Science.gov

Sample records for site specific flow

  1. Site-specific protein modification using immobilized sortase in batch and continuous-flow systems

    PubMed Central

    Witte, Martin D.; Wu, Tongfei; Guimaraes, Carla P.; Theile, Christopher S.; Blom, Annet E.M.; Ingram, Jessica R.; Li, Zeyang; Kundrat, Lenka; Goldberg, Shalom D.; Ploegh, Hidde L.

    2016-01-01

    Transpeptidation catalyzed by sortase A allows the preparation of proteins that are site-specifically and homogeneously modified with a wide variety of functional groups, such as fluorophores, PEG moieties, lipids, glycans, bioorthogonal reactive groups and affinity handles. This protocol describes immobilization of sortase A on a solid support (sepharose beads). Immobilization of sortase A simplifies downstream purification of a protein of interest after labeling of its N- or C- terminus. Small batch and larger scale continuous flow reactions require only a limited amount of enzyme. The immobilized enzyme can be reused for multiple cycles of protein modification reactions. The described protocol also works with a Ca2+-independent variant of sortase A with increased catalytic activity. This heptamutant variant of sortase A (7M) was generated by combining previously published mutations and this immobilized enzyme can used for the modification of calcium-senstive substrates or in instances where low temperatures are needed. Preparation of immobilized sortase A takes 1–2 days. Batch reactions take 3–12 hours and flow reactions proceed at 0.5 mL per hour, depending on the geometry of the reactor used. PMID:25719269

  2. Detection of Site-Specific Blood Flow Variation in Humans during Running by a Wearable Laser Doppler Flowmeter.

    PubMed

    Iwasaki, Wataru; Nogami, Hirofumi; Takeuchi, Satoshi; Furue, Masutaka; Higurashi, Eiji; Sawada, Renshi

    2015-01-01

    Wearable wireless physiological sensors are helpful for monitoring and maintaining human health. Blood flow contains abundant physiological information but it is hard to measure blood flow during exercise using conventional blood flowmeters because of their size, weight, and use of optic fibers. To resolve these disadvantages, we previously developed a micro integrated laser Doppler blood flowmeter using microelectromechanical systems technology. This micro blood flowmeter is wearable and capable of stable measurement signals even during movement. Therefore, we attempted to measure skin blood flow at the forehead, fingertip, and earlobe of seven young men while running as a pilot experiment to extend the utility of the micro blood flowmeter. We measured blood flow in each subject at velocities of 6, 8, and 10 km/h. We succeeded in obtaining stable measurements of blood flow, with few motion artifacts, using the micro blood flowmeter, and the pulse wave signal and motion artifacts were clearly separated by conducting frequency analysis. Furthermore, the results showed that the extent of the changes in blood flow depended on the intensity of exercise as well as previous work with an ergometer. Thus, we demonstrated the capability of this wearable blood flow sensor for measurement during exercise. PMID:26445047

  3. Detection of Site-Specific Blood Flow Variation in Humans during Running by a Wearable Laser Doppler Flowmeter

    PubMed Central

    Iwasaki, Wataru; Nogami, Hirofumi; Takeuchi, Satoshi; Furue, Masutaka; Higurashi, Eiji; Sawada, Renshi

    2015-01-01

    Wearable wireless physiological sensors are helpful for monitoring and maintaining human health. Blood flow contains abundant physiological information but it is hard to measure blood flow during exercise using conventional blood flowmeters because of their size, weight, and use of optic fibers. To resolve these disadvantages, we previously developed a micro integrated laser Doppler blood flowmeter using microelectromechanical systems technology. This micro blood flowmeter is wearable and capable of stable measurement signals even during movement. Therefore, we attempted to measure skin blood flow at the forehead, fingertip, and earlobe of seven young men while running as a pilot experiment to extend the utility of the micro blood flowmeter. We measured blood flow in each subject at velocities of 6, 8, and 10 km/h. We succeeded in obtaining stable measurements of blood flow, with few motion artifacts, using the micro blood flowmeter, and the pulse wave signal and motion artifacts were clearly separated by conducting frequency analysis. Furthermore, the results showed that the extent of the changes in blood flow depended on the intensity of exercise as well as previous work with an ergometer. Thus, we demonstrated the capability of this wearable blood flow sensor for measurement during exercise. PMID:26445047

  4. Detection of Site-Specific Blood Flow Variation in Humans during Running by a Wearable Laser Doppler Flowmeter.

    PubMed

    Iwasaki, Wataru; Nogami, Hirofumi; Takeuchi, Satoshi; Furue, Masutaka; Higurashi, Eiji; Sawada, Renshi

    2015-10-05

    Wearable wireless physiological sensors are helpful for monitoring and maintaining human health. Blood flow contains abundant physiological information but it is hard to measure blood flow during exercise using conventional blood flowmeters because of their size, weight, and use of optic fibers. To resolve these disadvantages, we previously developed a micro integrated laser Doppler blood flowmeter using microelectromechanical systems technology. This micro blood flowmeter is wearable and capable of stable measurement signals even during movement. Therefore, we attempted to measure skin blood flow at the forehead, fingertip, and earlobe of seven young men while running as a pilot experiment to extend the utility of the micro blood flowmeter. We measured blood flow in each subject at velocities of 6, 8, and 10 km/h. We succeeded in obtaining stable measurements of blood flow, with few motion artifacts, using the micro blood flowmeter, and the pulse wave signal and motion artifacts were clearly separated by conducting frequency analysis. Furthermore, the results showed that the extent of the changes in blood flow depended on the intensity of exercise as well as previous work with an ergometer. Thus, we demonstrated the capability of this wearable blood flow sensor for measurement during exercise.

  5. Hanford Site environmental management specification

    SciTech Connect

    Grygiel, M.L.

    1998-06-10

    The US Department of Energy, Richland Operations Office (RL) uses this Hanford Site Environmental Management Specification (Specification) to document top-level mission requirements and planning assumptions for the prime contractors involved in Hanford Site cleanup and infrastructure activities under the responsibility of the US Department of Energy, Office of Environmental Management. This Specification describes at a top level the activities, facilities, and infrastructure necessary to accomplish the cleanup of the Hanford Site and assigns this scope to Site contractors and their respective projects. This Specification also references the key National Environmental Policy Act of 1969 (NEPA), Comprehensive Environmental Response, Compensation, and Liability Act of 1980 (CERCLA), and safety documentation necessary to accurately describe the cleanup at a summary level. The information contained in this document reflects RL`s application of values, priorities, and critical success factors expressed by those involved with and affected by the Hanford Site project. The prime contractors and their projects develop complete baselines and work plans to implement this Specification. These lower-level documents and the data that support them, together with this Specification, represent the full set of requirements applicable to the contractors and their projects. Figure 1-1 shows the relationship of this Specification to the other basic Site documents. Similarly, the documents, orders, and laws referenced in this specification represent only the most salient sources of requirements. Current and contractual reference data contain a complete set of source documents.

  6. 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.

  7. Investigation of the Binding Interaction of Fatty Acids with Human G Protein-Coupled Receptor 40 Using a Site-Specific Fluorescence Probe by Flow Cytometry.

    PubMed

    Ren, Xiao-Min; Cao, Lin-Ying; Zhang, Jing; Qin, Wei-Ping; Yang, Yu; Wan, Bin; Guo, Liang-Hong

    2016-04-01

    Human G protein-coupled receptor 40 (hGPR40), with medium- and long-chain free fatty acids (FFAs) as its natural ligands, plays an important role in the enhancement of glucose-dependent insulin secretion. To date, information about the direct binding of FFAs to hGPR40 is very limited, and how carbon-chain length affects the activities of FFAs on hGPR40 is not yet understood. In this study, a fluorescein-fasiglifam analogue (F-TAK-875A) conjugate was designed and synthesized as a site-specific fluorescence probe to study the interaction of FFAs with hGPR40. hGPR40 was expressed in human embryonic kidney 293 cells and labeled with F-TAK-875A. By using flow cytometry, competitive binding of FFA and F-TAK-875A to hGPR40-expressed cells was measured. Binding affinities of 18 saturated FFAs, with carbon-chain lengths ranging from C6 to C23, were analyzed. The results showed that the binding potencies of FFAs to hGPR40 were dependent on carbon length. There was a positive correlation between length and binding potency for seven FFAs (C9-C15), with myristic acid (C15) showing the highest potency, 0.2% relative to TAK-875. For FFAs with a length of fewer than C9 or more than C15, they had very weak or no binding. Molecular docking results showed that the binding pocket of TAK-875 in hGPR40 could enclose FFAs with lengths of C15 or fewer. However, for FFAs with lengths longer than C15, part of the alkyl chain extended out of the binding pocket. This study provided insights into the structural dependence of FFAs binding to and activation of hGPR40.

  8. 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.

  9. 14. "SITE WORK, CIVIL, SITE PLAN." Test Area 1120. Specifications ...

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

    14. "SITE WORK, CIVIL, SITE PLAN." Test Area 1-120. Specifications No. OC2-55-72; Drawing No. 60-09-12; sheet 7 of 148; file no. 1320/58, Rev. C. Stamped: RECORD DRAWING - AS CONSTRUCTED. Below stamp: Contract no. 4338 Rev. C, Date: 16 April 1957. - Edwards Air Force Base, Air Force Rocket Propulsion Laboratory, Leuhman Ridge near Highways 58 & 395, Boron, Kern County, CA

  10. Site-Scale Saturated Zone Flow Model

    SciTech Connect

    G. Zyvoloski

    2003-12-17

    The purpose of this model report is to document the components of the site-scale saturated-zone flow model at Yucca Mountain, Nevada, in accordance with administrative procedure (AP)-SIII.lOQ, ''Models''. This report provides validation and confidence in the flow model that was developed for site recommendation (SR) and will be used to provide flow fields in support of the Total Systems Performance Assessment (TSPA) for the License Application. The output from this report provides the flow model used in the ''Site-Scale Saturated Zone Transport'', MDL-NBS-HS-000010 Rev 01 (BSC 2003 [162419]). The Site-Scale Saturated Zone Transport model then provides output to the SZ Transport Abstraction Model (BSC 2003 [164870]). In particular, the output from the SZ site-scale flow model is used to simulate the groundwater flow pathways and radionuclide transport to the accessible environment for use in the TSPA calculations. Since the development and calibration of the saturated-zone flow model, more data have been gathered for use in model validation and confidence building, including new water-level data from Nye County wells, single- and multiple-well hydraulic testing data, and new hydrochemistry data. In addition, a new hydrogeologic framework model (HFM), which incorporates Nye County wells lithology, also provides geologic data for corroboration and confidence in the flow model. The intended use of this work is to provide a flow model that generates flow fields to simulate radionuclide transport in saturated porous rock and alluvium under natural or forced gradient flow conditions. The flow model simulations are completed using the three-dimensional (3-D), finite-element, flow, heat, and transport computer code, FEHM Version (V) 2.20 (software tracking number (STN): 10086-2.20-00; LANL 2003 [161725]). Concurrently, process-level transport model and methodology for calculating radionuclide transport in the saturated zone at Yucca Mountain using FEHM V 2.20 are being

  11. PERFORMING QUALITY FLOW MEASUREMENTS AT MINE SITES

    EPA Science Inventory

    Accurate flow measurement data is vital to research, monitoring, and remediation efforts at mining sites. This guidebook has been prepared to provide a summary of information relating to the performance of low measurements, and how this information can be applied at mining sites....

  12. DOE site-specific threat assessment

    SciTech Connect

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

    1985-07-12

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

  13. 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

  14. RADIATING BONDI AND COOLING SITE FLOWS

    SciTech Connect

    Mathews, William G.; Guo, Fulai

    2012-08-01

    Steady accretion of a radiating gas onto a central mass point is described and compared to classic Bondi accretion. Radiation losses are essential for accretion flows to be observed. Unlike Bondi flows, radiating Bondi flows pass through a sonic point at a finite radius and become supersonic near the center. The morphology of all radiating flows is described by a single dimensionless parameter proportional to M-dot /MT{sub s} where T{sub s} is the gas temperature at the sonic point. In radiating Bondi flows the relationship between the mass accretion rate and central mass, M-dot {proportional_to}M{sup p} with p {approx} 1, differs significantly from the quadratic dependence in classical Bondi flows, M-dot {proportional_to}M{sup 2}. Mass accretion rates onto galaxy or cluster-centered black holes estimated from traditional and radiating Bondi flows are significantly different. In radiating Bondi flows the gas temperature increases at large radii, as in the cores of many galaxy groups and clusters, allowing radiating Bondi flows to merge naturally with gas arriving from their cluster environments. Some radiating flows cool completely before reaching the center of the flow, and this also occurs in cooling site flows, in which there is no central gravitating mass.

  15. Dancing in Place: Site-Specific Work

    ERIC Educational Resources Information Center

    Metal-Corbin, Josie

    2012-01-01

    In her lecture the 2012 NDA Scholar/Artist, Josie Metal-Corbin, chronicles four decades of working with artists, educators, librarians, and scientists. The kinetic language of dance and the visual impact of specific environments provide provocative opportunities for collaboration, wherein the site becomes the framework or map for the dance design.…

  16. 60% Review technical specifications, Deaf Smith Site

    SciTech Connect

    Gast, R.A.

    1987-08-01

    The enclosed documentation for the 60% Review Technical Specifications, Deaf Smith Site includes: Solicitation Documents which represent the eventual Federal Acquisition Regulations (FARs) and Department of Energy Acquisition Regulations (DEARs) that will comprise a segment of the contractual documents for bidders attention; Contract Clauses that will become integral parts for the Fixed Price Construction Contracts applicable to the Exploratory Shaft Facility; Special Contract Requirements that will become contract provisions requiring specific contractor attention; Technical Specifications which have been completed for 60% submission, and the current list of 241 Contract Drawings that have been separately forwarded for review and comment.

  17. Site-Specific PEGylation of Therapeutic Proteins

    PubMed Central

    Dozier, Jonathan K.; Distefano, Mark D.

    2015-01-01

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

  18. 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

  19. 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

  20. Specific Impulse and Mass Flow Rate Error

    NASA Technical Reports Server (NTRS)

    Gregory, Don A.

    2005-01-01

    Specific impulse is defined in words in many ways. Very early in any text on rocket propulsion a phrase similar to .specific impulse is the thrust force per unit propellant weight flow per second. will be found.(2) It is only after seeing the mathematics written down does the definition mean something physically to scientists and engineers responsible for either measuring it or using someone.s value for it.

  1. Hanford Site Treated Effluent Disposal Facility process flow sheet

    SciTech Connect

    Bendixsen, R.B.

    1993-04-01

    This report presents a novel method of using precipitation, destruction and recycle factors to prepare a process flow sheet. The 300 Area Treated Effluent Disposal Facility (TEDF) will treat process sewer waste water from the 300 Area of the Hanford Site, located near Richland, Washington, and discharge a permittable effluent flow into the Columbia River. When completed and operating, the TEDF effluent water flow will meet or exceed water quality standards for the 300 Area process sewer effluents. A preliminary safety analysis document (PSAD), a preconstruction requirement, needed a process flow sheet detailing the concentrations of radionuclides, inorganics and organics throughout the process, including the effluents, and providing estimates of stream flow quantities, activities, composition, and properties (i.e. temperature, pressure, specific gravity, pH and heat transfer rates). As the facility begins to operate, data from process samples can be used to provide better estimates of the factors, the factors can be entered into the flow sheet and the flow sheet will estimate more accurate steady state concentrations for the components. This report shows how the factors were developed and how they were used in developing a flow sheet to estimate component concentrations for the process flows. The report concludes with how TEDF sample data can improve the ability of the flow sheet to accurately predict concentrations of components in the process.

  2. 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.

  3. 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...

  4. Site Specific Evaluation of Multisensor Capacitance Probes

    NASA Astrophysics Data System (ADS)

    Rowland, R. A.; Guber, A. K.; Pachepsky, Y.; Gish, T. J.; Daughtry, C. S.

    2007-12-01

    Multisensor capacitance probes (MCPs) are widely used for measuring soil water content (SWC) at the field scale. Although manufacturers supply a generic MCP calibration, many researchers recognize that MCPs should be calibrated for specific field conditions. MCPs measurements are typically associated with small soil volumes, and are subsequently scaled up to the plot or field scale. Research is needed to understand how representative are these measurements for water monitoring studies that operate with the elementary area from one to tens square meters. The objectives of this study were: (a) to test the accuracy of SWC field measurements using generic and laboratory MCP calibrations; (b) to test applicability of a single MCP calibration for SWC measurements at different depths; and (c) to compare the accuracy of two and three-parameter equations using scaled frequency (SF). Four 1x1 m plots were equipped with MCPs to measure SWC at 9 depths at the OPE3 USDA-ARS research site at Beltsville, MD. Within each plot, three undisturbed soil cores were taken with a 100 cm3 soil auger. SWC sampling was made on three different dates when soil water contents were distinctly different. To compare MCP measurements with observed SWC, the SF was converted into SWC using: (a) the manufacturer generic calibration; and (b) calibration obtained in laboratory for a mesic Aquic Hapludult soil. Parameters of three different calibration equations were also obtained by fitting the equations to the water contents measurements at the plots. This fit was done: (a) for all observations regardless the depth, (b) for observations at each genetic horizon, and (c) for each depth separately. Results show that the manufacturer and the laboratory calibrations provided a satisfactory fit to the field-measured SWC at depths of 30, 40 and 50 cm. The fit was about two times less accurate at depths of 10, 20, 60, 70 80 and 90 cm. A minor improvement was obtained at depths of 10 and 20 cm after

  5. 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.

  6. Calibration of the Site-Scale Saturated Zone Flow Model

    SciTech Connect

    G. A. Zyvoloski

    2001-06-28

    The purpose of the flow calibration analysis work is to provide Performance Assessment (PA) with the calibrated site-scale saturated zone (SZ) flow model that will be used to make radionuclide transport calculations. As such, it is one of the most important models developed in the Yucca Mountain project. This model will be a culmination of much of our knowledge of the SZ flow system. The objective of this study is to provide a defensible site-scale SZ flow and transport model that can be used for assessing total system performance. A defensible model would include geologic and hydrologic data that are used to form the hydrogeologic framework model; also, it would include hydrochemical information to infer transport pathways, in-situ permeability measurements, and water level and head measurements. In addition, the model should include information on major model sensitivities. Especially important are those that affect calibration, the direction of transport pathways, and travel times. Finally, if warranted, alternative calibrations representing different conceptual models should be included. To obtain a defensible model, all available data should be used (or at least considered) to obtain a calibrated model. The site-scale SZ model was calibrated using measured and model-generated water levels and hydraulic head data, specific discharge calculations, and flux comparisons along several of the boundaries. Model validity was established by comparing model-generated permeabilities with the permeability data from field and laboratory tests; by comparing fluid pathlines obtained from the SZ flow model with those inferred from hydrochemical data; and by comparing the upward gradient generated with the model with that observed in the field. This analysis is governed by the Office of Civilian Radioactive Waste Management (OCRWM) Analysis and Modeling Report (AMR) Development Plan ''Calibration of the Site-Scale Saturated Zone Flow Model'' (CRWMS M&O 1999a).

  7. 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.

  8. 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.

  9. 40 CFR 89.414 - Air flow measurement specifications.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 21 2013-07-01 2013-07-01 false Air flow measurement specifications... Emission Test Procedures § 89.414 Air flow measurement specifications. (a) The air flow measurement method used must have a range large enough to accurately measure the air flow over the engine operating...

  10. 40 CFR 89.414 - Air flow measurement specifications.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 20 2014-07-01 2013-07-01 true Air flow measurement specifications. 89... Test Procedures § 89.414 Air flow measurement specifications. (a) The air flow measurement method used must have a range large enough to accurately measure the air flow over the engine operating...

  11. 40 CFR 89.415 - Fuel flow measurement specifications.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 21 2012-07-01 2012-07-01 false Fuel flow measurement specifications... Emission Test Procedures § 89.415 Fuel flow measurement specifications. The fuel flow rate measurement instrument must have a minimum accuracy of 2 percent of the engine maximum fuel flow rate. The...

  12. 40 CFR 91.417 - Fuel flow measurement specifications.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 21 2012-07-01 2012-07-01 false Fuel flow measurement specifications... Procedures § 91.417 Fuel flow measurement specifications. (a) Fuel flow measurement is required only for raw testing but is allowed for dilute testing. (b) The fuel flow rate measurement instrument must have...

  13. 40 CFR 89.415 - Fuel flow measurement specifications.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 20 2014-07-01 2013-07-01 true Fuel flow measurement specifications... Emission Test Procedures § 89.415 Fuel flow measurement specifications. The fuel flow rate measurement instrument must have a minimum accuracy of 2 percent of the engine maximum fuel flow rate. The...

  14. 40 CFR 89.414 - Air flow measurement specifications.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 21 2012-07-01 2012-07-01 false Air flow measurement specifications... Emission Test Procedures § 89.414 Air flow measurement specifications. (a) The air flow measurement method used must have a range large enough to accurately measure the air flow over the engine operating...

  15. 40 CFR 91.417 - Fuel flow measurement specifications.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 20 2014-07-01 2013-07-01 true Fuel flow measurement specifications... Procedures § 91.417 Fuel flow measurement specifications. (a) Fuel flow measurement is required only for raw testing but is allowed for dilute testing. (b) The fuel flow rate measurement instrument must have...

  16. 40 CFR 89.415 - Fuel flow measurement specifications.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 20 2011-07-01 2011-07-01 false Fuel flow measurement specifications... Emission Test Procedures § 89.415 Fuel flow measurement specifications. The fuel flow rate measurement instrument must have a minimum accuracy of 2 percent of the engine maximum fuel flow rate. The...

  17. 40 CFR 91.417 - Fuel flow measurement specifications.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 21 2013-07-01 2013-07-01 false Fuel flow measurement specifications... Procedures § 91.417 Fuel flow measurement specifications. (a) Fuel flow measurement is required only for raw testing but is allowed for dilute testing. (b) The fuel flow rate measurement instrument must have...

  18. 40 CFR 89.415 - Fuel flow measurement specifications.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 21 2013-07-01 2013-07-01 false Fuel flow measurement specifications... Emission Test Procedures § 89.415 Fuel flow measurement specifications. The fuel flow rate measurement instrument must have a minimum accuracy of 2 percent of the engine maximum fuel flow rate. The...

  19. 40 CFR 91.417 - Fuel flow measurement specifications.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 20 2011-07-01 2011-07-01 false Fuel flow measurement specifications... Procedures § 91.417 Fuel flow measurement specifications. (a) Fuel flow measurement is required only for raw testing but is allowed for dilute testing. (b) The fuel flow rate measurement instrument must have...

  20. 40 CFR 90.417 - Fuel flow measurement specifications.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... specifications of 40 CFR part 1065, subpart C, instead of those in this paragraph (b). ... 40 Protection of Environment 20 2014-07-01 2013-07-01 true Fuel flow measurement specifications... Gaseous Exhaust Test Procedures § 90.417 Fuel flow measurement specifications. (a) Fuel flow...

  1. 40 CFR 90.417 - Fuel flow measurement specifications.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... specifications of 40 CFR part 1065, subpart C, instead of those in this paragraph (b). ... 40 Protection of Environment 21 2012-07-01 2012-07-01 false Fuel flow measurement specifications... Gaseous Exhaust Test Procedures § 90.417 Fuel flow measurement specifications. (a) Fuel flow...

  2. 40 CFR 90.417 - Fuel flow measurement specifications.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... specifications of 40 CFR part 1065, subpart C, instead of those in this paragraph (b). ... 40 Protection of Environment 21 2013-07-01 2013-07-01 false Fuel flow measurement specifications... Gaseous Exhaust Test Procedures § 90.417 Fuel flow measurement specifications. (a) Fuel flow...

  3. 40 CFR 90.417 - Fuel flow measurement specifications.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... specifications of 40 CFR part 1065, subpart C, instead of those in this paragraph (b). ... 40 Protection of Environment 20 2011-07-01 2011-07-01 false Fuel flow measurement specifications... Gaseous Exhaust Test Procedures § 90.417 Fuel flow measurement specifications. (a) Fuel flow...

