticha, F. Douglas; Hanley, Luke

    2011-03-14

    The small molecular analyte 3,5-dibromotyrosine (Br2Y) and chitosan-alginate polyelectrolyte multilayers (PEM) with and without adsorbed Br2Y were analyzed by laser desorption postionization mass spectrometry (LDPI-MS). LDPI-MS using 7.87 eV laser and tunable 8 ? 12.5 eV synchrotron vacuum ultraviolet (VUV) radiation found that desorption of clusters from Br2Y films allowed detection by≤8 eV single photon ionization. Thermal desorption and electronic structure calculations determined the ionization energy of Br2Y to be ~;;8.3?0.1 eV and further indicated that the lower ionization energies of clusters permitted their detection at≤8 eV photon energies. However, single photon ionization could only detect Br2Y adsorbed within PEMs when using either higher photon energies or matrix addition to the sample. All samples were also analyzed by 25 keV Bi3 + secondary ion mass spectrometry (SIMS), with the negative ion spectra showing strong parent ion signal which complemented that observed by LDPI-MS. The negative ion SIMS depended strongly on the high electron affinity of this specific analyte and the analyte?s condensed phase environment.

  6. Precursor ion scan profiles of acylcarnitines by atmospheric pressure thermal desorption chemical ionization tandem mass spectrometry.

    PubMed

    Paglia, Giuseppe; D'Apolito, Oceania; Corso, Gaetano

    2008-12-01

    The fatty acyl esters of L-carnitine (acylcarnitines) are useful biomarkers for the diagnosis of some inborn errors of metabolism analyzed by liquid chromatography/tandem mass spectrometry. In this study the acylcarnitines were analyzed by atmospheric pressure thermal desorption chemical ionization using a commercial tandem mass spectrometer (APTDCI-MS/MS). The method is based on the precursor ion scan mode determination of underivatized acylcarnitines desorbed from samples by a hot desolvation gas flow and ionized by a corona pin discharge. During desorption/ionization step the temperature induces the degradation of acylcarnitines; nevertheless, the common fragment to all acylcarnitines [MH-59](+) is useful for analyzing their profile. APTDCI parameters, including angle of collection and incidence, gas flows and temperatures, were optimized for acylcarnitines. The experiments were performed drying 2 microL of an equimolar mixture of acylcarnitine standards on a glass slide. The specificity was evaluated by comparing product ion spectra and the precursor ion spectra of 85 m/z of acylcarnitines obtained by the APTDCI method and by electrospray ionization flow injection analysis (ESI-FIA). The method was also employed to analyze acylcarnitines extracted from a pathological dried blood spot and a control. The method enables analysis of biological samples and recognition of some acylcarnitines that are diagnostic markers of inherited metabolic diseases. The intrinsic high-throughput analysis of the ambient desorption ionization methods offers a new opportunity either for its potential application in clinical chemistry and for the expanded screening of some inborn errors of metabolism.

  7. Efficient multicyclic sorption and desorption of lead ions on facilely prepared poly(m-phenylenediamine) particles with extremely strong chemoresistance.

    PubMed

    Huang, Mei-Rong; Lu, Hong-Jie; Li, Xin-Gui

    2007-09-01

    Nitric acid, hydrochloric acid and EDTA were carefully chosen as desorbent to systematically evaluate the adsorption/desorption performance of the Pb(2+)-adsorbing fine microparticles of poly(m-phenylenediamine). The sorption/desorption efficiency was maximized by optimizing desorption condition including the desorbent concentration, contact time, and desorption mode. The variation of the solution pH with Pb(2+) desorption was recorded to speculate the desorption mechanism. The practical reusability of the microparticles was elaborated through the sorption-desorption cycle experiments in an optimum condition. It was found that the desorption was very rapid with an equilibrium time of several minutes. A strong dependence of the desorbability on the species and concentration of the desorbents was observed. When 20 mM EDTA was chosen as the desorbent, the highest desorptivity was up to 94.2% that was much higher than those using nitric and hydrochloric acids. A successive sorption-desorption study employing nitric acid indicated that the microparticles could be simply regenerated and reutilized for more than 5 cycles together with Pb(2+) re-adsorption efficiency of about 50% and accumulative Pb(2+) adsorption capacity of up to 720.4 mg L(-1). Facilely prepared, extremely chemoresistant and cost-effective PmPD microparticles would be potentially used for multicyclic sorption of lead ions from aqueous solution.

  8. Site-specific cleavage by metal ion cofactors and inhibitors of M1 RNA, the catalytic subunit of RNase P from Escherichia coli.

    PubMed Central

    Kazakov, S; Altman, S

    1991-01-01

    The location of phosphate residues involved in specific centers for binding of metal ions in M1 RNA, the catalytic RNA subunit of RNase P from Escherichia coli, was determined by analysis of induction of cleavage of RNA by metal ions. At pH 9.5, Mg2+ catalyzes cleavage of M1 RNA at five principal sites. Under certain conditions, Mn2+ and Ca2+ can each replace Mg2+ as the cofactor in the processing of precursor tRNAs by M1 RNA and P RNA, the RNA subunit of RNase P from Bacillus subtilis. These cations, as well as various metal ion inhibitors of the catalytic activity of M1 RNA, also promote cleavage of M1 RNA in a specific manner. Certain conditions that affect the catalytic activity of M1 RNA also alter the rate of metal ion-induced cleavage at the various sites. From these results and a comparison of cleavage of M1 RNA with that of a deletion mutant of M1 RNA and of P RNA, we have identified two different centers for binding of metal ions in M1 RNA that are important for the processing of the precursor to tRNA(Tyr) from E. coli. There is also a center for the binding of metal ions in the substrate, close to the site of cleavage by M1 RNA. Images PMID:1718000

  9. Unravelling the secrets of Cs controlled secondary ion formation: Evidence of the dominance of site specific surface chemistry, alloying and ionic bonding

    NASA Astrophysics Data System (ADS)

    Wittmaack, Klaus

    2013-03-01

    Exposure of ion bombarded solids to Cs gives rise to a very strong enhancement of the yields of negatively charged secondary ions and, concurrently, to a lowering of positive ion yields. The phenomena have been explored in a large number of experimental and theoretical studies but attempts to clarify the mechanism of ion formation were not as successful as assumed. This review examines the state of the art in Cs controlled secondary ion mass spectrometry (SIMS) in great detail, with due consideration of low-energy alkali-ion scattering. In very basic studies on alkali induced secondary ion yield changes, sub-monolayer quantities of Cs or Li were deposited on the sample surface, followed by low-fluence ion bombardment, to avoid significant damage. If SIMS is applied to characterise the composition of solid materials, the simplest approach to achieving sample erosion as well as high negative-ion yields is bombardment with primary ions of Cs. Two other methods of sample loading with Cs provide more flexibility, (i) exposure to a collimated beam of Cs vapour and concurrent bombardment with high-energy non-Cs ions and (ii) the mixed-beam approach involving quasi-simultaneous bombardment with Cs and Xe ions. Both concepts have the advantage that undesirable sample overload with Cs can be avoided. High Cs concentrations reduce the formation probability of target specific molecular ions and lower the yields of all types of positive secondary ions, including Cs+, M+, X+, MCs+ and XCs+ (M and X denoting matrix and impurity elements). Quantitative SIMS analysis using MCs+ and XCs+ ions appears feasible, provided the Cs coverage is kept below about 5%. The semi-classical model of resonant charge transfer, also known as the tunnelling model, has long been considered a solid framework for the interpretation of Cs and Li based SIMS data. The model predicts ionisation probabilities for cases in which, at shallow distances from the surface, the affinity (ionisation) level of the

  10. Unravelling the secrets of Cs controlled secondary ion formation: Evidence of the dominance of site specific surface chemistry, alloying and ionic bonding

    NASA Astrophysics Data System (ADS)

    Wittmaack, Klaus

    2013-03-01

    Exposure of ion bombarded solids to Cs gives rise to a very strong enhancement of the yields of negatively charged secondary ions and, concurrently, to a lowering of positive ion yields. The phenomena have been explored in a large number of experimental and theoretical studies but attempts to clarify the mechanism of ion formation were not as successful as assumed. This review examines the state of the art in Cs controlled secondary ion mass spectrometry (SIMS) in great detail, with due consideration of low-energy alkali-ion scattering.In very basic studies on alkali induced secondary ion yield changes, sub-monolayer quantities of Cs or Li were deposited on the sample surface, followed by low-fluence ion bombardment, to avoid significant damage. If SIMS is applied to characterise the composition of solid materials, the simplest approach to achieving sample erosion as well as high negative-ion yields is bombardment with primary ions of Cs. Two other methods of sample loading with Cs provide more flexibility, (i) exposure to a collimated beam of Cs vapour and concurrent bombardment with high-energy non-Cs ions and (ii) the mixed-beam approach involving quasi-simultaneous bombardment with Cs and Xe ions. Both concepts have the advantage that undesirable sample overload with Cs can be avoided. High Cs concentrations reduce the formation probability of target specific molecular ions and lower the yields of all types of positive secondary ions, including Cs+, M+, X+, MCs+ and XCs+ (M and X denoting matrix and impurity elements). Quantitative SIMS analysis using MCs+ and XCs+ ions appears feasible, provided the Cs coverage is kept below about 5%.The semi-classical model of resonant charge transfer, also known as the tunnelling model, has long been considered a solid framework for the interpretation of Cs and Li based SIMS data. The model predicts ionisation probabilities for cases in which, at shallow distances from the surface, the affinity (ionisation) level of the

  11. Swift heavy ion irradiation of Pt nanocrystals: II. Structural changes and H desorption

    SciTech Connect

    Giulian, R.; Araujo, L.L.; Kluth, P.; Sprouster, D.J.; Schnohr, C.S.; Byrne, A.P.; Ridgway, M.C.

    2014-09-24

    The structural properties and H desorption from embedded Pt nanocrystals (NCs) following irradiation with swift heavy ions were investigated as a function of energy and fluence. From x-ray absorption near-edge spectroscopy analysis, Pt-H bonding was identified in NCs annealed in a forming gas (95% N{sub 2} + 5% H{sub 2}) ambient. The H content decreased upon irradiation and the desorption process was NC-size dependent such that larger NCs required a higher fluence to achieve a H-free state. Pt-H bonding and NC dissolution both perturbed the NC structural parameters (coordination number, bond-length and mean-square relative displacement) as determined with extended x-ray absorption fine structure measurements.

  12. Effect of the Surface on Charge Reduction and Desorption Kinetics of Soft Landed Peptide Ions

    SciTech Connect

    Hadjar, Omar; Wang, Peng; Futrell, Jean H.; Laskin, Julia

    2009-06-01

    Charge reduction and desorption kinetics of ions and neutral molecules produced by soft-landing of mass-selected singly and doubly protonated Gramicidin S (GS) on different surfaces was studied using time dependant in situ secondary ion mass spectrometry (SIMS) integrated in a specially designed Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) research instrument. Soft-landing targets utilized in this study included inert self-assembled monolayers (SAMs) of 1-dodecane thiol (HSAM) and its fluorinated analog (FSAM) on gold and hydrophilic carboxyl-terminated (COOH-SAM) and amine-terminated (NH2-SAM) SAM surfaces. We observed efficient neutralization of soft-landed ions on the COOH-SAM surface, partial retention of only one proton on the HSAM surface and efficient retention of two protons on the FSAM surface. Slow desorption rates measured experimentally indicate fairly strong binding between peptide molecules and SAM surfaces with the binding energy of 20-25 kcal/mol.

  13. Laser-induced thermal desorption facilitates postsource decay of peptide ions.

    PubMed

    Kim, Shin Hye; Lee, Aera; Song, Jae Yong; Han, Sang Yun

    2012-05-01

    We investigated the thermal mechanism involved in laser desorption/ionization (LDI) of thermally labile molecules from the flat surfaces of amorphous Si (a-Si) and crystalline Si (c-Si). a-Si was selected for this study because of its thermal property, such as low thermal conductivity; thus, it was predicted to be highly susceptible to laser-induced surface heating. By virtue of lack of surface nanostructures, the flat surfaces offer a simple model system to focus on the thermal mechanism, avoiding other effects, including possible non-thermal contributions that can arise from the physical existence of surface nanostructures. For the energetics study, the internal energies of substituted benzylpyridinium ions produced by LDI on the bare and coated surfaces of a-Si and c-Si were obtained using the survival yield method. The results, including LDI thresholds, ion yields, and internal energies all suggested that the LDI mechanism would be indeed thermal, which is most likely promoted by thermal desorption caused by laser-induced surface heating. In addition, the LDI process driven by laser-induced thermal desorption (LITD) was also found to be capable of depositing an excessive internal energy in resulting LDI ions, which underwent a dissociation. It exhibited the essentially same features as in postsource decay (PSD) in MALDI-TOF/TOF mass spectrometry. We report that the LDI process by LITD offers not only a way of intact ionization but also a facile means for PSD of peptide ions, which this work demonstrates is well suited to peptide sequencing using TOF/TOF mass spectrometry.

  14. Quantitation of berberine chloride in human urine by use of selected ion monitoring in the field desorption mode.

    PubMed

    Miyazaki, H; Shirai, E; Ishibashi, M; Hosoi, K; Shibata, S; Iwanaga, M

    1978-10-01

    A method is described for the microdetermination of berberine chloride in human urine by a field desorption mass spectrometry selected ion monitoring system using a deuterium labelled analogue of berberine chloride as an internal standard. Prior to the quantitation of berberine in human urine, the fundamental problems related to field desorption selected ion monitoring, such as quality of emitters, amounts of sample loading, and the programming rate of the emitter current, were statistically investigated in detail. Berberine chloride can be determined in a concentration of 10 ng ml-1 in human urine by the method described. The analytical results were compared with those from gas chromatography mass spectrometry selected ion monitoring in the chemical ionization mode suggesting that the reliability of field desorption selected ion monitoring may be almost equivalent to that of gas chromatography chemical ionization selected ion monitoring.

  15. Desorption of cluster ions from solid Ne by low-energy ion impact.

    PubMed

    Tachibana, T; Fukai, K; Koizumi, T; Hirayama, T

    2010-12-01

    We investigated Ne(+) ions and Ne(n)(+) (n = 2-20) cluster ions desorbed from the surface of solid Ne by 1.0 keV Ar(+) ion impact. Kinetic energy analysis shows a considerably narrower energy distribution for Ne(n)(+) (n ≥ 3) ions than for Ne(n)(+) (n = 1, 2) ions. The dependence of ion yields on Ne film thickness indicates that cluster ions (n ≥ 3) are desorbed only from relatively thick films. We conclude that desorbed ions grow into large cluster ions during the outflow of deep bulk atoms to the vacuum.

  16. Site-Specific Preparation of Intact Solid-Liquid Interfaces by Label-Free In Situ Localization and Cryo-Focused Ion Beam Lift-Out.

    PubMed

    Zachman, Michael J; Asenath-Smith, Emily; Estroff, Lara A; Kourkoutis, Lena F

    2016-12-01

    Scanning transmission electron microscopy (STEM) allows atomic scale characterization of solid-solid interfaces, but has seen limited applications to solid-liquid interfaces due to the volatility of liquids in the microscope vacuum. Although cryo-electron microscopy is routinely used to characterize hydrated samples stabilized by rapid freezing, sample thinning is required to access the internal interfaces of thicker specimens. Here, we adapt cryo-focused ion beam (FIB) "lift-out," a technique recently developed for biological specimens, to prepare intact internal solid-liquid interfaces for high-resolution structural and chemical analysis by cryo-STEM. To guide the milling process we introduce a label-free in situ method of localizing subsurface structures in suitable materials by energy dispersive X-ray spectroscopy (EDX). Monte Carlo simulations are performed to evaluate the depth-probing capability of the technique, and show good qualitative agreement with experiment. We also detail procedures to produce homogeneously thin lamellae, which enable nanoscale structural, elemental, and chemical analysis of intact solid-liquid interfaces by analytical cryo-STEM. This work demonstrates the potential of cryo-FIB lift-out and cryo-STEM for understanding physical and chemical processes at solid-liquid interfaces.

  17. Organic surfaces excited by low-energy ions: atomic collisions, molecular desorption and buckminsterfullerenes.

    PubMed

    Delcorte, Arnaud

    2005-10-07

    This article reviews the recent progress in the understanding of kiloelectronvolt particle interactions with organic solids, including atomic displacements in a light organic medium, vibrational excitation and desorption of fragments and entire molecules. This new insight is the result of a combination of theoretical and experimental approaches, essentially molecular dynamics (MD) simulations and secondary ion mass spectrometry (SIMS). Classical MD simulations provide us with a detailed microscopic view of the processes occurring in the bombarded target, from the collision cascade specifics to the scenarios of molecular emission. Time-of-flight SIMS measures the mass and energy distributions of sputtered ionized fragments and molecular species, a precious source of information concerning their formation, desorption, ionization and delayed unimolecular dissociation in the gas phase. The mechanisms of energy transfer and sputtering are compared for bulk molecular solids, organic overlayers on metal and large molecules embedded in a low-molecular weight matrix. These comparisons help understand some of the beneficial effects of metal substrates and matrices for the analysis of molecules by SIMS. In parallel, I briefly describe the distinct ionization channels of molecules sputtered from organic solids and overlayers. The specific processes induced by polyatomic projectile bombardment, especially fullerenes, are discussed on the basis of new measurements and calculations. Finally, the perspective addresses the state-of-the-art and potential developments in the fields of surface modification and analysis of organic materials by kiloelectronvolt ion beams.

  18. Rapid determination of nicotine in urine by direct thermal desorption ion trap mass spectrometry

    SciTech Connect

    Wise, M.B.; Ilgner, R.H.; Guerin, M.R.

    1990-01-01

    The measurement of nicotine and cotinine in physiological fluids (urine, blood serum, and saliva) is widely used as a means of assessing human exposure to environmental tobacco smoke (ETS). Although numerous analytical methods exist for these measurements, they generally involve extensive sample preparation which increases cost and decreases sample throughput. We report the use of thermal desorption directly into an ion trap mass spectrometer (ITMS) for the rapid determination of nicotine and cotinine in urine. A 1{mu}L aliquot of urine is injected into a specially designed inlet and flash vaporized directly into an ITMS through an open-split capillary restrictor interface. Isobutane chemical ionization is used to generate (M+H){sup +} ions of the analytes and collision induced dissociation is used to generate characteristic fragment ions which are used to confirm their identity. Quantification is achieved by integrating the ion current for the characteristic ions and comparing with an external working curve. Detection limits are approximately 50 pg per analyte and the sample turnaround time is approximately 3 minutes without the need for extensive sample preparation. 12 refs., 5 figs.

  19. Rapid determination of drugs and semivolatile organics by direct thermal desorption ion trap mass spectrometry

    SciTech Connect

    Wise, M.B.; Ilgner, R.H.; Buchanan, M.V.; Guerin, M.R.

    1991-01-01

    Direct thermal desorption of analytes into an ion trap mass spectrometer (ITMS) is being investigated as a technique for the rapid screening of a wide variety of samples for target semivolatile organic compounds. This includes the direct detection of drugs in physiological fluids, semivolatile organic pollutants in water and waste samples, and air pollutants collected on sorbent cartridges. In order to minimize the analysis time, chromatographic separation is not performed on the sample prior to introduction into the ITMS. Instead, selective chemical ionization and tandem mass spectrometry (MS/MS) are used achieve the specificity required for the target analytes. Detection limits are typically 10--50 ppb using a 1 uL aliquot of a liquid sample without preconcentration. Sample turn-around time is 2 to 5 minutes and 3 to 5 target analytes can be quantitatively determined simultaneously. 6 figs.

  20. Leidenfrost Phenomenon-assisted Thermal Desorption (LPTD) and Its Application to Open Ion Sources at Atmospheric Pressure Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Saha, Subhrakanti; Chen, Lee Chuin; Mandal, Mridul Kanti; Hiraoka, Kenzo

    2013-03-01

    This work describes the development and application of a new thermal desorption technique that makes use of the Leidenfrost phenomenon in open ion sources at atmospheric pressure for direct mass spectrometric detection of ultratrace levels of illicit, therapeutic, and stimulant drugs, toxicants, and peptides (molecular weight above 1 kDa) in their unaltered state from complex real world samples without or with minor sample pretreatment. A low temperature dielectric barrier discharge ion source was used throughout the experiments and the analytical figures of merit of this technique were investigated. Further, this desorption technique coupled with other ionization sources such as electrospray ionization (ESI) and dc corona discharge atmospheric pressure chemical ionization (APCI) in open atmosphere was also investigated. The use of the high-resolution `Exactive Orbitrap' mass spectrometer provided unambiguous identification of trace levels of the targeted compounds from complex mixtures and background noise; the limits of detection for various small organic molecules and peptides treated with this technique were at the level of parts per trillion and 10-9 M, respectively. The high sensitivity of the present technique is attributed to the spontaneous enrichment of analyte molecules during the slow evaporation of the solvent, as well as to the sequential desorption of molecules from complex mixtures based on their volatilities. This newly developed desorption technique is simple and fast, while molecular ions are observed as the major ions.

  1. Structural characterization of phospholipids by matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry.

    PubMed

    Marto, J A; White, F M; Seldomridge, S; Marshall, A G

    1995-11-01

    Matrix-assisted laser desorption/ionization (MALDI) Fourier transform ion cyclotron resonance mass spectrometry provides for structural analysis of the principal biological phospholipids: glycerophosphatidylcholine, -ethanolamine, -serine, and -inositol. Both positive and negative molecular or quasimolecular ions are generated in high abundance. Isolated molecular ions may be collisionally activated in the source side of a dual trap mass analyzer, yielding fragments serving to identify the polar head group (positive ion mode) and fatty acid side chains (negative ion mode). Azimuthal quadrupolar excitation following collisionally activated dissociation refocuses productions close to the solenoid axis; subsequent transfer of product ions to the analyzer ion trap allows for high-resolution mass analysis. Cyro-cooling of the sample probe with liquid nitrogen greatly reduces matrix adduction encountered in the negative ion mode.

  2. [Adsorption-desorption Characteristics of Fermented Rice Husk for Ferrous and Sulfur Ions].