  4. Tissue specificity of endothelin binding sites

    SciTech Connect

    Bolger, G.T.; Liard, F.; Krogsrud, R.; Thibeault, D.; Jaramillo, J. )

    1990-09-01

    A measurement was made of the binding of 125I-labeled endothelin (125I-ET) to crude membrane fractions prepared from rat aorta, atrium, ventricle, portal vein, trachea, lung parenchyma, vas deferens, ileum, bladder, and guinea-pig taenia coli and lung parenchyma. Scatchard analysis of 125I-ET binding in all tissues indicated binding to a single class of saturable sites. The affinity and density of 125I-ET binding sites varied between tissues. The Kd of 125I-ET binding was approximately 0.5 nM for rat aorta, trachea, lung parenchyma, ventricle, bladder, and vas deferens, and guinea-pig taenia coli and lung parenchyma, 1.8 nM for rat portal vein and atrium, and 3.3 nM for ileum. The Bmax of 125I-ET binding had the following rank order of density in rat tissues: trachea greater than lung parenchyma = vas deferens much greater than aorta = portal vein = atrium greater than bladder greater than ventricle = ileum. The properties of 125I-ET endothelin binding were characterized in rat ventricular membranes. 125I-ET binding was time dependent, reaching a maximum within 45-60 min at 25 degrees C. The calculated microassociation constant was 9.67 x 10(5) s-1 M-1. Only 15-20% of 125I-ET dissociated from its binding site even when dissociation was studied as long as 3 h. Preincubation of ventricular membranes with ET prevented binding of 125I-ET. 125I-ET binding was destroyed by boiling of ventricular membranes and was temperature, pH, and cation (Ca2+, Mg2+, and Na+) dependent.

  5. 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...

  6. 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... CONTACT: Gerri Flemming, Office of External Affairs, Department of Energy, Savannah River...

  7. 40 CFR 89.415 - Fuel flow measurement specifications.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Fuel flow measurement specifications... PROGRAMS (CONTINUED) CONTROL OF EMISSIONS FROM NEW AND IN-USE NONROAD COMPRESSION-IGNITION ENGINES Exhaust Emission Test Procedures § 89.415 Fuel flow measurement specifications. The fuel flow rate...

  8. 40 CFR 91.417 - Fuel flow measurement specifications.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Fuel flow measurement specifications... PROGRAMS (CONTINUED) CONTROL OF EMISSIONS FROM MARINE SPARK-IGNITION ENGINES Gaseous Exhaust Test Procedures § 91.417 Fuel flow measurement specifications. (a) Fuel flow measurement is required only for...

  9. 40 CFR 90.417 - Fuel flow measurement specifications.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Fuel flow measurement specifications... PROGRAMS (CONTINUED) CONTROL OF EMISSIONS FROM NONROAD SPARK-IGNITION ENGINES AT OR BELOW 19 KILOWATTS Gaseous Exhaust Test Procedures § 90.417 Fuel flow measurement specifications. (a) Fuel flow...

  10. 40 CFR 86.314-79 - Fuel flow measurement specifications.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... percent of the measuring weight. (3) If the mass of fuel consumed is measured electronically (load cell... 40 Protection of Environment 19 2013-07-01 2013-07-01 false Fuel flow measurement specifications....314-79 Fuel flow measurement specifications. (a) The fuel flow rate measurement instrument must have...

  11. 40 CFR 89.414 - Air flow measurement specifications.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Air flow measurement specifications. 89.414 Section 89.414 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR... Emission Test Procedures § 89.414 Air flow measurement specifications. (a) The air flow measurement...

  12. 40 CFR 86.314-79 - Fuel flow measurement specifications.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... percent of the measuring weight. (3) If the mass of fuel consumed is measured electronically (load cell... 40 Protection of Environment 18 2010-07-01 2010-07-01 false Fuel flow measurement specifications....314-79 Fuel flow measurement specifications. (a) The fuel flow rate measurement instrument must have...

  13. 40 CFR 91.416 - Intake air flow measurement specifications.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Intake air flow measurement... Procedures § 91.416 Intake air flow measurement specifications. (a) If used, the engine intake air flow measurement method used must have a range large enough to accurately measure the air flow over the...

  14. 40 CFR 91.416 - Intake air flow measurement specifications.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 21 2012-07-01 2012-07-01 false Intake air flow measurement... Procedures § 91.416 Intake air flow measurement specifications. (a) If used, the engine intake air flow measurement method used must have a range large enough to accurately measure the air flow over the...

  15. 40 CFR 91.416 - Intake air flow measurement specifications.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 21 2013-07-01 2013-07-01 false Intake air flow measurement... Procedures § 91.416 Intake air flow measurement specifications. (a) If used, the engine intake air flow measurement method used must have a range large enough to accurately measure the air flow over the...

  16. 40 CFR 91.416 - Intake air flow measurement specifications.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 20 2014-07-01 2013-07-01 true Intake air flow measurement... Procedures § 91.416 Intake air flow measurement specifications. (a) If used, the engine intake air flow measurement method used must have a range large enough to accurately measure the air flow over the...

  17. Site-specific labeling of RNA.

    PubMed

    Nilsen, Timothy W

    2013-03-01

    In this protocol, RNAs containing a specific internally labeled phosphate are generated. The entire transcript of interest is synthesized using in vitro transcription. It is then digested with RNase H in the presence of a complementary chimeric oligonucleotide of the sequence 5'-NNNddddNNNNNNN-3', where N is a 2'-O-methyl (2' OMe) ribonucleotide and d is a de-oxy-nu-cle-o-tide. RNase H specifically cleaves the RNA in the oligonucleotide-RNA hybrid at the phosphodiester bond opposite the 5'-most deoxynucleotide, creating 3'-hydroxyl and 5'-phosphate termini. After dephosphorylation of the 5' end of the 3' fragment with phosphatase, this terminus is labeled to high specific activity with [γ-(32)P]ATP. The fragments of the original RNA are then resealed with T4 DNA ligase in the presence of a splint (or bridge) oligonucleotide. These labeled RNAs can be used in subsequent procedures to probe RNA-protein or RNA-RNA interactions.

  18. Global and site specific multimedia (field) studies

    SciTech Connect

    Cutshall, N.H.; Guerin, M.R.

    1987-01-01

    Experience with radioactive fallout, with organic contaminants and with heavy metals has amply demonstrated that cross-media transfers are common and that understanding the transport, cycling, and fate of these contaminants requires a multimedia approach. Nonetheless, pollutants with similar physical and chemical attributes may follow markedly different pathways. The frequency of exceptions to predictions based on simplistic models is also sufficient to show that direct investigation of environmental contamination is essential to confirm validity of models used for conceptualizing a problem or for control. Modeling based on multimedia premises and regulatory controls that encompass multimedia considerations are challenged by a dilemma, however. First, the development of multimedia models or regulatory frameworks represents simplification and generalization. This is true for several reasons: (1) inadequate understanding of physical and environmental factors which control specific cross-media transfer; (2) the absence of specific data on certain multimedia pollutant concentrations; (3) even the most powerful computers do not have sufficient speed and capacity to deal with the known complexities of natural systems. On the other hand, for contaminants such as mercury, it may be necessary to include great detail; the overall distribution in the environment may be less important than the rate of some minor process. With sufficient experience and good judgment of what can be ignored, the simplifications and generalizations can be made. For the present, and for the foreseeable future, however, they absolutely must be accompanied by thorough field validation and monitoring.

  19. Source apportionment with site specific source profiles.

    PubMed

    Glover, D M; Hopke, P K; Vermette, S J; Landsberger, S; D'Auben, D R

    1991-03-01

    A receptor modeling study was performed to identify and apportion the sources of PM10 mass in Granite City, Illinois, an area of historic TSP nonattainment. Samples of the ambient aerosol were collected using a dichotomous sampler. Each sample was analyzed by x-ray fluorescence and instrumental neutron activation analysis. To begin the study, a factor analysis was performed. Two different chemical mass balance (CMB) analyses were then made. The first CMB analysis used only source profiles available from the literature while the second included twelve source profiles developed from dust samples collected in Granite City. Both CMB analyses used 20 of the 33 analyzed elements since many of the source profiles in the literature did not include the other thirteen elements. The results from both sets of CMB analyses were grouped by the predominate wind direction at the site during the time each sample was taken to identify the direction of each source relative to the sampler. It was found that regional sources were the primary contributors to the fine fraction while the coarse fraction was composed of material from local industries. These sources were generally the ones identified during the Regional Air Pollution Study previously conducted in the area. However, the emission profiles from these sources were observed to have changed between the studies. It was also found that the use of the locally generated profiles greatly improved the results of the CMB analysis.

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

    SciTech Connect

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

    1993-08-01

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

  1. Recharge and Lateral Groundwater Flow Boundary Conditions for the Saturated Zone Site-Scale Flow and Transport Model

    SciTech Connect

    S. James

    2004-10-06

    This analysis is designed to use existing modeling and analysis results as the basis for estimated groundwater flow rates into the saturated zone (SZ) site-scale model domains, both as recharge (infiltration) at the upper boundary (water table), and as underflow at the lateral boundaries. Specifically, this work compiles information on the recharge boundary conditions supplied to the base-case and alternate SZ site-scale flow models taken from (1) distributed recharge from the 1997 (D'Agnese et al. 1997 [DIRS 100131]) or 2001 (D'Agnese et al. 2002 [DIRS 158876]) SZ regional-scale (Death Valley Regional Flow System [DVRFS]) model; (2) recharge below the area of the 1997 (Wu et al. 1997 [DIRS 156453]) or 2003 (BSC 2004 [DIRS 169861]) unsaturated zone (UZ) site-scale flow model; and (3) focused recharge along Fortymile Wash. In addition, this analysis includes extraction of the groundwater flow rates simulated by the 1997 and 2001 DVRFS models coincident with the lateral boundaries of the SZ site-scale flow models. The fluxes from the 1997 DVRFS were used to calibrate the base-case SZ site-scale flow model. The 2001 DVRFS fluxes are used in the alternate SZ site-scale flow model.

  2. 40 CFR 228.6 - Specific criteria for site selection.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 25 2014-07-01 2014-07-01 false Specific criteria for site selection... selection. (a) In the selection of disposal sites, in addition to other necessary or appropriate factors...) Existence at or in close proximity to the site of any significant natural or cultural features of...

  3. 40 CFR 228.6 - Specific criteria for site selection.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 24 2010-07-01 2010-07-01 false Specific criteria for site selection... selection. (a) In the selection of disposal sites, in addition to other necessary or appropriate factors...; (10) Potentiality for the development or recruitment of nuisance species in the disposal site;...

  4. Site Specific Management of Cotton Production in the United States

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Site-specific management or precision agriculture, as it is evolving in large-scale crop production, offers promising new methods for managing cotton production for optimized yields, maximized profitability, and minimized environmental pollution. However, adaptation of site-specific theory and meth...

  5. 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...

  6. Site-specific crop management using geophysical proximal sensors

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Key components of site-specific crop management are (i) identifying the site-specific factors that influence within-field crop yield variation and (ii) spatially characterizing those factors. Geo-referenced measurements of apparent soil electrical conductivity (ECa) provide a potential means of cha...

  7. 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...

  8. Savannah River Site`s Site Specific Plan. Environmental restoration and waste management, fiscal year 1992

    SciTech Connect

    Not Available

    1991-08-01

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

  9. 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... Flemming, Office of External Affairs, Department of Energy, Savannah River Operations Office, P.O. Box...

  10. 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...-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...

  11. 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... of External Affairs, Department of Energy, Savannah River Operations Office, P.O. Box A, Aiken,...

  12. 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... CONTACT: Gerri Flemming, Office of External Affairs, Department of Energy, Savannah River...

  13. 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,...

  14. 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...

  15. 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...

  16. 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,...

  17. 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...

  18. 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,...

  19. 75 FR 82001 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-29

    ... 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... Affairs, Department of Energy, Savannah River Operations Office, P.O. Box A, Aiken, SC 29802; Phone:...

  20. 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,...

  1. 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,...

  2. 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...

  3. 76 FR 81487 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-28

    ... 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...

  4. 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,...

  5. 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,...

  6. 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,...

  7. 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... of External Affairs, Department of Energy, Savannah River Operations Office, P.O. Box A, Aiken,...

  8. 40 CFR 90.416 - Intake air flow measurement specifications.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Intake air flow measurement... Gaseous Exhaust Test Procedures § 90.416 Intake air flow measurement specifications. (a) If used, the engine intake air flow measurement method used must have a range large enough to accurately measure...

  9. 40 CFR 90.416 - Intake air flow measurement specifications.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 20 2014-07-01 2013-07-01 true Intake air flow measurement... Gaseous Exhaust Test Procedures § 90.416 Intake air flow measurement specifications. (a) If used, the engine intake air flow measurement method used must have a range large enough to accurately measure...

  10. 40 CFR 90.416 - Intake air flow measurement specifications.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 21 2013-07-01 2013-07-01 false Intake air flow measurement... Gaseous Exhaust Test Procedures § 90.416 Intake air flow measurement specifications. (a) If used, the engine intake air flow measurement method used must have a range large enough to accurately measure...

  11. 40 CFR 90.416 - Intake air flow measurement specifications.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 21 2012-07-01 2012-07-01 false Intake air flow measurement... Gaseous Exhaust Test Procedures § 90.416 Intake air flow measurement specifications. (a) If used, the engine intake air flow measurement method used must have a range large enough to accurately measure...

  12. 78 FR 40130 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-03

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION... CONTACT: Gerri Flemming, Office of External Affairs, Department of Energy, Savannah River...

  13. 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.

  14. 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

  15. Isotope specific arbitrary material flow meter

    DOEpatents

    Barty, Christopher P. J.; Post, John C.; Jones, Edwin

    2016-10-25

    A laser-based mono-energetic gamma-ray source is used to provide non-destructive and non-intrusive, quantitative determination of the absolute amount of a specific isotope contained within pipe as part of a moving fluid or quasi-fluid material stream.

  16. Protein assemblies by site-specific avidin-biotin interactions.

    PubMed

    Mori, Yutaro; Minamihata, Kosuke; Abe, Hiroki; Goto, Masahiro; Kamiya, Noriho

    2011-08-21

    Exploiting self-assembly systems with biological building blocks is of significant interest in the fabrication of advanced biomaterials. We assessed the potential use of site-specific ligand labeling of protein building blocks in designing functional protein self-assemblies by combining site-specifically biotinylated bacterial alkaline phosphatase (as a bidentate or tetradentate ligand unit) and streptavidin (as a tetrameric receptor). PMID:21731938

  17. Industrial energy conservation-center-pivot site specific irrigation. Final report, January 1995--December 1996

    SciTech Connect

    McCann, I.R.; King, B.A.; Brady, R.

    1996-12-27

    This project was to aid in the development and commercial transfer of site specific technology to industry and farmers. This report contains the results of data collected during the fall of 1996 on a site near Aberdeen, Idaho. This site was equipped to apply water at variable rates predetermined by a digital control map that resided in a computer controller. The flow rates were then adjusted to maintain desired pressure with an Adjustable Speed Drive. Energy consumption was monitored during implementation of site specific irrigation practices and normal irrigation practices. This final report covers the impact that site specific irrigation has on energy use on a irrigated small grain crop near Aberdeen, Idaho. 3 refs., 20 figs., 1 tab.

  18. Use of limited site-specific flood information in estimating flood peaks

    SciTech Connect

    Newton, D.W.; Herrin, J.C.; Roser, S.D.; Kibler, D.F.; Aron, G.; Wall, D.J.

    1984-07-01

    Long-term stream gage records are seldom available at locations where flood-frequency estimates are required. As a result, most estimates are made by transferring information from nearby locations where flood records exist. Occasionally estimates of large past floods (historic flood information) and/or less than 10 years of gage record (short-record flood information) are available at the site. Procedures are developed and evaluated to systematically combine this limited site-specific flood information and regional flow-frequency estimates at ungaged sites or gaged sites with less than 10 years of record to obtain a more accurate flood peak estimate. 29 references, 23 figures, 31 tables.

  19. 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.

  20. Site-specific recombinases as tools for heterologous gene integration.

    PubMed

    Hirano, Nobutaka; Muroi, Tetsurou; Takahashi, Hideo; Haruki, Mitsuru

    2011-10-01

    Site-specific recombinases are the enzymes that catalyze site-specific recombination between two specific DNA sequences to mediate DNA integration, excision, resolution, or inversion and that play a pivotal role in the life cycles of many microorganisms including bacteria and bacteriophages. These enzymes are classified as tyrosine-type or serine-type recombinases based on whether a tyrosine or serine residue mediates catalysis. All known tyrosine-type recombinases catalyze the formation of a Holliday junction intermediate, whereas the catalytic mechanism of all known serine-type recombinases includes the 180° rotation and rejoining of cleaved substrate DNAs. Both recombinase families are further subdivided into two families; the tyrosine-type recombinases are subdivided by the recombination directionality, and the serine-type recombinases are subdivided by the protein size. Over more than two decades, many different site-specific recombinases have been applied to in vivo genome engineering, and some of them have been used successfully to mediate integration, deletion, or inversion in a wide variety of heterologous genomes, including those from bacteria to higher eukaryotes. Here, we review the recombination mechanisms of the best characterized recombinases in each site-specific recombinase family and recent advances in the application of these recombinases to genomic manipulation, especially manipulations involving site-specific gene integration into heterologous genomes. PMID:21822899

  1. 40 CFR 91.416 - Intake air flow measurement specifications.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 20 2011-07-01 2011-07-01 false Intake air flow measurement specifications. 91.416 Section 91.416 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) CONTROL OF EMISSIONS FROM MARINE SPARK-IGNITION ENGINES Gaseous Exhaust Test Procedures § 91.416 Intake air flow...

  2. Organic solvents identify specific ligand binding sites on protein surfaces.

    PubMed

    Liepinsh, E; Otting, G

    1997-03-01

    Enzymes frequently recognize substrates and pharmaceutical drugs through specific binding interactions in deep pockets on the protein surface. We show how the specificity-determining substrate binding site of hen egg-white lysozyme (HEWL) can be readily identified in aqueous solution by nuclear magnetic resonance spectroscopy using small organic solvent molecules as detection probes. Exchange of magnetization between the 1H nuclei of the protein and the ligands through dipole-dipole interactions is observed which allows the modeling of their position and orientation at the binding site. Combined with site-specific binding constants measured by titration experiments with different organic solvents, the method can provide important information for rational drug design. In addition, the lifetime of nonspecific interactions of HEWL with organic solvents is shown to be in the sub-nanosecond time range. PMID:9062927

  3. A grammar inference approach for predicting kinase specific phosphorylation sites.

    PubMed

    Datta, Sutapa; Mukhopadhyay, Subhasis

    2015-01-01

    Kinase mediated phosphorylation site detection is the key mechanism of post translational mechanism that plays an important role in regulating various cellular processes and phenotypes. Many diseases, like cancer are related with the signaling defects which are associated with protein phosphorylation. Characterizing the protein kinases and their substrates enhances our ability to understand the mechanism of protein phosphorylation and extends our knowledge of signaling network; thereby helping us to treat such diseases. Experimental methods for predicting phosphorylation sites are labour intensive and expensive. Also, manifold increase of protein sequences in the databanks over the years necessitates the improvement of high speed and accurate computational methods for predicting phosphorylation sites in protein sequences. Till date, a number of computational methods have been proposed by various researchers in predicting phosphorylation sites, but there remains much scope of improvement. In this communication, we present a simple and novel method based on Grammatical Inference (GI) approach to automate the prediction of kinase specific phosphorylation sites. In this regard, we have used a popular GI algorithm Alergia to infer Deterministic Stochastic Finite State Automata (DSFA) which equally represents the regular grammar corresponding to the phosphorylation sites. Extensive experiments on several datasets generated by us reveal that, our inferred grammar successfully predicts phosphorylation sites in a kinase specific manner. It performs significantly better when compared with the other existing phosphorylation site prediction methods. We have also compared our inferred DSFA with two other GI inference algorithms. The DSFA generated by our method performs superior which indicates that our method is robust and has a potential for predicting the phosphorylation sites in a kinase specific manner.

  4. Site- and species-specific hydrolysis rates of heroin.

    PubMed

    Szöcs, Levente; Orgován, Gábor; Tóth, Gergő; Kraszni, Márta; Gergó, Lajos; Hosztafi, Sándor; Noszál, Béla

    2016-06-30

    The hydroxide-catalyzed non-enzymatic, simultaneous and consecutive hydrolyses of diacetylmorphine (DAM, heroin) are quantified in terms of 10 site- and species-specific rate constants in connection with also 10 site- and species-specific acid-base equilibrium constants, comprising all the 12 coexisting species in solution. This characterization involves the major and minor decomposition pathways via 6-acetylmorphine and 3-acetylmorphine, respectively, and morphine, the final product. Hydrolysis has been found to be 18-120 times faster at site 3 than at site 6, depending on the status of the amino group and the rest of the molecule. Nitrogen protonation accelerates the hydrolysis 5-6 times at site 3 and slightly less at site 6. Hydrolysis rate constants are interpreted in terms of intramolecular inductive effects and the concomitant local electron densities. Hydrolysis fraction, a new physico-chemical parameter is introduced and determined to quantify the contribution of the individual microspecies to the overall hydrolysis. Hydrolysis fractions are depicted as a function of pH. PMID:27130543

  5. Adoption of site-specific variable rate sprinkler irrigation 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) technology has resulted in limited commercial adoption of the technology. Competing patents, liability and proprietary software have affected industry’s willingness to move into a new t...

  6. 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...

  7. 78 FR 14088 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-04

    ...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act requires that... Resort Drive, Savannah, GA 31421. FOR FURTHER INFORMATION CONTACT: Gerri Flemming, Office of External... recommendations to DOE-EM and site management in the areas of environmental restoration, waste management,...

  8. 75 FR 9885 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-04

    ...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463..., 200 Stoneridge Drive, Columbia, SC 29210. FOR FURTHER INFORMATION CONTACT: Sheron Smith, Office of... make recommendations to DOE-EM and site management in the areas of environmental restoration,...

  9. Site-specific Probabilistic Seismic Hazard Map of Himachal Pradesh, India. Part I. Site-specific Ground Motion Relations

    NASA Astrophysics Data System (ADS)

    Muthuganeisan, Prabhu; Raghukanth, S. T. G.

    2016-04-01

    This article presents four regional site-specific ground motion relations developed for the state of Himachal Pradesh in northwest Himalaya, situated in a seismically active region. These relations are developed from synthetic free surface ground motion databases obtained from a calibrated stochastic seismological model considering the characteristic properties of this specific region. The adopted methodology incorporates the site effects characterised through active MASW tests conducted in 22 important cities. The estimated ground motion levels from the developed relations are found to be in reasonable agreement with the recorded data.

  10. Is hyporheic flow an indicator for salmonid spawning site selection?

    NASA Astrophysics Data System (ADS)

    Benjankar, R. M.; Tonina, D.; Marzadri, A.; McKean, J. A.; Isaak, D.

    2015-12-01

    Several studies have investigated the role of hydraulic variables in the selection of spawning sites by salmonids. Some recent studies suggest that the intensity of the ambient hyporheic flow, that present without a salmon egg pocket, is a cue for spawning site selection, but others have argued against it. We tested this hypothesis by using a unique dataset of field surveyed spawning site locations and an unprecedented meter-scale resolution bathymetry of a 13.5 km long reach of Bear Valley Creek (Idaho, USA), an important Chinook salmon spawning stream. We used a two-dimensional surface water model to quantify stream hydraulics and a three-dimensional hyporheic model to quantify the hyporheic flows. Our results show that the intensity of ambient hyporheic flows is not a statistically significant variable for spawning site selection. Conversely, the intensity of the water surface curvature and the habitat quality, quantified as a function of stream hydraulics and morphology, are the most important variables for salmonid spawning site selection. KEY WORDS: Salmonid spawning habitat, pool-riffle system, habitat quality, surface water curvature, hyporheic flow

  11. Some specific features of the NMR study of fluid flows

    NASA Astrophysics Data System (ADS)

    Davydov, V. V.

    2016-07-01

    Some specific features of studying fluid flows with a NMR spectrometer are considered. The consideration of these features in the NMR spectrometer design makes it possible to determine the relative concentrations of paramagnetic ions and measure the longitudinal and transverse relaxation times ( T 1 and T 2, respectively) in fluid flows with an error no larger than 0.5%. This approach allows one to completely avoid errors in determining the state of a fluid from measured relaxation constants T 1 and T 2, which is especially urgent when working with medical suspensions and biological solutions. The results of an experimental study of fluid flows are presented.