    PubMed

    Xie, Xiao-mei; Liao, Min; Hua, Jia-yuan; Chen, Na; Zhang, Nan; Xu, Pei-zhi; Xie Kai-zhi; XU, Chang-xu; Liu, Guang-rong

    2015-10-01

    To understand the potential of rice husk to fix Fe2+ and S2- ions, the sorption of Fe2+ and S2- by fermented rice husk was studied by using batch incubation experiments in the present study. The effects of adsorption time, Fe2+ and S2- concentration, pH, the temperature and ionic strength in adsorption reaction solution on the sorption were investigated. Therefore, the stability of Fe2+ and S2- adsorbed by fermented rice husk was further validated by desorption experiments performed under similar conditions as adsorption. The results showed that, the adsorption kinetics of Fe2+ (r = 0.912 1) and S2- (r = 0.901 1) by fermented rice husk fits the Elovich kinetics equation, and Freundlich isotherm model could simulate the isotherm adsorption processes of Fe2+ (R2 = 0.965 1) and S2- (R2 = 0.936 6) on fermented rice husk was better than other models. The adsorption processes on fermented rice husk were non- preferential adsorption for Fe2+ and S2, while the adsorption process of Fe2+ on fermented rice husk was spontaneous reaction and the adsorption process of S2- was non-spontaneous reaction. The adsorption processes of Fe2+ and S2- on fermented rice husk were endothermic process since high temperature could benefit to the adsorption. The adsorption mechanism of Fe2+ on fermented rice husk was mainly controlled by coordination adsorption, the adsorption mechanism of S2- on fermented rice husk was mainly controlled by ligand exchange adsorption. The adsorption processes of Fe2+ and S2- on fermented rice husk showed greater pH adaptability which ranged from 1.50 to 11.50. With the increasing of ionic strength, the amount of adsorbed Fe2+ on fermented rice husk wasincreased in some extent, the amount of adsorbed S2- on fermented rice husk was slightly decreased, which further proved the adsorption of Fe2+ was major in inner sphere complexation and the adsorption of S2- was major in outer complexation. The desorption rates of Fe2+ and S2- which was adsorbed by fermented

  3. Comparison of sample pre-treatments for laser desorption ionization and secondary ion mass spectrometry imaging of Miscanthus x giganteus.

    PubMed

    Li, Zhen; Bohn, Paul W; Sweedler, Jonathan V

    2010-07-01

    Efforts to further the potential of the large perennial grass Miscanthusxgiganteus as a biofuel feedstock would be aided by the ability to image the chemical species present during the fuel production process. Toward this end, two mass spectrometry imaging (MSI) approaches have been investigated here-laser desorption/ionization mass spectrometry (LDI-MS) and secondary ion mass spectrometry (SIMS). As a first step, cross sections of Miscanthus were subjected to a variety of sample preparation methods to optimize conditions for MSI. For LDI-MS, a thin metal coating (2 nm thick Au) provided high quality signals of saccharide-related ions. The traditional matrix-assisted laser desorption/ionization matrix, 2,5-dihydroxybenzoic acid, also showed high efficiency for the desorption of saccharide-related ions. In contrast, with alpha-cyano-4-hydroxycinnamic acid matrix, these ions were nearly absent in the mass spectra. Direct laser ablation of untreated Miscanthus sections was also performed. High resolution images, where the fine structure of the vascular bundle could be clearly visualized, were obtained using SIMS. Although coating the sections with a nanometer thick Au layer can greatly enhance the quality of SIMS images, the coating had limited effect on secondary ion signal enhancement. Using the optimized mass spectrometry approaches described here, information on the spatial distribution of several saccharides was obtained.

  4. 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

  5. Ion-to-Neutral Ratios and Thermal Proton Transfer in Matrix-Assisted Laser Desorption/Ionization

    NASA Astrophysics Data System (ADS)

    Lu, I.-Chung; Chu, Kuan Yu; Lin, Chih-Yuan; Wu, Shang-Yun; Dyakov, Yuri A.; Chen, Jien-Lian; Gray-Weale, Angus; Lee, Yuan-Tseh; Ni, Chi-Kung

    2015-07-01

    The ion-to-neutral ratios of four commonly used solid matrices, α-cyano-4-hydroxycinnamic acid (CHCA), 2,5-dihydroxybenzoic acid (2,5-DHB), sinapinic acid (SA), and ferulic acid (FA) in matrix-assisted laser desorption/ionization (MALDI) at 355 nm are reported. Ions are measured using a time-of-flight mass spectrometer combined with a time-sliced ion imaging detector. Neutrals are measured using a rotatable quadrupole mass spectrometer. The ion-to-neutral ratios of CHCA are three orders of magnitude larger than those of the other matrices at the same laser fluence. The ion-to-neutral ratios predicted using the thermal proton transfer model are similar to the experimental measurements, indicating that thermal proton transfer reactions play a major role in generating ions in ultraviolet-MALDI.

  6. The dissociation kinetics of NO on Rh(111) as studied by temperature programmed static secondary ion mass spectrometry and desorption

    NASA Astrophysics Data System (ADS)

    Borg, H. J.; Reijerse, J. F. C.-J. M.; van Santen, R. A.; Niemantsverdriet, J. W.

    1994-12-01

    Temperature programmed static secondary ion mass spectrometry (TPSSIMS) and temperature programmed desorption (TPD) have been used to study the kinetics of adsorption, dissociation, and desorption of NO on Rh(111). At 100 K, NO adsorption is molecular and proceeds via mobile precursor state kinetics with a high initial sticking probability. SSIMS indicates the presence of two distinct NO adsorption states, indicative of threefold adsorption at low coverage, and occupation of bridge sites at higher coverages. Three characteristic coverage regimes appear with respect to NO dissociation. At low coverages θNO<0.25 ML, NO dissociates completely at temperatures between 275 and 340 K. If we neglect lateral interactions and assume pure first order dissociation kinetics, we find effective values for the activation barrier and preexponential factor of 40±6 kJ/mol and 106±1 s-1 for the dissociation of 0.15-0.20 ML NO. However, if we assume that a NO molecule needs an ensemble of three to four vacant sites in order to dissociate, the preexponential factor and activation energy are ˜1011 s-1 and 65 kJ/mol, in better agreement with transition state theory expectations. The Nads and Oads dissociation products desorb as N2 and O2, respectively, with desorption parameters Edes=118±10 kJ/mol and νdes=1010.1±1.0 s-1 for N2 in the zero coverage limit. At higher coverages, the desorption kinetics of N2 is strongly influenced by the presence of coadsorbed oxygen. In the medium coverage range 0.25<θNO<0.50 ML, part of the NO desorbs molecularly, with an estimated desorption barrier of 113±10 kJ/mol and a preexponential of 1013.5±1.0 s-1. Dissociation of NO becomes progressively inhibited due to site blocking, the onset shifting from 275 K at 0.25 ML to 400 K, coinciding with the NO desorption temperature, at a coverage of 0.50 ML. The accumulation of nitrogen and oxygen atoms on the highly covered surface causes a destabilization of the nitrogen atoms, which results in an

  7. Organic ion imaging of biological tissue with secondary ion mass spectrometry and matrix-assisted laser desorption/ionization.

    PubMed

    Todd, P J; Schaaff, T G; Chaurand, P; Caprioli, R M

    2001-04-01

    Organic secondary ion mass spectrometry (SIMS) and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry can be used to produce molecular images of samples. This is achieved through ionization from a clearly identified point on a flat sample, and performing a raster of the sample by moving the point of ionization over the sample surface. The unique analytical capabilities of mass spectrometry for mapping a variety of biological samples at the tissue level are discussed. SIMS provides information on the spatial distribution of the elements and low molecular mass compounds as well as molecular structures on these compounds, while MALDI yields spatial information about higher molecular mass compounds, including their distributions in tissues at very low levels, as well as information on the molecular structures of these compounds. Application of these methods to analytical problems requires appropriate instrumentation, sample preparation methodology, and a data presentation usually in a three-coordinate plot where x and y are physical dimensions of the sample and z is the signal amplitude. The use of imaging mass spectrometry is illustrated with several biological systems.

  8. Adsorption and Desorption of Nickel(II) Ions from Aqueous Solution by a Lignocellulose/Montmorillonite Nanocomposite

    PubMed Central

    Zhang, Xiaotao; Wang, Ximing

    2015-01-01

    A new and inexpensive lignocellulose/montmorillonite (LNC/MMT) nanocomposite was prepared by a chemical intercalation of LNC into MMT and was subsequently investigated as an adsorbent in batch systems for the adsorption-desorption of Ni(II) ions in an aqueous solution. The optimum conditions for the Ni(II) ion adsorption capacity of the LNC/MMT nanocomposite were studied in detail by varying parameters such as the initial Ni(II) concentration, the solution pH value, the adsorption temperature and time. The results indicated that the maximum adsorption capacity of Ni(II) reached 94.86 mg/g at an initial Ni(II) concentration of 0.0032 mol/L, a solution pH of 6.8, an adsorption temperature of 70°C, and adsorption time of 40 min. The represented adsorption kinetics model exhibited good agreement between the experimental data and the pseudo-second-order kinetic model. The Langmuir isotherm equation best fit the experimental data. The structure of the LNC/MMT nanocomposite was characterized by X-ray diffraction (XRD) and transmission electron microscopy (TEM), whereas the adsorption mechanism was discussed in combination with the results obtained from scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDX), and Fourier-transform infrared spectroscopy analyses (FTIR). The desorption capacity of the LNC/MMT nanocomposite depended on parameters such as HNO3 concentration, desorption temperature, and desorption time. The satisfactory desorption capacity of 81.34 mg/g was obtained at a HNO3 concentration, desorption temperature, and desorption time of 0.2 mol/L, 60 ºC, and 30 min, respectively. The regeneration studies showed that the adsorption capacity of the LNC/MMT nanocomposite was consistent for five cycles without any appreciable loss in the batch process and confirmed that the LNC/MMT nanocomposite was reusable. The overall study revealed that the LNC/MMT nanocomposite functioned as an effective adsorbent in the detoxification of Ni

  9. Adsorption and desorption of nickel(II) ions from aqueous solution by a lignocellulose/montmorillonite nanocomposite.

    PubMed

    Zhang, Xiaotao; Wang, Ximing

    2015-01-01

    A new and inexpensive lignocellulose/montmorillonite (LNC/MMT) nanocomposite was prepared by a chemical intercalation of LNC into MMT and was subsequently investigated as an adsorbent in batch systems for the adsorption-desorption of Ni(II) ions in an aqueous solution. The optimum conditions for the Ni(II) ion adsorption capacity of the LNC/MMT nanocomposite were studied in detail by varying parameters such as the initial Ni(II) concentration, the solution pH value, the adsorption temperature and time. The results indicated that the maximum adsorption capacity of Ni(II) reached 94.86 mg/g at an initial Ni(II) concentration of 0.0032 mol/L, a solution pH of 6.8, an adsorption temperature of 70°C, and adsorption time of 40 min. The represented adsorption kinetics model exhibited good agreement between the experimental data and the pseudo-second-order kinetic model. The Langmuir isotherm equation best fit the experimental data. The structure of the LNC/MMT nanocomposite was characterized by X-ray diffraction (XRD) and transmission electron microscopy (TEM), whereas the adsorption mechanism was discussed in combination with the results obtained from scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDX), and Fourier-transform infrared spectroscopy analyses (FTIR). The desorption capacity of the LNC/MMT nanocomposite depended on parameters such as HNO3 concentration, desorption temperature, and desorption time. The satisfactory desorption capacity of 81.34 mg/g was obtained at a HNO3 concentration, desorption temperature, and desorption time of 0.2 mol/L, 60 ºC, and 30 min, respectively. The regeneration studies showed that the adsorption capacity of the LNC/MMT nanocomposite was consistent for five cycles without any appreciable loss in the batch process and confirmed that the LNC/MMT nanocomposite was reusable. The overall study revealed that the LNC/MMT nanocomposite functioned as an effective adsorbent in the detoxification of Ni

  10. Quantification of Carbohydrates and Related Materials Using Sodium Ion Adducts Produced by Matrix-Assisted Laser Desorption Ionization

    NASA Astrophysics Data System (ADS)

    Ahn, Sung Hee; Park, Kyung Man; Moon, Jeong Hee; Lee, Seong Hoon; Kim, Myung Soo

    2016-11-01

    The utility of sodium ion adducts produced by matrix-assisted laser desorption ionization for the quantification of analytes with multiple oxygen atoms was evaluated. Uses of homogeneous solid samples and temperature control allowed the acquisition of reproducible spectra. The method resulted in a direct proportionality between the ion abundance ratio I([A + Na]+)/I([M + Na]+) and the analyte concentration, which could be used as a calibration curve. This was demonstrated for carbohydrates, glycans, and polyether diols with dynamic range exceeding three orders of magnitude.

  11. A new approach for detection of explosives based on ion mobility spectrometry and laser desorption/ionization on porous silicon

    NASA Astrophysics Data System (ADS)

    Kuzishchin, Yury; Kotkovskii, Gennadii; Martynov, Igor; Dovzhenko, Dmitriy; Chistyakov, Alexander

    2016-05-01

    We demonstrate a new way for detection ultralow concentration of explosives in this study. It combines an ion mobility spectrometry (IMS) and a promising method of laser desorption/ionization on silicon (DIOS). The DIOS is widely used in mass spectrometry due to the possibility of small molecule detection and high sensitivity. It is known that IMS based on laser ion source is a power method for the fast detection of ultralow concentration of organic molecules. However requirement of using high energy pulse ultraviolet laser increases weight and size of the device. The use of DIOS in an ion source of IMS could decrease energy pulse requirements and allows one to construct both compact and high sensitive device for analyzing gas and liquid probes. On the other hand mechanisms of DIOS in gas media is poorly studied, especially in case of nitroaromatic compounds. The investigation of the desorption/ionization on porous silicon (pSi) surface of nitroaromatic compounds has been carried out for 2,4,6-trinitrotoluene (TNT) using IMS and mass spectrometry (MS). It has been demonstrated that TNT ion formation in a gas medium is a complicated process and includes both an electron emission from the pSi surface with subsequent ion-molecular reactions in a gas phase and a proton transfer between pSi surface and TNT molecule.

  12. Conformation of Macromolecules in the Gas Phase: Use of Matrix-Assisted Laser Desorption Methods in Ion Chromatography

    NASA Astrophysics Data System (ADS)

    von Helden, Gert; Wyttenbach, Thomas; Bowers, Michael T.

    1995-03-01

    Conformational data for macromolecules in the gas phase have been obtained by the coupling of a matrix-assisted laser desorption ion source to an ion chromatograph. A series of polyethylene glycol (PEG) polymers "cationized" (converted to a cation) by sodium ions (Na^+PEG9 to Na^+PEG19) and a protonated neurotransmitter protein, bradykinin, were studied. Mobilities of Na^+PEG9 to Na^+PEG19 are reported. Detailed modeling of Na^+PEG9 with molecular mechanics methods indicates that the lowest energy structure has the Na^+ ion "solvated" by the polymer chain with seven oxygen atoms as nearest neighbors. The agreement between the model and experiment is within 1 percent for Na^+PEG9, Na^+PEG13, and Na^+PEG17, giving strong support to both the method and the deduced structures. Similar agreement was obtained in initial studies that modeled experimental data for arginine-protonated bradykinin.

  13. Soft X-Ray Photochemistry of Condensed Mixed Reactants: Thin Film Growth and Ion Desorption

    NASA Astrophysics Data System (ADS)

    Moore, Jerry Franklin, Jr.

    A novel process for the growth of thin film dielectric materials is presented. By condensing a mixture of reactive compounds onto a surface that is cooled under vacuum, a mixed molecular layer is formed. This layer can then be exposed to soft x-ray radiation to form a refractory thin film of dielectric material. By using either trimethylaluminum (TMA), silane, or tetramethylsilane (TMS) alone or in combination with water or ammonia, it was possible to grow oxide, nitride and carbide films. The growth of these films was generally seen to stop after 30A, and extended exposure to soft x -rays led to decomposition of the films into a more elemental state. The self-limiting growth at 30A was not observed for unmixed systems such as when aluminum carbide was grown from a TMA layer. The explanation for this is that the self-limiting growth is due to excitation of the reaction by substrate electrons, while there are enough electrons generated in the carbide to perpetuate growth indefinitely. Additionally, unlimited growth was observed for TMA and water mixtures excited by ultraviolet radiation (4.6eV). This effect is due to direct photon absorption in the layer that leads to reaction and film growth. Decomposition of the films was observed at extended exposures. It is likely that core excitation is the main cause of this phenomenon. A model that accounts for this decomposition, the relative absorption density of the substrate and the growing film, and the mean free path of the electrons in the film, is presented. The model demonstrates that a limited thickness can be expected when the cross section for film decomposition is significant and the film absorption density is relatively low. Observations of the desorbed ions from the condensed mixtures show that core excitation can lead directly to subsequent reactions. For example, OH^+ was formed from an initial excitation of O _2. The utility of stimulated desorption as a energy dependent probe of these condensed mixed

  14. An investigation of liquid secondary ion and laser desorption mass spectroscopy for the analysis of planar chromatograms

    SciTech Connect

    Dunphy, J.C.

    1990-11-01

    In the work described in this dissertation, interfaces between two mass spectrometric methods, liquid secondary ion mass spectrometry (LSIMS) and laser desorption/ionization Fourier transform mass spectrometry (LD/FTMS), and thin-layer chromatography (TLC) and slab gel electrophoresis were developed for bioanalytical applications. In an investigation of direct LSIMS for TLC analysis (TLC/LSIMS), mass spectra of bile acids and bile salts were characterized directly from high-performance TLC plates. The scanning ability of the LSIMS instrument was used to generate spatial profiles of the characteristic bile acid ions in the mass spectra. A procedure for the analysis of bile salts in dog bile was developed involving an extraction step, followed by TLC separation and direct TLC/LSIMS detection and semi-quantitation. For peptides, an experiment called ``selected-sequence monitoring`` was developed to locate target peptides related in structure in complex mixtures developed on TLC plates. Ions characteristic of the bradykinin and enkephalin peptides were used to generate spatial profiles of members of those peptide families on TLC plates. Using a Fourier transform mass spectrometer (FTMS), a fundamental investigation was conducted into the factors affecting the quality of analytical data obtained using direct laser desorption/ionization to produce mass spectra from TLC plates.

  15. An investigation of liquid secondary ion and laser desorption mass spectroscopy for the analysis of planar chromatograms

    SciTech Connect

    Dunphy, J.C.

    1990-11-01

    In the work described in this dissertation, interfaces between two mass spectrometric methods, liquid secondary ion mass spectrometry (LSIMS) and laser desorption/ionization Fourier transform mass spectrometry (LD/FTMS), and thin-layer chromatography (TLC) and slab gel electrophoresis were developed for bioanalytical applications. In an investigation of direct LSIMS for TLC analysis (TLC/LSIMS), mass spectra of bile acids and bile salts were characterized directly from high-performance TLC plates. The scanning ability of the LSIMS instrument was used to generate spatial profiles of the characteristic bile acid ions in the mass spectra. A procedure for the analysis of bile salts in dog bile was developed involving an extraction step, followed by TLC separation and direct TLC/LSIMS detection and semi-quantitation. For peptides, an experiment called selected-sequence monitoring'' was developed to locate target peptides related in structure in complex mixtures developed on TLC plates. Ions characteristic of the bradykinin and enkephalin peptides were used to generate spatial profiles of members of those peptide families on TLC plates. Using a Fourier transform mass spectrometer (FTMS), a fundamental investigation was conducted into the factors affecting the quality of analytical data obtained using direct laser desorption/ionization to produce mass spectra from TLC plates.

  16. Matrix-assisted laser desorption/ionization mass spectrometry method for selectively producing either singly or multiply charged molecular ions.

    PubMed

    Trimpin, Sarah; Inutan, Ellen D; Herath, Thushani N; McEwen, Charles N

    2010-01-01

    Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is noted for its ability to produce primarily singly charged ions. This is an attribute when using direct ionization for complex mixtures such as protein digests or synthetic polymers. However, the ability to produce multiply charged ions, as with electrospray ionization (ESI), has advantages such as extending the mass range on mass spectrometers with limited mass-to-charge (m/z) range and enhancing fragmentation for structural characterization. We designed and fabricated a novel field free transmission geometry atmopsheric pressure (AP) MALDI source mounted to a high-mass resolution Orbitrap Exactive mass spectrometer. We report the ability to produce at will either singly charged ions or highly charged ions using a MALDI process by simply changing the matrix or the matrix preparation conditions. Mass spectra with multiply charged ions very similar to those obtained with ESI of proteins such as cytochrome c and ubiquitin are obtained with low femtomole amounts applied to the MALDI target plate and for peptides such as angiotensin I and II with application of attomole amounts. Single scan acquisitions produce sufficient ion current even from proteins.

  17. Vitamin D-metabolites from human plasma and mass spectrometric analysis by fast heavy ion induced desorption

    NASA Astrophysics Data System (ADS)

    Fohlman, J.; Peterson, P. A.; Kamensky, I.; Håkansson, P.; Sundqvist, B.

    1982-07-01

    D-vitamin metabolites have been isolated from human serum employing chromatographic techniques. The serum carrier protein for vitamin D (DBP) was first isolated by immunosorbent chromatography. Lipid ligands associated with DBP were then extracted with hexane and separated by high pressure liquid chromatography (HPLC). Detection of vitamin D metabolites by their absorbance of ultraviolet light is not sufficiently sensitive to monitor all vitamin D derivatives from a few millilitres of serum. Therefore, further analyses are necessary to quantitate these compounds. We have begun to develop a mass spectrometric method to achieve a reliable, quantitative procedure. As a first step towards this goal a number of pure samples of vitamin D compounds have been studied in a time-of-flight mass spectrometer based on fast heavy ion induced desorption. All vitamin D compounds examined could be detected and identified by their molecular ion and fragment spectra.

  18. Molecular dynamics investigation of desorption and ion separation following picosecond infrared laser (PIRL) ablation of an ionic aqueous protein solution.

    PubMed

    Zou, J; Wu, C; Robertson, W D; Zhigilei, L V; Miller, R J D

    2016-11-28

    Molecular dynamics simulations were performed to characterize the ablation process induced by a picosecond infrared laser (PIRL) operating in the regime of desorption by impulsive vibrational excitation (DIVE) of a model peptide (lysozyme)/counter-ion system in aqueous solution. The simulations were performed for ablation under typical experimental conditions found within a time-of-flight mass spectrometer (TOF-MS), that is in vacuum with an applied electric field (E = ± 10(7) V/m), for up to 2 ns post-ablation and compared to the standard PIRL-DIVE ablation condition (E = 0 V/m). Further, a simulation of ablation under an extreme field condition (E = 10(10) V/m) was performed for comparison to extend the effective dynamic range of the effect of the field on charge separation. The results show that the plume dynamics were retained under a typical TOF-MS condition within the first 1 ns of ablation. Efficient desorption was observed with more than 90% of water molecules interacting with lysozyme stripped off within 1 ns post-ablation. The processes of ablation and desolvation of analytes were shown to be independent of the applied electric field and thus decoupled from the ion separation process. Unlike under the extreme field conditions, the electric field inside a typical TOF-MS was shown to modify the ions' motion over a longer time and in a soft manner with no enhancement to fragmentation observed as compared to the standard PIRL-DIVE. The study indicates that the PIRL-DIVE ablation mechanism could be used as a new, intrinsically versatile, and highly sensitive ion source for quantitative mass spectrometry.

  19. Molecular dynamics investigation of desorption and ion separation following picosecond infrared laser (PIRL) ablation of an ionic aqueous protein solution

    NASA Astrophysics Data System (ADS)

    Zou, J.; Wu, C.; Robertson, W. D.; Zhigilei, L. V.; Miller, R. J. D.

    2016-11-01

    Molecular dynamics simulations were performed to characterize the ablation process induced by a picosecond infrared laser (PIRL) operating in the regime of desorption by impulsive vibrational excitation (DIVE) of a model peptide (lysozyme)/counter-ion system in aqueous solution. The simulations were performed for ablation under typical experimental conditions found within a time-of-flight mass spectrometer (TOF-MS), that is in vacuum with an applied electric field (E = ± 107 V/m), for up to 2 ns post-ablation and compared to the standard PIRL-DIVE ablation condition (E = 0 V/m). Further, a simulation of ablation under an extreme field condition (E = 1010 V/m) was performed for comparison to extend the effective dynamic range of the effect of the field on charge separation. The results show that the plume dynamics were retained under a typical TOF-MS condition within the first 1 ns of ablation. Efficient desorption was observed with more than 90% of water molecules interacting with lysozyme stripped off within 1 ns post-ablation. The processes of ablation and desolvation of analytes were shown to be independent of the applied electric field and thus decoupled from the ion separation process. Unlike under the extreme field conditions, the electric field inside a typical TOF-MS was shown to modify the ions' motion over a longer time and in a soft manner with no enhancement to fragmentation observed as compared to the standard PIRL-DIVE. The study indicates that the PIRL-DIVE ablation mechanism could be used as a new, intrinsically versatile, and highly sensitive ion source for quantitative mass spectrometry.

  20. Negative Ion In-Source Decay Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry for Sequencing Acidic Peptides

    NASA Astrophysics Data System (ADS)

    McMillen, Chelsea L.; Wright, Patience M.; Cassady, Carolyn J.

    2016-05-01

    Matrix-assisted laser desorption/ionization (MALDI) in-source decay was studied in the negative ion mode on deprotonated peptides to determine its usefulness for obtaining extensive sequence information for acidic peptides. Eight biological acidic peptides, ranging in size from 11 to 33 residues, were studied by negative ion mode ISD (nISD). The matrices 2,5-dihydroxybenzoic acid, 2-aminobenzoic acid, 2-aminobenzamide, 1,5-diaminonaphthalene, 5-amino-1-naphthol, 3-aminoquinoline, and 9-aminoacridine were used with each peptide. Optimal fragmentation was produced with 1,5-diaminonphthalene (DAN), and extensive sequence informative fragmentation was observed for every peptide except hirudin(54-65). Cleavage at the N-Cα bond of the peptide backbone, producing c' and z' ions, was dominant for all peptides. Cleavage of the N-Cα bond N-terminal to proline residues was not observed. The formation of c and z ions is also found in electron transfer dissociation (ETD), electron capture dissociation (ECD), and positive ion mode ISD, which are considered to be radical-driven techniques. Oxidized insulin chain A, which has four highly acidic oxidized cysteine residues, had less extensive fragmentation. This peptide also exhibited the only charged localized fragmentation, with more pronounced product ion formation adjacent to the highly acidic residues. In addition, spectra were obtained by positive ion mode ISD for each protonated peptide; more sequence informative fragmentation was observed via nISD for all peptides. Three of the peptides studied had no product ion formation in ISD, but extensive sequence informative fragmentation was found in their nISD spectra. The results of this study indicate that nISD can be used to readily obtain sequence information for acidic peptides.

  1. 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

  2. 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.

  3. Mechanisms for Excited Neutrals and Negative and Positive Ion Desorption from Surfaces.

    DTIC Science & Technology

    1985-10-01

    covalent and Auger stimultd. ionic systems, desorpt. ( RASD ) adsorbates aDuring+ the modification process (step 3),Xc can always result from X via...rescnant contributions (i.e., the DA and RASD contributions) were separated from the MPCI and ASD contributions (10,33]: and 3. the spectral lineshapes...con- " tribution, and the Ti .,3p -1 CIS spectrum [10] Re Psonan OH’decor) representing the RASD \\ / contribution. The fold ,f* 0KO S of the 0 K EELS

  4. Generation of highly charged peptide and protein ions by atmospheric pressure matrix-assisted infrared laser desorption/ionization ion trap mass spectrometry.

    PubMed

    König, Simone; Kollas, Oliver; Dreisewerd, Klaus

    2007-07-15

    We show that highly charged ions can be generated if a pulsed infrared laser and a glycerol matrix are employed for atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry with a quadrupole ion trap. Already for small peptides like bradykinin, doubly protonated ions form the most abundant analyte signal in the mass spectra. The center of the charge-state distribution increases with the size of the analyte. For example, insulin is detected with a most abundant ion signal corresponding to a charge state of four, whereas for cytochrome c, the 10 times protonated ion species produces the most intense signal. Myoglobin is observed with up to 13 charges. The high m/z ratios allow us to use the Paul trap for the detection of MALDI-generated protein ions that are, owing to their high molecular weight, not amenable in their singly protonated charge state. Formation of multiple charges critically depends on the addition of diluted acid to the analyte-matrix solution. Tandem mass spectra generated by collision-induced dissociation of doubly charged peptides are also presented. The findings allow speculations about the involvement of electrospray ionization processes in these MALDI experiments.

  5. 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)

  6. Rapid analysis of animal drug residues by microcolumn solid-phase extraction and thermal desorption-ion trap mass spectrometry

    SciTech Connect

    Barshick, S.A.; Buchanan, M.V.

    1994-11-01

    A new approach was developed for the rapid and quantitative determination of an anthelmintic drug, phenothiazine, in milk. The technique involves a simple extraction procedure using a C{sub 18} microcolumn disc, followed by thermal desorption of the analyte from the disc directly into an ion trap mass spectrometer. The compounds are selectively ionized by isobutane chemical ionization and detected by tandem mass spectrometry. With this approach, 10 ppb detection limits were achieved with as little as 100 {mu}L mild and only 10 min of analysis time. This approach was used to analyze samples of milk taken from a cow administered a one-time therapeutic dose of phenothiazine. The target compound could be detected at 56 post-dosage, corresponding to a concentration of 30 ppb. 13 refs., 3 figs., 2 tabs.

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. Biosorption of Cr(VI) ions from aqueous solutions: kinetics, equilibrium, thermodynamics and desorption studies.

    PubMed

    Singha, Biswajit; Das, Sudip Kumar

    2011-05-01

    Cr(VI) is a major water pollutant from industrial effluent whose concentration is to be reduced within the permissible limit. Present study reports a systematic evaluation of six different natural adsorbents for the removal of Cr(VI) from aqueous solutions in batch process. The adsorption kinetic data were best described by pseudo-second order model. The values of mass transfer coefficient for Cr(VI) adsorption indicated that the velocity of the adsorbate transport from the bulk to the solid phase was quite fast. The effective diffusivity of Cr(VI) removal for all the adsorbents were of the order of 10(-10) m(2)/s which suggested chemisorption of the process. The adsorption process was jointly controlled by film diffusion and intraparticle diffusion. Maximum monolayer adsorption capacities onto the natural adsorbents used were comparable to the other natural adsorbents used by other researchers. The thermodynamic studies and sorption energy calculation using Dubinin-Radushkevich isotherm model indicated that the adsorption processes were endothermic and chemical in nature. FT-IR studies were carried out to understand the type of functional groups responsible for Cr(VI) binding process. Desorption study was carried out with different concentration of NaOH solutions. Application study was carried out using electroplating industrial wastewater.

  12. UV laser induced desorption of CsI and RbI ion clusters

    NASA Astrophysics Data System (ADS)

    Fernández-Lima, F. A.; Ponciano, C. R.; Filho, H. D. Fonseca; Pedrero, E.; Chaer Nascimento, M. A.; da Silveira, E. F.

    2006-09-01

    Experimental results of laser sputtering of cesium and rubidium iodide secondary ions are presented. A TOF mass spectrometer, operating in linear mode, continuous extraction for positive or negative ions, was used for the analysis of (CsI) nCs +, (CsI) nI -, (RbI) nRb + and (RbI) nI - ion emission as a function of the laser irradiance. Experimental data show that the cluster ion emission yields decrease exponentially with n, for all the laser irradiances applied. Theoretical analysis of the clusters structure was performed using density functional theory at the B3LYP/LACV3P level, for the positive and negative cluster series. A quasi-equilibrium evolution of the clusters is proposed to extract a parameter characteristic of the cluster recombination process: the effective temperature. The hypothesis of the atomic species' recombination (during the expansion of a high density highly ionized cloud) leading to cluster formation is confirmed to some extent in a second set of experiments: the UV laser ablation of a mixed and non-mixed cesium iodide and potassium bromide targets. These experiments show that the emission yields contain contributions from both the recombination process and from the sample stoichiometry, even for high laser irradiances.

  13. 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.

  14. 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.

  15. Isotherms and Kinetics of Water Vapor Sorption/Desorption for Surface Films of Polyion-Surfactant Ion Complex Salts.

    PubMed

    Gustavsson, Charlotte; Piculell, Lennart

    2016-07-14

    Thin films of "complex salts" (CS = ionic surfactants with polymeric counterions) have recently been shown to respond to humidity changes in ambient air by changing their liquid crystalline structure. We here report isotherms and kinetics of water sorption/desorption for ∼10-100 μm films of alkyltrimethylammonium polyacrylate CS, measured in a dynamic gravimetric vapor sorption instrument over a 0-95% relative humidity (RH) range. The sorption per ion pair was similar to that observed for common ionomers. A kinetic model for the water exchange is presented, assuming that the "external" transport between the vapor reservoir and the film surface is rate-determining. The model predicts that the water content, after a small stepwise change of the reservoir RH, should vary exponentially with time, with a time constant proportional to both the slope of the sorption isotherm and the film thickness. These predictions were confirmed for our films over large RH ranges, and the external mass transfer coefficient in our setup was calculated from the experimental data. Expressions derived for the Biot number (ratio of characteristic times for internal and external water transport) for the considered limiting case strongly indicate that external water transport should quite generally affect, or even dominate, the measured kinetics for similarly thin hydrated films.

  16. Adsorption and desorption behavior of copper ions on Na-montmorillonite: effect of rhamnolipids and pH.

    PubMed

    Ozdemir, Günseli; Yapar, Saadet

    2009-07-30

    In this work, the effects of an anionic biosurfactant, rhamnolipid (RL), and pH on the adsorption and desorption of Cu(2+) ions on Na-montmorillonite were investigated. Adsorption studies were conducted through the addition of Cu(2+) to the dispersions containing pristine- and/or RL-modified clay. In the case of pristine clay, RL was also added simultaneously with the Cu(2+). The effect of pH was studied in the range between 1.0 and 8.0. The highest adsorption capacity was obtained at the pH of 4.7-4.8. Among the models including the Langmuir, Freundlich and Dubinin-Kaganer-Radushkevich isotherms; Langmuir isotherm gave a better fit to the experimental data. The most suitable fit for the adsorption kinetics of Cu(2+) was obtained with a pseudo-second-order model. It was determined that the adsorption capacity of the pristine clay is comparable with that of the activated carbon and the modification of clay with RL causes an increase in the adsorption rate due to the distribution of clay platelets in the solution.

  17. Vacuum compatible sample positioning device for matrix assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry imaging

    PubMed Central

    Aizikov, Konstantin; Smith, Donald F.; Chargin, David A.; Ivanov, Sergei; Lin, Tzu-Yung; Heeren, Ron M. A.; O’Connor, Peter B.

    2011-01-01

    The high mass accuracy and resolving power of Fourier transform ion cyclotron resonance mass spectrometers (FT-ICR MS) make them ideal mass detectors for mass spectrometry imaging (MSI), promising to provide unmatched molecular resolution capabilities. The intrinsic low tolerance of FT-ICR MS to RF interference, however, along with typically vertical positioning of the sample, and MSI acquisition speed requirements present numerous engineering challenges in creating robotics capable of achieving the spatial resolution to match. This work discusses a two-dimensional positioning stage designed to address these issues. The stage is capable of operating in ∼1 × 10–8 mbar vacuum. The range of motion is set to 100 mm × 100 mm to accommodate large samples, while the positioning accuracy is demonstrated to be less than 0.4 micron in both directions under vertical load over the entire range. This device was integrated into three different matrix assisted laser desorption/ionization (MALDI) FT-ICR instruments and showed no detectable RF noise. The “oversampling” MALDI-MSI experiments, under which the sample is completely ablated at each position, followed by the target movement of the distance smaller than the laser beam, conducted on the custom-built 7T FT-ICR MS demonstrate the stability and positional accuracy of the stage robotics which delivers high spatial resolution mass spectral images at a fraction of the laser spot diameter. PMID:21639522

  18. Oscillations in the stability of consecutive chemical bonds revealed by ion-induced desorption.

    PubMed

    Ossowski, Jakub; Rysz, Jakub; Krawiec, Mariusz; Maciazek, Dawid; Postawa, Zbigniew; Terfort, Andreas; Cyganik, Piotr

    2015-01-19

    While it is a common concept in chemistry that strengthening of one bond results in weakening of the adjacent ones, no results have been published on if and how this effect protrudes further into the molecular backbone. By binding molecules to a surface in the form of a self-assembled monolayer, the strength of a primary bond can be selectively altered. Herein, we report that by using secondary-ion mass spectrometry, we are able to detect for the first time positional oscillations in the stability of consecutive bonds along the adsorbed molecule, with the amplitudes diminishing with increasing distance from the molecule-metal interface. To explain these observations, we have performed molecular dynamics simulations and DFT calculations. These show that the oscillation effects in chemical-bond stability have a very general nature and break the translational symmetry in molecules.

  19. Ultrasensitive characterization of site-specific glycosylation of affinity-purified haptoglobin from lung cancer patient plasma using 10 μm i.d. porous layer open tubular liquid chromatography-linear ion trap collision-induced dissociation/electron transfer dissociation mass spectrometry.

    PubMed

    Wang, Dongdong; Hincapie, Marina; Rejtar, Tomas; Karger, Barry L

    2011-03-15

    Site-specific analysis of protein glycosylation is important for biochemical and clinical research efforts. Glycopeptide analysis using liquid chromatography-collision-induced dissociation/electron transfer dissociation mass spectrometry (LC-CID/ETD-MS) allows simultaneous characterization of the glycan structure and attached peptide site. However, due to the low ionization efficiency of glycopeptides during electrospray ionization, 200-500 fmol of sample per injection is needed for a single LC-MS run, which makes it challenging for the analysis of limited amounts of glycoprotein purified from biological matrixes. To improve the sensitivity of LC-MS analysis for glycopeptides, an ultranarrow porous layer open tubular (PLOT) LC column (2.5 m × 10 μm i.d.) was coupled to a linear ion trap (LTQ) collision-induced dissociation/electron transfer dissociation mass spectrometer to provide sensitive analysis of N-linked protein glycosylation heterogeneity. The potential of the developed method is demonstrated by the characterization of site-specific glycosylation using haptoglobin (Hpt) as a model protein. To limit the amount of haptoglobin to low picomole amounts of protein, we affinity purified it from 1 μL of pooled lung cancer patient plasma. A total of 26 glycoforms/glycan compositions on three Hpt tryptic glycopeptides were identified and quantified from 10 LC-MS runs with a consumption of 100 fmol of Hpt digest (13 ng of protein, 10 fmol per injection). Included in this analysis was the determination of the glycan occupancy level. At this sample consumption level, the high sensitivity of the PLOT LC-LTQ-CID/ETD-MS system allowed glycopeptide identification and structure determination, along with relative quantitation of glycans presented on the same peptide backbone, even for low abundant glycopeptides at the ∼100 amol level. The PLOT LC-MS system is shown to have sufficient sensitivity to allow characterization of site-specific protein glycosylation from trace

  20. 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...

  1. Adsorption and desorption of Cu(II), Cd(II) and Pb(II) ions using chitosan crosslinked with epichlorohydrin-triphosphate as the adsorbent.

    PubMed

    Laus, Rogério; Costa, Thiago G; Szpoganicz, Bruno; Fávere, Valfredo T

    2010-11-15

    In this study, chitosan (CTS) was crosslinked with both epichlorohydrin (ECH) and triphosphate (TPP), by covalent and ionic crosslinking, respectively. The resulting new CTS-ECH-TPP adsorbent was characterized by CHN analysis, EDS, FTIR spectroscopy, TGA and DSC, and the adsorption and desorption of Cu(II), Cd(II) and Pb(II) ions in aqueous solution were investigated. Potentiometric studies were also performed and revealed three titratable protons for each pK(a) value of 5.14, 6.76 and 9.08. The results obtained showed that the optimum pH values for adsorption were 6.0 for Cu(II), 7.0 for Cd(II) and 5.0 for Pb(II). The kinetics study demonstrated that the adsorption process proceeded according to the pseudo-second-order model. Three isotherm models (Langmuir, Freundlich and Dubinin-Radushkevich) were employed in the analysis of the adsorption equilibrium data. The Langmuir model resulted in the best fit and the new adsorbent had maximum adsorption capacities for Cu(II), Cd(II) and Pb(II) ions of 130.72, 83.75 and 166.94 mg g(-1), respectively. Desorption studies revealed that HNO(3) and HCl were the best eluents for desorption of Cu(II), Cd(II) and Pb(II) ions from the crosslinked chitosan.

  2. 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.

  3. 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.

  4. A mass spectrometric system for analyzing thermal desorption spectra of ion-implanted argon and cesium in tungsten. Ph.D. Thesis

    NASA Technical Reports Server (NTRS)

    Wood, G. M., Jr.

    1974-01-01

    A mass spectrometric system for determining the characteristics of materials used in instrumental development and aerospace applications was developed. The desorption spectra of cesium that was ion-implanted into polycrystalline tungsten and the effects on the spectra of bombardment of the tungsten by low energy (70 eV) electrons were investigated. Work function changes were measured by the retarding potential diode method. Flash desorption characteristics were observed and gas-reaction mechanisms of the surface of heated metal filaments were studied. Desorption spectra were measured by linearly increasing the sample temperature at a selected rate, the temperature cycling being generated from a ramp-driven dc power supply, with the mass spectrometer tuned to a mass number of interest. Results of the study indicate an anomolous desorption mechanism following an electron bombardment of the sample surface. The enhanced spectra are a function of the post-bombardment time and energy and are suggestive of an increased concentration of cesium atoms, up to 10 or more angstroms below the surface.

  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. Evaluation of combined matrix-assisted laser desorption/ionization time-of-flight and matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry experiments for peptide mass fingerprinting analysis.

    PubMed

    da Silva, David; Wasselin, Thierry; Carré, Vincent; Chaimbault, Patrick; Bezdetnaya, Lina; Maunit, Benoît; Muller, Jean-François

    2011-07-15

    Peptide Mass Fingerprinting (PMF) is still of significant interest in proteomics because it allows a large number of complex samples to be rapidly screened and characterized. The main part of post-translational modifications is generally preserved. In some specific cases, PMF suffers from ambiguous or unsuccessful identification. In order to improve its reliability, a combined approach using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) and matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FTICRMS) was evaluated. The study was carried out on bovine serum albumin (BSA) digest. The influence of several important parameters (the matrix, the sample preparation method, the amount of the analyte) on the MOWSE score and the protein sequence coverage were evaluated to allow the identification of specific effects. A careful investigation of the sequence coverage obtained by each kind of experiment ensured the detection of specific peptides for each experimental condition. Results highlighted that DHB-FTICRMS and DHB- or CHCA-TOFMS are the most suited combinations of experimental conditions to achieve PMF analysis. The association (convolution) of the data obtained by each of these techniques ensured a significant increase in the MOWSE score and the protein sequence coverage.

  7. Detection of Non-aromatic Organic Compounds in Meteorites using Imaging Laser Desorption/Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Scott, J. R.; Hinman, N. W.; Richardson, C. D.; Mahon, R. C.; McJunkin, T. R.

    2009-12-01

    Our most extensive understanding of extraterrestrial organic matter is based on what has been learned from meteorites that have been delivered naturally to Earth. Meteorites have been analyzed by a variety of techniques ranging from extensive sample preparation with extraction and subsequent chromatography to direct laser desorption mass spectrometry (LDMS). While extraction studies have reported a variety of organics (e.g., aliphatic and aromatic hydrocarbons, ketones, aldehydes, and amino acids), LDMS studies have only reported polycyclic aromatic hydrocarbons (PAHs). This is rather surprising considering that Yan et al. (Talanta 2007, 72, 634-641) reported that even a small amount of PAH enables the detection of organics that are not otherwise ionized during the desorption event from minerals. Therefore, we have begun re-investigating meteorites because, regardless of the source of the organic compounds, the presences of PAHs should allow other organic molecules to be observed using imaging laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry (LD-FTICR-MS). Indeed, we have mapped meteorites (e.g., EETA 79001) and found many mass-to-charge peaks that are non-aromatic as determined by analysis of their mass defects. Mapping also revealed that the distribution of organics is heterogeneous, which necessitates the collection of a mass spectrum from a single laser shot so that minor peaks of interest are not lost in signal averaging. These studies have implications for analyzing future returned samples from Mars or elsewhere with minimal preparation or damage.