  12. Site Specific Advisory Board initiative, evaluation survey results supplementary appendix: Summary of individual site results

    SciTech Connect

    1996-08-01

    This Appendix presents results of the Site-Specific Advisory Board (SSAB) Initiative for each of the 11 sites that participated in the survey. These individual results are a supplement to the June 1996 Summary Report which presented overall survey results. Results are presented in 11 sections, arranged alphabetically by site. Each section includes a series of figures and tables that parallel those presented in the Summary Report. To facilitate comparison, figures are presented both for the individual site and for the overall long survey. The sequence of sections is: Fernald, Hanford, Idaho, Los Alamos, Monticello, Nevada, Pantex, Rocky Flats, St. Louis, Sandia, and Savannah River.

  13. Site-Specific Covalent Labeling of RNA by Enzymatic Transglycosylation.

    PubMed

    Alexander, Seth C; Busby, Kayla N; Cole, Christian M; Zhou, Cun Yu; Devaraj, Neal K

    2015-10-14

    We demonstrate the site-specific incorporation of nucleobase derivatives bearing fluorophores or affinity labels into a short RNA stem loop recognition motif by exchange of a guanine residue. The RNA-TAG (transglycosylation at guanosine) is carried out by a bacterial (E. coli) tRNA guanine transglycosylase (TGT), whose natural substrate is the nitrogenous base PreQ1. Remarkably, we have successfully incorporated large functional groups including biotin, BODIPY, thiazole orange, and Cy7 through a polyethylene glycol linker attached to the exocyclic amine of PreQ1. Larger RNAs, such as mRNA transcripts, can be site-specifically labeled if they possess the 17-nucleotide hairpin recognition motif. The RNA-TAG methodology could facilitate the detection and manipulation of RNA molecules by enabling the direct incorporation of functional artificial nucleobases using a simple hairpin recognition element. PMID:26393285

  14. Site-specific gene therapy for cardiovascular disease

    PubMed Central

    Fishbein, Ilia; Chorny, Michael; Levy, Robert J

    2010-01-01

    Gene therapy holds considerable promise for the treatment of cardiovascular disease and may provide novel therapeutic solutions for both genetic disorders and acquired pathophysiologies such as arteriosclerosis, heart failure and arrhythmias. Recombinant DNA technology and the sequencing of the human genome have made a plethora of candidate therapeutic genes available for cardiovascular diseases. However, progress in the field of gene therapy for cardiovascular disease has been modest; one of the key reasons for this limited progress is the lack of gene delivery systems for localizing gene therapy to specific sites to optimize transgene expression and efficacy. This review summarizes progress made toward the site-specific delivery of cardiovascular gene therapy and highlights selected promising novel approaches. PMID:20205054

  15. 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.

  16. Site-Specific Biomolecule Labeling with Gold Clusters

    PubMed Central

    Ackerson, Christopher J.; Powell, Richard D.; Hainfeld, James F.

    2013-01-01

    Site-specific labeling of biomolecules in vitro with gold clusters can enhance the information content of electron cryomicroscopy experiments. This chapter provides a practical overview of well-established techniques for forming biomolecule/gold cluster conjugates. Three bioconjugation chemistries are covered: Linker-mediated bioconjugation, direct gold–biomolecule bonding, and coordination-mediated bonding of nickel(II) nitrilotriacetic acid (NTA)-derivatized gold clusters to polyhistidine (His)-tagged proteins. PMID:20887859

  17. 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. PMID:27356886

  18. 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.

  19. 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.

  20. 40 CFR 89.414 - Air flow measurement specifications.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 20 2011-07-01 2011-07-01 false Air flow measurement specifications. 89.414 Section 89.414 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) CONTROL OF EMISSIONS FROM NEW AND IN-USE NONROAD COMPRESSION-IGNITION ENGINES Exhaust Emission Test Procedures § 89.414 Air...

  1. 40 CFR 90.416 - Intake air flow measurement specifications.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 20 2011-07-01 2011-07-01 false Intake air flow measurement specifications. 90.416 Section 90.416 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) CONTROL OF EMISSIONS FROM NONROAD SPARK-IGNITION ENGINES AT OR BELOW 19 KILOWATTS Gaseous Exhaust Test Procedures §...

  2. 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

  3. A saturated zone site-scale flow model for Yucca mountain

    SciTech Connect

    Eddebbarh, Al Aziz

    2008-01-01

    A saturated zone site-scale flow model (YMSZFM) was developed for licensing requirements for the Yucca Mountain nuclear waste repository to incorporate recent data and analyses including recent stratigraphic and water-level data from Nye County wells, single-and multiple-well hydraulic testing data, and recent hydrochemistry data. Analyses include use of data from the 2004 transient Death Valley Regional (ground-water) Flow System (DVRFS) model, the 2003 unsaturated zone flow model, and the latest hydrogeologic framework model (HFM). This model includes: (1) the latest understanding of SZ flow, (2) enhanced model validation and uncertainty analyses, (3) improved locations and definitions of fault zones, (4) refined grid resolution (500-to 250-m grid spacing), and (5) use of new data. The flow model was completed using the three-dimensional, Finite-Element Heat and Mass Transfer computer code (FEHM). The SZ site-scale flow model was calibrated with the commercial parameter estimation code, PEST to achieve a minimum difference between observed water levels and predicted water levels, and also between volumetric/mass flow rates along specific boundary segments as supplied by the DVRFS. A total of 161 water level and head measurements with varied weights were used for calibration. A comparison between measured water-level data and the potentiometric surface yielded an RMSE of 20.7 m (weighted RMSE of 8.8 m). The calibrated model was used to generate flow paths and specific discharge predictions. Model confidence was built by comparing: (l) calculated to observed hydraulic heads, and (2) calibrated to measured permeabilities (and therefore specific discharge). In addition, flowpaths emanating from below the repository footprint are consistent with those inferred both from gradients of measured head and from independent water-chemistry data. Uncertainties in the SZ site-scale flow model were quantified because all uncertainty contributes to inaccuracy in system

  4. Specific [(3)H]tryptophan binding sites in rat brain.

    PubMed

    Wong, P T; Lee, H S; Tan, C H; Teo, W L

    1989-01-01

    [(3)H]Tryptophan binds to a single population of sites in the rat cortical synaptosomal membranes. The binding is reversible and follows the law of mass action. By saturation studies using increasing concentration of [(3)H]tryptophan with decreasing specific radioactivity, the apparent K(d) obtained was approx. 0.8 ?M and the B(max) 110 pmol/mg protein. However, the IC(50) obtained for unlabelled tryptophan in displacing [(3)H]tryptophan binding (3.5 nM) was 0.26 ?M. All six naturally occurring aromatic amino acids studied displaced [(3)H]tryptophan binding with tryptophan and phenylalanine showing higher apparent affinity than histidine, tyrosine, dihydroxyphenylalanine and 5-hydroxytryptophan. These binding sites are proteins in nature as they are sensitive to trypsin and ?-chymotrypsin. It is observed that about 37% of the sites seem to be protected from the proteolytic enzymes by the membrane structure. Furthermore, they are extremely sensitive to phospholipase A(2) presumably because altered membrane phospholipids conduce a conformational change in the binding protein. A considerable degree of stereospecificity was demonstrated with the affinity for l-tryptophan about 90 times higher than that for d-tryptophan. The affinity for l-phenylalanine was 8 times higher than that for d-phenylalanine. Ligand specificity for the aromatic amino acids is remarkable as hydrocinnamic acid, 2-phenylethylamine, 5-hydroxytryptamine, histamine, dopamine, ?-aminobutyric acid, glutamic acid and taurine did not displace [(3)H]tryptophan binding. Therefore, these sites are termed aromatic amino acid binding sites (AABS). Whether or not AABS are involved in neuromodulation at the synapse awaits clarification. If so, the endogenous ligand for the AABS may well be tryptophan.

  5. 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.

  6. Site assessors take note: Water doesn`t always flow downhill

    SciTech Connect

    Shuey, R.W. |

    1996-05-01

    With increasing frequency, geologists are being called as expert witnesses to testify in court that water does not necessarily flow downhill--a fact that has been overlooked by the environmental consulting industry. Environmental site assessments that are performed quickly by unqualified people and within the bounds of very tight budgets are inaccurate because contaminated groundwater from downgradient sites is showing up in upgradient wells. Much of the litigation involving groundwater contamination revolves around the fact that groundwater environments vary--water can behave differently in one environment than it does in another. The regional environment considers the characteristics of groundwater movement in a geologic environment encompassing many square miles, whereas the local or site-specific environment may involve only a single property. Although groundwater at a regional level tends to flow in the direction of the slope of regional topography, many surface and subsurface characteristics will affect the direction of groundwater flow before it reaches the water table.

  7. Hydrazide Reactive Peptide Tags for Site-Specific Protein Labeling

    PubMed Central

    Eldridge, Glenn M.; Weiss, Gregory A.

    2011-01-01

    New site-specific protein labeling (SSPL) reactions for targeting specific, short peptides could be useful for the real time detection of proteins inside of living cells. One SSPL approach matches bioorthogonal reagents with complementary peptides. Here, hydrazide reactive peptides were selected from phage-displayed libraries using reaction-based selections. Selection conditions included washes of varying pH and treatment with NaCNBH3 in order to specifically select reactive carbonyl containing peptides. Selected peptides were fused to T4 lysozyme or synthesized on filter paper for colorimetric assays of the peptide-hydrazide interaction. A peptide-lysozyme protein fusion demonstrated specific, covalent labeling by the Hydrazide Reactive (HyRe) peptides in crude bacterial cell lysates, sufficient for the specific detection of an over-expressed protein fusion. Chemical synthesis of a short HyRe tag variant and subsequent reaction with two structurally distinct hydrazide probes produced covalent adducts observable by MALDI-TOF MS and MS/MS. Rather than isolating reactive carbonyl-containing peptides, we observed reaction with the N–terminal His of HyRe tag 114, amino acid sequence HKSNHSSKNRE, which attacks the hydrazide carbonyl at neutral pH. However, at the pH used during selection wash steps (<6.0), an alternative imine-containing product is formed that can be reduced with sodium cyanoborohydride. MSMS further reveals that this low pH product forms an adduct on Ser6. Further optimization of the novel bimolecular reaction described here could provide a useful tool for in vivo protein labeling and bioconjugate synthesis. The reported selection and screening methods could be widely applicable to the identification of peptides capable of other site-specific protein labeling reactions with bioorthogonal reagents. PMID:21905743

  8. Specific binding sites for muramyl peptides on murine macrophages

    SciTech Connect

    Silverman, D.H.S.; Krueger, J.M.; Karnovsky, M.L.

    1986-03-15

    Two radiolabeled (/sup 125/I) muramyl peptide derivatives of high specific activity were prepared: a tripeptide with an iodinated C-terminal tyrosine methyl ester (Ligand I), and a muramyl tripeptide with a C-terminal lysine derivatized with Bolton-Hunter reagent (Ligand II). These were used to characterize binding of muramyl peptides to monolayers of murine macrophages. Saturable high-affinity binding to resident, caseinate-elicited, and Listeria-activated peritoneal cells was observed with both radioligands. Binding affinities varied with the state of activation of the macrophages, and K/sub D/ values ranged from 48 +/- 33 pM (for resident macrophages, Ligand I) to 1020 +/- 90 pM (for activated macrophages, Ligand II). Specific binding sites were also found on a macrophage-derived cell line. The ability of several unlabeled muramyl peptides to compete with Ligands I and II for their binding sites was tested. Competition was stereospecific and correlated with known biological activities of these compounds (i.e., immunoadjuvanticity, pyrogenicity, and somnogenicity). The sites identified here for Ligands I and II may mediate some of the effects that muramyl peptides have previously been demonstrated to have on macrophages.

  9. 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

  10. Reaction kinetics of some important site-specific endonucleases.

    PubMed Central

    Hinsch, B; Kula, M R

    1981-01-01

    Reaction kinetics of the site-specific endonucleases BamHI, BgIII, C1aI, EcoRI, HpaII, PstI, SaII, SmaI, and XorII were investigated employing some frequently used substrates. Six of these enzymes could be analyzed under steady-state conditions. Kinetic data were obtained from progress curves applying an integrated Michaelis-Menten equation. KM ranged from 4 x 10(-9) M to 4 x 10(-11) M. Activities also spanned two orders of magnitude. In the case of C1aI the analysis of the pre-steady-state kinetics ("burst reaction") allowed the assessment of several rate constants. The rate-limiting step is the very slow dissociation of the enzyme-product complex (0.22 min(-1)). This complex is formed from the enzyme-bound nicked intermediate at a rate of 1.7 min(-1). The introduction of the first cut is again faster by a factor of about 6. SmaI and XorII resembled C1aI in their kinetics. The burst reaction can be used for the easy and unambiguous determination of molar concentrations of site-specific endonucleases in any preparation, which is free of non-specific DNases. PMID:6269074

  11. Towards soft robotic devices for site-specific drug delivery.

    PubMed

    Alici, Gursel

    2015-01-01

    Considerable research efforts have recently been dedicated to the establishment of various drug delivery systems (DDS) that are mechanical/physical, chemical and biological/molecular DDS. In this paper, we report on the recent advances in site-specific drug delivery (site-specific, controlled, targeted or smart drug delivery are terms used interchangeably in the literature, to mean to transport a drug or a therapeutic agent to a desired location within the body and release it as desired with negligibly small toxicity and side effect compared to classical drug administration means such as peroral, parenteral, transmucosal, topical and inhalation) based on mechanical/physical systems consisting of implantable and robotic drug delivery systems. While we specifically focus on the robotic or autonomous DDS, which can be reprogrammable and provide multiple doses of a drug at a required time and rate, we briefly cover the implanted DDS, which are well-developed relative to the robotic DDS, to highlight the design and performance requirements, and investigate issues associated with the robotic DDS. Critical research issues associated with both DDSs are presented to describe the research challenges ahead of us in order to establish soft robotic devices for clinical and biomedical applications. PMID:26415110

  12. Towards soft robotic devices for site-specific drug delivery.

    PubMed

    Alici, Gursel

    2015-01-01

    Considerable research efforts have recently been dedicated to the establishment of various drug delivery systems (DDS) that are mechanical/physical, chemical and biological/molecular DDS. In this paper, we report on the recent advances in site-specific drug delivery (site-specific, controlled, targeted or smart drug delivery are terms used interchangeably in the literature, to mean to transport a drug or a therapeutic agent to a desired location within the body and release it as desired with negligibly small toxicity and side effect compared to classical drug administration means such as peroral, parenteral, transmucosal, topical and inhalation) based on mechanical/physical systems consisting of implantable and robotic drug delivery systems. While we specifically focus on the robotic or autonomous DDS, which can be reprogrammable and provide multiple doses of a drug at a required time and rate, we briefly cover the implanted DDS, which are well-developed relative to the robotic DDS, to highlight the design and performance requirements, and investigate issues associated with the robotic DDS. Critical research issues associated with both DDSs are presented to describe the research challenges ahead of us in order to establish soft robotic devices for clinical and biomedical applications.

  13. Site-specific DNA transesterification catalyzed by a restriction enzyme

    PubMed Central

    Sasnauskas, Giedrius; Connolly, Bernard A.; Halford, Stephen E.; Siksnys, Virginijus

    2007-01-01

    Most restriction endonucleases use Mg2+ to hydrolyze phosphodiester bonds at specific DNA sites. We show here that BfiI, a metal-independent restriction enzyme from the phospholipase D superfamily, catalyzes both DNA hydrolysis and transesterification reactions at its recognition site. In the presence of alcohols such as ethanol or glycerol, it attaches the alcohol covalently to the 5′ terminus of the cleaved DNA. Under certain conditions, the terminal 3′-OH of one DNA strand can attack the target phosphodiester bond in the other strand to create a DNA hairpin. Transesterification reactions on DNA with phosphorothioate linkages at the target bond proceed with retention of stereoconfiguration at the phosphorus, indicating, uniquely for a restriction enzyme, a two-step mechanism. We propose that BfiI first makes a covalent enzyme–DNA intermediate, and then it resolves it by a nucleophilic attack of water or an alcohol, to yield hydrolysis or transesterification products, respectively. PMID:17267608

  14. Thymocyte plasma membrane: the location of specific glucocorticoid binding sites

    SciTech Connect

    Sergeev, P.V.; Kalinin, G.V.; Dukhanin, A.S.

    1987-01-01

    In modern molecular endocrinology it is now possible to determine the localization of receptors for biologically active substances with the aid of ligands, with high affinity for the receptor, immobilized on polymers. The purpose of this paper is to study the ability of hydrocortisone (HC), immobilized on polyvinylpyrrolidone (PVP-HC), to reduce binding of tritium-HC by thymocytes of adrenalectomized rats. It is determined that specific binding sites for HC on rat thymocytes are also accessible for PVP-HC, which, due to the fact that this immobilized version of HC does not penetrate into the cell, leads to the conclusion that the binding sites for HC itself are located in the plasma membrane.

  15. Using site-specific soil samples as a substitution for improved hydrological and nonpoint source predictions.

    PubMed

    Chen, Lei; Wang, Guobo; Zhong, Yucen; Zhao, Xin; Shen, Zhenyao

    2016-08-01

    Soil databases are one of the most important inputs for watershed models, and the quality of soil properties affects how well a model performs. The objectives of this study were to (1) quantify the sensitivity of model outputs to soil properties and to (2) use site-specific soil properties as a substitution for more accurate hydrological and nonpoint source (H/NPS) predictions. Soil samples were collected from a typical mountainous watershed in China, and the impacts of soil sample parameters on H/NPS predictions were quantified using the Soil and Water Assessment Tool (SWAT). The most sensitive parameters related to predicting flow, sediment, and total phosphorus (TP) mainly were the soil hydrological, the channel erosion processes, and the initial soil chemical environment, respectively. When the site-specific soil properties were used, the uncertainties (coefficient of variation) related to predicting the hydrology, sediment and TP decreased by 75∼80 %, 75∼84 %, and 46∼61 %, respectively. Based on changes in the Nash-Sutcliff coefficient, the model performance improved by 4.9 and 19.45 % for the hydrological and sediment model, accordingly. However, site-specific soil properties did not contribute to better TP predictions because of the high spatial variability of the soil P concentrations across the large watershed. Thus, although site-specific soil samples can be used to obtain more accurate H/NPS predictions, more sampling sites are required to apply this method in large watersheds. PMID:27146539

  16. Using site-specific soil samples as a substitution for improved hydrological and nonpoint source predictions.

    PubMed

    Chen, Lei; Wang, Guobo; Zhong, Yucen; Zhao, Xin; Shen, Zhenyao

    2016-08-01

    Soil databases are one of the most important inputs for watershed models, and the quality of soil properties affects how well a model performs. The objectives of this study were to (1) quantify the sensitivity of model outputs to soil properties and to (2) use site-specific soil properties as a substitution for more accurate hydrological and nonpoint source (H/NPS) predictions. Soil samples were collected from a typical mountainous watershed in China, and the impacts of soil sample parameters on H/NPS predictions were quantified using the Soil and Water Assessment Tool (SWAT). The most sensitive parameters related to predicting flow, sediment, and total phosphorus (TP) mainly were the soil hydrological, the channel erosion processes, and the initial soil chemical environment, respectively. When the site-specific soil properties were used, the uncertainties (coefficient of variation) related to predicting the hydrology, sediment and TP decreased by 75∼80 %, 75∼84 %, and 46∼61 %, respectively. Based on changes in the Nash-Sutcliff coefficient, the model performance improved by 4.9 and 19.45 % for the hydrological and sediment model, accordingly. However, site-specific soil properties did not contribute to better TP predictions because of the high spatial variability of the soil P concentrations across the large watershed. Thus, although site-specific soil samples can be used to obtain more accurate H/NPS predictions, more sampling sites are required to apply this method in large watersheds.

  17. Site-specific S-Acylation of Influenza Virus Hemagglutinin

    PubMed Central

    Brett, Katharina; Kordyukova, Larisa V.; Serebryakova, Marina V.; Mintaev, Ramil R.; Alexeevski, Andrei V.; Veit, Michael

    2014-01-01

    S-Acylation of hemagglutinin (HA), the main glycoprotein of influenza viruses, is an essential modification required for virus replication. Using mass spectrometry, we have previously demonstrated specific attachment of acyl chains to individual acylation sites. Whereas the two cysteines in the cytoplasmic tail of HA contain only palmitate, stearate is exclusively attached to a cysteine positioned at the end of the transmembrane region (TMR). Here we analyzed recombinant viruses containing HA with exchange of conserved amino acids adjacent to acylation sites or with a TMR cysteine shifted to a cytoplasmic location to identify the molecular signal that determines preferential attachment of stearate. We first developed a new protocol for sample preparation that requires less material and might thus also be suitable to analyze cellular proteins. We observed cell type-specific differences in the fatty acid pattern of HA: more stearate was attached if human viruses were grown in mammalian compared with avian cells. No underacylated peptides were detected in the mass spectra, and even mutations that prevented generation of infectious virus particles did not abolish acylation of expressed HA as demonstrated by metabolic labeling experiments with [3H]palmitate. Exchange of conserved amino acids in the vicinity of an acylation site had a moderate effect on the stearate content. In contrast, shifting the TMR cysteine to a cytoplasmic location virtually eliminated attachment of stearate. Thus, the location of an acylation site relative to the transmembrane span is the main signal for stearate attachment, but the sequence context and the cell type modulate the fatty acid pattern. PMID:25349209

  18. 75 FR 983 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-07

    ...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463... Crowne Plaza Hotel, 130 Shipyard Drive, Hilton Head, SC 29928. FOR FURTHER INFORMATION CONTACT: Sheron... the Board is to make recommendations to DOE-EM in the areas of environmental restoration,...

  19. 78 FR 16260 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-14

    ...-Specific Advisory Board, Savannah River Site (78 FR 14088). This document makes a correction to that notice... Federal Register of March 4, 2013, in FR Doc. 2013-04875, on page 14088, please make the following... address is Hilton Garden Inn, 1065 Stevens Creek Road, Augusta, GA 30907. The reason for this change...

  20. Rational Design of Antirheumatic Prodrugs Specific for Sites of Inflammation

    PubMed Central

    Onuoha, Shimobi C.; Ferrari, Mathieu; Sblattero, Daniele

    2015-01-01

    Objective Biologic drugs, such as the anti–tumor necrosis factor (anti‐TNF) antibody adalimumab, have represented a breakthrough in the treatment of rheumatoid arthritis. Yet, concerns remain over their lack of efficacy in a sizable proportion of patients and their potential for systemic side effects such as infection. Improved biologic prodrugs specifically targeted to the site of inflammation have the potential to alleviate current concerns surrounding biologic anticytokine therapies. The purpose of this study was to design, construct, and evaluate in vitro and ex vivo the targeting and antiinflammatory capacity of activatable bispecific antibodies. Methods Activatable dual variable domain (aDVD) antibodies were designed and constructed to target intercellular adhesion molecule 1 (ICAM‐1), which is up‐regulated at sites of inflammation, and anti‐TNF antibodies (adalimumab and infliximab). These bispecific molecules included an external arm that targets ICAM‐1 and an internal arm that comprises the therapeutic domain of an anti‐TNF antibody. Both arms were linked to matrix metalloproteinase (MMP)–cleavable linkers. The constructs were tested for their ability to bind and neutralize both in vitro and ex vivo targets. Results Intact aDVD constructs demonstrated significantly reduced binding and anti‐TNF activity in the prodrug formulation as compared to the parent antibodies. Human synovial fluid and physiologic concentrations of MMP enzyme were capable of cleaving the external domain of the antibody, revealing a fully active molecule. Activated antibodies retained the same binding and anti‐TNF inhibitory capacities as the parent molecules. Conclusion The design of a biologic prodrug with enhanced specificity for sites of inflammation (synovium) and reduced specificity for off‐target TNF is described. This construct has the potential to form a platform technology that is capable of enhancing the therapeutic index of drugs for the treatment of

  1. 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

  2. Site-specific polymer modification of therapeutic proteins.

    PubMed

    Kochendoerfer, Gerd G

    2005-12-01

    Recent advances in chemoselective ligation technology have made possible the modification of proteins with polymers in a site-specific and controlled manner. These approaches rely on the incorporation of chemoselective anchors into the protein backbone by either chemical or recombinant means, and subsequent modification with a polymer carrying a complementary linker. As a result, the assembly process and the covalent structure of the resulting protein-polymer conjugate are completely controlled, enabling the rational optimization of drug properties, in particular efficacy and pharmacokinetic properties. Application of chemoselective ligation technologies to cytokines and chemokines has led to the generation of new lead proteins for use as erythropoietic agents and HIV fusion inhibitors.

  3. Chemical tags for site-specific fluorescent labeling of biomolecules.

    PubMed

    Freidel, Christoph; Kaloyanova, Stefka; Peneva, Kalina

    2016-06-01

    This review focuses on the various approaches to covalently attach a chromophore to a biomolecule of interest in site-specific manner. Novel methods like inverse electron-demand Diels-Alder reaction, Pictet-Spengler ligation and enzyme tags like SNAP and Halo-tags are critically discussed and compared to established techniques like copper-free click reaction and native chemical ligation. Selected examples in which the tags have been exploited for in vitro or in vivo imaging are reviewed and evaluated. PMID:26969255

  4. 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

  5. Site-specific dual ink dip pen nanolithography

    NASA Astrophysics Data System (ADS)

    Nafday, Omkar A.; Haaheim, Jason R.; Villagran, Fredy; Levesque, Tom

    2009-05-01

    The ability to deposit two different materials with nanoscale precision at user specified locations is a very important attribute of dip pen nanolithography (DPN). However, the potential of DPN goes beyond simple deposition since DPN used in conjunction with lateral force microscopy (LFM) allows site-specific investigations of nanoscale properties. In this work, we use two different inks, 16-Mercaptohexadecanoic acid (MHA) and 1-octadenethiol (ODT) to show sitespecific dual ink DPN enabled exclusively by our proprietary software. A diamond-dot pattern was created by using a layer-to-layer alignment (LLA) algorithm which enables the MHA (diamond) to be written concentric with the ODT (central dot) pattern. This simple demonstration of multi-ink DPN is not specific to alkanethiol ink systems, but is also applicable to other multi-material patterning, interaction and exchange studies.

  6. Savannah River Site production reactor technical specifications. K Production Reactor

    SciTech Connect

    1996-02-01

    These technical specifications are explicit restrictions on the operation of the Savannah River Site K Production Reactor. They are designed to preserve the validity of the plant safety analysis by ensuring that the plant is operated within the required conditions bounded by the analysis, and with the operable equipment that is assumed to mitigate the consequences of an accident. Technical specifications preserve the primary success path relied upon to detect and respond to accidents. This report describes requirements on thermal-hydraulic limits; limiting conditions for operation and surveillance for the reactor, power distribution control, instrumentation, process water system, emergency cooling and emergency shutdown systems, confinement systems, plant systems, electrical systems, components handling, and special test exceptions; design features; and administrative controls.

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

    PubMed

    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

  8. Multiscale prediction of patient-specific platelet function under flow.

    PubMed

    Flamm, Matthew H; Colace, Thomas V; Chatterjee, Manash S; Jing, Huiyan; Zhou, Songtao; Jaeger, Daniel; Brass, Lawrence F; Sinno, Talid; Diamond, Scott L

    2012-07-01

    During thrombotic or hemostatic episodes, platelets bind collagen and release ADP and thromboxane A(2), recruiting additional platelets to a growing deposit that distorts the flow field. Prediction of clotting function under hemodynamic conditions for a patient's platelet phenotype remains a challenge. A platelet signaling phenotype was obtained for 3 healthy donors using pairwise agonist scanning, in which calcium dye-loaded platelets were exposed to pairwise combinations of ADP, U46619, and convulxin to activate the P2Y(1)/P2Y(12), TP, and GPVI receptors, respectively, with and without the prostacyclin receptor agonist iloprost. A neural network model was trained on each donor's pairwise agonist scanning experiment and then embedded into a multiscale Monte Carlo simulation of donor-specific platelet deposition under flow. The simulations were compared directly with microfluidic experiments of whole blood flowing over collagen at 200 and 1000/s wall shear rate. The simulations predicted the ranked order of drug sensitivity for indomethacin, aspirin, MRS-2179 (a P2Y(1) inhibitor), and iloprost. Consistent with measurement and simulation, one donor displayed larger clots and another presented with indomethacin resistance (revealing a novel heterozygote TP-V241G mutation). In silico representations of a subject's platelet phenotype allowed prediction of blood function under flow, essential for identifying patient-specific risks, drug responses, and novel genotypes.

  9. 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

  10. Highly efficient site-specific transgenesis in cancer cell lines

    PubMed Central

    2012-01-01

    Background Transgenes introduced into cancer cell lines serve as powerful tools for identification of genes involved in cancer. However, the random nature of genomic integration site of a transgene highly influences the fidelity, reliability and level of its expression. In order to alleviate this bottleneck, we characterized the potential utility of a novel PhiC31 integrase-mediated site-specific insertion system (PhiC31-IMSI) for introduction of transgenes into a pre-inserted docking site in the genome of cancer cells. Methods According to this system, a “docking-site” was first randomly inserted into human cancer cell lines and clones with a single copy were selected. Subsequently, an “incoming” vector containing the gene of interest was specifically inserted in the docking-site using PhiC31. Results Using the Pc-3 and SKOV-3 cancer cell lines, we showed that transgene insertion is reproducible and reliable. Furthermore, the selection system ensured that all surviving stable transgenic lines harbored the correct integration site. We demonstrated that the expression levels of reporter genes, such as green fluorescent protein and luciferase, from the same locus were comparable among sister, isogenic clones. Using in vivo xenograft studies, we showed that the genetically altered cancer cell lines retain the properties of the parental line. To achieve temporal control of transgene expression, we coupled our insertion strategy with the doxycycline inducible system and demonstrated tight regulation of the expression of the antiangiogenic molecule sFlt-1-Fc in Pc-3 cells. Furthermore, we introduced the luciferase gene into the insertion cassette allowing for possible live imaging of cancer cells in transplantation assays. We also generated a series of Gateway cloning-compatible intermediate cassettes ready for high-throughput cloning of transgenes and demonstrated that PhiC31-IMSI can be achieved in a high throughput 96-well plate format. Conclusions The novel

  11. Influence of Quasi-Specific Sites on Kinetics of Target DNA Search by a Sequence-Specific DNA-Binding Protein

    PubMed Central

    2015-01-01

    Functions of transcription factors require formation of specific complexes at particular sites in cis-regulatory elements of genes. However, chromosomal DNA contains numerous sites that are similar to the target sequences recognized by transcription factors. The influence of such “quasi-specific” sites on functions of the transcription factors is not well understood at present by experimental means. In this work, using fluorescence methods, we have investigated the influence of quasi-specific DNA sites on the efficiency of target location by the zinc finger DNA-binding domain of the inducible transcription factor Egr-1, which recognizes a 9 bp sequence. By stopped-flow assays, we measured the kinetics of Egr-1’s association with a target site on 143 bp DNA in the presence of various competitor DNAs, including nonspecific and quasi-specific sites. The presence of quasi-specific sites on competitor DNA significantly decelerated the target association by the Egr-1 protein. The impact of the quasi-specific sites depended strongly on their affinity, their concentration, and the degree of their binding to the protein. To quantitatively describe the kinetic impact of the quasi-specific sites, we derived an analytical form of the apparent kinetic rate constant for the target association and used it for fitting to the experimental data. Our kinetic data with calf thymus DNA as a competitor suggested that there are millions of high-affinity quasi-specific sites for Egr-1 among the 3 billion bp of genomic DNA. This study quantitatively demonstrates that naturally abundant quasi-specific sites on DNA can considerably impede the target search processes of sequence-specific DNA-binding proteins. PMID:26502071

  12. Site Specific Genetic Incorporation of Azidophenylalanine in Schizosaccharomyces pombe.

    PubMed

    Shao, Nan; Singh, N Sadananda; Slade, Susan E; Jones, Alexandra M E; Balasubramanian, Mohan K

    2015-01-01

    The diversity of protein functions is impacted in significant part by the chemical properties of the twenty amino acids, which are used as building blocks for nearly all proteins. The ability to incorporate unnatural amino acids (UAA) into proteins in a site specific manner can vastly expand the repertoire of protein functions and also allows detailed analysis of protein function. In recent years UAAs have been incorporated in a site-specific manner into proteins in a number of organisms. In nearly all cases, the amber codon is used as a sense codon, and an orthogonal tRNA/aminoacyl-tRNA synthetase (RS) pair is used to generate amber suppressing tRNAs charged with the UAA. In this work, we have developed tools to incorporate the cross-linking amino acid azido-phenylalanine (AzF) through the use of bacterial tRNA(Tyr) and a modified version of TyrRS, AzFRS, in Schizosaccharomyces pombe, which is an attractive model organism for the study of cell behavior and function. We have incorporated AzF into three different proteins. We show that the majority of AzF is modified to amino-phenyl alanine, but protein cross-linking was still observed. These studies set the stage for exploitation of this new technology for the analysis of S. pombe proteins.

  13. Site-specific criteria for the completion of landfill aftercare.

    PubMed

    Laner, David; Fellner, Johann; Brunner, Paul H

    2012-09-01

    Municipal solid waste (MSW) landfills need to be managed after closure to assure long-term environmental compatibility. Aftercare can be completed when the authorities consider the landfill not likely to pose a threat to humans and the environment. In this work, a methodology for deriving site-specific aftercare completion criteria is presented and its application is illustrated via a case study. The evaluation method combines models addressing waste emission behavior, long-term barrier performance, and pollutant migration to assess the potential impact of landfill emissions on the environment. Based on the definition of acceptable impact levels at certain points of compliance, scenario- and pollutant-specific aftercare completion criteria are derived. The methodology was applied to a closed MSW landfill in Austria and potential aftercare durations were determined. While landfill gas emissions may become environmentally tolerable within decades at the site, leachate-related aftercare measures were expected to be necessary for centuries (primarily as a result of ammonium). Although the evaluation comes with large uncertainties, it allows for linking aftercare intensity and duration with respect to an environmentally compatible state of the landfill in the absence of aftercare. However, further case studies including regulatory review and acceptance are needed to use the methodology in a decision support tool on aftercare completion.

  14. Site Specific Genetic Incorporation of Azidophenylalanine in Schizosaccharomyces pombe

    PubMed Central

    Shao, Nan; Singh, N. Sadananda; Slade, Susan E.; Jones, Alexandra M. E.; Balasubramanian, Mohan K.

    2015-01-01

    The diversity of protein functions is impacted in significant part by the chemical properties of the twenty amino acids, which are used as building blocks for nearly all proteins. The ability to incorporate unnatural amino acids (UAA) into proteins in a site specific manner can vastly expand the repertoire of protein functions and also allows detailed analysis of protein function. In recent years UAAs have been incorporated in a site-specific manner into proteins in a number of organisms. In nearly all cases, the amber codon is used as a sense codon, and an orthogonal tRNA/aminoacyl-tRNA synthetase (RS) pair is used to generate amber suppressing tRNAs charged with the UAA. In this work, we have developed tools to incorporate the cross-linking amino acid azido-phenylalanine (AzF) through the use of bacterial tRNATyr and a modified version of TyrRS, AzFRS, in Schizosaccharomyces pombe, which is an attractive model organism for the study of cell behavior and function. We have incorporated AzF into three different proteins. We show that the majority of AzF is modified to amino-phenyl alanine, but protein cross-linking was still observed. These studies set the stage for exploitation of this new technology for the analysis of S. pombe proteins. PMID:26597962

  15. Site Specific Cleavage Mediated by MMPs Regulates Function of Agrin

    PubMed Central

    McFarlane, Ainsley; Xie, Irene; Overall, Christopher M.; Stetefeld, Jörg

    2012-01-01

    Background Agrin is the key inducer of postsynaptic differentiations at the neuromuscular junction. The multidomain heparan sulfate proteoglycan is mediating via its N-terminal segment the interaction with laminin, whereas the C-terminal portion is responsible for Dystroglycan binding and clustering of the Acetylcholine receptor. Matrix metalloproteinases (MMP) are known to play essential roles in matrix remodeling, degradation and regulation of extracellular signaling networks. Principal Findings Site-specific processing of Agrin provides key insight into regulatory effects of Matrix metalloproteinases (MMPs). Here, we present a detailed study of agrin processing by different MMPs together with a molecular understanding of binding and cleavage at both terminal fragments. The data suggest for a regulatory effect of MMP cleavage at particularly important functional sites of agrin. Cleave of agrin abolishes the agrin-laminin complex formation and the Acetylcholine receptor clustering at the neuromuscular junction. Conclusion/Significance Agrin is a target of specific MMP processing resulting in agrin subfragments with different regulatory activities. MMP processing is a powerful tool to regulate extracellular signaling networks. PMID:22984437

  16. Unsteady Flow in a Supersonic Turbine with Variable Specific Heats

    NASA Technical Reports Server (NTRS)

    Dorney, Daniel J.; Griffin, Lisa W.; Huber, Frank; Sondak, Douglas L.; Turner, James (Technical Monitor)

    2001-01-01

    Modern high-work turbines can be compact, transonic, supersonic, counter-rotating, or use a dense drive gas. The vast majority of modern rocket turbine designs fall into these Categories. These turbines usually have large temperature variations across a given stage, and are characterized by large amounts of flow unsteadiness. The flow unsteadiness can have a major impact on the turbine performance and durability. For example, the Space Transportation Main Engine (STME) fuel turbine, a high work, transonic design, was found to have an unsteady inter-row shock which reduced efficiency by 2 points and increased dynamic loading by 24 percent. The Revolutionary Reusable Technology Turbopump (RRTT), which uses full flow oxygen for its drive gas, was found to shed vortices with such energy as to raise serious blade durability concerns. In both cases, the sources of the problems were uncovered (before turbopump testing) with the application of validated, unsteady computational fluid dynamics (CFD) to the designs. In the case of the RRTT and the Alternate Turbopump Development (ATD) turbines, the unsteady CFD codes have been used not just to identify problems, but to guide designs which mitigate problems due to unsteadiness. Using unsteady flow analyses as a part of the design process has led to turbine designs with higher performance (which affects temperature and mass flow rate) and fewer dynamics problems. One of the many assumptions made during the design and analysis of supersonic turbine stages is that the values of the specific heats are constant. In some analyses the value is based on an average of the expected upstream and downstream temperatures. In stages where the temperature can vary by 300 to 500 K, however, the assumption of constant fluid properties may lead to erroneous performance and durability predictions. In this study the suitability of assuming constant specific heats has been investigated by performing three-dimensional unsteady Navier

  17. Site-specific basal body duplication in Chlamydomonas.

    PubMed

    O'Toole, Eileen T; Dutcher, Susan K

    2014-02-01

    Correct centriole/basal body positioning is required for numerous biological processes, yet how the cell establishes this positioning is poorly understood. Analysis of centriolar/basal body duplication provides a key to understanding basal body positioning and function. Chlamydomonas basal bodies contain structural features that enable specific triplet microtubules to be specified. Electron tomography of cultures enriched in mitotic cells allowed us to follow basal body duplication and identify a specific triplet at which duplication occurs. Probasal bodies elongate in prophase, assemble transitional fibers (TF) and are segregated with a mature basal body near the poles of the mitotic spindle. A ring of nine-singlet microtubules is initiated at metaphase, orthogonal to triplet eight. At telophase/cytokinesis, triplet microtubule blades assemble first at the distal end, rather than at the proximal cartwheel. The cartwheel undergoes significant changes in length during duplication, which provides further support for its scaffolding role. The uni1-1 mutant contains short basal bodies with reduced or absent TF and defective transition zones, suggesting that the UNI1 gene product is important for coordinated probasal body elongation and maturation. We suggest that this site-specific basal body duplication ensures the correct positioning of the basal body to generate landmarks for intracellular patterning in the next generation.

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

    PubMed

    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.

  19. Site-specific basal body duplication in Chlamydomonas.

    PubMed

    O'Toole, Eileen T; Dutcher, Susan K

    2014-02-01

    Correct centriole/basal body positioning is required for numerous biological processes, yet how the cell establishes this positioning is poorly understood. Analysis of centriolar/basal body duplication provides a key to understanding basal body positioning and function. Chlamydomonas basal bodies contain structural features that enable specific triplet microtubules to be specified. Electron tomography of cultures enriched in mitotic cells allowed us to follow basal body duplication and identify a specific triplet at which duplication occurs. Probasal bodies elongate in prophase, assemble transitional fibers (TF) and are segregated with a mature basal body near the poles of the mitotic spindle. A ring of nine-singlet microtubules is initiated at metaphase, orthogonal to triplet eight. At telophase/cytokinesis, triplet microtubule blades assemble first at the distal end, rather than at the proximal cartwheel. The cartwheel undergoes significant changes in length during duplication, which provides further support for its scaffolding role. The uni1-1 mutant contains short basal bodies with reduced or absent TF and defective transition zones, suggesting that the UNI1 gene product is important for coordinated probasal body elongation and maturation. We suggest that this site-specific basal body duplication ensures the correct positioning of the basal body to generate landmarks for intracellular patterning in the next generation. PMID:24166861

  20. 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

  1. Site-specific investigations on aquifer thermal energy storage for space and process cooling

    NASA Astrophysics Data System (ADS)

    Brown, D. R.

    1991-08-01

    The Pacific Northwest Laboratory (PNL) has completed three preliminary site-specific feasibility studies that investigated aquifer thermal energy storage (ATES) for reducing space and process cooling costs. Chilled water stored in an ATES system could be used to meet all or part of the process and/or space cooling loads at the three facilities investigated. Seasonal or diurnal chill ATES systems could be significantly less expensive than a conventional electrically-driven, load-following chiller system at one of the three sites, depending on the cooling water loop return temperature and presumed future electricity escalation rate. For the other two sites investigated, a chill ATES system would be economically competitive with conventional chillers if onsite aquifer characteristics were improved. Well flow rates at one of the sites were adequate, but the expected thermal recovery efficiency was too low. The reverse of this situation was found at the other site, where the thermal recovery efficiency was expected to be adequate, but well flow rates were too low.

  2. Site-specific fab fragment biotinylation at the conserved nucleotide binding site for enhanced Ebola detection.

    PubMed

    Mustafaoglu, Nur; Alves, Nathan J; Bilgicer, Basar

    2015-07-01

    The nucleotide binding site (NBS) is a highly conserved region between the variable light and heavy chains at the Fab domains of all antibodies, and a small molecule that we identified, indole-3-butyric acid (IBA), binds specifically to this site. Fab fragment, with its small size and simple production methods compared to intact antibody, is good candidate for use in miniaturized diagnostic devices and targeted therapeutic applications. However, commonly used modification techniques are not well suited for Fab fragments as they are often more delicate than intact antibodies. Fab fragments are of particular interest for sensor surface functionalization but immobilization results in damage to the antigen binding site and greatly reduced activity due to their truncated size that allows only a small area that can bind to surfaces without impeding antigen binding. In this study, we describe an NBS-UV photocrosslinking functionalization method (UV-NBS(Biotin) in which a Fab fragment is site-specifically biotinylated with an IBA-EG11-Biotin linker via UV energy exposure (1 J/cm(2)) without affecting its antigen binding activity. This study demonstrates successful immobilization of biotinylated Ebola detecting Fab fragment (KZ52 Fab fragment) via the UV-NBS(Biotin) method yielding 1031-fold and 2-fold better antigen detection sensitivity compared to commonly used immobilization methods: direct physical adsorption and NHS-Biotin functionalization, respectively. Utilization of the UV-NBS(Biotin) method for site-specific conjugation to Fab fragment represents a proof of concept use of Fab fragment for various diagnostic and therapeutic applications with numerous fluorescent probes, affinity molecules and peptides.

  3. Specific Initiation Site for Simian Virus 40 Deoxyribonucleic Acid Replication

    PubMed Central

    Thoren, Marilyn M.; Sebring, Edwin D.; Salzman, Norman P.

    1972-01-01

    Replicating simian virus 40 (SV40) deoxyribonucleic acid (DNA) molecules have been isolated under conditions in which the newly synthesized DNA is uniformly labeled with 3H-thymidine. These newly synthesized strands are released from the replicative intermediate molecules by alkaline treatment, and it has been possible to isolate single-stranded SV40 DNA which varies in size from 157,000 daltons (from molecules that are 10% replicated) to 1,360,000 daltons (85% replicated). The rates of duplex formation of newly synthesized DNA have been used to relate their genetic complexity to the extent of DNA replication. As DNA replication proceeds, the time required to effect 50% renaturation of the newly synthesized DNA increases at a proportional rate. The data establish that DNA replication is not initiated at random, but rather that there is a single specific initiation site for DNA replication. PMID:4342054

  4. Site-specific recombinases: molecular machines for the Genetic Revolution.

    PubMed

    Olorunniji, Femi J; Rosser, Susan J; Stark, W Marshall

    2016-03-15

    The fields of molecular genetics, biotechnology and synthetic biology are demanding ever more sophisticated molecular tools for programmed precise modification of cell genomic DNA and other DNA sequences. This review presents the current state of knowledge and development of one important group of DNA-modifying enzymes, the site-specific recombinases (SSRs). SSRs are Nature's 'molecular machines' for cut-and-paste editing of DNA molecules by inserting, deleting or inverting precisely defined DNA segments. We survey the SSRs that have been put to use, and the types of applications for which they are suitable. We also discuss problems associated with uses of SSRs, how these problems can be minimized, and how recombinases are being re-engineered for improved performance and novel applications.

  5. 2'-modified nucleosides for site-specific labeling of oligonucleotides

    NASA Technical Reports Server (NTRS)

    Krider, Elizabeth S.; Miller, Jeremiah E.; Meade, Thomas J.

    2002-01-01

    We report the synthesis of 2'-modified nucleosides designed specifically for incorporating labels into oligonucleotides. Conversion of these nucleosides to phosphoramidite and solid support-bound derivatives proceeds in good yield. Large-scale synthesis of 11-mer oligonucleotides possessing the 2'-modified nucleosides is achieved using these derivatives. Thermal denaturation studies indicate that the presence of 2'-modified nucleosides in 11-mer duplexes has minimal destabilizing effects on the duplex structure when the nucleosides are placed at the duplex termini. The powerful combination of phosphoramidite and support-bound derivatives of 2'-modified nucleosides affords the large-scale preparation of an entirely new class of oligonucleotides. The ability to synthesize oligonucleotides containing label attachment sites at 3', intervening, and 5' locations of a duplex is a significant advance in the development of oligonucleotide conjugates.

  6. Reliable multicast protocol specifications flow control and NACK policy

    NASA Technical Reports Server (NTRS)

    Callahan, John R.; Montgomery, Todd L.; Whetten, Brian

    1995-01-01

    This appendix presents the flow and congestion control schemes recommended for RMP and a NACK policy based on the whiteboard tool. Because RMP uses a primarily NACK based error detection scheme, there is no direct feedback path through which receivers can signal losses through low buffer space or congestion. Reliable multicast protocols also suffer from the fact that throughput for a multicast group must be divided among the members of the group. This division is usually very dynamic in nature and therefore does not lend itself well to a priori determination. These facts have led the flow and congestion control schemes of RMP to be made completely orthogonal to the protocol specification. This allows several differing schemes to be used in different environments to produce the best results. As a default, a modified sliding window scheme based on previous algorithms are suggested and described below.

  7. Development of site-specific water quality criteria for copper

    SciTech Connect

    Giere, M.A.; McIntyre, D.O.; DeGraeve, G.M.

    1995-12-31

    Under its current operating system, the final effluent from a copper mining facility consistently meets its effluent limitation for copper. A change in mining practices to solution mining will result in a decrease in the hardness of the final effluent. The reduced hardness of the effluent will lower the effluent limit for copper to a concentration which cannot be achieved. The water-effect ratio (WER) procedure was selected to develop a site-specific criterion continuous concentration for copper for the effluent and it`s receiving stream. WER procedures followed those described in EPA`s ``Interim Guidance on Determination and Use of Water-Effect Ratios for Metals`` (1994). Three WER determinations were made using simulated downstream water as the site water. 48-hour acute Ceriodaphnia dubia and 96-hour acute fathead minnow toxicity tests were selected as the primary and secondary tests, respectively for use in the WER determinations. The results of the three WER determinations will be presented, as will the process used for predicting future effluent quality and permit compliance.