  8. Core excitation and decay in rare gas mono- and multilayers on a metal surface: screening, deexcitation, and desorption of neutrals and ions

    NASA Astrophysics Data System (ADS)

    Rocker, G.; Feulner, P.; Scheuerer, R.; Zhu, L.; Menzel, D.

    1990-06-01

    In order to investigate the modification of excitation and decay of core holes by condensation and adsorption in the simplest possible cases, as well as the coupling to atomic motion, we have studied the Ar2p and Kr3d excitation regions in Ar and Kr mono- and multilayers on Ru(001). Using synchrotron radiation from BESSY (Berlin), total and Auger electron yields and yields of desorbing ions and neutrals, as function of photon energy, as well as decay electron spectra for specific primary excitations have been measured. The main results are: Multilayers: Energies for resonant core excitations are shifted to higher values by 0.6 to 1 eV compared to free atoms; for Kr, surface (smaller shifts) and bulk excitations can be distinguished. Autoionization and normal Auger spectra are clearly different, as in the gas phase. Besides desorption of neutral atoms as in the valence region, singly and doubly charged ions as well as ionic clusters are desorbed. Monolayers: The shift of resonant excitation energies relative to the gas phase is smaller than for condensed layers. Decay spectra for resonant and non-resonant excitations are identical, as for strongly coupled chemisorbates, proving that charge exchange with the metal is fast compared to core decay. As in the valence region, only neutral atoms desorb. The results shed light on the screening and charge transfer behaviour and on the mechanisms of stimulated desorption which are operative in them.

  9. Identification of amino acids by material enhanced laser desorption/ionisation mass spectrometry (MELDI-MS) in positive- and negative-ion mode

    NASA Astrophysics Data System (ADS)

    Hashir, Muhammad Ahsan; Stecher, Guenther; Mayr, Stefan; Bonn, Guenther K.

    2009-01-01

    In the present study, different silica gel modifications were evaluated for their application as target surface for material enhanced laser desorption/ionisation mass spectrometric (MELDI-MS) investigation of amino acids. 4,4'-Azodianiline (ADA-silica) modified silica gel was successfully employed for the qualitative analysis of amino acids in positive- and in negative-ion mode. Further no derivatisation of amino acids was necessary, as the introduced system allowed the direct analysis of targets and delivered spectra with excellent signal intensity and signal-to-noise ratio within a few minutes. The influence of surface chemistry, ionisation mode and the nature of analytes on signal intensity was studied and discussed. Detection limit of 2.10 pg (10 fmol) was achieved by employing ADA-silica in positive-ion mode. Finally, xylem saps from different types of trees were analysed. This proved the high performance and excellent behaviour of the introduced target surface material.

  10. Ion thermalization using pressure transients in a quadrupole ion trap coupled to a vacuum matrix-assisted laser desorption ionization source and a reflectron time-of-flight mass analyzer.

    PubMed

    Papanastasiou, D; Belgacem, O; Sudakov, M; Raptakis, E

    2008-05-01

    Efficient trapping and detection of intact peptide ions is demonstrated in a quadrupole ion trap (QIT) coupled to an external vacuum matrix-assisted laser desorption ionization (MALDI) source. Deactivation of metastable ions generated by MALDI is achieved in a pressure transient environment inside the QIT established by pulsing gas to access the higher pressures required for fast thermalization, without affecting vacuum conditions in the ion source and time-of-flight (TOF) mass analyzer. Pressure transients are experimentally determined and a threshold of approximately 10 mTorr is identified where internally excited ions, which commonly observed to dissociate upon injection in a QIT, are stabilized. Fragment-free spectra are presented for a set of peptides by using 2,5-dihydroxybenzoic acid (DHB) as a matrix, and significantly reduced fragmentation is observed by using a-cyano-4-hydroxycinnamic acid (CHCA). Intact peptide spectra of a protein tryptic digest are also recorded with CHCA. The process of translational cooling for externally injected ions in a dynamic pressure environment is visualized by using ion trajectory simulations that employ hard sphere collisions. Statistical theory of dynamic equilibrium of ions stored in rf fields is applied to our QIT to characterize a translationally thermalized ion cloud, to explain observed ejection efficiency into the TOF mass analyzer, and to further discuss collisional deactivation of metastable ions.

  11. Removal of Co(II), Cu(II) and Pb(II) ions by polymer based 2-hydroxyethyl methacrylate: thermodynamics and desorption studies

    PubMed Central

    2012-01-01

    Removal thermodynamics and desorption studies of some heavy metal ions such as Co(II), Cu(II) and Pb(II) by polymeric surfaces such as poly 2-hydroxyethyl methacrylate (PHEMA) and copolymer 2-hydroxyethyl methacrylate with monomer methyl methacrylate P(MMA-HEMA) as adsorbent surfaces from aqueous single solution were investigated with respect to the changes in pH of solution, adsorbent composition, contact time and temperature in the individual aqueous solution. The linear correlation coefficients of Langmuir and Freundlich isotherms were obtained and the results revealed that the Langmuir isotherm fitted the experiment results better than Freundlich isotherm. Using the Langmuir model equation, the monolayer removal capacity of PHEMA surface was found to be 0.7388, 0.8396 and 3.0367 mg/g for Co(II), Cu(ΙΙ) and Pb(II) ions and removal capacity of P(MMA-HEMA) was found to be 28.8442, 31.1526 and 31.4465 mg/g for Co(II), Cu(ΙΙ) and Pb(II) ions, respectively. Changes in the standard Gibbs free energy (ΔG0), standard enthalpy (ΔH0) and standard entropy (ΔS0) showed that the removals of mentioned ions onto PHEMA and P(MMA-HEMA) are spontaneous and exothermic at 293–323 K. The maximum desorption efficiency was 75.26% for Pb(II) using 0.100 M HNO3, 70.10% for Cu(II) using 0.100 M HCl, 59.20% for 0.100 M HCl 63.67% Co(II). PMID:23369255

  12. Removal of Co(II), Cu(II) and Pb(II) ions by polymer based 2-hydroxyethyl methacrylate: thermodynamics and desorption studies.

    PubMed

    Moradi, Omid; Mirza, Behrooz; Norouzi, Mehdi; Fakhri, Ali

    2012-12-22

    Removal thermodynamics and desorption studies of some heavy metal ions such as Co(II), Cu(II) and Pb(II) by polymeric surfaces such as poly 2-hydroxyethyl methacrylate (PHEMA) and copolymer 2-hydroxyethyl methacrylate with monomer methyl methacrylate P(MMA-HEMA) as adsorbent surfaces from aqueous single solution were investigated with respect to the changes in pH of solution, adsorbent composition, contact time and temperature in the individual aqueous solution. The linear correlation coefficients of Langmuir and Freundlich isotherms were obtained and the results revealed that the Langmuir isotherm fitted the experiment results better than Freundlich isotherm. Using the Langmuir model equation, the monolayer removal capacity of PHEMA surface was found to be 0.7388, 0.8396 and 3.0367 mg/g for Co(II), Cu(ΙΙ) and Pb(II) ions and removal capacity of P(MMA-HEMA) was found to be 28.8442, 31.1526 and 31.4465 mg/g for Co(II), Cu(ΙΙ) and Pb(II) ions, respectively. Changes in the standard Gibbs free energy (ΔG0), standard enthalpy (ΔH0) and standard entropy (ΔS0) showed that the removals of mentioned ions onto PHEMA and P(MMA-HEMA) are spontaneous and exothermic at 293-323 K. The maximum desorption efficiency was 75.26% for Pb(II) using 0.100 M HNO3, 70.10% for Cu(II) using 0.100 M HCl, 59.20% for 0.100 M HCl 63.67% Co(II).

  13. Quantitation of lysergic acid diethylamide in urine using atmospheric pressure matrix-assisted laser desorption/ionization ion trap mass spectrometry.

    PubMed

    Cui, Meng; McCooeye, Margaret A; Fraser, Catharine; Mester, Zoltán

    2004-12-01

    A quantitative method was developed for analysis of lysergic acid diethylamide (LSD) in urine using atmospheric pressure matrix-assisted laser desorption/ionization ion trap mass spectrometry (AP MALDI-ITMS). Following solid-phase extraction of LSD from urine samples, extracts were analyzed by AP MALDI-ITMS. The identity of LSD was confirmed by fragmentation of the [M + H](+) ion using tandem mass spectrometry. The quantification of LSD was achieved using stable-isotope-labeled LSD (LSD-d(3)) as the internal standard. The [M + H](+) ion fragmented to produce a dominant fragment ion, which was used for a selected reaction monitoring (SRM) method for quantitative analysis of LSD. SRM was compared with selected ion monitoring and produced a wider linear range and lower limit of quantification. For SRM analysis of samples of LSD spiked in urine, the calibration curve was linear in the range of 1-100 ng/mL with a coefficient of determination, r(2), of 0.9917. This assay was used to determine LSD in urine samples and the AP MALDI-MS results were comparable to the HPLC/ ESI-MS results.

  14. 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...

  15. 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.

  16. 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...

  17. Calibration laws based on multiple linear regression applied to matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry.

    PubMed

    Williams, D Keith; Chadwick, M Ashley; Williams, Taufika Islam; Muddiman, David C

    2008-12-01

    Operation of any mass spectrometer requires implementation of mass calibration laws to translate experimentally measured physical quantities into a m/z range. While internal calibration in Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) offers several attractive features, including exposure of calibrant and analyte ions to identical experimental conditions (e.g. space charge), external calibration affords simpler pulse sequences and higher throughput. The automatic gain control method used in hybrid linear trap quadrupole (LTQ) FT-ICR-MS to consistently obtain the same ion population is not readily amenable to matrix-assisted laser desorption/ionization (MALDI) FT-ICR-MS, due to the heterogeneous nature and poor spot-to-spot reproducibility of MALDI. This can be compensated for by taking external calibration laws into account that consider magnetic and electric fields, as well as relative and total ion abundances. Herein, an evaluation of external mass calibration laws applied to MALDI-FT-ICR-MS is performed to achieve higher mass measurement accuracy (MMA).

  18. Ion Yields in the Coupled Chemical and Physical Dynamics Model of Matrix-Assisted Laser Desorption/Ionization

    NASA Astrophysics Data System (ADS)

    Knochenmuss, Richard

    2015-08-01

    The Coupled Chemical and Physical Dynamics (CPCD) model of matrix assisted laser desorption ionization has been restricted to relative rather than absolute yield comparisons because the rate constant for one step in the model was not accurately known. Recent measurements are used to constrain this constant, leading to good agreement with experimental yield versus fluence data for 2,5-dihydroxybenzoic acid. Parameters for alpha-cyano-4-hydroxycinnamic acid are also estimated, including contributions from a possible triplet state. The results are compared with the polar fluid model, the CPCD is found to give better agreement with the data.

  19. Rapid identification of gallotannins from Chinese galls by matrix-assisted laser desorption/ionization time-of-flight quadrupole ion trap mass spectrometry.

    PubMed

    Zhu, Fan; Cai, Yi-Zhong; Xing, Jie; Ke, Jinxia; Zhan, Zhaoqi; Corke, Harold

    2009-06-01

    Chinese gall, a conventional traditional Chinese medicine, contains high levels of gallotannins. A rapid method for direct analysis of the gallotannins without using any troublesome sample pretreatments was developed using matrix-assisted laser desorption/ionization time-of-flight quadrupole ion trap mass spectrometry (MALDI-QIT-TOF MS) to successfully identify the gallotannin components in the crude extract of Chinese galls within several minutes. The high quality of the MS and MS(2) spectra acquired clearly showed that hydrolysable tannins in Chinese galls were identified as a series of the gallotannins with degrees of polymerization (DP) of 4-11 galloyl units. The MS(2) data indicated that the identified gallotannins with DP of 4-7 galloyl units had clear fragmentation with loss of 1-5 galloyl units which were further deprived of 1-3 water moieties. This technique may be used for rapid evaluation and screening of hydrolysable tannins in medicinal plants.

  20. Soft-landing ion mobility of silver clusters for small-molecule matrix-assisted laser desorption ionization mass spectrometry and imaging of latent fingerprints.

    PubMed

    Walton, Barbara L; Verbeck, Guido F

    2014-08-19

    Matrix-assisted laser desorption ionization (MALDI) imaging is gaining popularity, but matrix effects such as mass spectral interference and damage to the sample limit its applications. Replacing traditional matrices with silver particles capable of equivalent or increased photon energy absorption from the incoming laser has proven to be beneficial for low mass analysis. Not only can silver clusters be advantageous for low mass compound detection, but they can be used for imaging as well. Conventional matrix application methods can obstruct samples, such as fingerprints, rendering them useless after mass analysis. The ability to image latent fingerprints without causing damage to the ridge pattern is important as it allows for further characterization of the print. The application of silver clusters by soft-landing ion mobility allows for enhanced MALDI and preservation of fingerprint integrity.

  1. Comparing Laser Desorption Ionization and Atmospheric Pressure Photoionization Coupled to Fourier Transform Ion Cyclotron Resonance Mass Spectrometry To Characterize Shale Oils at the Molecular Level

    USGS Publications Warehouse

    Cho, Yunjo; Jin, Jang Mi; Witt, Matthias; Birdwell, Justin E.; Na, Jeong-Geol; Roh, Nam-Sun; Kim, Sunghwan

    2013-01-01

    Laser desorption ionization (LDI) coupled to Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) was used to analyze shale oils. Previous work showed that LDI is a sensitive ionization technique for assessing aromatic nitrogen compounds, and oils generated from Green River Formation oil shales are well-documented as being rich in nitrogen. The data presented here demonstrate that LDI is effective in ionizing high-double-bond-equivalent (DBE) compounds and, therefore, is a suitable method for characterizing compounds with condensed structures. Additionally, LDI generates radical cations and protonated ions concurrently, the distribution of which depends upon the molecular structures and elemental compositions, and the basicity of compounds is closely related to the generation of protonated ions. This study demonstrates that LDI FT-ICR MS is an effective ionization technique for use in the study of shale oils at the molecular level. To the best of our knowledge, this is the first time that LDI FT-ICR MS has been applied to shale oils.

  2. 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.

  3. 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.

  4. Energy scaling of the ion-induced desorption yield for perpendicular collisions of Ar and U with stainless steel in the energy range of 5 and 100 MeV/u

    SciTech Connect

    Kollmus, H.; Kraemer, A.; Bender, M.; Bellachioma, M. C.; Reich-Sprenger, H.; Mahner, E.; Hedlund, E.; Westerberg, L.; Malyshev, O. B.; Leandersson, M.; Edqvist, E.

    2009-03-15

    For the GSI future project Facility for Antiproton and Ion Research a beam intensity of 10{sup 12} U{sup 28+}ions/s is planned to be extracted from the GSI heavy ion synchrotron SIS18. Measurements performed in 2001 showed that the beam lifetime of the ions in the synchrotron is decreasing with increasing number of injected particles due to vacuum instabilities caused by ion-induced desorption. The injection energy for the SIS18 is about 10 MeV/u and U{sup 28+} ions are accelerated to 200 MeV/u limited by the magnetic rigidity for the low charge state. The aim of this work was to measure the desorption yield as a function of the impact energy from injection to extraction of SIS18 at GSI. Low energy yields at 5.0, 9.7, and 17.7 MeV/u were measured at the Cyclotron of The Svedberg Laboratory in Uppsala. High energy yields at 40, 80, and 100 MeV/u were measured at SIS18 of GSI in a different setup. It was found that the desorption yield scales with the electronic energy loss (dE/dx){sub el}{sup n}, with n between 2 and 3, decreasing for increasing impact energy above the Bragg maximum.

  5. 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.

  6. 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.

  7. 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

  8. Analysis of cancer cell lipids using matrix-assisted laser desorption/ionization 15-T Fourier transform ion cyclotron resonance mass spectrometry.

    PubMed

    Yang, Hyo-Jik; Park, Kyu Hwan; Lim, Dong Wan; Kim, Hyun Sik; Kim, Jeongkwon

    2012-03-30

    A combination of methodologies using the extremely high mass accuracy and resolution of 15-T Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS) was introduced for the identification of intact cancer cell phospholipids. Lipids from a malignant glioma cell line were initially analyzed at a resolution of >200,000 and identified by setting the mass tolerance to ±1 mDa using matrix-assisted laser desorption/ionization (MALDI) 15-T FT-ICR MS in positive ion mode. In most cases, a database search of potential lipid candidates using the exact masses of the lipids yielded only one possible chemical composition. Extremely high mass accuracy (<0.1 ppm) was then attained by using previously identified lipids as internal standards. This, combined with an extremely high resolution (>800,000), yielded well-resolved isotopic fine structures allowing for the identification of lipids by MALDI 15-T FT-ICR MS without using tandem mass spectrometric (MS/MS) analysis. Using this method, a total of 38 unique lipids were successfully identified.

  9. Petroleomic Analysis of Bio- Oils from the Fast Pyrolysis or Biomass: Laser Desorption Ionization-Linear Ion Trap-Orbitrap mass Spectrometry Approach

    SciTech Connect

    Smith, Erica A.; Lee, Young Jin

    2010-08-23

    Fast pyrolysis of biomass produces bio-oils that can be upgraded into biofuels. Despite similar physical properties to petroleum, the chemical properties of bio-oils are quite different and their chemical compositions, particularly those of non-volatile compounds, are not well-known. Here, we report the first time attempt at analyzing bio-oils using high-resolution mass spectrometry (MS), which employed laser desorption ionization-linear ion trap-Orbitrap MS. Besides a few limitations, we could determine chemical compositions for over 100 molecular compounds in a bio-oil sample produced from the pyrolysis of a loblolly pine tree. These compounds consist of 3-6 oxygens and 9-17 double-bond equivalents (DBEs). Among those, O{sub 4} compounds with a DBE of 9-13 were most abundant. Unlike petroleum oils, the lack of nearby molecules within a {+-}2 Da mass window for major components enabled clear isolation of precursor ions for subsequent MS/MS structural investigations. Petroleomic analysis and a comparison to low-mass components in hydrolytic lignin suggest that they are dimers and trimers of depolymerized lignin.

  10. Evidence for phosphorylation of serine 753 in CFTR using a novel metal-ion affinity resin and matrix-assisted laser desorption mass spectrometry.

    PubMed Central

    Neville, D. C.; Rozanas, C. R.; Price, E. M.; Gruis, D. B.; Verkman, A. S.; Townsend, R. R.

    1997-01-01

    The cystic fibrosis transmembrane conductance regulator (CFTR) gene encodes an apical membrane Cl- channel regulated by protein phosphorylation. To identify cAMP-dependent protein kinase (PKA)-phosphorylated residues in full-length CFTR, immobilized metal-ion affinity chromatography (IMAC) was used to selectively purify phosphopeptides. The greater specificity of iron-loaded (Fe3+) nitrilotriacetic (NTA). Sepharose compared to iminodiacetic acid (IDA) metal-chelating matrices was demonstrated using a PKA-phosphorylated recombinant NBD1-R protein from CFTR. Fe(3+)-loaded NTA Sepharose preferentially bound phosphopeptides, whereas acidic and poly-His-containing peptides were co-purified using the conventional IDA matrices. IMAC using NTA Sepharose enabled the selective recovery of phosphopeptides and identification of phosphorylated residues from a complex proteolytic digest. Phosphopeptides from PKA-phosphorylated full-length CFTR, generated in Hi5 insect cells using a baculovirus expression system, were purified using NTA Sepharose. Phosphopeptides were identified using matrix-assisted laser desorption mass spectrometry (MALDI/MS) with post-source decay (PSD) analysis and collision-induced dissociation (CID) experiments. Phosphorylated peptides were identified by mass and by the metastable loss of HPO3 and H3PO4 from the parent ions. Peptide sequence and phosphorylation at CFTR residues 660Ser, 737Ser, and 795Ser were confirmed using MALDI/PSD analysis. Peptide sequences and phosphorylation at CFTR residues 700Ser, 712Ser, 768Ser, and 813Ser were deduced from peptide mass, metastable fragment ion formation, and PKA consensus sequences. Peptide sequence and phosphorylation at residue 753Ser was confirmed using MALDI/CID analysis. This is the first report of phosphorylation of 753Ser in full-length CFTR. PMID:9385646

  11. 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 ...

  12. 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…

  13. 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.

  14. 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, ...

  15. 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 ...

  16. 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 ...

  17. 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

  18. 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.

  19. 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.

  20. Laser-induced liquid bead ion desorption-MS of protein complexes from blue-native gels, a sensitive top-down proteomic approach.

    PubMed

    Sokolova, Lucie; Wittig, Ilka; Barth, Hans-Dieter; Schägger, Hermann; Brutschy, Bernhard; Brandt, Ulrich

    2010-04-01

    We have developed an experimental approach that combines two powerful methods for proteomic analysis of large membrane protein complexes: blue native electrophoresis (BNE or BN-PAGE) and laser-induced liquid bead ion desorption (LILBID) MS. Protein complexes were separated by BNE and eluted from the gel. The masses of the constituents of the multiprotein complexes were obtained by LILBID MS, a detergent-tolerant method that is especially suitable for the characterisation of membrane proteins. High sensitivity and small sample volumes required for LILBID MS resulted in low demands on sample quantity. Eluate from a single band allowed assessing the mass of an entire multiprotein complex and its subunits. The method was validated with mitochondrial NADH:ubiquinone reductase from Yarrowia lipolytica. For this complex of 947 kDa, typically 30 microg or 32 pmol were sufficient to obtain spectra from which the subunit composition could be analysed. The resolution of this electrophoretic small-scale approach to the purification of native complexes was improved markedly by further separation on a second dimension of BNE. Starting from a subcellular fraction obtained by differential centrifugation, this allowed the purification and analysis of the constituents of a large multiprotein complex in a single LILBID spectrum.

  1. Activation processes and polyethylene formation on a phillips model catalyst studied by laser ablation, laser desorption, and static secondary ion mass spectrometry.