  8. Site-specific anticancer effects of dietary flavonoid quercetin.

    PubMed

    Sak, Katrin

    2014-01-01

    Food-derived flavonoid quercetin, widely distributed in onions, apples, and tea, is able to inhibit growth of various cancer cells indicating that this compound can be considered as a good candidate for anticancer therapy. Although the exact mechanism of this action is not thoroughly understood, behaving as antioxidant and/or prooxidant as well as modulating different intracellular signalling cascades may all play a certain role. Such inhibitory activity of quercetin has been shown to depend first of all on cell lines and cancer types; however, no comprehensive site-specific analysis of this effect has been published. In this review article, cytotoxicity constants of quercetin measured in various human malignant cell lines of different origin were compiled from literature and a clear cancer selective action was demonstrated. The most sensitive malignant sites for quercetin revealed to be cancers of blood, brain, lung, uterine, and salivary gland as well as melanoma whereas cytotoxic activity was higher in more aggressive cells compared to the slowly growing cells showing that the most harmful cells for the organism are probably targeted. More research is needed to overcome the issues of poor water solubility and relatively low bioavailability of quercetin as the major obstacles limiting its clinical use. PMID:24377461

  9. 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

  10. Interplay of Proximal Flow Confluence and Distal Flow Divergence in Patient-Specific Vertebrobasilar System.

    PubMed

    Yin, Xiaoping; Huang, Xu; Feng, Yundi; Tan, Wenchang; Liu, Huaijun; Huo, Yunlong

    2016-01-01

    Approximately one-quarter of ischemic strokes involve the vertebrobasilar arterial system that includes the upstream flow confluence and downstream flow divergence. A patient-specific hemodynamic analysis is needed to understand the posterior circulation. The objective of this study is to determine the distribution of hemodynamic parameters in the vertebrobasilar system, based on computer tomography angiography images. Here, the interplay of upstream flow confluence and downstream flow divergence was hypothesized to be a determinant factor for the hemodynamic distribution in the vertebrobasilar system. A computational fluid dynamics model was used to compute the flow fields in patient-specific vertebrobasilar models (n = 6). The inlet and outlet boundary conditions were the aortic pressure waveform and flow resistances, respectively. A 50% reduction of total outlet area was found to induce a ten-fold increase in surface area ratio of low time-averaged wall shear stress (i.e., TAWSS ≤ 4 dynes/cm2). This study enhances our understanding of the posterior circulation associated with the incidence of atherosclerotic plaques. PMID:27467755

  11. Interplay of Proximal Flow Confluence and Distal Flow Divergence in Patient-Specific Vertebrobasilar System

    PubMed Central

    Yin, Xiaoping; Huang, Xu; Feng, Yundi; Tan, Wenchang; Liu, Huaijun

    2016-01-01

    Approximately one-quarter of ischemic strokes involve the vertebrobasilar arterial system that includes the upstream flow confluence and downstream flow divergence. A patient-specific hemodynamic analysis is needed to understand the posterior circulation. The objective of this study is to determine the distribution of hemodynamic parameters in the vertebrobasilar system, based on computer tomography angiography images. Here, the interplay of upstream flow confluence and downstream flow divergence was hypothesized to be a determinant factor for the hemodynamic distribution in the vertebrobasilar system. A computational fluid dynamics model was used to compute the flow fields in patient-specific vertebrobasilar models (n = 6). The inlet and outlet boundary conditions were the aortic pressure waveform and flow resistances, respectively. A 50% reduction of total outlet area was found to induce a ten-fold increase in surface area ratio of low time-averaged wall shear stress (i.e., TAWSS ≤ 4 dynes/cm2). This study enhances our understanding of the posterior circulation associated with the incidence of atherosclerotic plaques. PMID:27467755

  12. Interplay of Proximal Flow Confluence and Distal Flow Divergence in Patient-Specific Vertebrobasilar System.

    PubMed

    Yin, Xiaoping; Huang, Xu; Feng, Yundi; Tan, Wenchang; Liu, Huaijun; Huo, Yunlong

    2016-01-01

    Approximately one-quarter of ischemic strokes involve the vertebrobasilar arterial system that includes the upstream flow confluence and downstream flow divergence. A patient-specific hemodynamic analysis is needed to understand the posterior circulation. The objective of this study is to determine the distribution of hemodynamic parameters in the vertebrobasilar system, based on computer tomography angiography images. Here, the interplay of upstream flow confluence and downstream flow divergence was hypothesized to be a determinant factor for the hemodynamic distribution in the vertebrobasilar system. A computational fluid dynamics model was used to compute the flow fields in patient-specific vertebrobasilar models (n = 6). The inlet and outlet boundary conditions were the aortic pressure waveform and flow resistances, respectively. A 50% reduction of total outlet area was found to induce a ten-fold increase in surface area ratio of low time-averaged wall shear stress (i.e., TAWSS ≤ 4 dynes/cm2). This study enhances our understanding of the posterior circulation associated with the incidence of atherosclerotic plaques.

  13. 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

  14. Investigation of non-specific signals in nanoporous flow-through and flow-over based sensors.

    PubMed

    Kumar, Neeraj; Froner, Elena; Guider, Romain; Scarpa, Marina; Bettotti, Paolo

    2014-03-21

    Porous materials are ideal hosts to fabricate high sensitivity devices. Their large specific area and the possibility to modify the type and the strength of the matrix-analyte interactions allow the realization of sensors with finely tailored characteristics. In this article, we investigate how mass transport across the nanoporous structure influences the response due to the non-specific signal by comparing flow-through versus flow-over geometries. We observed a systematic overestimation of the sensitivity for porous substrate devices made of closed-ended pores compared with open-ended pore ones. Our analysis shows that such an effect is due to (unbound) analytes or contaminants that remain trapped within the pores and are not removed by rinsing of the sample. This result was verified by measuring similar samples in both flow through and flow over configurations, as well as their residual response after blockage of all their active sites. We also notice that sensors based on free-standing membranes show similar results independent of the fact that mass transport is induced by either an external pressure source or simply by Brownian motions.

  15. 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

  16. Inducible site-specific recombination in myelinating cells.

    PubMed

    Doerflinger, Nathalie H; Macklin, Wendy B; Popko, Brian

    2003-01-01

    To explore the function of genes expressed by myelinating cells we have developed a model system that allows for the inducible ablation of predetermined genes in oligodendrocytes and Schwann cells. The Cre/loxP recombination system provides the opportunity to generate tissue-specific somatic mutations in mice. We have used a fusion protein between the Cre recombinase and a mutated ligand-binding domain of the human estrogen receptor (CreER(T)) to obtain inducible, site-specific recombination. CreER(T) expression was placed under the transcriptional control of the regulatory sequences of the myelin proteolipid protein (PLP) gene, which is abundantly expressed in oligodendrocytes and to a lesser extent in Schwann cells. The CreER(T) fusion protein translocated to the nucleus and mediated the recombination of a LacZ reporter transgene in myelinating cells of PLP/CreER(T) mice injected with the synthetic steroid tamoxifen. In untreated animals CreER(T) remained cytoplasmic, and there was no evidence of recombination. The PLP/ CreER(T) animals should be very useful in elucidating and distinguishing a particular gene's function in the formation and maintenance of the myelin sheath and in analyzing mature oligodendrocyte function in pathological conditions. PMID:12481300

  17. Site-specific protein labeling with SNAP-tags.

    PubMed

    Cole, Nelson B

    2013-09-24

    Site-specific labeling of cellular proteins with chemical probes is a powerful tool for studying protein function in living cells. A number of small peptide and protein tags have been developed that can be labeled with synthetic probes with high efficiencies and specificities and provide flexibility not available with fluorescent proteins. The SNAP-tag is a modified form of the DNA repair enzyme human O(6)-alkylguanine-DNA-alkyltransferase, and undergoes a self-labeling reaction to form a covalent bond with O(6)-benzylguanine (BG) derivatives. BG can be modified with a wide variety of fluorophores and other reporter compounds, generally without affecting the reaction with the SNAP-tag. In this unit, basic strategies for labeling SNAP-tag fusion proteins, both for live cell imaging and for in vitro analysis, are described. This includes a description of a releasable SNAP-tag probe that allows the user to chemically cleave the fluorophore from the labeled SNAP-tag fusion. In vitro labeling of purified SNAP-tag fusions is briefly described.

  18. Flow-specific physical properties of coconut flours

    NASA Astrophysics Data System (ADS)

    Manikantan, Musuvadi R.; Kingsly Ambrose, Rose P.; Alavi, Sajid

    2015-10-01

    Coconut milk residue and virgin coconut oil cake are important co-products of virgin coconut oil that are used in the animal feed industry. Flour from these products has a number of potential human health benefits and can be used in different food formulations. The objective of this study was to find out the flow-specific physical properties of coconut flours at three moisture levels. Coconut milk residue flour with 4.53 to 8.18% moisture content (w.b.) had bulk density and tapped density of 317.37 to 312.65 and 371.44 to 377.23 kg m-3, respectively; the corresponding values for virgin coconut oil cake flour with 3.85 to 7.98% moisture content (wet basis) were 611.22 to 608.68 and 663.55 to 672.93 kg m-3, respectively. The compressibility index and Hausner ratio increased with moisture. The angle of repose increased with moisture and ranged from 34.12 to 36.20 and 21.07 to 23.82° for coconut milk residue flour and virgin coconut oil cake flour, respectively. The coefficient of static and rolling friction increased with moisture for all test surfaces, with the plywood offering more resistance to flow than other test surfaces. The results of this study will be helpful in designing handling, flow, and processing systems for coconut milk residue and virgin coconut oil cake flours.

  19. Flow Simulation to Enable Patient Specific Virtual Surgical Planning

    NASA Astrophysics Data System (ADS)

    Jansen, Kenneth; Taylor, Charles; Mueller, Jens

    2003-11-01

    The current paradigm for interventional and surgery planning for the treatment of cardiovascular disease relies exclusively on diagnostic imaging data to define the present state of the patient, empirical data to evaluate the efficacy of prior treatments for similar patients, and the judgement of the surgeon to decide on a preferred treatment. The individual variability and inherent complexity of human biological systems is such that diagnostic imaging and empirical data alone are insufficient to predict the outcome of a given treatment for an individual patient. We have proposed a new paradigm of predictive medicine in which the physician utilizes computational tools to construct and evaluate a combined anatomic/physiologic model to predict differential changes in blood flow for alternative treatment plans for an individual patient. Ideally, these systems would provide an integrated set of image segmentation, geometric solid modeling, automatic finite element mesh generation, computational mechanics and scientific visualization tools accessible through an intuitive human-computer interface. In this talk we focus on the flow simulation aspects of this project. Error estimators for transient flow analyses have been developed and implemented to focus computational resources on the areas where they may have provide the greatest improvement. We will describe these error estimators and apply them to adaptive as well as uniform refinement simulations and compare the accuracy and performance to available experimental data in porcine bypass models that have been carried out specifically for this purpose.

  20. DephosSite: a machine learning approach for discovering phosphotase-specific dephosphorylation sites.

    PubMed

    Wang, Xiaofeng; Yan, Renxiang; Song, Jiangning

    2016-01-01

    Protein dephosphorylation, which is an inverse process of phosphorylation, plays a crucial role in a myriad of cellular processes, including mitotic cycle, proliferation, differentiation, and cell growth. Compared with tyrosine kinase substrate and phosphorylation site prediction, there is a paucity of studies focusing on computational methods of predicting protein tyrosine phosphatase substrates and dephosphorylation sites. In this work, we developed two elegant models for predicting the substrate dephosphorylation sites of three specific phosphatases, namely, PTP1B, SHP-1, and SHP-2. The first predictor is called MGPS-DEPHOS, which is modified from the GPS (Group-based Prediction System) algorithm with an interpretable capability. The second predictor is called CKSAAP-DEPHOS, which is built through the combination of support vector machine (SVM) and the composition of k-spaced amino acid pairs (CKSAAP) encoding scheme. Benchmarking experiments using jackknife cross validation and 30 repeats of 5-fold cross validation tests show that MGPS-DEPHOS and CKSAAP-DEPHOS achieved AUC values of 0.921, 0.914 and 0.912, for predicting dephosphorylation sites of the three phosphatases PTP1B, SHP-1, and SHP-2, respectively. Both methods outperformed the previously developed kNN-DEPHOS algorithm. In addition, a web server implementing our algorithms is publicly available at http://genomics.fzu.edu.cn/dephossite/ for the research community.

  1. Lunar heat flow: Regional prospective of the Apollo landing sites

    NASA Astrophysics Data System (ADS)

    Siegler, M. A.; Smrekar, S. E.

    2014-01-01

    reexamine the Apollo Heat Flow Experiment in light of new orbital data. Using three-dimensional thermal conduction models, we examine effects of crustal thickness, density, and radiogenic abundance on measured heat flow values at the Apollo 15 and 17 sites. These models show the importance of regional context on heat flux measurements. We find that measured heat flux can be greatly altered by deep subsurface radiogenic content and crustal density. However, total crustal thickness and the presence of a near-surface radiogenic-rich ejecta provide less leverage, representing only minor (<1.5 mW m-2) perturbations on surface heat flux. Using models of the crust implied by Gravity Recovery and Interior Laboratory results, we found that a roughly 9-13 mW m-2 mantle heat flux best approximate the observed heat flux. This equates to a total mantle heat production of 2.8-4.1 × 1011 W. These heat flow values could imply that the lunar interior is slightly less radiogenic than the Earth's mantle, perhaps implying that a considerable fraction of terrestrial mantle material was incorporated at the time of formation. These results may also imply that heat flux at the crust-mantle boundary beneath the Procellarum potassium, rare earth element, and phosphorus (KREEP) Terrane (PKT) is anomalously elevated compared to the rest of the Moon. These results also suggest that a limited KREEP-rich layer exists beneath the PKT crust. If a subcrustal KREEP-rich layer extends below the Apollo 17 landing site, required mantle heat flux can drop to roughly 7 mW m-2, underlining the need for future heat flux measurements outside of the radiogenic-rich PKT region.

  2. Modeling Groundwater Flow and Infiltration at Potential Low-Level Radioactive Waste Disposal Sites in Taiwan

    NASA Astrophysics Data System (ADS)

    Arnold, B. W.; Lee, C.; Ma, C.; Knowlton, R. G.

    2006-12-01

    Taiwan is evaluating representative sites for the potential disposal of low-level radioactive waste (LLW), including consideration of shallow land burial and cavern disposal concepts. A representative site for shallow land burial is on a small island in the Taiwan Strait with basalt bedrock. The shallow land burial concept includes an engineered cover to limit infiltration into the waste disposal cell. A representative site for cavern disposal is located on the southeast coast of Taiwan. The tunnel system for this disposal concept would be several hundred meters below the mountainous land surface in argillite bedrock. The LLW will consist of about 966,000 drums, primarily from the operation and decommissioning of four nuclear power plants. Sandia National Laboratories and the Institute of Nuclear Energy Research have collaborated to develop performance assessment models to evaluate the long-term safety of LLW disposal at these representative sites. Important components of the system models are sub-models of groundwater flow in the natural system and infiltration through the engineered cover for the shallow land burial concept. The FEHM software code was used to simulate groundwater flow in three-dimensional models at both sites. In addition, a higher-resolution two-dimensional model was developed to simulate flow through the engineered tunnel system at the cavern site. The HELP software was used to simulate infiltration through the cover at the island site. The primary objective of these preliminary models is to provide a modeling framework, given the lack of site-specific data and detailed engineering design specifications. The steady-state groundwater flow model at the island site uses a specified recharge boundary at the land surface and specified head at the island shoreline. Simulated groundwater flow vectors are extracted from the FEHM model along a cross section through one of the LLW disposal cells for utilization in radionuclide transport simulations in

  3. 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

  4. Monomeric site-specific nucleases for genome editing

    PubMed Central

    Kleinstiver, Benjamin P.; Wolfs, Jason M.; Kolaczyk, Tomasz; Roberts, Alanna K.; Hu, Sherry X.; Edgell, David R.

    2012-01-01

    Targeted manipulation of complex genomes often requires the introduction of a double-strand break at defined locations by site-specific DNA endonucleases. Here, we describe a monomeric nuclease domain derived from GIY-YIG homing endonucleases for genome-editing applications. Fusion of the GIY-YIG nuclease domain to three-member zinc-finger DNA binding domains generated chimeric GIY-zinc finger endonucleases (GIY-ZFEs). Significantly, the I-TevI-derived fusions (Tev-ZFEs) function in vitro as monomers to introduce a double-strand break, and discriminate in vitro and in bacterial and yeast assays against substrates lacking a preferred 5′-CNNNG-3′ cleavage motif. The Tev-ZFEs function to induce recombination in a yeast-based assay with activity on par with a homodimeric Zif268 zinc-finger nuclease. We also fused the I-TevI nuclease domain to a catalytically inactive LADGLIDADG homing endonuclease (LHE) scaffold. The monomeric Tev-LHEs are active in vivo and similarly discriminate against substrates lacking the 5′-CNNNG-3′ motif. The monomeric Tev-ZFEs and Tev-LHEs are distinct from the FokI-derived zinc-finger nuclease and TAL effector nuclease platforms as the GIY-YIG domain alleviates the requirement to design two nuclease fusions to target a given sequence, highlighting the diversity of nuclease domains with distinctive biochemical properties suitable for genome-editing applications. PMID:22566637

  5. 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.

  6. Oral bioavailability of chromium from a specific site

    SciTech Connect

    Witmer, C.M.; Harris, R. ); Shupack, S.I. )

    1991-05-01

    Analysis of soil from a specific site in New Jersey indicated a low level of sodium and chromium present as a calcium compound. Chromium was then administered orally to young, mature male rats at a level of 240 {mu}g/kg for 14 days as chromium-contaminated soil, as CaCrO{sub 4}, and as an equimolar mixture of the soil and calcium salts for 14 days. The rats were sacrificed 24 hours after the last dosing, and tissues were taken immediately for chromium analysis. Blood, muscle, and liver contained the highest levels of chromium in these animals, although kidney contained the highest concentration per gram of tissue. Total amount of chromium in the tissues was less than 2% of the administered chromium. In a study of the excretion of chromium, the animals were dosed orally for 8 days and the chromium in feces and urine was determined on days 1, 2, 7, and 8. The animals administered the chromium in soil had higher levels of chromium in both urine and feces on all days compared to the group fed the CaCrO{sub 4}. The total recovery of chromium in any of the 2-day periods was less than 50% of the chromium administered during that period.

  7. Site-specific risk assessment in contaminated vegetable gardens.

    PubMed

    Sipter, Emese; Rózsa, Eniko; Gruiz, Katalin; Tátrai, Erzsébet; Morvai, Veronika

    2008-04-01

    A field survey was carried on in Gyöngyösoroszi, Hungary, near to an abandoned lead/zinc mine to analyse the metal contamination of flooded and non-flooded vegetable gardens, and to evaluate the health risks to local population. Contamination levels of arsenic, cadmium, lead, mercury and zinc were measured in soil and homegrown vegetable samples and bioconcentration factors and hazard indices were calculated. The high metal contents of flooded vegetable gardens were caused by floods, the results indicated significant differences between flooded and non-flooded vegetable gardens. The most accumulating vegetable was sorrel, the most mobile elements were cadmium and lead. Arsenic was not available for vegetables. The health risk was calculated for two exposure routes: ingestion of soil and ingestion of vegetables. The site-specific exposure parameters were established after a population based survey and a special equation was created to calculate the health risk due to homegrown vegetable consumption. The highest risk was associated with ingestion of vegetables, the most hazardous element being lead. The hazard index did not exceed the threshold value of one in flooded or non-flooded gardens. The analyses of health risk indicated that despite the high metal concentrations of soil the contamination of vegetable gardens does not pose an unacceptable risk to the inhabitants of the village. PMID:18191173

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

    PubMed

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

    2015-05-01

    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 (M w 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

  9. Site specific plan. [Environmental Restoration and Waste Management, Savannah River Site

    SciTech Connect

    Hutchison, J.; Jernigan, G.

    1989-12-01

    The Environmental Restoration and Waste Management Five-Year Plan (FYP) covers the period for FY 1989 through FY 1995. The plan establishes a Department of Energy -- Headquarters (DOE-HQ) agenda for cleanup and compliance against which overall progress can be measured. The FYP covers three areas: Corrective Activities, Environmental Restoration, and Waste Management Operations. Corrective Activities are those activities necessary to bring active or standby facilities into compliance with local, state, and federal environmental regulations. Environmental restoration activities include the assessment and cleanup of surplus facilities and inactive waste sites. Waste management operations includes the treatment, storage, and disposal of wastes which are generated as a result of ongoing operations. This Site Specific Plan (SSP) has been prepared by the Savannah River Site (SRS) in order to show how environmental restoration and waste management activities that were identified during the preparation of the FYP will be implemented, tracked, and reported. The SSP describes DOE Savannah River (DOE-SR) and operating contractor, Westinghouse Savannah River Company (WSRC), organizations that are responsible, for undertaking the activities identified in this plan. 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. 8 refs., 46 figs., 23 tabs.

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

    PubMed

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

    2012-09-01

    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.

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

    PubMed

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

    2012-09-01

    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. PMID:22861645

  12. Understanding site-specific PSHA results by hazard deaggregation into site intensities

    NASA Astrophysics Data System (ADS)

    Klügel, Jens-Uwe

    2016-04-01

    From 1998 till 2015 Swiss Nuclear Power Plants sponsored a set of comprehensive site-specific PSHA-studies (PEGASOS, PEGASOS Refinement Project) to define review level earthquakes as well as the input for their plant specific probabilistic risk assessments. The studies were performed following the US SSHAC procedures at their most elaborated level 4. Safety experts and risk analysts of Swiss Nuclear Power Plants recently have been mandated to implement the final results of the studies in their risk assessment studies. For an in depth understanding of the consequences of the hazard on practical decision making it is reasonable to compare the new studies with the original hazard assessment studies used for the development of the seismic design basis of the plants. These studies were performed in terms of intensity. For the comparison a hazard deaggregation methodology was developed that allows for the conversion of standard uniform hazard spectra (UHS) into site-intensity (factors) hazard curves. The method was applied for the nuclear power plant Goesgen using the PEGASOS hazard. The results were compared with the results of earlier hazard studies as well as with actual deterministic and probabilistic hazard studies performed independently from the PEGASOS study in terms of EMS-98 intensities. The comparison revealed that the results of the PEGASOS study led to site intensity factors comparable with the results of studies from the 1970-ies. The study may have under predicted the safety importance of historical large earthquakes like the Basel earthquake of 1356. Therefore, an important conclusion is that probabilistic hazard studies for critical infrastructures have to be accompanied by an independent physics-based study (modelling hazard assessment) that allows to perform a safety evaluation of historical earthquakes. The paper presents the deaggregation methodology and the results of its application.

  13. 30 CFR 46.11 - Site-specific hazard awareness training.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... STONE, SURFACE CLAY, COLLOIDAL PHOSPHATE, OR SURFACE LIMESTONE MINES. § 46.11 Site-specific hazard... hazard awareness training for each mine. (d) Site-specific hazard awareness training is information...

  14. 30 CFR 46.11 - Site-specific hazard awareness training.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... STONE, SURFACE CLAY, COLLOIDAL PHOSPHATE, OR SURFACE LIMESTONE MINES. § 46.11 Site-specific hazard... hazard awareness training for each mine. (d) Site-specific hazard awareness training is information...

  15. 30 CFR 46.11 - Site-specific hazard awareness training.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... STONE, SURFACE CLAY, COLLOIDAL PHOSPHATE, OR SURFACE LIMESTONE MINES. § 46.11 Site-specific hazard... hazard awareness training for each mine. (d) Site-specific hazard awareness training is information...

  16. 30 CFR 46.11 - Site-specific hazard awareness training.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... STONE, SURFACE CLAY, COLLOIDAL PHOSPHATE, OR SURFACE LIMESTONE MINES. § 46.11 Site-specific hazard... hazard awareness training for each mine. (d) Site-specific hazard awareness training is information...

  17. 30 CFR 46.11 - Site-specific hazard awareness training.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... STONE, SURFACE CLAY, COLLOIDAL PHOSPHATE, OR SURFACE LIMESTONE MINES. § 46.11 Site-specific hazard... hazard awareness training for each mine. (d) Site-specific hazard awareness training is information...

  18. 75 FR 56526 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-16

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION... Environmental Management Site-Specific Advisory Board (EM SSAB), Portsmouth. The Federal Advisory Committee Act... areas of environmental restoration, waste management and related activities. Tentative Agenda...

  19. 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

  20. Unsaturated water flow at the Hanford site: a review of literature and annotated bibliography

    SciTech Connect

    Gee, G.W.; Heller, P.R.

    1985-05-01

    As an initial part of a performance assessment task for the Hanford Waste Management Plan, we have reviewed research done over a number of years on unsaturated water flow at the Hanford site near Richland, Washington. This work will be helpful in assessing the probability that water infiltrating the ground surface may eventually contribute to ground-water recharge at the site. Reports done primarily by Atlantic Richfield Hanford, Rockwell Hanford Operations, and Pacific Northwest Laboratory were reviewed for their pertinence to unsaturated water flow and specifically for information that could help resolve the question of whether recharge of the unconfined aquifer by natural precipitation (meteoric water) is occurring on the Hanford site and, if so, what are the expected ranges of recharge. The reports that we reviewed are primarily technical reports detailing the physical and hydrologic characteristics of soils and sediments at specific locations on the Hanford site, or describing studies that have either monitored or simulated such parameters as surface evaporation, soil moisture storage, and deep drainage (recharge). The appendix of this report provides abstracts and annotations on 24 key technical reports on subjects related to estimation of recharge at Hanford. 66 refs.

  1. The dynamics of pain: Evidence for simultaneous site-specific habituation and site-nonspecific sensitization in thermal pain

    PubMed Central

    Jepma, Marieke; Jones, Matt; Wager, Tor D.

    2014-01-01

    Repeated exposure to noxious stimuli changes their painfulness, due to multiple adaptive processes in the peripheral and central nervous system. Somewhat paradoxically, repeated stimulation can produce an increase (sensitization) or a decrease (habituation) in pain. Adaptation processes may also be body-site-specific or operate across body sites, and considering this distinction may help explain the conditions under which habituation vs. sensitization occurs. To dissociate the effects of site-specific and site-nonspecific adaptation processes, we examined reported pain in 100 participants during counterbalanced sequences of noxious thermal stimulation on multiple skin sites. Analysis of pain ratings revealed two opposing sequential effects: repeated stimulations of the same skin site produced temperature-dependent habituation, whereas repeated stimulations across different sites produced sensitization. Stimulation trials were separated by ~20 seconds and sensitization was unrelated to the distance between successively stimulated sites, suggesting that neither temporal nor spatial summation occurred. To explain these effects, we propose a dynamic model with two adaptation processes, one site-specific and one site-nonspecific. The model explains 93% of the variance in the group-mean pain ratings after controlling for current stimulation temperature, with its estimated parameters showing evidence for habituation for the site-specific process and sensitization for the site-nonspecific process. The two pain-adaptation processes revealed in this study, and the ability to disentangle them, may hold keys to understanding multiple pain-regulatory mechanisms and their disturbance in chronic-pain syndromes. Perspective This article presents novel evidence for simultaneous site-specific habituation and site-nonspecific sensitization in thermal pain, which can be disentangled (and the direction and strength of each process estimated) by a dynamic model. The dissociation of site-specific

  2. Overall Ventilation System Flow Network Calculation for Site Recommendation

    SciTech Connect

    Jeff J. Steinhoff

    2001-08-02

    The scope of this calculation is to determine ventilation system resistances, pressure drops, airflows, and operating cost estimates for the Site Recommendation (SR) design as detailed in the ''Site Recommendation Subsurface Layout'' (BSC (Bechtel SAIC Company) 2001a). The statutory limit for emplacement of waste in Yucca Mountain is 70,000 metric tons of uranium (MTU) and is considered the base case for this report. The objective is to determine the overall repository system ventilation flow network for the monitoring phase during normal operations and to provide a basis for the system description document design descriptions. Any values derived from this calculation will not be used to support construction, fabrication, or procurement. The work scope is identified in the ''Technical Work Plan for Subsurface Design Section FY01 Work Activities'' (CRWMS M&O 2001, pp. 6 and 13). In accordance with the technical work plan this calculation was prepared in accordance with AP-3.12Q, ''Calculations'' and other procedures invoked by AP-3.12Q. It also incorporates the procedure AP-SI1.Q, ''Software Management''.

  3. 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.

  4. SITE SPECIFIC REFERENCE PERSON PARAMETERS AND DERIVED CONCENTRATION STANDARDS FOR THE SAVANNAH RIVER SITE

    SciTech Connect

    Jannik, T.

    2013-03-14

    The purpose of this report is twofold. The first is to develop a set of behavioral parameters for a reference person specific for the Savannah River Site (SRS) such that the parameters can be used to determine dose to members of the public in compliance with Department of Energy (DOE) Order 458.1 “Radiation Protection of the Public and the Environment.” A reference person is a hypothetical, gender and age aggregation of human physical and physiological characteristics arrived at by international consensus for the purpose of standardizing radiation dose calculations. DOE O 458.1 states that compliance with the annual dose limit of 100 mrem (1 mSv) to a member of the public may be demonstrated by calculating the dose to the maximally exposed individual (MEI) or to a representative person. Historically, for dose compliance, SRS has used the MEI concept, which uses adult dose coefficients and adult male usage parameters. Beginning with the 2012 annual site environmental report, SRS will be using the representative person concept for dose compliance. The dose to a representative person will be based on 1) the SRS-specific reference person usage parameters at the 95th percentile of appropriate national or regional data, which are documented in this report, 2) the reference person (gender and age averaged) ingestion and inhalation dose coefficients provided in DOE Derived Concentration Technical Standard (DOE-STD-1196-2011), and 3) the external dose coefficients provided in the DC_PAK3 toolbox. The second purpose of this report is to develop SRS-specific derived concentration standards (DCSs) for all applicable food ingestion pathways, ground shine, and water submersion. The DCS is the concentration of a particular radionuclide in water, in air, or on the ground that results in a member of the public receiving 100 mrem (1 mSv) effective dose following continuous exposure for one year. In DOE-STD-1196-2011, DCSs were developed for the ingestion of water, inhalation of

  5. The implications of episodic nonequilibrium fracture-matrix flow on site suitability and total system performance

    SciTech Connect

    Nitao, J.J.; Buscheck, T.A.; Chesnut, D.A.

    1992-04-01

    We apply our work on fracture- and matrix-dominated flow to develop a conceptual model of hydrological flow processes in the unsaturated zone at Yucca Mountain. The possibility of fracture-dominated flow is discussed, and various deductions are made on its impact on natural and total system performance, site characterization activities, and site suitability determination.

  6. Configuration and specifications of an Unmanned Aerial Vehicle (UAV) for early site specific weed management.

    PubMed

    Torres-Sánchez, Jorge; López-Granados, Francisca; De Castro, Ana Isabel; Peña-Barragán, José Manuel

    2013-01-01

    A new aerial platform has risen recently for image acquisition, the Unmanned Aerial Vehicle (UAV). This article describes the technical specifications and configuration of a UAV used to capture remote images for early season site- specific weed management (ESSWM). Image spatial and spectral properties required for weed seedling discrimination were also evaluated. Two different sensors, a still visible camera and a six-band multispectral camera, and three flight altitudes (30, 60 and 100 m) were tested over a naturally infested sunflower field. The main phases of the UAV workflow were the following: 1) mission planning, 2) UAV flight and image acquisition, and 3) image pre-processing. Three different aspects were needed to plan the route: flight area, camera specifications and UAV tasks. The pre-processing phase included the correct alignment of the six bands of the multispectral imagery and the orthorectification and mosaicking of the individual images captured in each flight. The image pixel size, area covered by each image and flight timing were very sensitive to flight altitude. At a lower altitude, the UAV captured images of finer spatial resolution, although the number of images needed to cover the whole field may be a limiting factor due to the energy required for a greater flight length and computational requirements for the further mosaicking process. Spectral differences between weeds, crop and bare soil were significant in the vegetation indices studied (Excess Green Index, Normalised Green-Red Difference Index and Normalised Difference Vegetation Index), mainly at a 30 m altitude. However, greater spectral separability was obtained between vegetation and bare soil with the index NDVI. These results suggest that an agreement among spectral and spatial resolutions is needed to optimise the flight mission according to every agronomical objective as affected by the size of the smaller object to be discriminated (weed plants or weed patches).

  7. Configuration and specifications of an Unmanned Aerial Vehicle (UAV) for early site specific weed management.

    PubMed

    Torres-Sánchez, Jorge; López-Granados, Francisca; De Castro, Ana Isabel; Peña-Barragán, José Manuel

    2013-01-01

    A new aerial platform has risen recently for image acquisition, the Unmanned Aerial Vehicle (UAV). This article describes the technical specifications and configuration of a UAV used to capture remote images for early season site- specific weed management (ESSWM). Image spatial and spectral properties required for weed seedling discrimination were also evaluated. Two different sensors, a still visible camera and a six-band multispectral camera, and three flight altitudes (30, 60 and 100 m) were tested over a naturally infested sunflower field. The main phases of the UAV workflow were the following: 1) mission planning, 2) UAV flight and image acquisition, and 3) image pre-processing. Three different aspects were needed to plan the route: flight area, camera specifications and UAV tasks. The pre-processing phase included the correct alignment of the six bands of the multispectral imagery and the orthorectification and mosaicking of the individual images captured in each flight. The image pixel size, area covered by each image and flight timing were very sensitive to flight altitude. At a lower altitude, the UAV captured images of finer spatial resolution, although the number of images needed to cover the whole field may be a limiting factor due to the energy required for a greater flight length and computational requirements for the further mosaicking process. Spectral differences between weeds, crop and bare soil were significant in the vegetation indices studied (Excess Green Index, Normalised Green-Red Difference Index and Normalised Difference Vegetation Index), mainly at a 30 m altitude. However, greater spectral separability was obtained between vegetation and bare soil with the index NDVI. These results suggest that an agreement among spectral and spatial resolutions is needed to optimise the flight mission according to every agronomical objective as affected by the size of the smaller object to be discriminated (weed plants or weed patches). PMID:23483997

  8. Configuration and Specifications of an Unmanned Aerial Vehicle (UAV) for Early Site Specific Weed Management

    PubMed Central

    Torres-Sánchez, Jorge; López-Granados, Francisca; De Castro, Ana Isabel; Peña-Barragán, José Manuel

    2013-01-01

    A new aerial platform has risen recently for image acquisition, the Unmanned Aerial Vehicle (UAV). This article describes the technical specifications and configuration of a UAV used to capture remote images for early season site- specific weed management (ESSWM). Image spatial and spectral properties required for weed seedling discrimination were also evaluated. Two different sensors, a still visible camera and a six-band multispectral camera, and three flight altitudes (30, 60 and 100 m) were tested over a naturally infested sunflower field. The main phases of the UAV workflow were the following: 1) mission planning, 2) UAV flight and image acquisition, and 3) image pre-processing. Three different aspects were needed to plan the route: flight area, camera specifications and UAV tasks. The pre-processing phase included the correct alignment of the six bands of the multispectral imagery and the orthorectification and mosaicking of the individual images captured in each flight. The image pixel size, area covered by each image and flight timing were very sensitive to flight altitude. At a lower altitude, the UAV captured images of finer spatial resolution, although the number of images needed to cover the whole field may be a limiting factor due to the energy required for a greater flight length and computational requirements for the further mosaicking process. Spectral differences between weeds, crop and bare soil were significant in the vegetation indices studied (Excess Green Index, Normalised Green-Red Difference Index and Normalised Difference Vegetation Index), mainly at a 30 m altitude. However, greater spectral separability was obtained between vegetation and bare soil with the index NDVI. These results suggest that an agreement among spectral and spatial resolutions is needed to optimise the flight mission according to every agronomical objective as affected by the size of the smaller object to be discriminated (weed plants or weed patches). PMID:23483997

  9. Integrating hydrograph modeling with real-time flow monitoring to generate hydrograph-specific sampling schemes

    NASA Astrophysics Data System (ADS)

    Gall, Heather E.; Jafvert, Chad T.; Jenkinson, Byron

    2010-11-01

    Automated sample collection for water quality research and evaluation generally is performed by simple time-paced or flow-weighted sampling protocols. However, samples collected on strict time-paced or flow-weighted schemes may not adequately capture all elements of storm event hydrographs (i.e., rise, peak, and recession). This can result in inadequate information for calculating chemical mass flux over storm events. In this research, an algorithm was developed to guide automated sampling of hydrographs based on storm-specific information. A key element of the new "hydrograph-specific sampling scheme" is the use of a hydrograph recession model for predicting the hydrograph recession curve, during which flow-paced intervals are calculated for scheduling the remaining samples. The algorithm was tested at a tile drained Midwest agricultural site where real-time flow data were processed by a programmable datalogger that in turn activated an automated sampler at the appropriate sampling times to collect a total of twenty samples during each storm event independent of the number of sequential hydrographs generated. The utility of the algorithm was successfully tested with hydrograph data collected at both a tile drain and agricultural ditch, suggesting the potential for general applicability of the method. This sampling methodology is flexible in that the logic can be adapted for use with any hydrograph recession model; however, in this case a power law equation proved to be the most practical model.

  10. Lipopolysaccharide Specific Immunochromatography Based Lateral Flow Assay for Serogroup Specific Diagnosis of Leptospirosis in India

    PubMed Central

    Vanithamani, Shanmugam; Shanmughapriya, Santhanam; Narayanan, Ramasamy; Raja, Veerapandian; Kanagavel, Murugesan; Sivasankari, Karikalacholan; Natarajaseenivasan, Kalimuthusamy

    2015-01-01

    Background Leptospirosis is a re-emerging infectious disease that is under-recognized due to low-sensitivity and cumbersome serological tests. MAT is the gold standard test and it is the only serogroup specific test used till date. Rapid reliable alternative serogroup specific tests are needed for surveillance studies to identify locally circulating serogroups in the study area. Methods/Principal Findings In the present investigation the serological specificity of leptospiral lipopolysaccharides (LPS) was evaluated by enzyme linked immunosorbent assay (ELISA), dot blot assay and rapid immunochromatography based lateral flow assay (ICG-LFA). Sera samples from 120 MAT positive cases, 174 cases with febrile illness other than leptospirosis, and 121 seronegative healthy controls were evaluated for the diagnostic sensitivity and specificity of the developed assays. LPS was extracted from five locally predominant circulating serogroups including: Australis (27.5%), Autumnalis (11.7%), Ballum (25.8%), Grippotyphosa (12.5%), Pomona (10%) and were used as antigens in the diagnostics to detect IgM antibodies in patients’ sera. The sensitivity observed by IgM ELISA and dot blot assay using various leptospiral LPS was >90% for homologous sera. Except for Ballum LPS, no other LPS showed cross-reactivity to heterologous sera. An attempt was made to develop LPS based ICG-LFA for rapid and sensitive serogroup specific diagnostics of leptospirosis. The developed ICG-LFA showed sensitivity in the range between 93 and 100% for homologous sera. The Wilcoxon analysis showed LPS based ICG-LFA did not differ significantly from the gold standard MAT (P>0.05). Conclusion The application of single array of LPS for serogroup specific diagnosis is first of its kind. The developed assay could potentially be evaluated and employed for as MAT alternative. PMID:26340095

  11. Recharge and Lateral Groundwater Flow Boundary Conditions for the Saturated Zone Site-Scale Flow and Transport Model

    SciTech Connect

    B. Arnold; T. Corbet

    2001-12-18

    The purpose of the flow boundary conditions analysis is to provide specified-flux boundary conditions for the saturated zone (SZ) site-scale flow and transport model. This analysis is designed to use existing modeling and analysis results as the basis for estimated groundwater flow rates into the SZ site-scale model domain, both as recharge at the upper (water table) boundary and as underflow at the lateral boundaries. The objective is to provide consistency at the boundaries between the SZ site-scale flow model and other groundwater flow models. The scope of this analysis includes extraction of the volumetric groundwater flow rates simulated by the SZ regional-scale flow model to occur at the lateral boundaries of the SZ site-scale flow model and the internal qualification of the regional-scale model for use in this analysis model report (AMR). In addition, the scope includes compilation of information on the recharge boundary condition taken from three sources: (1) distributed recharge as taken from the SZ regional-scale flow model, (2) recharge below the area of the unsaturated zone (UZ) site-scale flow model, and (3) focused recharge along the Fortymile Wash channel.

  12. Site-Specific Reference Person Parameters and Derived Concentration Standards for the Savannah River Site

    SciTech Connect

    Stone, Daniel K.; Higley, Kathryn A.; Jannik, G. Timothy

    2014-05-01

    The U.S. Department of Energy Order 458.1 states that the compliance with the 1 mSv annual dose constraint to a member of the public may be demonstrated by calculating dose to the maximally exposed individual (MEI) or to a representative person. Historically, the MEI concept was used for dose compliance at the Savannah River Site (SRS) using adult dose coefficients and adult male usage parameters. For future compliance, SRS plans to use the representative person concept for dose estimates to members of the public. The representative person dose will be based on the reference person dose coefficients from the U.S. DOE Derived Concentration Technical Standard and on usage parameters specific to SRS for the reference and typical person. Usage parameters and dose coefficients were determined for inhalation, ingestion and external exposure pathways. The parameters for the representative person were used to calculate and tabulate SRS-specific derived concentration standards (DCSs) for the pathways not included in DOE-STD-1196-2011.

  13. Site-Specific Reference Person Parameters and Derived Concentration Standards for the Savannah River Site

    DOE PAGES

    Stone, Daniel K.; Higley, Kathryn A.; Jannik, G. Timothy

    2014-05-01

    The U.S. Department of Energy Order 458.1 states that the compliance with the 1 mSv annual dose constraint to a member of the public may be demonstrated by calculating dose to the maximally exposed individual (MEI) or to a representative person. Historically, the MEI concept was used for dose compliance at the Savannah River Site (SRS) using adult dose coefficients and adult male usage parameters. For future compliance, SRS plans to use the representative person concept for dose estimates to members of the public. The representative person dose will be based on the reference person dose coefficients from the U.S.more » DOE Derived Concentration Technical Standard and on usage parameters specific to SRS for the reference and typical person. Usage parameters and dose coefficients were determined for inhalation, ingestion and external exposure pathways. The parameters for the representative person were used to calculate and tabulate SRS-specific derived concentration standards (DCSs) for the pathways not included in DOE-STD-1196-2011.« less

  14. Base-flow measurements at partial-record sites on small streams in South Carolina

    USGS Publications Warehouse

    Barker, Carroll

    1986-01-01

    This report contains site descriptions and base-flow data collected at 362 partial-record sites in South Carolina. These data include site name, site description, latitude, longitude, drainage area, instantaneous streamflow, and date of the streamflow measurement. The base-flow data can be used as an aid to estimate low flow characteristics at ungaged locations on streams in South Carolina. Partial record data collection sites were established in all physiographic provinces except the lower Coastal Plain. Data collection sites were not established in the lower Coastal Plain because of the widespread occurrence of zero during drought periods in all but the larger streams. (USGS)

  15. Mapping potential of digitized aerial photographs and space images for site-specific crop management

    NASA Astrophysics Data System (ADS)

    Nielsen, Gerald A.; Long, Daniel S.; Queen, Lloyd P.

    1996-11-01

    In site-specific crop management, treatments (e.g., fertilizer and herbicides) are applied precisely where they are needed. Global positioning system receivers allow accurate navigation of field implements and creation of crop yield maps. Remote sensing products help producers explain the wide range of yields shown on these maps and become the basis for digitized field management maps. Previous sources of remote sensing products for agriculture did not provide services that generated a sustained demand by crop producers, often because data were not delivered quickly enough. Public Access Resource Centers could provide a nearly uninterrupted electronic flow of data from NASA's MODIS and other sensors that could help producers and their advisors monitor crop conditions. This early warning/opportunity system would provide a low-cost way to discover conditions that merit examination on the ground. High-spatial-resolution digital aerial photographs or data from new commercial satellite companies would provide the basis for site-specific treatments. These detailed data are too expensive to acquire often and must be timed so as to represent differences in water supply characteristics and crop yield potentials. Remote sensing products must be linked to specific prescriptions that crop produces use to control operations and improve outcomes.

  16. Optimal mapping of site-specific multivariate soil properties.

    PubMed

    Burrough, P A; Swindell, J

    1997-01-01

    This paper demonstrates how geostatistics and fuzzy k-means classification can be used together to improve our practical understanding of crop yield-site response. Two aspects of soil are important for precision farming: (a) sensible classes for a given crop, and (b) their spatial variation. Local site classifications are more sensitive than general taxonomies and can be provided by the method of fuzzy k-means to transform a multivariate data set with i attributes measured at n sites into k overlapping classes; each site has a membership value mk for each class in the range 0-1. Soil variation is of interest when conditions vary over patches manageable by agricultural machinery. The spatial variation of each of the k classes can be analysed by computing the variograms of mk over the n sites. Memberships for each of the k classes can be mapped by ordinary kriging. Areas of class dominance and the transition zones between them can be identified by an inter-class confusion index; reducing the zones to boundaries gives crisp maps of dominant soil groups that can be used to guide precision farming equipment. Automation of the procedure is straightforward given sufficient data. Time variations in soil properties can be automatically incorporated in the computation of membership values. The procedures are illustrated with multi-year crop yield data collected from a 5 ha demonstration field at the Royal Agricultural College in Cirencester, UK. PMID:9573478

  17. SITE-SPECIFIC MEASUREMENTS OF RESIDENTIAL RADON PROTECTION CATEGORY

    EPA Science Inventory

    The report describes a series of benchmark measurements of soil radon potential at seven Florida sites and compares the measurements with regional estimates of radon potential from the Florida radon protection map. The measurements and map were developed under the Florida Radon R...

  18. 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... Site-Specific Advisory Board (EM SSAB), Idaho National Laboratory. The Federal Advisory Committee Act... to Cleanup Idaho National Laboratory Site Wide Review--CERCLA Long-Term Ecological Program...

  19. 75 FR 51450 - Environmental Management Site-Specific Advisory Board Chairs

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-20

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

  20. 76 FR 17118 - Environmental Management Site-Specific Advisory Board Chairs

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-28

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

  1. 75 FR 6018 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-05

    ... 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... the Board is to make recommendations to DOE-EM and site management in the areas of...

  2. 78 FR 49738 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-15

    ... 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... and site management in the areas of environmental restoration, waste management, and...

  3. 77 FR 55813 - Environmental Management Site-Specific Advisory Board Chairs

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-11

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

  4. 75 FR 8050 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-23

    ... 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... and site management in the areas of environmental restoration, waste management, and...

  5. 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 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,...

  6. 78 FR 64932 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-30

    ... 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,...

  7. 78 FR 28207 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-14

    ... 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... and site management in the areas of environmental restoration, waste management, and...

  8. 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 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,...

  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 open meeting. SUMMARY: This notice announces a meeting of the Site-Wide Environmental Impact Statement (EIS) Committee of the Environmental Management Site- Specific Advisory Board (EM SSAB), Nevada....

  10. 78 FR 68431 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-14

    ... 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... and site management in the areas of environmental restoration, waste management, and...

  11. 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 Open Meeting. SUMMARY: This notice announces a meeting of the Site-Wide Environmental Impact Statement (EIS) Committee of the Environmental Management Site- Specific Advisory Board (EM SSAB), Nevada....

  12. Site-specific reference person parameters and derived concentration standards for the Savannah River Site.

    PubMed

    Stone, Daniel K; Higley, Kathryn A; Jannik, G Timothy

    2014-05-01

    The U.S. Department of Energy Order 458.1 states that the compliance with the 1 mSv annual dose constraint to a member of the public may be demonstrated by calculating dose to the maximally exposed individual (MEI) or to a representative person. Historically, the MEI concept was used for dose compliance at the Savannah River Site (SRS) using adult dose coefficients and adult male usage parameters. For future compliance, SRS plans to use the representative person concept for dose estimates to members of the public. The representative person dose will be based on the reference person dose coefficients from the U.S. DOE Derived Concentration Technical Standard and on usage parameters specific to SRS for the reference and typical person. Usage parameters and dose coefficients were determined for inhalation, ingestion and external exposure pathways. The reference intake for air, water, meat, dairy, freshwater fish, saltwater invertebrates, produce (fruits and vegetables), and grains for the 95th percentile are 17.4 m d, 2.19 L d, 220.6 g d, 674 cm d, 66.4 g d, 23.0 g d, 633.4 g d (448.5 g dand 631.7 g d) and 251.3 g d, respectively. For the 50th percentile: 13.4 m d, 0.809 L d, 86.4 g d, 187 cm d, 8.97 g d, 3.04 g d, 169.5 g d (45.9 g d and 145.6 g d), 101.3 g d, respectively. These parameters for the representative person were used to calculate and tabulate SRS-specific derived concentration standards (DCSs) for the pathways not included in DOE-STD-1196-2011.

  13. Simulation-Based Approach for Site-Specific Optimization of Hydrokinetic Turbine Arrays

    NASA Astrophysics Data System (ADS)

    Sotiropoulos, F.; Chawdhary, S.; Yang, X.; Khosronejad, A.; Angelidis, D.