    PubMed

    Aubriet, Frédéric; Muller, Jean-François; Poleunis, Claude; Bertrand, Patrick; Di Croce, Pascal G; Grange, Paul

    2006-03-01

    Since the discovery of the Phillips catalysts, there still is much uncertainty concerning their activation, their molecular structure, the nature of the active chromium sites, and the polymerization mechanisms. Surface techniques are not easy to be used for such study according to the nonconductive behavior of the support. Therefore, model Phillips catalyst is elaborated by spin coating a trivalent chromium precursor on a silicon wafer. The surface characterization of this model catalyst is conducted by laser ablation mass spectrometry (LA-MS), laser desorption/ionization mass spectrometry (LDI-MS), and static secondary ion mass spectrometry (s-SIMS), at different steps of its preparation. To validate our approach, a comparison is also made between the model and the real Philips catalyst. Moreover, the model catalyst efficiency for polyethylene synthesis is evaluated and allows us to discuss the validity of the mechanisms previously proposed to explain the catalytic process. The characterization of Phillips model catalyst by mass spectrometry allows us to better understand the activation processes of such catalyst. Depending on the activation temperature, chromium oxide species are formed and anchored at the support surface. They consist mainly in mono-chromium sites at high temperature. The chromium valence is hexavalent. This model catalyst is active for the polymerization of ethylene. A pseudo-oligomer molecular weight distribution is observed by LA-MS, whereas s-SIMS allows us to elucidate the anchorage of the polymer at activate chromium surface sites.

  2. 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.

  3. 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

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. MoS2/Ag nanohybrid: A novel matrix with synergistic effect for small molecule drugs analysis by negative-ion matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

    PubMed

    Zhao, Yaju; Deng, Guoqing; Liu, Xiaohui; Sun, Liang; Li, Hui; Cheng, Quan; Xi, Kai; Xu, Danke

    2016-09-21

    This paper reports a facile synthesis of molybdenum disulfide nanosheets/silver nanoparticles (MoS2/Ag) hybrid and its use as an effective matrix in negative ion matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The nanohybrid exerts a strong synergistic effect, leading to high performance detection of small molecule analytes including amino acids, peptides, fatty acids and drugs. The enhancement of laser desorption/ionization (LDI) efficiency is largely attributed to the high surface roughness and large surface area for analyte adsorption, better dispersibility, increased thermal conductivity and enhanced UV energy absorption as compared to pure MoS2. Moreover, both Ag nanoparticles and the edge of the MoS2 layers function as deprotonation sites for proton capture, facilitating the charging process in negative ion mode and promoting formation of negative ions. As a result, the MoS2/Ag nanohybrid proves to be a highly attractive matrix in MALDI-TOF MS, with desired features such as high desorption/ionization efficiency, low fragmentation interference, high salt tolerance, and no sweet-spots for mass signal. These characteristic properties allowed for simultaneous analysis of eight different drugs and quantification of acetylsalicylic acid in the spiked human serum. This work demonstrates for the first time the fabrication and application of a novel MoS2/Ag hybrid, and provides a new platform for use in the rapid and high throughput analysis of small molecules by mass spectrometry.

  13. Desorption and ionization mechanisms in desorption atmospheric pressure photoionization.

    PubMed

    Luosujärvi, Laura; Arvola, Ville; Haapala, Markus; Pól, Jaroslav; Saarela, Ville; Franssila, Sami; Kotiaho, Tapio; Kostiainen, Risto; Kauppila, Tiina J

    2008-10-01

    The factors influencing desorption and ionization in newly developed desorption atmospheric pressure photoionization-mass spectrometry (DAPPI-MS) were studied. Redirecting the DAPPI spray was observed to further improve the versatility of the technique: for dilute samples, parallel spray with increased analyte signal was found to be the best suited, while for more concentrated samples, the orthogonal spray with less risk for contamination is recommended. The suitability of various spray solvents and sampling surface materials was tested for a variety of analytes with different polarities and molecular weights. As in atmospheric pressure photoionization, the analytes formed [M + H](+), [M - H](-), M(+*), M(-*), [M - H + O](-), or [M - 2H + 2O](-) ions depending on the analyte, spray solvent, and ionization mode. In positive ion mode, anisole and toluene as spray solvents promoted the formation of M(+*) ions and were therefore best suited for the analysis of nonpolar compounds (anthracene, benzo[a]pyrene, and tetracyclone). Acetone and hexane were optimal spray solvents for polar compounds (MDMA, testosterone, and verapamil) since they produced intensive [M + H](+) ion peaks of the analytes. In negative ion mode, the type of spray solvent affected the signal intensity, but not the ion composition. M(-*) ions were formed from 1,4-dinitrobenzene, and [M - H + O](-) and [M - 2H + 2O](-) ions from 1,4-naphthoquinone, whereas acidic compounds (naphthoic acid and paracetamol) formed [M - H](-) ions. The tested sampling surfaces included various materials with different thermal conductivities. The materials with low thermal conductivity, i.e., polymers like poly(methyl methacrylate) and poly(tetrafluoroethylene) (Teflon) were found to be the best, since they enable localized heating of the sampling surface, which was found to be essential for efficient analyte desorption. Nevertheless, the sampling surface material did not affect the ionization mechanisms.

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. Characterization of silver ions adsorbed on gold nanorods: surface analysis by using surface-assisted laser desorption/ionization time-of-flight mass spectrometry.

    PubMed

    Niidome, Yasuro; Nakamura, Yuki; Honda, Kanako; Akiyama, Yasuyuki; Nishioka, Koji; Kawasaki, Hideya; Nakashima, Naotoshi

    2009-04-07

    Surface-assisted laser desorption/ionization time-of-flight mass spectrometry (SALDI-MS) indicated AgBr2-, which adsorbed on gold nanorod surfaces, was a key material to control the anisotropic growth of gold nanorods.

  1. Rapid Profiling of Bovine and Human Milk Gangliosides by Matrix-Assisted Laser Desorption/Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

    PubMed Central

    Lee, Hyeyoung; An, Hyun Joo; Lerno, Larry A.; German, J. Bruce; Lebrilla, Carlito B.

    2010-01-01

    Gangliosides are anionic glycosphingolipids widely distributed in vertebrate tissues and fluids. Their structural and quantitative expression patterns depend on phylogeny and are distinct down to the species level. In milk, gangliosides are exclusively associated with the milk fat globule membrane. They may participate in diverse biological processes but more specifically to host-pathogen interactions. However, due to the molecular complexities, the analysis needs extensive sample preparation, chromatographic separation, and even chemical reaction, which makes the process very complex and time-consuming. Here, we describe a rapid profiling method for bovine and human milk gangliosides employing matrix-assisted desorption/ionization (MALDI) Fourier transform ion cyclotron resonance (FTICR) mass spectrometry (MS). Prior to the analyses of biological samples, milk ganglioside standards GM3 and GD3 fractions were first analyzed in order to validate this method. High mass accuracy and high resolution obtained from MALDI FTICR MS allow for the confident assignment of chain length and degree of unsaturation of the ceramide. For the structural elucidation, tandem mass spectrometry (MS/MS), specifically as collision-induced dissociation (CID) and infrared multiphoton dissociation (IRMPD) were employed. Complex ganglioside mixtures from bovine and human milk were further analyzed with this method. The samples were prepared by two consecutive chloroform/methanol extraction and solid phase extraction. We observed a number of differences between bovine milk and human milk. The common gangliosides in bovine and human milk are NeuAc-NeuAc-Hex-Hex-Cer (GD3) and NeuAc-Hex-Hex-Cer (GM3); whereas, the ion intensities of ganglioside species are different between two milk samples. Kendrick mass defect plot yields grouping of ganglioside peaks according to their structural similarities. Gangliosides were further probed by tandem MS to confirm the compositional and structural assignments

  2. Tandem time-of-flight mass spectrometer for photodissociation of biopolymer ions generated by matrix-assisted laser desorption ionization (MALDI-TOF-PD-TOF) using a linear-plus-quadratic potential reflectron.

    PubMed

    Oh, Joo Yeon; Moon, Jeong Hee; Kim, Myung Soo

    2004-08-01

    A tandem time-of-flight mass spectrometer for the study of photodissociation of biopolymer ions generated by matrix-assisted laser desorption ionization was designed and constructed. A reflectron with linear and quadratic (LPQ) potential components was used. Characteristics of the LPQ reflectron and its utility as the second stage analyzer of the tandem mass spectrometer were investigated. Performance of the instrument was tested by observing photodissociation of [M + H](+) from angiotensin II, a prototype polypeptide. Quality of the photodissociation tandem mass spectrum was almost comparable to that of the post-source decay spectrum. Monoisotopic selection of the parent ion was possible, which was achieved through the ion beam-laser beam synchronization. General theoretical considerations needed for a successful photodissociation of large biopolymer ions are also presented.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. Experimental Investigations of the Internal Energy of Molecules Evaporated via Laser-induced Acoustic Desorption into a Fourier-transform Ion Cyclotron Resonance Mass Spectrometer (LIAD/FT-ICR)

    PubMed Central

    Shea, Ryan C.; Petzold, Christopher J.; Liu, Ji-ang; Kenttämaa, Hilkka I.

    2008-01-01

    The internal energy of neutral gas-phase organic and biomolecules, evaporated by means of laser-induced acoustic desorption (LIAD) into a Fourier-transform ion cyclotron resonance mass spectrometer (FT-ICR), was investigated through several experimental approaches. The desorbed molecules were demonstrated not to undergo degradation during the desorption process by collecting LIAD-evaporated molecules and subjecting them to analysis by electrospray ionization/quadrupole ion trap mass spectrometry. Previously established gas-phase basicity (GB) values were remeasured for LIAD-evaporated organic molecules and biomolecules with the use of the bracketing method. No endothermic reactions were observed. The remeasured basicity values are in close agreement with the values reported in the literature. The amount of internal energy deposited during LIAD is concluded to be less than a few kcal/mol. Chemical ionization with a series of proton transfer reagents was employed to obtain a breakdown curve for a protonated dipeptide, val-pro, evaporated by LIAD. Comparison of this breakdown curve with a previously published analogous curve obtained by using substrate-assisted laser desorption (SALD) to evaporate the peptide suggests that the molecules evaporated via LIAD have less internal energy than those evaporated via SALD. PMID:17263513

  11. Analysis of the site-specific carbon isotope composition of propane by gas source isotope ratio mass spectrometer

    NASA Astrophysics Data System (ADS)

    Piasecki, Alison; Sessions, Alex; Lawson, Michael; Ferreira, A. A.; Neto, E. V. Santos; Eiler, John M.

    2016-09-01

    Site-specific isotope ratio measurements potentially provide valuable information about the formation and degradation of complex molecules-information that is lost in conventional bulk isotopic measurements. Here we discuss the background and possible applications of such measurements, and present a technique for studying the site-specific carbon isotope composition of propane at natural abundance based on mass spectrometric analysis of the intact propane molecule and its fragment ions. We demonstrate the feasibility of this approach through measurements of mixtures of natural propane and propane synthesized with site-specific 13C enrichment, and we document the limits of precision of our technique. We show that mass balance calculations of the bulk δ13C of propane based on our site-specific measurements is generally consistent with independent constraints on bulk δ13C. We further demonstrate the accuracy of the technique, and illustrate one of its simpler applications by documenting the site-specific carbon isotope signature associated with gas phase diffusion of propane, confirming that our measurements conform to the predictions of the kinetic theory of gases. This method can be applied to propane samples of moderate size (tens of micromoles) isolated from natural gases. Thus, it provides a means of studying the site-specific stable isotope systematics of propane at natural isotope abundances on sample sizes that are readily recovered from many natural environments. This method may also serve as a model for future techniques that apply high-resolution mass spectrometry to study the site-specific isotopic distributions of larger organic molecules, with potential applications to biosynthesis, forensics and other geochemical subjects.

  12. Structure and Composition of Air-Plane Soots and Surrogates Analyzed by Raman Spectroscopy and Laser/Ions Desorption Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Ortega, Ismael; Chazallon, Bertrand; Carpentier, Yvain; Irimiea, Cornelia; Focsa, Cristian; Ouf, François-Xavier; Salm, François; Delhaye, David; Gaffié, Daniel; Yon, Jérôme

    2015-04-01

    Aviation alters the composition of the atmosphere globally and can thus drive climate change and ozone depletion [1]. An aircraft exhaust plume contains species emitted by the engines, species formed in the plume from the emitted species and atmospheric species that become entrained into the plume. The majority of emitted species (gases and soot particles) are produced by the combustion of kerosene with ambient air in the combustion chamber of the engine. Emissions of soot particles by air-planes produce persistent contrails in the upper troposphere in ice-supersaturated air masses that contribute to cloudiness and impact the radiative properties of the atmosphere. These aerosol-cloud interactions represent one of the largest sources of uncertainty in global climate models [2]. Though the formation of atmospheric ice particles has been studied since many years [3], there are still numerous opened questions on nucleation properties of soot particles [4], as the ice nucleation experiments showed a large spread in results depending on the nucleation mode chosen and origin of the soot produced. Most likely one of the reasons behind these discrepancies resides in the different physico-chemical properties (composition, structure) of soot particles produced in different conditions, e.g. with respect to fuel or combustion techniques. In this work, we use Raman microscopy (266, 514 and 785 nm excitation) and ablation techniques (SIMS, Secondary Ions Mass Spectrometry, and Laser Desorption Mass Spectrometry) to characterize soot particles produced from air-plane at different engine regimes simulating a landing and taking-off (LTO) cycle. First, the spectral parameters of the first-order Raman band of various soot samples, collected from three different sources in the frame of the MERMOSE project (http://mermose.onera.fr/): PowerJet SaM-146 turbofan (four engine regimes), CAST generator (propane fuel, four different global equivalence ratios), and Kerosene laboratory flame

  13. 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

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. 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

  20. 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.

  1. Evaluation of a novel approach for peptide sequencing: laser-induced acoustic desorption combined with P(OCH(3))(2)(+) chemical ionization and collision-activated dissociation in a Fourier transform ion cyclotron resonance mass spectrometer.

    PubMed

    Somuramasami, Jayalakshmi; Kenttämaa, Hilkka I

    2007-03-01

    A novel mass spectrometric method has been developed for obtaining sequence information on small peptides. The peptides are desorbed as intact neutral molecules into a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR) by means of laser-induced acoustic desorption (LIAD). Reactions of the neutral peptides with the dimethoxyphosphenium ion, P(OCH(3))(2)(+), occur predominantly by addition of the peptide to P(OCH(3))(2)(+) followed by the loss of two methanol molecules, thus yielding product ions with the composition (peptide + P - 2H)(+). Upon sustained off-resonance irradiation for collision-activated dissociation (SORI-CAD), the (peptide + P - 2H)(+) ions undergo successive losses of CO and NHCHR or H(2)O, CO, and NHCHR to yield sequence-related fragment ions in addition to the regular a(n)- and b(n)-type ions. Under the same conditions, SORI-CAD of the analogous protonated peptides predominantly yields the regular a(n)- and b(n)-type ions. The mechanisms of the reactions of peptides with P(OCH(3))(2)(+) and the dissociation of the (peptide + P - 2H)(+) ions were examined by using model peptides and molecular orbital calculations.

  2. Evaluation of a Novel Approach for Peptide Sequencing: Laser-induced Acoustic Desorption Combined with P(OCH3)2+ Chemical Ionization and Collision-activated Dissociation in a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer

    PubMed Central

    Somuramasami, Jayalakshmi; Kenttämaa, Hilkka I.

    2007-01-01

    A novel mass spectrometric method has been developed for obtaining sequence information on small peptides. The peptides are desorbed as intact neutral molecules into a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR) by means of laser-induced acoustic desorption (LIAD). Reactions of the neutral peptides with the dimethoxyphosphenium ion, P(OCH3)2+, occur predominantly by addition of the peptide to P(OCH3)2+ followed by the loss of two methanol molecules, thus yielding product ions with the composition (peptide + P − 2H)+. Upon sustained off-resonance irradiation for collision-activated dissociation (SORI-CAD), the (peptide + P − 2H)+ ions undergo successive losses of CO and NH = CHR or H2O, CO, and NH = CHR to yield sequence-related fragment ions in addition to the regular an- and bn-type ions. Under the same conditions, SORI-CAD of the analogous protonated peptides predominantly yields the regular an- and bn-type ions. The mechanisms of the reactions of peptides with P(OCH3)2+ and the dissociation of the (peptide + P − 2H)+ ions were examined by using model peptides and molecular orbital calculations. PMID:17157527

  3. 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.

  4. Development of ultralow energy (1-10 eV) ion scattering spectrometry coupled with reflection absorption infrared spectroscopy and temperature programmed desorption for the investigation of molecular solids.

    PubMed

    Bag, Soumabha; Bhuin, Radha Gobinda; Methikkalam, Rabin Rajan J; Pradeep, T; Kephart, Luke; Walker, Jeff; Kuchta, Kevin; Martin, Dave; Wei, Jian

    2014-01-01

    Extremely surface specific information, limited to the first atomic layer of molecular surfaces, is essential to understand the chemistry and physics in upper atmospheric and interstellar environments. Ultra low energy ion scattering in the 1-10 eV window with mass selected ions can reveal extremely surface specific information which when coupled with reflection absorption infrared (RAIR) and temperature programmed desorption (TPD) spectroscopies, diverse chemical and physical properties of molecular species at surfaces could be derived. These experiments have to be performed at cryogenic temperatures and at ultra high vacuum conditions without the possibility of collisions of neutrals and background deposition in view of the poor ion intensities and consequent need for longer exposure times. Here we combine a highly optimized low energy ion optical system designed for such studies coupled with RAIR and TPD and its initial characterization. Despite the ultralow collision energies and long ion path lengths employed, the ion intensities at 1 eV have been significant to collect a scattered ion spectrum of 1000 counts/s for mass selected CH2(+).

  5. Development of ultralow energy (1–10 eV) ion scattering spectrometry coupled with reflection absorption infrared spectroscopy and temperature programmed desorption for the investigation of molecular solids

    SciTech Connect

    Bag, Soumabha; Bhuin, Radha Gobinda; Methikkalam, Rabin Rajan J.; Pradeep, T.; Kephart, Luke; Walker, Jeff; Kuchta, Kevin; Martin, Dave; Wei, Jian

    2014-01-15

    Extremely surface specific information, limited to the first atomic layer of molecular surfaces, is essential to understand the chemistry and physics in upper atmospheric and interstellar environments. Ultra low energy ion scattering in the 1–10 eV window with mass selected ions can reveal extremely surface specific information which when coupled with reflection absorption infrared (RAIR) and temperature programmed desorption (TPD) spectroscopies, diverse chemical and physical properties of molecular species at surfaces could be derived. These experiments have to be performed at cryogenic temperatures and at ultra high vacuum conditions without the possibility of collisions of neutrals and background deposition in view of the poor ion intensities and consequent need for longer exposure times. Here we combine a highly optimized low energy ion optical system designed for such studies coupled with RAIR and TPD and its initial characterization. Despite the ultralow collision energies and long ion path lengths employed, the ion intensities at 1 eV have been significant to collect a scattered ion spectrum of 1000 counts/s for mass selected CH{sub 2}{sup +}.

  6. 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

  7. Stir-bar sorptive extraction and thermal desorption-ion mobility spectrometry for the determination of trinitrotoluene and l,3,5-trinitro-l,3,5-triazine in water samples.

    PubMed

    Lokhnauth, John K; Snow, Nicholas H

    2006-02-10

    Stir-bar sorptive extraction (SBSE) is interfaced to ion mobility spectrometry (IMS) for the rapid detection of trace analytes, with the explosives, trinitrotoluene (TNT) and l,3,5-trinitro-l,3,5-triazine (RDX) shown as examples. SBSE retains its inherent advantages as a sensitive, straightforward, solventless, and inexpensive method. Additionally, the new SBSE-IMS technique exhibits excellent sensitivity, has onsite field analysis capabilities and provides the potential to detect and quantitate analytes that are difficult to accomplish using gas chromatography (GC) or high-performance liquid chromatography (HPLC). The SBSE-IMS technique is shown to be an effective method for the low-level detection of TNT and RDX from water with method standard deviation of 8.6% for TNT and 6.6% for RDX. The short desorption time of 60 s and analysis time of less than 20 ms along with limits of detection of 0.1 ng/mL for TNT and 1.5 ng/mL for RDX and render the method potentially useful for trace analysis. Desorption profiles showing the kinetics of analyte transfer from the stir-bar into the IMS are shown and discussed; the SBSE-IMS configuration shows very rapid desorption from the stir-bar, with the analytes completely transferred in most cases, in under 1 min.

  8. Direct analysis of the products of sequential cleavages of peptides and proteins affinity-bound to immobilized metal ion beads by matrix-assisted laser desorption/ionization mass spectrometry.

    PubMed

    Qian, X; Zhou, W; Khaledi, M G; Tomer, K B

    1999-10-15

    Consecutive enzymatic reactions on analytes affinity-bound to immobilized metal ion beads with subsequent direct analysis of the products by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry have been used for detecting protein synthesis errors occuring at the N-terminus. The usefulness of this method was demonstrated by analyzing two commercially available recombinant HIV proteins with affinity tags at the N-terminus, and histatin-5, a peptide with multiple histidine residues. The high specificity, sensitivity, and speed of analysis make this method especially useful in obtaining N-terminal sequencing information of histidine-tagged recombinant proteins.

  9. 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

  10. 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.

  11. 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

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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

  19. 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

  20. 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.

  1. 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

  2. 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

  3. 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.

  4. 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.