    2014-12-01

    A simulation-based approach has been developed to enable site-specific optimization of tidal and current turbine arrays in real-life waterways. The computational code is based on the St. Anthony Falls Laboratory Virtual StreamLab (VSL3D), which is able to carry out high-fidelity simulations of turbulent flow and sediment transport processes in rivers and streams taking into account the arbitrary geometrical complexity characterizing natural waterways. The computational framework can be used either in turbine-resolving mode, to take into account all geometrical details of the turbine, or with the turbines parameterized as actuator disks or actuator lines. Locally refined grids are employed to dramatically increase the resolution of the simulation and enable efficient simulations of multi-turbine arrays. Turbine/sediment interactions are simulated using the coupled hydro-morphodynamic module of VSL3D. The predictive capabilities of the resulting computational framework will be demonstrated by applying it to simulate turbulent flow past a tri-frame configuration of hydrokinetic turbines in a rigid-bed turbulent open channel flow as well as turbines mounted on mobile bed open channels to investigate turbine/sediment interactions. The utility of the simulation-based approach for guiding the optimal development of turbine arrays in real-life waterways will also be discussed and demonstrated. This work was supported by NSF grant IIP-1318201. Simulations were carried out at the Minnesota Supercomputing Institute.

  14. Characterization of nicotine binding to the rat brain P/sub 2/ preparation: the identification of multiple binding sites which include specific up-regulatory site(s)

    SciTech Connect

    Sloan, J.W.

    1984-01-01

    These studies show that nicotine binds to the rat brain P/sub 2/ preparation by saturable and reversible processes. Multiple binding sites were revealed by the configuration of saturation, kinetic and Scatchard plots. A least squares best fit of Scatchard data using nonlinear curve fitting programs confirmed the presence of a very high affinity site, an up-regulatory site, a high affinity site and one or two low affinity sites. Stereospecificity was demonstrated for the up-regulatory site where (+)-nicotine was more effective and for the high affinity site where (-)-nicotine had a higher affinity. Drugs which selectively up-regulate nicotine binding site(s) have been identified. Further, separate very high and high affinity sites were identified for (-)- and (+)-(/sup 3/H)nicotine, based on evidence that the site density for the (-)-isomer is 10 times greater than that for the (+)-isomer at these sites. Enhanced nicotine binding has been shown to be a statistically significant phenomenon which appears to be a consequence of drugs binding to specific site(s) which up-regulate binding at other site(s). Although Scatchard and Hill plots indicate positive cooperatively, up-regulation more adequately describes the function of these site(s). A separate up-regulatory site is suggested by the following: (1) Drugs vary markedly in their ability to up-regulate binding. (2) Both the affinity and the degree of up-regulation can be altered by structural changes in ligands. (3) Drugs with specificity for up-regulation have been identified. (4) Some drugs enhance binding in a dose-related manner. (5) Competition studies employing cold (-)- and (+)-nicotine against (-)- and (+)-(/sup 3/H)nicotine show that the isomers bind to separate sites which up-regulate binding at the (-)- and (+)-nicotine high affinity sites and in this regard (+)-nicotine is more specific and efficacious than (-)-nicotine.

  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. Hydrogeologic Framework Model for the Saturated Zone Site Scale flow and Transport Model

    SciTech Connect

    T. Miller

    2004-11-15

    The purpose of this report is to document the 19-unit, hydrogeologic framework model (19-layer version, output of this report) (HFM-19) with regard to input data, modeling methods, assumptions, uncertainties, limitations, and validation of the model results in accordance with AP-SIII.10Q, Models. The HFM-19 is developed as a conceptual model of the geometric extent of the hydrogeologic units at Yucca Mountain and is intended specifically for use in the development of the ''Saturated Zone Site-Scale Flow Model'' (BSC 2004 [DIRS 170037]). Primary inputs to this model report include the GFM 3.1 (DTN: MO9901MWDGFM31.000 [DIRS 103769]), borehole lithologic logs, geologic maps, geologic cross sections, water level data, topographic information, and geophysical data as discussed in Section 4.1. Figure 1-1 shows the information flow among all of the saturated zone (SZ) reports and the relationship of this conceptual model in that flow. The HFM-19 is a three-dimensional (3-D) representation of the hydrogeologic units surrounding the location of the Yucca Mountain geologic repository for spent nuclear fuel and high-level radioactive waste. The HFM-19 represents the hydrogeologic setting for the Yucca Mountain area that covers about 1,350 km2 and includes a saturated thickness of about 2.75 km. The boundaries of the conceptual model were primarily chosen to be coincident with grid cells in the Death Valley regional groundwater flow model (DTN: GS960808312144.003 [DIRS 105121]) such that the base of the site-scale SZ flow model is consistent with the base of the regional model (2,750 meters below a smoothed version of the potentiometric surface), encompasses the exploratory boreholes, and provides a framework over the area of interest for groundwater flow and radionuclide transport modeling. In depth, the model domain extends from land surface to the base of the regional groundwater flow model (D'Agnese et al. 1997 [DIRS 100131], p 2). For the site-scale SZ flow model, the HFM

  17. 75 FR 19630 - Environmental Management Site-Specific Advisory Board Charter Renewal

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-15

    ... Environmental Management Site-Specific Advisory Board Charter Renewal Pursuant to Section 14(a)(2)(A) of the...-Specific Advisory Board will be renewed for a two-year period beginning April 11, 2010. The Board provides... renewal of the Environmental Management Site- Specific Advisory Board has been determined to be...

  18. Monitoring and Evaluation of Environmental Flow Prescriptions for Five Demonstration Sites of the Sustainable Rivers Project

    USGS Publications Warehouse

    Konrad, Christopher P.

    2010-01-01

    The Nature Conservancy has been working with U.S. Army Corps of Engineers (Corps) through the Sustainable Rivers Project (SRP) to modify operations of dams to achieve ecological objectives in addition to meeting the authorized purposes of the dams. Modifications to dam operations are specified in terms of environmental flow prescriptions that quantify the magnitude, duration, frequency, and seasonal timing of releases to achieve specific ecological outcomes. Outcomes of environmental flow prescriptions implemented from 2002 to 2008 have been monitored and evaluated at demonstration sites in five rivers: Green River, Kentucky; Savannah River, Georgia/South Carolina; Bill Williams River, Arizona; Big Cypress Creek, Texas; and Middle Fork Willamette River, Oregon. Monitoring and evaluation have been accomplished through collaborative partnerships of federal and state agencies, universities, and nongovernmental organizations.

  19. 78 FR 56871 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-16

    ... 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...

  20. 78 FR 10611 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-14

    ... 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...

  1. 75 FR 7577 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-22

    ... 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...

  2. 76 FR 8359 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-14

    ... 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...

  3. 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...

  4. Monitoring Protein Misfolding by Site-Specific Labeling of Proteins In Vivo

    PubMed Central

    Hsieh, Tzung-yang; Nillegoda, Nadinath B.; Tyedmers, Jens; Bukau, Bernd; Mogk, Axel; Kramer, Günter

    2014-01-01

    Incorporating fluorescent amino acids by suppression of the TAG amber codon is a useful tool for site-specific labeling of proteins and visualizing their localization in living cells. Here we use a plasmid encoded orthogonal tRNA/aminoacyl-tRNA synthetase pair to site-specifically label firefly luciferase with the environmentally sensitive fluorescent amino acid, 3-(6-acetylnaphthalen-2-ylamino)-2- aminopropanoic acid (ANAP) and explore the detectability of conformational changes in labeled luciferase in the yeast cytoplasm. We find that ANAP labeling efficiency is greatly increased in [PSI+] cells and show that analysis of the ANAP fluorescence emission by confocal imaging allows for tracking the thermal unfolding and aggregation of luciferase in vivo. Furthermore we demonstrate that flow cytometry can be used to study conformational changes in luciferase and chaperone-mediated refolding in quantitative terms and at the level of single cells. This experimental setup for the first time allows for the direct analysis of the folding state of a protein in living cells and may serve as valuable new tool for examining mechanisms of protein folding, misfolding and aggregation. PMID:24915041

  5. Site-specific variability in BTEX biodegradation under denitrifying conditions

    SciTech Connect

    Kao, C.M.; Borden, R.C.

    1997-03-01

    Laboratory microcosm experiments were conducted to evaluate the feasibility of benzene, toluene, ethylbenzene, m-xylene, and o-xylene (BTEX) biodegradation under denitrifying conditions. Nine different sources of inocula, including contaminated and uncontaminated soil cores from four different sites and activated sludge, were used to establish microcosms. BTEX was not degraded under denitrifying conditions in microcosms inoculated with aquifer material from Rocky Point and Traverse City. However, rapid depletion of glucose under denitrifying conditions was observed in microcosms containing Rocky Point aquifer material. TEX degradation was observed in microcosms containing Rocky Point aquifer material. TEX degradation was observed in microcosms containing aquifer material from Fort Bragg and Sleeping Bear Dunes and sewage sludge. Benzene was recalcitrant in all microcosms tested. The degradation of o-xylene ceased after toluene, ethylbenzene, and m-xylene were depleted in the Fort Bragg and sludge microcosms, but o-xylene continued to degrade in microcosms with contaminated Sleeping Bear Dunes soil. The most probable number (MPN) of denitrifiers in these nine different inocula were measured using a microtiter technique. There was no correlation between the MPN of denitrifiers and the TEX degradation rate under denitrifying conditions. Experimental results indicate that the degradation sequence and TEX degradation rate under denitrifying conditions may differ among sites. Results also indicate that denitrification alone may not be a suitable bioremediation technology for gasoline-contaminated aquifers because of the inability of denitrifiers to degrade benzene.

  6. The Sim-SEQ Project: Comparison of Selected Flow Models for the S-3 Site

    SciTech Connect

    Mukhopadhyay, Sumit; Doughty, Christine A.; Bacon, Diana H.; Li, Jun; Wei, Lingli; Yamamoto, Hajime; Gasda, Sarah E.; Hosseini, Seyyed; Nicot, Jean-Philippe; Birkholzer, Jens

    2015-05-23

    Sim-SEQ is an international initiative on model comparison for geologic carbon sequestration, with an objective to understand and, if possible, quantify model uncertainties. Model comparison efforts in Sim-SEQ are at present focusing on one specific field test site, hereafter referred to as the Sim-SEQ Study site (or S-3 site). Within Sim-SEQ, different modeling teams are developing conceptual models of CO2 injection at the S-3 site. In this paper, we select five flow models of the S-3 site and provide a qualitative comparison of their attributes and predictions. These models are based on five different simulators or modeling approaches: TOUGH2/EOS7C, STOMP-CO2e, MoReS, TOUGH2-MP/ECO2N, and VESA. In addition to model-to-model comparison, we perform a limited model-to-data comparison, and illustrate how model choices impact model predictions. We conclude the paper by making recommendations for model refinement that are likely to result in less uncertainty in model predictions.

  7. Site Specific Analysis of Recent CSMIP Downhole Array Data

    NASA Astrophysics Data System (ADS)

    Haddadi, H.; Graizer, V.; Shakal, A.

    2003-12-01

    California Strong Motion Instrumentation Program (CSMIP) started operating downhole arrays in 1989 to provide essential data for studying the effects of local soil conditions. As of September 2003, 19 downhole arrays were instrumented, 13 of those with cooperation of California Department of Transportation (Caltrans). More than 90 low amplitude recordings from earthquakes with 2.0site. The velocities obtained by correlation analysis agree with those of suspension logging. The M4.8 earthquake of September 3, 2002 is recorded at Los Angeles Obregon Park downhole array. The array was installed in 2000 and its local site geology consists of deep alluvium over sandstone. The accelerometers are installed at the surface and depth of 69 m. The recordings of the earthquake are used to correlate seismic wave motion at the surface and depth in horizontal and vertical directions. The S- and P- wave velocities obtained by correlation analysis are compared with those of suspension logging method. The new geotechnical array at Aptos in Santa Cruz is designed to study the effects of the cliff on seismic ground motion. The accelerometers are located at the surface and planned to install at depth of 30 m. Also, a three components accelerometer recorder is installed about 15 m south of the borehole toward the seacliff near bluff. The low

  8. Thermopolis/East Thermopolis, Wyoming site-specific development analysis

    SciTech Connect

    Burgess-Lyon, P.

    1981-06-01

    Some of the topics addressed are: what the area is like currently in terms of its land use, economics, and demographics; reservoir potentials; how the reservoir might be developed; marketing the final product; financial assistance for development; the legal aspects of development; and barriers to possible development. Some specific topics discussed are: leasing and permitting; heat exchangers for geothermal heating systems; and corrosion, scaling, and materials selection. (MHR)

  9. 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.

  10. Anatomical site-specific contributions of pneumococcal virulence determinants

    PubMed Central

    Shenoy, Anukul T.; Orihuela, Carlos J.

    2016-01-01

    Streptococcus pneumoniae is an opportunistic pathogen globally associated with significant morbidity and mortality. It is capable of causing a wide range of diseases including sinusitis, conjunctivitis, otitis media, pneumonia, bacteraemia, sepsis, and meningitis. While its capsular polysaccharide is indispensible for invasive disease, and opsonising antibodies against the capsule are the basis for the current vaccines, a long history of biomedical research indicates that other components of this Gram-positive bacterium are also critical for virulence. Herein we review the contribution of pneumococcal virulence determinants to survival and persistence in the context of distinct anatomical sites. We discuss how these determinants allow the pneumococcus to evade mucociliary clearance during colonisation, establish lower respiratory tract infection, resist complement deposition and opsonophagocytosis in the bloodstream, and invade secondary tissues such as the central nervous system leading to meningitis. We do so in a manner that highlights both the critical role of the capsular polysaccharide and the accompanying and necessary protein determinants. Understanding the complex interplay between host and pathogen is necessary to find new ways to prevent pneumococcal infection. This review is an attempt to do so with consideration for the latest research findings. PMID:27635368

  11. Anatomical site-specific contributions of pneumococcal virulence determinants

    PubMed Central

    Shenoy, Anukul T.; Orihuela, Carlos J.

    2016-01-01

    Streptococcus pneumoniae is an opportunistic pathogen globally associated with significant morbidity and mortality. It is capable of causing a wide range of diseases including sinusitis, conjunctivitis, otitis media, pneumonia, bacteraemia, sepsis, and meningitis. While its capsular polysaccharide is indispensible for invasive disease, and opsonising antibodies against the capsule are the basis for the current vaccines, a long history of biomedical research indicates that other components of this Gram-positive bacterium are also critical for virulence. Herein we review the contribution of pneumococcal virulence determinants to survival and persistence in the context of distinct anatomical sites. We discuss how these determinants allow the pneumococcus to evade mucociliary clearance during colonisation, establish lower respiratory tract infection, resist complement deposition and opsonophagocytosis in the bloodstream, and invade secondary tissues such as the central nervous system leading to meningitis. We do so in a manner that highlights both the critical role of the capsular polysaccharide and the accompanying and necessary protein determinants. Understanding the complex interplay between host and pathogen is necessary to find new ways to prevent pneumococcal infection. This review is an attempt to do so with consideration for the latest research findings.

  12. Expanding the Scope of Site-Specific Recombinases for Genetic and Metabolic Engineering

    PubMed Central

    Gaj, Thomas; Sirk, Shannon J.; Barbas, Carlos F.

    2014-01-01

    Site-specific recombinases are tremendously valuable tools for basic research and genetic engineering. By promoting high-fidelity DNA modifications, site-specific recombination systems have empowered researchers with unprecedented control over diverse biological functions, enabling countless insights into cellular structure and function. The rigid target specificities of many sites-specific recombinases, however, have limited their adoption in fields that require highly flexible recognition abilities. As a result, intense effort has been directed toward altering the properties of site-specific recombination systems by protein engineering. Here, we review key developments in the rational design and directed molecular evolution of site-specific recombinases, highlighting the numerous applications of these enzymes across diverse fields of study. PMID:23982993

  13. Cooperative non-specific DNA binding by octamerizing lambda cI repressors: a site-specific thermodynamic analysis.

    PubMed

    Pray, T R; Burz, D S; Ackers, G K

    1998-10-01

    Relationships between dimerization and site-specific binding have been characterized previously for wild-type and mutant cI repressors at the right operator (OR) of bacteriophage lambda DNA. However, the roles of higher-order oligomers (tetramers and octamers) that are also formed from these cI molecules have remained elusive. In this study, a clear correlation has been established between repressor oligomerization and non-specific DNA-binding activity. A modification of the quantitative DNase I footprint titration technique has been used to evaluate the degree of saturation of non-specific, OR-flanking lambda DNA by cI repressor oligomers. With the exception of one mutant, only those repressors capable of octamerizing were found to exhibit non-specific DNA-binding activity. The non-specific interaction was accurately modeled using either a one-dimensional, univalent, site-specific Ising lattice approximation, or a more traditional, multivalent lattice approach. It was found that non-specific DNA-binding by repressor oligomers is highly cooperative and energetically independent from site-specific binding at OR. Furthermore, the coupling free energy resolved for non-specific binding was similar to that of site-specific binding for each repressor, suggesting that similar structural elements may mediate the cooperative component of both binding processes. It is proposed that the state of assembly of the repressor molecule modulates its relative affinity for specific and non-specific DNA sequences. These specificities are allosterically regulated by the transmission of assembly-state information from the C-terminal domain, which mediates self-association and cooperativity, to the N-terminal domain, which primarily mediates DNA-binding. While dimers have a high affinity for their cognate sites within OR, tetramers and octamers may preferentially recognize non-specific DNA sequences. The concepts and findings developed in this study may facilitate quantitative

  14. Tissue-specific N-glycosylation, site-specific oligosaccharide patterns and lentil lectin recognition of rat Thy-1.

    PubMed Central

    Parekh, R B; Tse, A G; Dwek, R A; Williams, A F; Rademacher, T W

    1987-01-01

    To examine the extent to which protein structure and tissue-type influence glycosylation, we have determined the oligosaccharide structures at each of the three glycosylation sites (Asn-23, 74 and 98) of the cell surface glycoprotein Thy-1 isolated from rat brain and thymus. The results show that there is tissue-specificity of glycosylation and that superimposed on this is a significant degree of site-specificity. On the basis of the site distribution of oligosaccharides, we find that no Thy-1 molecules are in common between the two tissues despite the amino acid sequences being identical. We suggest, therefore, that by controlling N-glycosylation a tissue creates an unique set of glycoforms (same polypeptide but with oligosaccharides that differ either in sequence or disposition). The structures at each of the three sites were also determined for the thymocyte Thy-1 that binds to lentil lectin (Thy-1 L+) and for that which does not (Thy-1 L-). Segregation of intact thymus Thy-1 into two distinct sets of glycoforms by lentil lectin was found to be due to the structures at site 74. Analysis of oligosaccharide structures at the 'passenger' sites (23 and 98) suggests that either Thy-1 L+ and Thy-1 L- molecules are made in different cell-types or that the biosynthesis of oligosaccharides at one site is influenced by the glycosylation at other sites. PMID:2886334

  15. 78 FR 69657 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-20

    ... 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... Board is to make recommendations to DOE-EM and site management in the areas of environmental...

  16. 78 FR 22255 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-15

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

  17. 77 FR 39234 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-02

    ... Environmental Management Site-Specific Advisory Board, Northern New Mexico AGENCY: Department of Energy. 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...

  18. 75 FR 8051 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-23

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

  19. 75 FR 51026 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-18

    ... 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...

  20. 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... Board is to make recommendations to DOE-EM and site management in the areas of environmental...

  1. 77 FR 50488 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-21

    ... 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...

  2. 78 FR 36543 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-18

    ... 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 19379 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-14

    ... 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...

  4. 75 FR 65615 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-26

    ... 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. 77 FR 63300 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-16

    ... 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...

  6. 77 FR 16021 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-19

    ... 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...

  7. 77 FR 37390 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-21

    ... 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...

  8. 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...

  9. 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...

  10. 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...

  11. On-the-go nitrogen sensing and fertilizer control for site-specific crop management

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In-field site-specific nitrogen (N) management increases crop yield, reduces N application to minimize the risk of nitrate contamination of ground water, and thus reduces farming cost. Real-time N sensing and fertilization is required for efficient N management. An ‘on-the-go’ site-specific N manage...

  12. A cyclopropene-modified nucleotide for site-specific RNA labeling using genetic alphabet expansion transcription.

    PubMed

    Eggert, F; Kath-Schorr, S

    2016-06-01

    Site-specific RNA modification with methyl cyclopropene moieties is performed by T7 in vitro transcription. An existing unnatural base is functionalized with a cyclopropene moiety and used in transcription reactions to produce site-specifically cyclopropene-modified RNA molecules. The posttranscriptional inverse electron demand Diels-Alder cycloaddition reaction with a selected tetrazine-fluorophore conjugate is demonstrated.

  13. A cyclopropene-modified nucleotide for site-specific RNA labeling using genetic alphabet expansion transcription.

    PubMed

    Eggert, F; Kath-Schorr, S

    2016-06-01

    Site-specific RNA modification with methyl cyclopropene moieties is performed by T7 in vitro transcription. An existing unnatural base is functionalized with a cyclopropene moiety and used in transcription reactions to produce site-specifically cyclopropene-modified RNA molecules. The posttranscriptional inverse electron demand Diels-Alder cycloaddition reaction with a selected tetrazine-fluorophore conjugate is demonstrated. PMID:27181840

  14. 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... Site-Specific Advisory Board (EM SSAB), Northern New Mexico. The Federal Advisory Committee Act (Pub. L... Mexico Citizens' Advisory Board (NNMCAB), 94 Cities of Gold Road, Santa Fe, NM 87506. Phone (505)...

  15. 76 FR 39080 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-07-05

    ... 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 (INL) 101. INL EM Budget. Calcine Path Forward. Advanced Mixed Waste Treatment...

  16. 78 FR 58294 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-23

    ... 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... SSAB, Idaho National Laboratory, welcomes the attendance of the public at its advisory...

  17. 77 FR 76475 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-28

    ... 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... Laboratory/ICP Public Involvement/ Communications Sodium Bearing Waste Treatment Plant Update ICP End...

  18. 75 FR 82004 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-29

    ... 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...

  19. 75 FR 56527 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-16

    ... 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.... Overview Legacy Management--Long-Term Land Use at Idaho National Laboratory. Integrated Waste...

  20. 76 FR 68179 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-03

    ... Management Site-Specific Advisory Board, Idaho National Laboratory (76 FR 66917). This document makes a... page at: http://inlcab.energy.gov/ . Correction In the Federal Register of October 28, 2011, in FR Doc... Environmental Management Site-Specific Advisory Board, Idaho National Laboratory AGENCY: Department of...

  1. 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...

  2. 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...

  3. 75 FR 9590 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-03

    ... 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...

  4. 77 FR 38276 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-27

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

  5. 77 FR 65374 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-26

    ... 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/ICP Public Involvement/ Communications Public Participation: The EM SSAB,...

  6. 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...

  7. 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...

  8. 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... Site-Specific Advisory Board (EM SSAB), Idaho National Laboratory. The Federal Advisory Committee Act...--Future Work Plan Public Participation: The EM SSAB, Idaho National Laboratory, welcomes the attendance...

  9. 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...

  10. 76 FR 53888 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-30

    ... 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...

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

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-23

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

  12. 75 FR 346 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-05

    ... 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... Decision. Public Participation: The EM SSAB, Idaho National Laboratory, welcomes the attendance of...

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

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-07

    ... Environmental Management Site-Specific Advisory Board Chairs AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... environmental restoration, waste management, and related activities. Tentative Agenda Topics: Wednesday,...

  14. 76 FR 20651 - Environmental Management Site-Specific Advisory Board Chairs

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-13

    ... Environmental Management Site-Specific Advisory Board Chairs (76 FR 17118). This notice announces the... Environmental Management Site-Specific Advisory Board Chairs AGENCY: Department of Energy. ACTION: Notice of cancellation of open meeting. SUMMARY: On March 28, 2011, in FR Doc. 2011-7243, on page 17118, the...

  15. 76 FR 63613 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-13

    ... 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....

  16. 78 FR 26635 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-07

    ... Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy. ACTION: Notice of... of open meeting announcing a meeting on May 16, 2013 of the Environmental Management Site-Specific Advisory Board, Paducah (78 FR 25064). This document makes a correction to that notice. FOR...

  17. 78 FR 61348 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-03

    ..., 2013 of the Environmental Management Site-Specific Advisory Board, Portsmouth (78 FR 56871). This... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy. ACTION: Notice of Cancellation of Open Meeting. SUMMARY: On September 16, 2013, in FR Doc. 2013-22453, on page...

  18. 76 FR 4645 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-26

    ... 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....

  19. 78 FR 59012 - Environmental Management Site-Specific Advisory Board Chairs

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-25

    ... Environmental Management Site-Specific Advisory Board Chairs AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... environmental restoration, waste management, and related activities. Tentative Agenda Topics: Wednesday,...