  5. Ionic Adsorption and Desorption of CNT Nanoropes

    PubMed Central

    Shang, Jun-Jun; Yang, Qing-Sheng; Yan, Xiao-Hui; He, Xiao-Qiao; Liew, Kim-Meow

    2016-01-01

    A nanorope is comprised of several carbon nanotubes (CNTs) with different chiralities. A molecular dynamic model is built to investigate the ionic adsorption and desorption of the CNT nanoropes. The charge distribution on the nanorope is obtained by using a modified gradient method based on classical electrostatic theory. The electrostatic interactions among charged carbon atoms are calculated by using the Coulomb law. It was found here that the charged nanorope can adsorb heavy metal ions, and the adsorption and desorption can be realized by controlling the strength of applied electric field. The distance between the ions and the nanorope as well as the amount of ions have an effect on the adsorption capacity of the nanorope. The desorption process takes less time than that of adsorption. The study indicates that the CNT nanorope can be used as a core element of devices for sewage treatment. PMID:28335306

  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. On two site-specific nitrite-sensing nanocomposites having a core-shell structure: Construction, characterization and sensing performance

    NASA Astrophysics Data System (ADS)

    Kadeerhazi, Muhetaer; Ali, Azam; Bekhit, Alaa El-Din

    2017-01-01

    This paper reported two site-specific nitrite-sensing nanocomposite samples having a core-shell structure, where Fe3O4 nanoparticles were used as core, two rhodamine derivatives served as chemosensor and MCM-41 was applied as supporting host, respectively. These composite samples and their structure were analyzed and confirmed SEM/TEM, XRD, N2 adsorption/desorption, magnetic feature, IR and thermogravimetric analysis. Their nitrite sensing performance was discussed based on emission quenching, with limit of detection as low as 1.2 μM. Detailed analysis suggested that these composite samples followed a static sensing mechanism based on an additive reaction between NO+ and chemosensors. After being quenched by nitrite, these samples could be recovered by sulphamic acid.

  9. 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.

  10. Site-Specific Antagonists to Tetrodotoxin and Saxitoxin

    DTIC Science & Technology

    2016-05-10

    site is probably a pocket in the sodium -channel protein 9.5 A wide, 6 A tall, and 5 A deep, containing one ion-pairing and 4 hydrogen-bonding sites...common to both TTX and STX. There are 1 or 2 sites unique to either toxin. If glutamate 387 of rat brain sodium channel were taken as the anionic site...the specific chemical structures of the tetrodotoxin (TTX)/saxitoxin (STX) binding site on the voltage-gated sodium channel protein. It is hoped that

  11. Light-stimulated cargo release from a core–shell structured nanocomposite for site-specific delivery

    SciTech Connect

    Cai, Yun; Ling, Li; Li, Xiaofang; Chen, Meng; Su, Likai

    2015-03-15

    This paper reported a core–shell structured site-specific delivery system with a light switch triggered by low energy light (λ=510 nm). Its core was composed of supermagnetic Fe{sub 3}O{sub 4} nanoparticles for magnetic guiding and targeting. Its outer shell consisted of mesoporous silica molecular sieve MCM-41 which offered highly ordered hexagonal tunnels for cargo capacity. A light switch N1-(4aH-cyclopenta[1,2-b:5,4-b′]dipyridin-5(5aH)-ylidene)benzene-1, 4-diamine (CBD) was covalently grafted into these hexagonal tunnels, serving as light stimuli acceptor with loading content of 1.1 μM/g. This composite was fully characterized and confirmed by SEM, TEM, XRD patterns, N{sub 2} adsorption/desorption, thermogravimetric analysis, IR, UV–vis absorption and emission spectra. Experimental data suggested that this composite had a core as wide as 150 nm and could be magnetically guided to specific sites. Its hexagonal tunnels were as long as 180 nm. Upon light stimuli of “on” and “off” states, controllable release was observed with short release time of ~900 s (90% capacity). - Graphical abstract: A core–shell structured site-specific delivery system with a light switch triggered by yellow light was constructed. Controllable release was observed with short release time of ~900 s (90% capacity). - Highlights: • A core–shell structured site-specific delivery system was constructed. • It consisted of Fe{sub 3}O{sub 4} core and MCM-41 shell grafted with light switch. • This delivery system was triggered by low energy light. • Controllable release was observed with short release time of ~900 s.

  12. Ultraviolet laser desorption/ionization mass spectrometry of single-core and multi-core polyaromatic hydrocarbons under variable conditions of collisional cooling: insights into the generation of molecular ions, fragments and oligomers.

    PubMed

    Gámez, Francisco; Hortal, Ana R; Martínez-Haya, Bruno; Soltwisch, Jens; Dreisewerd, Klaus

    2014-11-01

    The ultraviolet laser desorption/ionization of polyaromatic hydrocarbons (PAHs) has been investigated under different background pressures of an inert gas (up to 1.2 mbar of N2) in the ion source of a hybrid, orthogonal-extracting time-of-flight mass spectrometer (oTOF-MS). The study includes an ensemble of six model PAHs with isolated single polyaromatic cores and four ones with multiple cross-linked aromatic and polyaromatic cores. In combination with a weak ion extraction field, the variation of the buffer gas pressure allowed to control the degree of collisional cooling of the desorbed PAHs and, thus, to modulate their decomposition into fragments. The dominant fragmentation channels observed are related to dehydrogenation of the PAHs, in most cases through the cleavage of even numbers of C-H bonds. Breakage of C-C bonds leading to the fragmentation of rings, side chains and core linkages is also observed, in particular, at low buffer gas pressures. The precise patterns of the combined fragmentation processes vary significantly between the PAHs. The highest abundances of molecular PAH ions and cleanest mass spectra were consistently obtained at the highest buffer gas pressure of 1.2 mbar. The effective quenching of the fragmentation pathways at this elevated pressure improves the sensitivity and data interpretation for analytical applications, although the fragmentation of side chains and of bonds between (poly)aromatic cores is not completely suppressed in all cases. Moreover, these results suggest that the detected fragments are generated through thermal equilibrium processes rather than as a result of rapid photolysis. This assumption is further corroborated by a laser desorption/ionization post-source decay analysis using an axial time-of-flight MS. In line with these findings, covalent oligomers of the PAHs, which are presumably formed by association of two or more dehydrogenated fragments, are detected with higher abundances at the lower buffer gas

  13. Laser desorption from a room temperature ionic liquid

    NASA Astrophysics Data System (ADS)

    Harris, Peter Ronald

    We report laser desorption from a Room Temperature Ionic Liquid (RTIL) as a novel source for time of flight mass spectrometry. We use the 2nd harmonic of an Nd:YAG laser to deposit intensities of 1-50 MW/cm2 via backside illumination onto our RTIL desorption sample. A microstructured metal grid situated on top of a glass microscope slide coated with RTIL serves as our desorption sample. The RTIL we use, 1-Butyl, 3-Methylimidazolium Hexafluorophosphate, remains liquid at pressures below 10-8 torr. The use of liquid desorption sample allows for improved surface conditions, homogeneity and sample life as compared to Matrix Assisted Laser Desorption Ionization (MALDI) techniques. Our desorption technique is also unique as it allows the study of both multiphoton and acoustic desorption processes within the same time of flight spectra. Our technique yields intrinsically high resolution, low noise data. We observe differences between ion species in their preference for desorption by a particular desorption method. Specifically, we observe desorption solely by acoustic means of an entire RTIL molecule adducted with an RTIL cation. Finally, we report the applicability of this technique for the desorption of biomolecules.

  14. Desorption in Mass Spectrometry.

    PubMed

    Usmanov, Dilshadbek Tursunbayevich; Ninomiya, Satoshi; Chen, Lee Chuin; Saha, Subhrakanti; Mandal, Mridul Kanti; Sakai, Yuji; Takaishi, Rio; Habib, Ahsan; Hiraoka, Kenzo; Yoshimura, Kentaro; Takeda, Sen; Wada, Hiroshi; Nonami, Hiroshi

    2017-01-01

    In mass spectrometry, analytes must be released in the gas phase. There are two representative methods for the gasification of the condensed samples, i.e., ablation and desorption. While ablation is based on the explosion induced by the energy accumulated in the condensed matrix, desorption is a single molecular process taking place on the surface. In this paper, desorption methods for mass spectrometry developed in our laboratory: flash heating/rapid cooling, Leidenfrost phenomenon-assisted thermal desorption (LPTD), solid/solid friction, liquid/solid friction, electrospray droplet impact (EDI) ionization/desorption, and probe electrospray ionization (PESI), will be described. All the methods are concerned with the surface and interface phenomena. The concept of how to desorb less-volatility compounds from the surface will be discussed.

  15. Desorption in Mass Spectrometry

    PubMed Central

    Usmanov, Dilshadbek Tursunbayevich; Ninomiya, Satoshi; Chen, Lee Chuin; Saha, Subhrakanti; Mandal, Mridul Kanti; Sakai, Yuji; Takaishi, Rio; Habib, Ahsan; Hiraoka, Kenzo; Yoshimura, Kentaro; Takeda, Sen; Wada, Hiroshi; Nonami, Hiroshi

    2017-01-01

    In mass spectrometry, analytes must be released in the gas phase. There are two representative methods for the gasification of the condensed samples, i.e., ablation and desorption. While ablation is based on the explosion induced by the energy accumulated in the condensed matrix, desorption is a single molecular process taking place on the surface. In this paper, desorption methods for mass spectrometry developed in our laboratory: flash heating/rapid cooling, Leidenfrost phenomenon-assisted thermal desorption (LPTD), solid/solid friction, liquid/solid friction, electrospray droplet impact (EDI) ionization/desorption, and probe electrospray ionization (PESI), will be described. All the methods are concerned with the surface and interface phenomena. The concept of how to desorb less-volatility compounds from the surface will be discussed. PMID:28337398

  16. Aminoglycoside antibiotics: A-site specific binding to 16S

    NASA Astrophysics Data System (ADS)

    Baker, Erin Shammel; Dupuis, Nicholas F.; Bowers, Michael T.

    2009-06-01

    The A-site of 16S rRNA, which is a part of the 30S ribosomal subunit involved in prokaryotic translation, is a well known aminoglycoside binding site. Full characterization of the conformational changes undergone at the A-site upon aminoglycoside binding is essential for development of future RNA/drug complexes; however, the massiveness of 16S makes this very difficult. Recently, studies have found that a 27 base RNA construct (16S27) that comprises the A-site subdomain of 16S behaves similarly to the whole A-site domain. ESI-MS, ion mobility and molecular dynamics methods were utilized in this study to analyze the A-site of 16S27 before and after the addition of ribostamycin (R), paromomycin (P) and lividomycin (L). The ESI mass spectrum for 16S27 alone illustrated both single-stranded 16S27 and double-stranded (16S27)2 complexes. Upon aminoglycoside addition, the mass spectra showed that only one aminoglycoside binds to 16S27, while either one or two bind to (16S27)2. Ion mobility measurements and molecular dynamics calculations were utilized in determining the solvent-free structures of the 16S27 and (16S27)2 complexes. These studies found 16S27 in a hairpin conformation while (16S27)2 existed as a cruciform. Only one aminoglycoside binds to the single A-site of the 16S27 hairpin and this attachment compresses the hairpin. Since two A-sites exist for the (16S27)2 cruciform, either one or two aminoglycosides may bind. The aminoglycosides compress the A-sites causing the cruciform with just one aminoglycoside bound to be larger than the cruciform with two bound. Non-specific binding was not observed in any of the aminoglycoside/16S27 complexes.

  17. Stable isotope, site-specific mass tagging for protein identification

    DOEpatents

    Chen, Xian

    2006-10-24

    Proteolytic peptide mass mapping as measured by mass spectrometry provides an important method for the identification of proteins, which are usually identified by matching the measured and calculated m/z values of the proteolytic peptides. A unique identification is, however, heavily dependent upon the mass accuracy and sequence coverage of the fragment ions generated by peptide ionization. The present invention describes a method for increasing the specificity, accuracy and efficiency of the assignments of particular proteolytic peptides and consequent protein identification, by the incorporation of selected amino acid residue(s) enriched with stable isotope(s) into the protein sequence without the need for ultrahigh instrumental accuracy. Selected amino acid(s) are labeled with .sup.13C/.sup.15N/.sup.2H and incorporated into proteins in a sequence-specific manner during cell culturing. Each of these labeled amino acids carries a defined mass change encoded in its monoisotopic distribution pattern. Through their characteristic patterns, the peptides with mass tag(s) can then be readily distinguished from other peptides in mass spectra. The present method of identifying unique proteins can also be extended to protein complexes and will significantly increase data search specificity, efficiency and accuracy for protein identifications.

  18. Field desorption of Na and Cs from graphene on iridium

    NASA Astrophysics Data System (ADS)

    Bernatskii, D. P.; Pavlov, V. G.

    2015-08-01

    Field electron and desorption microscopy has been used to study specific features of the field desorption of sodium and cesium ions adsorbed on the surface of iridium with graphene. It was found that adsorbed sodium atoms most strongly reduce the work function on graphene islands situated over densely packed faces of iridium. A strong electric field qualitatively similarly affects the sodium and cesium desorption processes from a field emitter to give two desorption phases and has no noticeable effect on the disintegration of the graphene layer.

  19. Site-specific semisynthetic variant of human hemoglobin

    SciTech Connect

    Hefta, S.A.; Lyle, S.B.; Busch, M.R.; Harris, D.E.; Matthew, J.B.; Gurd, F.R.N.

    1988-02-01

    A single round of Edman degradation was employed to remove the NH/sub 2/-terminal valine from isolated ..cap alpha.. chains of human hemoglobin. Reconstitution of normal ..beta.. chains with truncated or substituted ..cap alpha.. chains was used to form truncated (des-Val/sup 1/-..cap alpha..1) and substituted (((1-/sup 13/C)Gly/sup 1/)..cap alpha..1) tetrameric hemoglobin analogs. Structural homology of the analogs with untreated native hemoglobin was established by using several spectroscopic and physical methods. Functional studies indicate that the reconstituted tetrameric protein containing des-Val/sup 1/-..cap alpha.. chains has a higher affinity for oxygen, is less influenced by chloride ions or 2,3-biphosphoglycerate, and shows lower cooperativity than native hemoglobin. These results confirm the key functional role of the ..cap alpha..-chain NH/sub 2/ terminus in mediating cooperative oxygen binding across the dimer interface. The NH/sub 2/-terminal pK/sub 1/2/ value was determined for the (/sup 13/C)glycine-substituted analog to be 7.46 +/- 0.09 at 15/sup 0/C in the carbon monoxide-liganded form. This value, measured directly by /sup 13/C NMR, agrees with the determination made by the less-direct /sup 13/CO/sub 2/ method and confirms the role of this residue as a contributor to the alkaline Bohr effect; however, it is consistent with the presence of an NH/sub 2/-terminal salt bridge to the carboxylate of Arg-141 of the ..cap alpha.. chain in the liganded form.

  20. Initial velocities of positive and negative protein molecule-ions produced in matrix-assisted ultraviolet laser desorption using a liquid matrix

    NASA Astrophysics Data System (ADS)

    Dominic Chan, T.-W.; Thomas, Ioan; Colburn, A. W.; Derrick, Peter J.

    1994-06-01

    The initial axial velocities for the positive and negative cytochrome c molecule-ions desorbed from a liquid matrix (3-nitro-benzyl alcohol) using a 17 ns ultraviolet laser (266 nm) have been determined. The method employed was based upon measurement of ion flight times through a field-free path co-axial with the ion optical axis. The possible interferences, such as energy deficits, due to the presence of electric fields were avoided by using a grid-electrode placed at a very short distance from the sample stage. The potential of this electrode was maintained at the same potential as the sample stage, thereby creating a narrow field-free region within which ion generation took place. Systematic variations of the potential at a second grid-electrode caused a gradual shift of the ion flight times, which could be related to the initial ion velocities. The ion velocities were obtained by correlating the measured time-shifts with values from theoretical analysis. The positive and negative molecule-ions were found to have axial velocities of 840±70 and 750±40 ms -1, respectively.

  1. 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

  2. In situ site-specific specimen preparation for atom probe tomography.

    PubMed

    Thompson, K; Lawrence, D; Larson, D J; Olson, J D; Kelly, T F; Gorman, B

    2007-01-01

    Techniques for the rapid preparation of atom-probe samples extracted directly from a Si wafer are presented and discussed. A systematic mounting process to a standardized microtip array allows approximately 12 samples to be extracted from a near-surface region and mounted for subsequent focused-ion-beam sharpening in a short period of time, about 2h. In addition, site-specific annular mill extraction techniques are demonstrated that allow specific devices or structures to be removed from a Si wafer and analyzed in the atom-probe. The challenges presented by Ga-induced implantation and damage, particularly at a standard ion-beam accelerating voltage of 30 keV, are shown and discussed. A significant reduction in the extent of the damaged regions through the application of a low-energy "clean-up" ion beam is confirmed by atom-probe analysis of the damaged regions. The Ga+ penetration depth into {100} Si at 30 keV is approximately 40 nm. Clean-up with either a 5 or 2 keV beam reduces the depth of damaged Si to approximately 5 nm and <1 nm, respectively. Finally, a NiSi sample was extracted from a Si wafer, mounted to a microtip array, sharpened, cleaned up with a 5 keV beam and analyzed in the atom probe. The current results demonstrate that specific regions of interest can be accessed and preserved throughout the sample-preparation process and that this preparation method leads to high-quality atom probe analysis of such nano-structures.

  3. 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

  4. 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...

  5. 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...

  6. 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...

  7. 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...

  8. 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...

  9. 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...

  10. 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...

  11. 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...

  12. 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...

  13. 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,...

  14. 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,...

  15. 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...

  16. 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...

  17. 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....

  18. 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...

  19. 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...

  20. 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....

  1. 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...

  2. 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...

  3. 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...

  4. 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...

  5. 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...

  6. 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,...

  7. 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...

  8. 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,...

  9. 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...

  10. 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...

  11. 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...

  12. 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...

  13. 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...

  14. 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...

  15. 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...

  16. 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...

  17. 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...

  18. 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...

  19. 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...

  20. 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...

  1. 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...

  2. 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)...

  3. 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,...

  4. 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...

  5. 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...

  6. 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...

  7. 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...

  8. 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....

  9. 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...

  10. 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...

  11. 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...

  12. 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...

  13. 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...

  14. 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...

  15. 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...

  16. 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...

  17. 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...

  18. 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....

  19. 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...

  20. 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,...

  1. 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...

  2. 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...

  3. 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....

  4. 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...

  5. 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...

  6. 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...

  7. 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...

  8. 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:...

  9. 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:...

  10. 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...

  11. Site-Specific Ser/Thr/Tyr Phosphoproteome of Sinorhizobium meliloti at Stationary Phase.

    PubMed

    Liu, Tao; Tian, Chang Fu; Chen, Wen Xin

    2015-01-01

    Sinorhizobium meliloti, a facultative microsymbiont of alfalfa, should fine-tune its cellular processes to live saprophytically in soils characterized with limited nutrients and diverse stresses. In this study, TiO2 enrichment and LC-MS/MS were used to uncover the site-specific Ser/Thr/Tyr phosphoproteome of S. meliloti in minimum medium at stationary phase. There are a total of 96 unique phosphorylated sites, with a Ser/Thr/Tyr distribution of 63:28:5, in 77 proteins. Phosphoproteins identified in S. meliloti showed a wide distribution pattern regarding to functional categories, such as replication, transcription, translation, posttranslational modification, transport and metabolism of amino acids, carbohydrate, inorganic ion, succinoglycan etc. Ser/Thr/Tyr phosphosites identified within the conserved motif in proteins of key cellular function indicate a crucial role of phosphorylation in modulating cellular physiology. Moreover, phosphorylation in proteins involved in processes related to rhizobial adaptation was also discussed, such as those identified in SMa0114 and PhaP2 (polyhydroxybutyrate synthesis), ActR (pH stress and microaerobic adaption), SupA (potassium stress), chaperonin GroEL2 (viability and potentially symbiosis), and ExoP (succinoglycan synthesis and secretion). These Ser/Thr/Tyr phosphosites identified herein would be helpful for our further investigation and understanding of the role of phosphorylation in rhizobial physiology.

  12. Amorphous Semiconductor Nanowires Created by Site-Specific Heteroatom Substitution with Significantly Enhanced Photoelectrochemical Performance.

    PubMed

    He, Ting; Zu, Lianhai; Zhang, Yan; Mao, Chengliang; Xu, Xiaoxiang; Yang, Jinhu; Yang, Shihe

    2016-08-23

    Semiconductor nanowires that have been extensively studied are typically in a crystalline phase. Much less studied are amorphous semiconductor nanowires due to the difficulty for their synthesis, despite a set of characteristics desirable for photoelectric devices, such as higher surface area, higher surface activity, and higher light harvesting. In this work of combined experiment and computation, taking Zn2GeO4 (ZGO) as an example, we propose a site-specific heteroatom substitution strategy through a solution-phase ions-alternative-deposition route to prepare amorphous/crystalline Si-incorporated ZGO nanowires with tunable band structures. The substitution of Si atoms for the Zn or Ge atoms distorts the bonding network to a different extent, leading to the formation of amorphous Zn1.7Si0.3GeO4 (ZSGO) or crystalline Zn2(GeO4)0.88(SiO4)0.12 (ZGSO) nanowires, respectively, with different bandgaps. The amorphous ZSGO nanowire arrays exhibit significantly enhanced performance in photoelectrochemical water splitting, such as higher and more stable photocurrent, and faster photoresponse and recovery, relative to crystalline ZGSO and ZGO nanowires in this work, as well as ZGO photocatalysts reported previously. The remarkable performance highlights the advantages of the ZSGO amorphous nanowires for photoelectric devices, such as higher light harvesting capability, faster charge separation, lower charge recombination, and higher surface catalytic activity.

  13. Conformational effects on cationization of poly(ethylene glycol) by alkali metal ions in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

    NASA Astrophysics Data System (ADS)

    Shimada, Kayori; Matsuyama, Shigetomo; Saito, Takeshi; Kinugasa, Shinichi; Nagahata, Ritsuko; Kawabata, Shin-Ichirou

    2005-12-01

    Conformational effects of polymer chains on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) were studied by using an equimolar mixture of uniform poly(ethylene glycol)s (PEGs) and by molecular dynamics simulations. Uniform PEGs with degrees of polymerization n = 8-39 were separated from commercial PEG samples by preparative supercritical fluid chromatography. MALDI-TOFMS spectra of an equimolar mixture of the uniform PEGs in aqueous ethanol were measured by adding a mixture of 2,5-dihydroxybenzoic acid (as a matrix reagent) and five alkali metal chlorides (LiCl, NaCl, KCl, RbCl, and CsCl). After optimization of the matrix concentration and laser power, five types of adduct cationized by Li+, Na+, K+, Rb+, and Cs+ could be identified simultaneously in the same spectrum. In the lower molecular-mass region around 103, the spectral intensity increase rapidly with increasing molecular mass of PEG; this rapid increase in the spectral intensity started at a lower molecular mass for smaller adduct cations. Molecular dynamics simulations were used to calculated the affinity of PEG for the adduct cations. These experimental and simulated results showed that the observed spectral intensities in MALDI-TOFMS were markedly affected by the species of adduct cations and the degree of polymerization of the PEG, and that they were dependent on the stability of the PEG-cation complex.

  14. Characterization of gallotannins from Astronium species by flow injection analysis- electrospray ionization-ion trap-tandem mass spectrometry and matrix-assisted laser desorption/ionization time-of- flight mass spectrometry.

    PubMed

    da Silva, Viviane Cândida; Napolitano, Assunta; Eletto, Daniela; Rodrigues, Clenilson Martins; Pizza, Cosimo; Vilegas, Wagner

    2011-01-01

    The species Astronium urundeuva (Allemao) Engl. and Astronium graveolens Jacq., which are used in Brazilian folk medicine to treat allergies, inflammation, diarrhea and ulcers, were investigated for their composition. The aim of this study was to define a rapid and reliable analytical approach, based on the flow-injection analysis-electrospray ionization-ion trap-tandem mass spectrometry (FIA-ESI-IT-MS-MS) and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-ToF-MS), to investigate the full range of hydrolyzable tannins present in the extracts of these Astronium species. The MALDI-ToF-MS analysis allowed us to ascertain the presence of hydrolysable tannins in both Astronium species as a series of gallotannins with degrees of polymerization of 7 to 13 galloyl units. Moreover, the analysis by FIA-ESI-IT-MS-MS, as well as confirming this result and chemically defining gallotannins as galloylglucose compounds, highlighted the presence of further classes of hydrolysable tannins, such as hexahydrodiphenoyl esters of glucose and some gallic acid derivatives, providing information about their structure by a careful study of their fragmentation patterns. Finally, the evaluation of the number of positional isomers of gallotannins occurring in both Astronium species was obtained by high-performance liquid chromatography-electrospray ionization-ion trap mass spectrometry (HPLC/ESI-IT-MS). This is the first mass spectrometric evidence relating to the existence of gallotannins in Astronium genus.

  15. On-chip solid-phase extraction pre-concentration/focusing substrates coupled to atmospheric pressure matrix-assisted laser desorption/ionization ion trap mass spectrometry for high sensitivity biomolecule analysis.

    PubMed

    Navare, Arti; Nouzova, Marcela; Noriega, Fernando G; Hernández-Martínez, Salvador; Menzel, Christoph; Fernández, Facundo M

    2009-02-01

    Atmospheric pressure matrix-assisted laser desorption/ionization (AP-MALDI) has proven a convenient and rapid method for ion production in the mass spectrometric (MS) analysis of biomolecules. AP-MALDI and electrospray ionization (ESI) sources are easily interchangeable in most mass spectrometers. However, AP-MALDI suffers from less-than-optimal sensitivity due to ion losses during transport from the atmosphere into the vacuum of the mass spectrometer. Here, we study the signal-to-noise ratio (S/N) gains observed when an on-chip dynamic pre-concentration/focusing approach is coupled to AP-MALDI for the MS analysis of neuropeptides and protein digests. It was found that, in comparison with conventional AP-MALDI targets, focusing targets showed (1) a sensitivity enhancement of approximately two orders of magnitude with S/N gains of 200-900 for hydrophobic substrates, and 150-400 for weak cation-exchange (WCX) substrates; (2) improved detection limits as low as 5 fmol/microL for standard peptides; (3) significantly reduced matrix background; and (4) higher inter-day reproducibility. The improved sensitivity allowed successful tandem mass spectrometric (MS/MS) sequencing of dilute solutions of a derivatized tryptic digest of a protein standard, and enabled the first reported AP-MALDI MS detection of neuropeptides from Aedes aegypti mosquito heads.

  16. Sample metallization for performance improvement in desorption/ionization of kilodalton molecules: quantitative evaluation, imaging secondary ion MS, and laser ablation.

    PubMed

    Delcorte, A; Bour, J; Aubriet, F; Muller, J-F; Bertrand, P

    2003-12-15

    The metallization procedure, proposed recently for signal improvement in organic secondary ion mass spectrometry (SIMS) (Delcorte, A.; Médard, N.; Bertrand, P. Anal.Chem. 2002, 74, 4955)., has been thoroughly tested for a set of kilodalton molecules bearing various functional groups: Irganox 1010, polystyrene, polyalanine, and copper phthalocyanine. In addition to gold, we evaluate the effect of silver evaporation as a sample treatment prior to static SIMS analysis. Ion yields, damage cross sections, and emission efficiencies are compared for Ag- and Au-metallized molecular films, pristine coatings on silicon, and submonolayers of the same molecules adsorbed on silver and gold. The results are sample-dependent but as an example, the yield enhancement calculated for metallized Irganox films with respect to untreated coatings is larger than 2 orders of magnitude for the quasimolecular ion and a factor of 1-10 for characteristic fragments. Insights into the emission processes of quasimolecular ions from metallized surfaces are deduced from kinetic energy distribution measurements. The advantage of the method for imaging SIMS applications is illustrated by the study of a nonuniform coating of polystyrene oligomers on a 100-microm polypropylene film. The evaporated metal eliminates sample charging and allows us to obtain enhanced quality images of characteristic fragment ions as well as reasonably contrasted chemical mappings for cationized PS oligomers and large PP chain segments. Finally, we report on the benefit of using metal evaporation as a sample preparation procedure for laser ablation mass spectrometry. Our results show that the fingerprint spectra of Au-covered polystyrene, polypropylene, and Irganox films can be readily obtained under 337-nm irradiation, a wavelength for which the absorption of polyolefins is low. This is probably because the gold clusters embedded in the sample surface absorb and transfer the photon energy to the surrounding organic medium.

  17. 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.

  18. 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.

  19. Metabolomic profiling of prostate cancer by matrix assisted laser desorption/ionization-Fourier transform ion cyclotron resonance mass spectrometry imaging using Matrix Coating Assisted by an Electric Field (MCAEF).

    PubMed

    Wang, Xiaodong; Han, Jun; Hardie, Darryl B; Yang, Juncong; Pan, Jingxi; Borchers, Christoph H

    2016-12-23

    In this work, we combined the use of two MALDI matrices (quercetin and 9-aminoacridine), a recently developed new matrix coating technique - matrix coating assisted by an electric field (MCAEF), and matrix-assisted laser desorption/ionization - Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FTICRMS) to detect and image endogenous compounds in the cancerous and non-cancerous regions of three human prostate cancer (stage II) tissue specimens. After three rounds of imaging data acquisitions (i.e., quercetin for positive and negative ion detection and 9-aminoacridine for negative ion detection), and metabolite identification, a total of 1091 metabolites including 1032 lipids and 59 other metabolites were routinely detected and successfully localized. Of these compounds, 250 and 217 were only detected in either the cancerous or the non-cancerous regions respectively, although we cannot rule out the presence of these metabolites at concentrations below the detection limit. In addition, 152 of the other 624 metabolites showed differential distributions (p<0.05, t-test) between the two regions of the tissues. Further studies on a larger number of clinical specimens will need to be carried out to confirm this large number of apparently cancer-related metabolites. The successful determination of the spatial locations and abundances of these endogenous biomolecules indicated significant metabolism abnormalities - e.g., increased energy charge and under-expression of neutral acyl glycerides, in the prostate cancer samples. To our knowledge, this work has resulted in MALDI-MS imaging of the largest group of metabolites in prostate cancer thus far and demonstrated the importance of using complementary matrices for comprehensive metabolomic imaging by MALDI-MS. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.

  20. 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. ...

  1. 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...

  2. 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...

  3. 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...

  4. 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...

  5. 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...

  6. 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...

  7. 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...

  8. 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)....

  9. 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...

  10. 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. ...

  11. 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...

  12. 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...

  13. Light-stimulated cargo release from a core-shell structured nanocomposite for site-specific delivery

    NASA Astrophysics Data System (ADS)

    Cai, Yun; Ling, Li; Li, Xiaofang; Chen, Meng; Su, Likai

    2015-03-01

    This paper reported a core-shell structured site-specific delivery system with a light switch triggered by low energy light (λ=510 nm). Its core was composed of supermagnetic Fe3O4 nanoparticles for magnetic guiding and targeting. Its outer shell consisted of mesoporous silica molecular sieve MCM-41 which offered highly ordered hexagonal tunnels for cargo capacity. A light switch N1-(4aH-cyclopenta[1,2-b:5,4-b‧]dipyridin-5(5aH)-ylidene)benzene-1,4-diamine (CBD) was covalently grafted into these hexagonal tunnels, serving as light stimuli acceptor with loading content of 1.1 μM/g. This composite was fully characterized and confirmed by SEM, TEM, XRD patterns, N2 adsorption/desorption, thermogravimetric analysis, IR, UV-vis absorption and emission spectra. Experimental data suggested that this composite had a core as wide as 150 nm and could be magnetically guided to specific sites. Its hexagonal tunnels were as long as 180 nm. Upon light stimuli of "on" and "off" states, controllable release was observed with short release time of ~900 s (90% capacity).

  14. Near-Atomic Three-Dimensional Mapping for Site-Specific Chemistry of 'Superbugs'.

    PubMed

    Adineh, Vahid R; Marceau, Ross K W; Velkov, Tony; Li, Jian; Fu, Jing

    2016-11-09

    Emergence of multidrug resistant Gram-negative bacteria has caused a global health crisis and last-line class of antibiotics such as polymyxins are increasingly used. The chemical composition at the cell surface plays a key role in antibiotic resistance. Unlike imaging the cellular ultrastructure with well-developed electron microscopy, the acquisition of a high-resolution chemical map of the bacterial surface still remains a technological challenge. In this study, we developed an atom probe tomography (APT) analysis approach to acquire mass spectra in the pulsed-voltage mode and reconstructed the 3D chemical distribution of atoms and molecules in the subcellular domain at the near-atomic scale. Using focused ion beam (FIB) milling together with micromanipulation, site-specific samples were retrieved from a single cell of Acinetobacter baumannii prepared as needle-shaped tips with end radii less than 60 nm, followed by a nanoscale coating of silver in the order of 10 nm. The significantly elevated conductivity provided by the metallic coating enabled successful and routine field evaporation of the biological material, with all the benefits of pulsed-voltage APT. In parallel with conventional cryo-TEM imaging, our novel approach was applied to investigate polymyxin-susceptible and -resistant strains of A. baumannii after treatment of polymyxin B. Acquired atom probe mass spectra from the cell envelope revealed characteristic fragments of phosphocholine from the polymyxin-susceptible strain, but limited signals from this molecule were detected in the polymyxin-resistant strain. This study promises unprecedented capacity for 3D nanoscale imaging and chemical mapping of bacterial cells at the ultimate 3D spatial resolution using APT.

  15. Application and field test of a mobile thermal desorption - single photon ionization - ion trap mass spectrometer (TD-SPI-ITMS) for trace detection of security relevant substances

    NASA Astrophysics Data System (ADS)

    Schramm, Elisabeth; Heindl, Thomas; Hölzer, Jasper; McNeish, Alexander; Puetz, Michael; Ries, Hermann; Schall, Patricia; Schulte-Ladbeck, Rasmus; Schultze, Rainer; Sklorz, Martin; Spieker, Gerd; Trebbe, Roman; Ulrich, Andreas; Wieser, Jochen; Zimmermann, Ralf

    2009-05-01

    The objective of this accomplished project funded by the German BMBF was to develop a single photon ionization ion trap mass spectrometer (SPI-ITMS) for detection of security relevant substances in complex matrices at low concentrations. The advantage of such a soft ionization technique is a reduction of target ion fragmentation allowing identification of signals from complex matrices and enabling MS/MS capability. To obtain low detection limits, the applied photon energy has to be below the ionization potential (IP) of the bulk matrix components. Therefore, photon energies between 8 eV (155 nm) and 12 eV (103 nm) are necessary which was achieved with newly developed electron beam excimer lamps (EBEL). They generate light at different wavelengths depending on the selected rare gas emitting wavelengths adapted to the analyzed substances. So, e.g. with a krypton-EBEL with 8.4 eV photon energy most narcotics can be ionized without notable fragmentation. Due to their higher IPs, EBEL with higher photon energy have to be used for most explosives. Very low false-positive and false-negative rates have been achieved using MS/MS studies. First field tests of a demonstrator provided the proof of principle.

  16. Rapid identification of betacyanins from Amaranthus tricolor, Gomphrena globosa, and Hylocereus polyrhizus by matrix-assisted laser desorption/ionization quadrupole ion trap time-of-flight mass spectrometry (MALDI-QIT-TOF MS).

    PubMed

    Cai, Yi-Zhong; Xing, Jie; Sun, Mei; Corke, Harold

    2006-09-06

    Natural betacyanins have attracted great attention as food colorants and potential antioxidants. Matrix-assisted laser desorption/ionization quadrupole ion trap time-of-flight mass spectrometry (MALDI-QIT-TOF MS) is a new and powerful technique for the identification of low molecular weight compounds. This study is the first to employ MALDI-QIT-TOF MS to rapidly identify, within a few minutes, a great number of betacyanins in crude extracts from Amaranthus tricolor seedlings, Gomphrena globosa flowers, and Hylocereus polyrhizus fruits. The fresh crude extract samples without any purification were directly used for MALDI-QIT-TOF MS analysis with 2,5-dihydroxybenzoic acid as a matrix. The MS2 and MS3 spectrometric data acquired could provide important characteristic information for structural elucidation of the betacyanins. Fourteen free and acylated betacyanins, belonging to amaranthin-type, betanin-type, and gomphrenin-type betacyanins, respectively, were identified. However, the related isomers should be differentiated with the aid of HPLC.

  17. Thermal desorption of deuterium implanted into beryllium

    SciTech Connect

    Markin, A.V.; Chernikov, V.N.; Zakharov, A.P.

    1995-09-01

    By means of TDS measurements it is shown that the desorption of deuterium from Be implanted with 5 keV D ions to fluences, {Phi}, from 1x10{sup 20} D/m{sup 2} to 1x10{sup 21} D/m{sup 2} proceeds in one high temperature stage B, while at {Phi} {ge} 1.2x10{sup 21}D/m{sup 2} one more stage A is added. The desorption maximum A is narrow and consists of two peaks A{sub 1} and A{sub 2} at about 460 K and 490 K, respectively. Peak A{sub 1} is attributed to the desorption of deuterium from the walls of opened channels formed under D ion implantation. Peak {sub A}2 is a consequence of the opening of a part of closed bubbles/channels to the outer surface. The position of maximum B shifts noticeably and nonsteadily on the fluence in a range from 850 to 1050 K. The origin of this maximum is the liberation of D atoms bound at vacancy complexes discussed previously by Wampler. The dependence of Tm(B) on the fluence is governed by the interaction of freely migrating D atoms with partly opened or fully closed gas cavity arrangements which are created under temperature ramping, but differently in specimens implanted with D ions to different fluences.

  18. Towards monitoring real-time cellular response using an integrated microfluidics-matrix assisted laser desorption ionisation/nanoelectrospray ionisation-ion mobility-mass spectrometry platform.

    PubMed

    Enders, J R; Marasco, C C; Kole, A; Nguyen, B; Sevugarajan, S; Seale, K T; Wikswo, J P; McLean, J A

    2010-11-01

    The combination of microfluidic cell trapping devices with ion mobility-mass spectrometry offers the potential for elucidating in real time the dynamic responses of small populations of cells to paracrine signals, changes in metabolite levels and delivery of drugs and toxins. Preliminary experiments examining peptides in methanol and recording the interactions of yeast and Jurkat cells with their superfusate have identified instrumental set-up and control parameters and online desalting procedures. Numerous initial experiments demonstrate and validate this new instrumental platform. Future outlooks and potential applications are addressed, specifically how this instrumentation may be used for fully automated systems biology studies of the significantly interdependent, dynamic internal workings of cellular metabolic and signalling pathways.

  19. High-resolution and site-specific scanning spreading resistance microscopy and its applications to silicon devices

    SciTech Connect

    Zhang, L.; Koike, M.; Takeno, S.; Hara, K.

    2012-11-06

    Due to the continuous reduction of the critical dimensions of semiconductor devices, it becomes very important to know the two dimensional (2D) doping profile for improving device performance. Scanning spreading resistance microscopy (SSRM) performed in high vacuum is a powerful technique for quantitative 2D-doping profiling, with high spatial resolution and wide dynamic range of carrier concentration, as well as capability of site-specific analysis for accurate position. In this paper, we review SSRM applications to source/drain engineering in Si devices and their correlation with device characteristics by demonstrating several case studies. Direct observation of (110)/(100) CMOSFETs clarified significant differences between both pFETs and nFETs on (110) and (100) silicon substrates, revealing 2D channeling effect of boron ion implantation in pFETs; as well as silicidation impact on junction leakage-current characteristics in nFETs. Furthermore, our sample-preparation breakthrough enables site-specific SSRM characterization within 60 nm ultra thin samples and therefore failure analysis of real SRAM devices, demonstrating the high potential of SSRM technology for further device scaling and for failure analysis.

  20. Dephosphorylation of intact glycoprotein to greatly improve digestion efficiency coupled with matrix-assisted laser desorption/ionization-Fourier transform ion cyclotron resonance mass spectrometric analysis.

    PubMed

    Li, Fenjie; Wang, Xiaodong; Liu, Yujie; Liu, Hui; Li, Zhili

    2013-07-17

    Sialylation is essential for a variety of cellular functions. Herein, we used bovine fetuin with three potential N-linked glycosylation sites containing complex-type glycan structures, four potential O-linked glycosylation sites and six potential phosphorylation sites as a model compound to develop a highly-efficient digestion strategy for sialylated glycoproteins and efficient enrichment strategy for sialylated glycopeptides using titanium dioxide. The former according to the process of alkaline phosphatase digestion followed by tryptic digestion and then proteinase K digestion could greatly improve the enzymatic efficiency on fetuin, and the latter could obviously enhance the enrichment efficiency for multisialylated glycopeptides using phosphoric acid solution as elution buffer. The mass spectra of the enriched glycopeptides derived from fetuin reveal that several series of the ion clusters with mass difference of 291 Da correspond to the presence of multisialylated glycopeptides. In addition, the approach was applied to characterize the sialylated status of α2-macroglobulin and transferrin, respectively, from the sera of healthy subjects and sex- and age-matched patients with thyroid cancer, and their spectra indicate that the change in the amount of the glycoforms containing different number of sialic acid (SA) residues from one glycosylation site may be used to differentiate between healthy subjects and cancer cases.

  1. Identification of water-soluble heavy crude oil organic-acids, bases, and neutrals by electrospray ionization and field desorption ionization fourier transform ion cyclotron resonance mass spectrometry.

    PubMed

    Stanford, Lateefah A; Kim, Sunghwan; Klein, Geoffrey C; Smith, Donald F; Rodgers, Ryan P; Marshall, Alan G

    2007-04-15

    We identify water-soluble (23 degrees C) crude oil NSO nonvolatile acidic, basic, and neutral crude oil hydrocarbons by negative-ion ESI and continuous flow FD FT-ICR MS at an average mass resolving power, m/deltam50% = 550,000. Of the 7000+ singly charged acidic species identified in South American crude oil, surprisingly, many are water-soluble, and much more so in pure water than in seawater. The truncated m/z distributions for water-soluble components exhibit preferential molecular weight, size, and heteroatom class influences on hydrocarbon solubility. Acidic water-soluble heteroatomic classes detected at >1% relative abundance include O, O2, O3, O4, OS, O2S, O3S, O4S, NO2, NO3, and NO4. Parent oil class abundance does not directly relate to abundance in the water-soluble fraction. Acidic oxygen-containing classes are most prevalent in the water-solubles, whereas acidic nitrogen-containing species are least soluble. In contrast to acidic nitrogen-containing heteroatomic classes, basic nitrogen classes are water-soluble. Water-soluble heteroatomic basic classes detected at >1% relative abundance include N, NO, NO2, NS, NS2, NOS, NO2S, N2, N2O, N2O2, OS, O2S, and O2S2.

  2. 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.

  3. Characterization of Site-Specific N-Glycopeptide Isoforms of α-1-Acid Glycoprotein from an Interlaboratory Study Using LC-MS/MS.

    PubMed

    Lee, Ju Yeon; Lee, Hyun Kyoung; Park, Gun Wook; Hwang, Heeyoun; Jeong, Hoi Keun; Yun, Ki Na; Ji, Eun Sun; Kim, Kwang Hoe; Kim, Jun Seok; Kim, Jong Won; Yun, Sung Ho; Choi, Chi-Won; Kim, Seung Il; Lim, Jong-Sun; Jeong, Seul-Ki; Paik, Young-Ki; Lee, Soo-Youn; Park, Jisook; Kim, Su Yeon; Choi, Young-Jin; Kim, Yong-In; Seo, Jawon; Cho, Je-Yoel; Oh, Myoung Jin; Seo, Nari; An, Hyun Joo; Kim, Jin Young; Yoo, Jong Shin

    2016-12-02

    Glycoprotein conformations are complex and heterogeneous. Currently, site-specific characterization of glycopeptides is a challenge. We sought to establish an efficient method of N-glycoprotein characterization using mass spectrometry (MS). Using alpha-1-acid glycoprotein (AGP) as a model N-glycoprotein, we identified its tryptic N-glycopeptides and examined the data reproducibility in seven laboratories running different LC-MS/MS platforms. We used three test samples and one blind sample to evaluate instrument performance with entire sample preparation workflow. 165 site-specific N-glycopeptides representative of all N-glycosylation sites were identified from AGP 1 and AGP 2 isoforms. The glycopeptide fragmentations by collision-induced dissociation or higher-energy collisional dissociation (HCD) varied based on the MS analyzer. Orbitrap Elite identified the greatest number of AGP N-glycopeptides, followed by Triple TOF and Q-Exactive Plus. Reproducible generation of oxonium ions, glycan-cleaved glycopeptide fragment ions, and peptide backbone fragment ions was essential for successful identification. Laboratory proficiency affected the number of identified N-glycopeptides. The relative quantities of the 10 major N-glycopeptide isoforms of AGP detected in four laboratories were compared to assess reproducibility. Quantitative analysis showed that the coefficient of variation was <25% for all test samples. Our analytical protocol yielded identification and quantification of site-specific N-glycopeptide isoforms of AGP from control and disease plasma sample.

  4. Surface magnetic contribution in zinc ferrite thin films studied by element- and site-specific XMCD hysteresis-loops

    NASA Astrophysics Data System (ADS)

    Mendoza Zélis, P.; Pasquevich, G. A.; Salcedo Rodríguez, K. L.; Sánchez, F. H.; Rodríguez Torres, C. E.

    2016-12-01

    Element- and site-specific magnetic hysteresis-loops measurements on a zinc ferrite (ZnFe2O4) thin film were performed by X-ray magnetic circular dichroism. Results show that iron in octahedral and tetrahedral sites of spinel structure are coupled antiferromagnetically between them, and when magnetic field is applied the magnetic moment of the ion located at octahedral sites aligns along the field direction. The magnetic measurements reveal a distinctive response of the surface with in-plane anisotropy and an effective anisotropy constant value of 12.6 kJ/m3. This effective anisotropy is due to the combining effects of demagnetizing field and, volume and surface magnetic anisotropies KV =3.1 kJ/m3 and KS =16 μJ/m2.

  5. Beryllium Desorption from Sediments

    NASA Astrophysics Data System (ADS)

    Boschi, V.; Willenbring, J. K.

    2015-12-01

    Beryllium isotopes have provided a useful tool in the field of geochronology and geomorphology over the last 25 years. The amount of cosmogenic meteoric 10Be and native 9Be absorbed to soils often scales with the residence time and chemical weathering of sediments in a landscape, respectively. Thus, the concentrations in river sediment may be used to quantify the denudation of specific watersheds. When deposited in ocean sediment, these concentrations are thought to record the history of denudation on Earth over the last ~10 Ma. The use of both isotopes often relies on the premise of beryllium retention to sediment surfaces in order to preserve a landscape's erosion and weathering signature. Changes in setting, en route from the soil to fluvial system to the ocean, can cause beryllium desorption and may preclude some applications of the 10Be/9Be system. Four mechanisms were tested to determine the desorption potential of beryllium including a reduction in pH, an increase in ionic strength and complexation with soluble organic and inorganic species. These processes have the potential to mobilize beryllium into solution. For example, by both reducing the pH and increasing the ionic strength, competition for adsorption sites increases, potentially liberating beryllium from the sediment surface. In addition, organic and inorganic ligands can complex beryllium causing it to become mobilized. To determine which of these alterations influence beryllium desorption and to quantify the effect, we prepared separate solutions of beryllium bound to minerals and organic compounds and measured beryllium concentrations in solution before and after adjusting the pH, ionic strength, and changing inorganic and organic ligand concentrations. We conclude from our observations that overall, beryllium sorbed to organic compounds was more resistant to desorption relative to mineral-associated beryllium. Among the methods tested, a reduction in pH resulted in the greatest amount of

  6. 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.

  7. 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.

  8. 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...

  9. Site-specific carbon deposition for hierarchically ordered core/shell-structured graphitic carbon with remarkable electrochemical performance.

    PubMed

    Lv, Yingying; Wu, Zhangxiong; Qian, Xufang; Fang, Yin; Feng, Dan; Xia, Yongyao; Tu, Bo; Zhao, Dongyuan

    2013-10-01

    A fascinating core-shell-structured graphitic carbon material composed of ordered microporous core and uniform mesoporous shell is fabricated for the first time through a site-specific chemical vapor deposition process by using a nanozeolite@mesostructured silica composite molecular sieve as the template. The mesostructure-directing agent cetyltrimethylammonium bromide in the shell of the template can be either burned off or carbonized so that it is successfully utilized as a pore switch to turn the shell of the template "on" or "off" to allow selective carbon deposition. The preferred carbon deposition process can be performed only in the inner microporous zeolite cores or just within the outer mesoporous shells, resulting in a zeolite-like ordered microporous carbon or a hollow mesoporous carbon. Full carbon deposition in the template leads to the new core-shell-structured microporous@mesoporous carbon with a nanographene-constructed framework for fast electron transport, a microporous nanocore with large surface area for high-capacity storage of lithium ions, a mesoporous shell with highly opened mesopores as a transport layer for lithium ions and electron channels to access inner cores. The ordered micropores are protected by the mesoporous shell, avoiding pore blockage as the formation of solid electrolyte interphase layers. Such a unique core-shell-structured microporous@mesoporous carbon material represents a newly established lithium ion storage model, demonstrating high reversible energy storage, excellent rate capability, and long cyclic stability.

  10. Comparison of in-gel and on-membrane digestion methods at low to sub-pmol level for subsequent peptide and fragment-ion mass analysis using matrix-assisted laser-desorption/ionization mass spectrometry.

    PubMed

    Courchesne, P L; Luethy, R; Patterson, S D

    1997-01-01

    The success of the mass spectrometric-based approaches for the identification of gel-separated proteins relies upon recovery of peptides, without high levels of ionization-suppressing contaminants, in solvents compatible with the mass spectrometer being employed. We sought to determine whether in-gel or on-membrane digestion provided a significant advantage when low to sub-pmol quantities of gel-separated proteins were analyzed by matrix-assisted laser-desorption/ionization mass spectrometry (MALDI-MS) with respect to the number and size of released peptides. Serial dilutions of five standard proteins of M(r) 17,000 to 97,000 (from 16 pmol to 125 fmol) were electrophoresed and subjected to in-gel digestion (using a microcolumn clean-up protocol, Courchesne, P.L. and Patterson, S. D., BioTechniques, 1997, in press) or on-membrane digestion following blotting to the PVDF-based membranes, Immobilon-P and Immobilon-CD. Peptide maps were able to be obtained for all proteins at the detection limit of each method (Immobilon-P and Immobilon-CD, 0.5 pmol; and in-gel, 125 fmol), and searches of Swiss-Prot or a non-redundant database (> 193000 entries) successfully identified all of the proteins, except beta-casein. Fragment-ion spectra using a curved-field reflector MALDI-MS were obtained from more than one peptide per protein at loads down to 250 fmol (except beta-casein). Using the uninterpreted data, a search of the nonredundant database and a six-way translation of GenBank dbEST (> 2,208,000 entries total) was able to identify myoglobin, carbonic anhydrase II, and phosphorylase b.

  11. 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...

  12. 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...

  13. 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:...

  14. 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.

  15. 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 ...

  16. 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...

  17. 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...

  18. 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....

  19. 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...

  20. 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....

  1. 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....

  2. 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...

  3. 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...

  4. 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...

  5. 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 ...

  6. 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...

  7. 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.

  8. 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...

  9. 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...

  10. 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...

  11. 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...

  12. 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...

  13. 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:...

  14. 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,...

  15. 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,...

  16. 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...

  17. 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,...

  18. 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,...

  19. 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,...

  20. 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...

  1. 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...

  2. 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,...

  3. 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,...

  4. 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,...

  5. 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,...

  6. 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,...

  7. 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,...

  8. 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...

  9. 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...

  10. 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...

  11. 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,...

  12. 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...

  13. 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...

  14. 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,...

  15. 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,...

  16. 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,...

  17. 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,...

  18. 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,...

  19. 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)...

  20. 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...

  1. 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...

  2. 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....

  3. 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....

  4. 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...

  5. 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

  6. 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.

  7. 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...

  8. 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...

  9. 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...

  10. 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'...

  11. 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...

  12. 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 ...

  13. 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.

  14. 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.

  15. 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-...

  16. 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.

  17. 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 §...

  18. 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...

  19. 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...

  20. 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...

  1. 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...

  2. 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 ...

  3. 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...

  4. 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:...

  5. 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...

  6. 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....

  7. 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...

  8. 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...

  9. 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...

  10. 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...

  11. 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...

  12. 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...

  13. 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...

  14. 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...

  15. 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…

  16. 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...

  17. 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 ...

  18. 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...

  19. 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.

  20. 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...

  1. 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.

  2. 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....

  3. 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...

  4. 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....

  5. 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...

  6. 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....

  7. 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....

  8. 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....

  9. 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....

  10. 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....

  11. 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....

  12. 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....

  13. 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....

  14. 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...

  15. 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...

  16. 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)...

  17. 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...

  18. 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. ...

  19. 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)...

  20. 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)...

  1. 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...

  2. 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......

  3. 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,...

  4. 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...

  5. 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....

  6. 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:...

  7. 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,...

  8. 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...

  9. 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...

  10. 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.

  11. Site-specific DOTA/europium-labeling of recombinant human relaxin-3 for receptor-ligand interaction studies.

    PubMed

    Zhang, Wei-Jie; Luo, Xiao; Liu, Ya-Li; Shao, Xiao-Xia; Wade, John D; Bathgate, Ross A D; Guo, Zhan-Yun

    2012-08-01

    natural or designed ligands with these receptors. Using this site-specific labeling strategy, other functional probes, such as fluorescent dyes, biotin, or nanoparticles could also be introduced to the A-chain N-terminal of the recombinant human relaxin-3. Additionally, we improved the time-resolved fluorescence assay for the DOTA-bound europium ion which paves the way for the use of DOTA as a lanthanide chelator for protein and peptide labeling in future studies.

  12. Characteristic tandem mass spectral features under various collision chemistries for site-specific identification of protein S-glutathionylation.

    PubMed

    Chou, Chi-Chi; Chiang, Bing-Yu; Lin, Jason Ching-Yao; Pan, Kuan-Ting; Lin, Chun-Hung; Khoo, Kay-Hooi

    2015-01-01

    Protein S-glutathionylation is a reversible post-translational modification widely implicated in redox regulated biological functions. Conventional biochemical methods, however, often do not allow such a mixed disulfide modification to be reliably identified on specific cysteine residues or be distinguished from other related oxidized forms. To develop more efficient mass spectrometry (MS)-based analytical strategies for this purpose, we first investigated the MS/MS fragmentation pattern of S-glutathionylated peptides under various dissociation modes, including collision-induced dissociation (CID), higher-energy C-trap dissociation (HCD), and electron transfer dissociation (ETD), using synthetic peptides derived from protein tyrosine phosphatase as models. Our results indicate that a MALDI-based high energy CID MS/MS on a TOF/TOF affords the most distinctive spectral features that would facilitate rapid and unambiguous identification of site-specific S-glutathionylation. For more complex proteomic samples best tackled by LC-MS/MS approach, we demonstrate that HCD performed on an LTQ-Orbitrap hybrid instrument fairs better than trap-based CID and ETD in allowing more protein site-specific S-glutathionylation to be confidently identified by direct database searching of the generated MS/MS dataset using Mascot. Overall, HCD afforded more peptide sequence-informative fragment ions retaining the glutathionyl modification with less neutral losses of side chains to compromise scoring. In conjunction with our recently developed chemo-enzymatic tagging strategy, our nanoLC-HCD-MS/MS approach is sufficiently sensitive to identify endogenous S-glutathionylated peptides prepared from non-stressed cells. It is anticipated that future applications to global scale analysis of protein S-glutathionylation will benefit further from current advances in both speed and mass accuracy afforded by HCD MS/MS mode on the Orbitrap series.

  13. Characteristic Tandem Mass Spectral Features Under Various Collision Chemistries for Site-Specific Identification of Protein S-Glutathionylation

    NASA Astrophysics Data System (ADS)

    Chou, Chi-Chi; Chiang, Bing-Yu; Lin, Jason Ching-Yao; Pan, Kuan-Ting; Lin, Chun-Hung; Khoo, Kay-Hooi

    2015-01-01

    Protein S-glutathionylation is a reversible post-translational modification widely implicated in redox regulated biological functions. Conventional biochemical methods, however, often do not allow such a mixed disulfide modification to be reliably identified on specific cysteine residues or be distinguished from other related oxidized forms. To develop more efficient mass spectrometry (MS)-based analytical strategies for this purpose, we first investigated the MS/MS fragmentation pattern of S-glutathionylated peptides under various dissociation modes, including collision-induced dissociation (CID), higher-energy C-trap dissociation (HCD), and electron transfer dissociation (ETD), using synthetic peptides derived from protein tyrosine phosphatase as models. Our results indicate that a MALDI-based high energy CID MS/MS on a TOF/TOF affords the most distinctive spectral features that would facilitate rapid and unambiguous identification of site-specific S-glutathionylation. For more complex proteomic samples best tackled by LC-MS/MS approach, we demonstrate that HCD performed on an LTQ-Orbitrap hybrid instrument fairs better than trap-based CID and ETD in allowing more protein site-specific S-glutathionylation to be confidently identified by direct database searching of the generated MS/MS dataset using Mascot. Overall, HCD afforded more peptide sequence-informative fragment ions retaining the glutathionyl modification with less neutral losses of side chains to compromise scoring. In conjunction with our recently developed chemo-enzymatic tagging strategy, our nanoLC-HCD-MS/MS approach is sufficiently sensitive to identify endogenous S-glutathionylated peptides prepared from non-stressed cells. It is anticipated that future applications to global scale analysis of protein S-glutathionylation will benefit further from current advances in both speed and mass accuracy afforded by HCD MS/MS mode on the Orbitrap series.

  14. HYDROGEN AND ITS DESORPTION IN RHIC.

    SciTech Connect

    HSEUH,H.C.

    2002-11-11

    Hydrogen is the dominating gas specie in room temperature, ultrahigh vacuum systems of particle accelerators and storage rings, such as the Relativistic Heavy Ion Collider (RHIC) at Brookhaven. Rapid pressure increase of a few decades in hydrogen and other residual gases was observed during RHIC's recent high intensity gold and proton runs. The type and magnitude of the pressure increase were analyzed and compared with vacuum conditioning, beam intensity, number of bunches and bunch spacing. Most of these pressure increases were found to be consistent with those induced by beam loss and/or electron stimulated desorption from electron multipacting.

  15. Laser desorption and matrix-assisted laser desorption/ionization mass spectrometry of 29-kDa Au:SR cluster compounds.

    PubMed

    Schaaff, T Gregory

    2004-11-01

    Positive and negative ions generated by laser-based ionization methods from three gold:thiolate cluster compounds are mass analyzed by time-of-flight mass spectrometry. The three compounds have similar inorganic core masses ( approximately 29 kDa, approximately 145 Au atoms) but different n-alkanethiolate ligands associated with each cluster compound (Au:SR, R = butane, hexane, dodecane). Irradiation of neat films (laser desorption/ionization) and films generated by dilution of the cluster compounds in an organic acid matrix (matrix-assisted laser desorption/ionization) with a nitrogen laser (337 nm) produced distinct ion abundances that are relevant to different structural aspects of the cluster compound. Laser desorption/ionization of neat Au:SR compound films produces ions consistent with the inorganic core mass (i.e., devoid of original hydrocarbon content). Matrix-assisted laser desorption/ionization produces either ions with m/z values consistent with the core mass of the cluster compounds or ions with m/z values consistent with the approximate molecular weight of the cluster compounds, depending on ionization conditions. The ion abundances, and ionization conditions under which they are detected, provide insight into desorption/ionization processes for these unique cluster compounds as well as other analytes typically studied by matrix-assisted laser desorption/ionization.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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

  10. 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

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. 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.

  4. 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

  5. Thermal helium desorption behavior in advanced ferritic steels

    NASA Astrophysics Data System (ADS)

    Kimura, Akihiko; Sugano, R.; Matsushita, Y.; Ukai, S.

    2005-02-01

    Thermal helium desorption measurements were performed to investigate the difference in the helium trapping and accumulation behavior among a reduced activation ferritic (RAF) steel and oxide dispersion strengthening (ODS) steels after implantation of He+ ions at room temperature. Thermal helium desorption spectra (THDS) were obtained during annealing to 1200 °C at a heating rate of 1 °C/s. The THDS of the ODS steels are very similar to that of the RAF steel, except for the presence of the peak in the temperature range from 800 to 1000 °C, where the α γ transformation related helium desorption from the γ-phase is considered to occur in the 9Cr-ODS martensitic steels. The fraction of helium desorption becomes larger at higher temperatures, and this trend is increased with the amount of implanted helium. In the 9Cr-ODS steels, the fraction of helium desorption by bubble migration mechanism was smaller than that in the RAF steel. This suggests that the bubble formation was suppressed in the ODS steels. In the 12Cr-ODS steel, the fraction of helium desorption by bubble migration reached more than 90%, suggesting that the trapping capacity of martensite phase in the 9Cr-ODS steel is rather large.

  6. 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

  7. Net Mineralization Response to Fertilizer Application and Site-Specific Setting in a No-Till Dryland Wheat Agroecosystem in the Pacific Northwest (USA)

    NASA Astrophysics Data System (ADS)

    Bruner, Emily A.; Brown, David J.; Carpenter-Boggs, Lynn

    2015-04-01

    Application of nitrogen (N) fertilizers is pivotal to maintaining agricultural productivity. Nutrient management is typically guided by a combined assessment of crop yield requirements, residual soil inorganic N concentration, and predicted N supply from organic matter. However, laboratory assays employed to forecast mineralization potential do not reflect in situ processes occurring in soils, processes that can vary spatially within a field. Furthermore, fertilizer application alters biogeochemical cycles through a variety of mechanisms including priming effects and microbial community alterations. This study investigates in-situ ammonification/nitrification rates utilizing mineralization cores as part of a five-year Site-Specific Climate-Friendly Farming (SCF) project. In-depth accounting of nitrate and ammonium production and flux was possible via a six bag mixed-bed ion exchange resin system. Soil cores (7.5 cm diameter by 15 cm deep) were isolated from the surrounding soil by three resin bags sealed in the top and bottom of individual plastic cylinders. Fifteen locations were selected across a commercial direct-seed wheat field based on statistical clustering of primary and secondary topographic variables. In each location surface soil-resin cores were installed in fertilized and unfertilized plots immediately after spring planting and removed before harvest. In situ ammonification/nitrification rates will be analyzed as a function of both fertilizer application and site-specific environmental characteristics as determined from soil moisture monitoring, soil characterization, and crop analysis at each measurement location. This site-specific information on N transformations and availability can then be used to guide site-specific crop management.

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. Isolation and properties of the acid site-specific endonuclease from mature eggs of the sea urchin Strongylocentrotus intermedius

    SciTech Connect

    Sibirtsev, Yu.T.; Konechnyi, A.A.; Rasskazov, V.A.

    1986-01-10

    An acid site-specific endonuclease has been detected in mature sea urchin eggs and cells of embryos at early stages of differentiation. Fractionation with ammonium sulfate, followed by chromatography on columns with DEAE, phosphocellulose, and hydroxyapatite resulted in an 18,000-fold purification. The molecular weight of the enzyme was determined at approx. 29,000, the optimum pH 5.5. The activity of the enzyme does not depend on divalent metal ions, EDTA, ATP, and tRNA, but it is modulated to a substantial degree by NaCl. The maximum rate of cleavage of the DNA supercoil (form I) is observed at 100 mM NaCl. Increasing the NaCl concentration to 350 mM only slightly lowers the rate of cleavage of form I, yielding form II, but entirely suppresses the accumulation of form III. Restriction analysis of the products of enzymatic hydrolysis of Co1E1 and pBR322 DNA showed that at the early stages of hydrolysis the enzyme exhibits pronounced specificity for definite sites, the number of which is 12 for Co1 E1 DNA and 8 sites for pBR322 DNA.

  4. Quantitative site-specific analysis of protein glycosylation by LC-MS using different glycopeptide-enrichment strategies.

    PubMed

    Wohlgemuth, Jessica; Karas, Michael; Eichhorn, Thomas; Hendriks, Robertus; Andrecht, Sven

    2009-12-15

    A common technique for analysis of protein glycosylation is HPLC coupled to mass spectrometry (LC-MS). However, analysis is challenging due to a low abundance of glycopeptides in complex protein digests, microheterogeneity at the glycosylation site, ion suppression effects, and competition for ionization by coeluting peptides. Specific sample preparation is necessary for a comprehensive and site-specific glycosylation analysis by MS. In this study we qualitatively compared hydrophilic interaction chromatography (HILIC) and hydrazine chemistry for the enrichment of all N-linked glycopeptides and titanium dioxide for capturing sialylated glycopeptides from a complex peptide mixture. Bare silica, microcrystalline cellulose, amino-, amide- (TSKgel Amide-80), and sulfobetaine-(ZIC-HILIC) bonded phases were evaluated for HILIC enrichment. The experiments revealed that ZIC-HILIC and TSKgel Amide-80 are very specific for capturing glycopeptides under optimized conditions. Quantitative analysis of N-glycosidase F-released and 2-aminobenzamide-labeled glycans of a ZIC-HILIC-enriched monoclonal antibody demonstrated that glycopeptides could be enriched without bias for particular glycan structures and without significant losses. Sialylated glycopeptides could be efficiently enriched by titanium dioxide and in addition to HILIC both methods enable a comprehensive analysis of protein glycosylation by MS. Enrichment of N-linked glycopeptides by hydrazine chemistry resulted in lower peptide recovery using a more complex enrichment scheme.

  5. 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.

  6. 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

  7. 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

  8. 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.

  9. 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

  10. 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

  11. 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

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. Desorption of cesium from granite under various aqueous conditions.

    PubMed

    Wang, Tsing-Hai; Li, Ming-Hsu; Wei, Yuan-Yaw; Teng, Shi-Ping

    2010-12-01

    In this work the desorption of cesium ions from crushed granite in synthetic groundwater (GW) and seawater (SW) was investigated. Results were compared with those obtained in deionized water (DW) and in two kinds of extraction solutions, namely: MgCl(2) and NaOAc (sodium acetate). In general, the desorption rate of Cs from crushed granite increased proportionally with initial Cs loadings. Also, amounts of desorbed Cs ions followed the tendency in the order SW>GW>NaOAc approximately equal MgCl(2)>DW solutions. This indicated that the utilization of extraction reagents for ion exchange will underestimate the Cs desorption behavior. Fitting these experimental data by Langmuir model showed that these extraction reagents have reduced Cs uptake by more than 90%, while only less than 1% of adsorbed Cs ions are still observed in GW and SW solutions in comparison to those in DW. Further SEM/EDS mapping studies clearly demonstrate that these remaining adsorbed Cs ions are at the fracture areas of biotite.

  20. 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