  20. Activity of site-specific endonucleases on complexes of plasmid DNA with multiwalled carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Egorova, V. P.; Krylova, H. V.; Lipnevich, I. V.; Veligura, A. A.; Shulitsky, B. G.; Asayonok, A. A.; Vaskovtsev, E. V.

    2016-08-01

    We have synthesized and investigated structural and functional properties of plasmid DNA complexes with multi-walled carbon nanotubes (MWCNTs) for detection of changes in structural state of the plasmid DNA at its recognition by site-specific endonuclease. It has been also established that the site-specific endonuclease is functionally active on the surface of MWCNTs.

  1. 77 FR 26273 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-03

    ... Environmental Management Site-Specific Advisory Board, Northern New Mexico AGENCY: Department of Energy, DoE... Site-Specific Advisory Board (EM SSAB), Northern New Mexico. The Federal Advisory Committee Act (Pub. L... New Mexico Citizens' Advisory Board (NNMCAB), 94 Cities of Gold Road, Santa Fe, NM 87506. Phone...

  2. 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...

  3. 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...

  4. 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...

  5. 75 FR 82001 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-29

    ... 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... 12, 2011, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak Ridge Turnpike, Oak Ridge,...

  6. 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,...

  7. 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...

  8. 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...

  9. 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...

  10. 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...

  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. 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....

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

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-19

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

  14. 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...

  15. 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...

  16. 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,...

  17. 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...

  18. 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...

  19. 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...

  20. 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...

  1. 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...

  2. 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...

  3. 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...

  4. 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...

  5. 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...

  6. 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...

  7. 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....

  8. 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...

  9. 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...

  10. 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...

  11. 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...

  12. 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...

  13. 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...

  14. 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...

  15. 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....

  16. 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...

  17. 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...

  18. 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...

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

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-19

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

  20. 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...

  1. 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,...

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

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 25 2012-07-01 2012-07-01 false Knowledge of labeling and site-specific information. 170.232 Section 170.232 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS WORKER PROTECTION STANDARD Standard for Pesticide Handlers § 170.232 Knowledge of labeling and site-specific...

  4. 76 FR 51362 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-18

    ... activities. Tentative Agenda 1. Update--Site-Specific Environmental Impact Statement Committee. 2. Update... advance of the meeting at the phone number listed above. Written statements may be filed with the Board... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice...

  5. 75 FR 64718 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-20

    ... 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... the areas of environmental restoration, waste management, and related activities. Tentative...

  6. Low affinity binding site clusters confer hox specificity and regulatory robustness.

    PubMed

    Crocker, Justin; Abe, Namiko; Rinaldi, Lucrezia; McGregor, Alistair P; Frankel, Nicolás; Wang, Shu; Alsawadi, Ahmad; Valenti, Philippe; Plaza, Serge; Payre, François; Mann, Richard S; Stern, David L

    2015-01-15

    In animals, Hox transcription factors define regional identity in distinct anatomical domains. How Hox genes encode this specificity is a paradox, because different Hox proteins bind with high affinity in vitro to similar DNA sequences. Here, we demonstrate that the Hox protein Ultrabithorax (Ubx) in complex with its cofactor Extradenticle (Exd) bound specifically to clusters of very low affinity sites in enhancers of the shavenbaby gene of Drosophila. These low affinity sites conferred specificity for Ubx binding in vivo, but multiple clustered sites were required for robust expression when embryos developed in variable environments. Although most individual Ubx binding sites are not evolutionarily conserved, the overall enhancer architecture-clusters of low affinity binding sites-is maintained and required for enhancer function. Natural selection therefore works at the level of the enhancer, requiring a particular density of low affinity Ubx sites to confer both specific and robust expression. PMID:25557079

  7. Gene therapy on demand: site specific regulation of gene therapy.

    PubMed

    Jazwa, Agnieszka; Florczyk, Urszula; Jozkowicz, Alicja; Dulak, Jozef

    2013-08-10

    Since 1990 when the first clinical gene therapy trial was conducted, much attention and considerable promise have been given to this form of treatment. Gene therapy has been used with success in patients suffering from severe combined immunodeficiency syndromes (X-SCID and ADA-deficiency), Leber's congenital amaurosis, hemophilia, β-thalassemia and adrenoleukodystrophy. Last year, the first therapeutic vector (Glybera) for treatment of lipoprotein lipase deficiency has been registered in the European Union. Nevertheless, there are still several numerous issues that need to be improved to make this technique more safe, effective and easily accessible for patients. Introduction of the therapeutic gene to the given cells should provide the level of expression which will restore the production of therapeutic protein to normal values or will provide therapeutic efficacy despite not fully physiological expression. However, in numerous diseases the expression of therapeutic genes has to be kept at certain level for some time, and then might be required to be switched off to be activated again when worsening of the symptoms may aggravate the risk of disease relapse. In such cases the promoters which are regulated by local conditions may be more required. In this article the special emphasis is to discuss the strategies of regulation of gene expression by endogenous stimuli. Particularly, the hypoxia- or miRNA-regulated vectors offer the possibilities of tight but, at the same time, condition-dependent and cell-specific expression. Such means have been already tested in certain pathophysiological conditions. This creates the chance for the translational approaches required for development of effective treatments of so far incurable diseases. PMID:23566848

  8. High-Resolution Flow Logging for Hydraulic Characterization of Boreholes and Aquifer Flow Zones at Contaminated Bedrock Sites

    NASA Astrophysics Data System (ADS)

    Williams, J. H.; Johnson, C. D.; Paillet, F. L.

    2004-05-01

    In the past, flow logging was largely restricted to the application of spinner flowmeters to determine flow-zone contributions in large-diameter production wells screened in highly transmissive aquifers. Development and refinement of tool-measurement technology, field methods, and analysis techniques has greatly extended and enhanced flow logging to include the hydraulic characterization of boreholes and aquifer flow zones at contaminated bedrock sites. State-of-the-art in flow logging will be reviewed, and its application to bedrock-contamination investigations will be presented. In open bedrock boreholes, vertical flows are measured with high-resolution flowmeters equipped with flexible rubber-disk diverters fitted to the nominal borehole diameters to concentrate flow through the measurement throat of the tools. Heat-pulse flowmeters measure flows in the range of 0.05 to 5 liters per minute, and electromagnetic flowmeters measure flows in the range of 0.3 to 30 liters per minute. Under ambient and low-rate stressed (either extraction or injection) conditions, stationary flowmeter measurements are collected in competent sections of the borehole between fracture zones identified on borehole-wall images. Continuous flow, fluid-resistivity, and temperature logs are collected under both sets of conditions while trolling with a combination electromagnetic flowmeter and fluid tool. Electromagnetic flowmeters are used with underfit diverters to measure flow rates greater than 30 liters per minute and suppress effects of diameter variations while trolling. A series of corrections are applied to the flow-log data to account for the zero-flow response, bypass, trolling, and borehole-diameter biases and effects. The flow logs are quantitatively analyzed by matching simulated flows computed with a numerical model to measured flows by varying the hydraulic properties (transmissivity and hydraulic head) of the flow zones. Several case studies will be presented that demonstrate

  9. Approaches and algorithms for groundwater flow modeling in support of site investigations and safety assessment of the Forsmark site, Sweden

    NASA Astrophysics Data System (ADS)

    Hartley, Lee; Joyce, Steven

    2013-09-01

    The Swedish Nuclear Fuel and Waste Management Company (SKB) has in 2011 finalized a safety assessment project, SR-Site, with the objective to assess the long term safety of a final repository for spent nuclear fuel at Forsmark in Northern Uppland of Sweden. Prior to the safety assessment, comprehensive site investigations were conducted at the Forsmark site to build understanding and characterize the site. An essential part of the site investigations were to describe hydrological properties and characteristics of the site and use this to assess the groundwater pathway. The geological structural context of the crystalline bedrock at Forsmark implied a fracture network concept was the natural description for interpreting site data and assessing the groundwater pathway. Of primary importance to the description of the fracture system was the assignment of down-borehole flow-logging measurements to individual fractures identified by imaging techniques, providing the basis to relate hydrogeological characteristics such as anisotropy and heterogeneity to the geological structural framework. Also, the key input quantities to the assessment of long-term safety can be closely related to the derived fracture flow-rate distributions. Key success factors for this project were to develop and test strategies for modeling methodologies, as described in this paper, from an early stage, hand-in-hand with the planning and phased acquisition of site data as well as successive safety assessments.

  10. Mapping site-specific endonuclease binding to DNA by direct imaging with AFM

    SciTech Connect

    Allison, D.P.; Thundat, T.; Doktycz, M.J.; Kerper, P.S.; Warmack, R.J.; Modrich, P.; Isfort, R.J.

    1995-12-31

    Physical mapping of DNA can be accomplished by direct AFM imaging of site specific proteins bound to DNA molecules. Using Gln-111, a mutant of EcoRI endonuclease with a specific affinity for EcoRI sites 1,000 times greater than wild type enzyme but with cleavage rate constants reduced by a factor of 10{sup 4}, the authors demonstrate site-specific mapping by direct AFM imaging. Images are presented showing specific-site binding of Gln-111 to plasmids having either one (pBS{sup +}) or two (pMP{sup 32}) EcoRI sites. Identification of the Gln-111/DNA complex is greatly enhanced by biotinylation of the complex followed by reaction with streptavidin gold prior to imaging. Image enhancement coupled with improvements in the preparation techniques for imaging large DNA molecules, such as lambda DNA (47 kb), has the potential to contribute to direct AFM restriction mapping of cosmid-sized genomic DNAs.

  11. Mapping site-specific endonuclease binding to DNA by direct imaging with atomic force microscopy (AFM)

    NASA Astrophysics Data System (ADS)

    Allison, David P.; Thundat, Thomas G.; Modrich, P.; Isfort, R. J.; Doktycz, Mitchel J.; Kerper, P. S.; Warmack, R. J.

    1995-04-01

    Physical mapping of DNA can be accomplished by direct AFM imaging of site specific proteins bound to DNA molecules. Using Gln-111, a mutant of EcoRI endonuclease with a specific affinity for EcoRI sites 1000 times greater than wild type enzyme but with cleavage rate constants reduced by a factor of 104, we demonstrate site-specific mapping by direct AFM imaging. Images are presented showing specific-site binding of Gln-111 to plasmids having either one (pBS+) or two (pMP32) EcoRI sites. Identification of the Gln-111/DNA complex is greatly enhanced by biotinylation of the complex followed by reaction with streptavidin gold prior to imaging. Image enhancement coupled with improvements in our preparation techniques for imaging large DNA molecules, such as lambda DNA (47 kb), has the potential to contribute to direct AFM restriction mapping of cosmid-sized genomic DNAs.

  12. Site-specific DNA recombination in mammalian cells by the Cre recombinase of bacteriophage P1.

    PubMed Central

    Sauer, B; Henderson, N

    1988-01-01

    The Cre protein encoded by the coliphage P1 is a 38-kDa protein that efficiently promotes both intra- and intermolecular synapsis and recombination of DNA both in Escherichia coli and in vitro. Recombination occurs at a specific site, called lox, and does not require any other protein factors. The Cre protein is shown here also to be able to cause synapsis of DNA and site-specific recombination in a mammalian cell line. A stable mouse cell line was established that expresses the Cre protein under the control of the Cd2+-inducible metallothionein I gene promoter. DNA recombination was monitored with DNA substrates containing two directly repeated lox sites. One such substrate is a circular plasmid with two directly repeated lox sites (lox2) flanking a marker gene and was introduced into cells by Ca3(PO4)2 transformation. As a second substrate we used a pseudorabies virus (a herpesvirus) containing a lox2 insertion designed to provide a sensitive detection system for recombination. In both cases, site-specific recombination in vivo is dependent on the presence of the Cre protein and occurs specifically at the 34-base-pair lox sites. These results demonstrate the controlled site-specific synapsis of DNA and recombination by a prokaryotic protein in mammalian cells and suggest that Cre-mediated site-specific recombination may be a useful tool for understanding and modulating genome rearrangements in eukaryotes. Images PMID:2839833

  13. Sequence- and Structure-Based Analysis of Tissue-Specific Phosphorylation Sites

    PubMed Central

    Karabulut, Nermin Pinar; Frishman, Dmitrij

    2016-01-01

    Phosphorylation is the most widespread and well studied reversible posttranslational modification. Discovering tissue-specific preferences of phosphorylation sites is important as phosphorylation plays a role in regulating almost every cellular activity and disease state. Here we present a comprehensive analysis of global and tissue-specific sequence and structure properties of phosphorylation sites utilizing recent proteomics data. We identified tissue-specific motifs in both sequence and spatial environments of phosphorylation sites. Target site preferences of kinases across tissues indicate that, while many kinases mediate phosphorylation in all tissues, there are also kinases that exhibit more tissue-specific preferences which, notably, are not caused by tissue-specific kinase expression. We also demonstrate that many metabolic pathways are differentially regulated by phosphorylation in different tissues. PMID:27332813

  14. Vortex design of a diagonal flow impeller with high specific speed

    NASA Astrophysics Data System (ADS)

    Kamada, Yoshihisa; Yamaguchi, Sumio; Sasaki, Kazuto; Inoue, Masahiro

    1986-09-01

    The 'vortex design' method applied to an axial flow compressor stage has been extended to a diagonal flow impeller with high specific speed. For a given type of vortex flow, the through flow problem is solved by the streamline curvature method, and a blade element is determined on the basis of this solution. However, for any vortex type except free vortex, the exit flow condition changes due to a secondary flow induced by vortices shed from the trailing edges. The given vortex type can be obtained by correcting this effect with a so-called secondary flow theory.The validity of this method has been examined in experiments on three kinds of vortex flows: free vortex type, and constant tangential velocity types with or without correction of the secondary flow effects.

  15. UNSAT-H Version 1. 0: unsaturated flow code documentation and applications for the Hanford Site

    SciTech Connect

    Fayer, M.J.; Gee, G.W.; Jones, T.L.

    1986-08-01

    Waste mangement practices at the Hanford Site have relied havily on near-surface burial. Predicting the future performance of any burial site in terms of the migration of buried contaminants requires a model capable of simulating water flow in the unsaturated soils above the buried waste. The model currently being developed to meet this need is UNSAT-H, which was developed at Pacific Northwest Laboratory for assessing the water dynamics of near-surface waste-disposal sites at the Hanfrod Site. The code will primarily be used to predict deep drainage (i.e., recharge) as a function of environmental conditions such as climate, soil type, and vegetation. UNSAT-H will also simulate various waste-management practices such as placing surface barriers over waste sites. UNSAT-H is a one-dimensional model that simulates the dynamics processes of infiltration, drainage, redistribution, surface evaporation, and uptake of water from soil by plants. UNSAT-H is designed to utilize two auxiliary codes. These codes are DATAINH, which is used to process the input data, and DATAOUT, which is used to process the UNSAT-H output. Operation of the code requires three separate steps. First, the problem to be simulated must be conceptualized in terms of boundary conditions, available data, and soil properties. Next, the data must be correctly formatted for input. Finally, the unput data must be processed, UNSAT-H run, and the output data processed for analysis. This report includes three examples of code use. In the first example, a benchmark test case is run in which the results of UNSAT-H simulations of infiltration are compared with an analytical solution and a numerical solution. The comparisons show excellent agreement for the specific test case, and this agreement provides vertification of the infiltration portion of the UNSAT-H code. The other two examples of code use are a simulation of a layered soil and one of plant transpiration.

  16. Demonstration of specific binding sites for /sup 3/H-RRR-alpha-tocopherol on human erythrocytes

    SciTech Connect

    Kitabchi, A.E.; Wimalasena, J.

    1982-01-01

    Previous work from our laboratory demonstrated specific binding sites for /sup 3/H-RRR-alpha-tocopherol (/sup 3/H-d alpha T) in membranes of rat adrenal cells. As tocopherol deficiency is associated with increased susceptibility of red blood cells to hemolysis, we investigated tocopherol binding sites in human RBCs. Erythrocytes were found to have specific binding sites for /sup 3/H-d alpha T that exhibited saturability and time and cell-concentration dependence as well as reversibility of binding. Kinetic studies of binding demonstrated two binding sites--one with high affinity (Ka of 2.6 x 10(7) M-1), low capacity (7,600 sites per cell) and the other with low affinity (1.2 x 10(6) M-1), high capacity (150,000 sites per cell). In order to localize the binding sites further, RBCs were fractionated and greater than 90% of the tocopherol binding was located in the membranes. Similar to the findings in intact RBCs, the membranes exhibited two binding sites with a respective Ka of 3.3 x 10(7) M-1 and 1.5 x 10(6) M-1. Specificity data for binding demonstrated 10% binding for RRR-gamma-tocopherol, but not other tocopherol analog exhibited competition for /sup 3/H-d alpha T binding sites. Instability data suggested a protein nature for these binding sites. Preliminary studies on Triton X-100 solubilized fractions resolved the binding sites to a major component with an Mr of 65,000 and a minor component with an Mr of 125,000. We conclude that human erythrocyte membranes contain specific binding sites for RRR-alpha-tocopherol. These sites may be of physiologic significance in the function of tocopherol on the red blood cell membrane.

  17. A reusable and specific protein A-coated piezoelectric biosensor for flow injection immunoassay.

    PubMed

    Lu, H C; Chen, H M; Lin, Y S; Lin, J W

    2000-01-01

    A hydrophilic matrix of periodate-oxidized dextran was used as a double-sided linker to covalently immobilize Staphylococcus aureus protein A (SpA) molecules onto a poly-L-lysine-modified piezoelectric crystal surface to improve their stability, activity, and binding specificity with human immunoglobulin G (IgG) in flow injection assays. The prepared sensing crystals displayed best sensitivity and reusability at a flow rate of 140 microL/min. A human IgG concentration as low as 0.3 nM can be detected by this system. Up to 19 successive assay repetitions were achieved without significant loss of sensitivity using the same crystal. The analysis of adsorption kinetics indicates that such a preparation can greatly increase the amount of available active human IgG binding sites on immobilized SpA. Hardly any response arising from unspecific binding was detected. In addition, the sensing crystal prepared by this method was found to retain activity better than one prepared via direct deposition when stored in either wet or dry states. Finally, the prepared SpA-coated crystals were applied to the affinity immobilization of polyclonal goat anti-Schistosoma japonicum glutathione-S-transferase (GST) and were able to subsequently detect GST and its genetically engineered mutant either in a purified form or in the crude cell lysate. PMID:10662499

  18. POTENTIAL EFFECTS OF FAULTS ON GROUNDWATER FLOW FOR THE YUCCA FLAT BASIN, NEVADA TEST SITE, NEVADA

    NASA Astrophysics Data System (ADS)

    Dickerson, R. P.; Fryer, W.

    2009-12-01

    The permeability changes resulting from finely comminuted material in fault cores and the fractured and brecciated rock in fault damage zones allows faults to channelize groundwater flow along the plane of the fault. The efficiency of faults as permeability structures depends on fault zone width, fault offset, depth at which the fault developed, type of faulted rock, extent of secondary mineralization, and fault orientation within current stress field. Studies of faulted volcanic rocks at Yucca Mountain, Nevada, indicate that fault zone width and brecciation increase with fault offset, that faulted welded tuff is more permeable than nonwelded or bedded tuff, and that non-hydrothermal secondary mineralization commonly diminishes fracture permeability. These results are applied to the groundwater conceptual flow model for Yucca Flat (YF) on the Nevada Test Site (NTS). Yucca Flat contains Tertiary volcanic rocks similar to thoise at Yucca Mountain deposited on Paleozoic carbonate rocks whose thickness is increased by local thrust-faults. The YF basin contains north-striking normal faults and is bordered by southwest-striking strike-slip faults to the south and east. Fault permeability values derived from faulted volcanic rocks at Yucca Mountain suggests that major normal faults in Yucca Flat potentially manifest permeability values along the fault plane equal to the highest values determined for volcanic aquifers. Numerous minor faults not assigned specific permeability values are assumed to imbue the basin with a hydraulic anisotropy favoring fault-parallel flow. In this scenario groundwater flows generally from north to south in the Yucca Flat basin, even as the head gradient is primarily towards the centrally located Yucca Fault, which acts as the main subsurface drainage feature within the basin. Studies show that the regional stress field has rotated clockwise such that southwest-striking strike-slip faults are currently under tension. In this scenario these

  19. 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. ...

  20. 78 FR 7767 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-04

    ... 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...

  1. 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...

  2. 77 FR 20014 - Environmental Management Site-Specific Advisory Board, Paducah, KY

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-03

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

  3. 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...

  4. 78 FR 32640 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-31

    ... 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: Rachel Blumenfeld, Deputy Designated Federal Officer, Department of...

  5. 78 FR 54460 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-04

    ... 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...

  6. 76 FR 61350 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-04

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

  7. 77 FR 59598 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-28

    ... 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...

  8. 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...

  9. 77 FR 51789 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-27

    ... 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...

  10. 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...

  11. 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...

  12. 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...

  13. 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...

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

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-12

    ... and Remediation Committee and Waste Management Committee of the Environmental Management Site-Specific... restoration, waste management, and related activities. Purpose of the Environmental Monitoring and Remediation... environmental remediation activities resulting from historical Los Alamos National Laboratory operations and,...

  15. 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. ...

  16. SMART GUIDANCE AND SMARTE - TOOLS FOR DEVELOPING SITE SPECIFIC REDEVELOPMENT PLANS

    EPA Science Inventory

    Site-specific Management Approaches and Redevelopment Tools (SMART) Guidance and its electronic counterpart, SMARTe are being developed jointly with the German Federal Ministry of Education and Research and the Interstate Technology Regulatory Council. These products will assist ...

  17. The calculation of surface orbital energies for specific types of active sites on dispersed metal catalysts

    SciTech Connect

    Augustine, R.L.; Lahanas, K.M.; Cole, F.

    1992-11-01

    An angular overlap calculation has been used to determine the s, p, and d orbital energy levels of the different types of surface sites present on dispersed metal catalysts. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.

  18. The calculation of surface orbital energies for specific types of active sites on dispersed metal catalysts

    SciTech Connect

    Augustine, R.L.; Lahanas, K.M.; Cole, F.

    1992-01-01

    An angular overlap calculation has been used to determine the s, p, and d orbital energy levels of the different types of surface sites present on dispersed metal catalysts. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.

  19. 75 FR 35446 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-22

    ... Environmental Management Site-Specific Advisory Board, Northern New Mexico AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... the areas of environmental restoration, waste management, and related activities. Tentative Agenda 1...

  20. 76 FR 48148 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-08

    ... Environmental Management Site-Specific Advisory Board, Hanford 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: Annual Tri-Party...

  1. 77 FR 31837 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-30

    ... 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... Energy Paducah Site Office, Post Office Box 1410, MS-103, Paducah, Kentucky 42001, (270)...

  2. 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)...

  3. 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...

  4. 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....

  5. 77 FR 66962 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-08

    ... Environmental Impact Statement Briefing/Update 3. Nye County Drilling Presentation 4. Industrial Sites-Closing... above. Written statements may be filed with the Board either before or after the meeting. Individuals... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice...

  6. 76 FR 21878 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-19

    .... Greater-Than-Class-C Draft Environmental Impact Statement (EIS) Committee Update. 3. Site-Wide EIS Update... Rupp at least seven days in advance of the meeting at the phone number listed above. Written statements... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice...

  7. 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.

  8. 76 FR 36101 - Environmental Management Site-Specific Advisory Board, Northern New Mexico; Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-21

    ... Site-Specific Advisory Board (EM SSAB), Northern New Mexico. The Federal Advisory Committee Act (Pub. L... Drive, Los Alamos, New Mexico. FOR FURTHER INFORMATION CONTACT: Menice Santistevan, Northern New Mexico... Board: The purpose of the Board is to make recommendations to DOE-EM and site management in the areas...

  9. Bioorthogonal Strategy for Bioprocessing of Specific-Site-Functionalized Enveloped Influenza-Virus-Like Particles

    PubMed Central

    2016-01-01

    Virus-like particles (VLPs) constitute a promising platform in vaccine development and targeted drug delivery. To date, most applications use simple nonenveloped VLPs as human papillomavirus or hepatitis B vaccines, even though the envelope is known to be critical to retain the native protein folding and biological function. Here, we present tagged enveloped VLPs (TagE-VLPs) as a valuable strategy for the downstream processing and monitoring of the in vivo production of specific-site-functionalized enveloped influenza VLPs. This two-step procedure allows bioorthogonal functionalization of azide-tagged nascent influenza type A hemagglutinin proteins in the envelope of VLPs through a strain-promoted [3 + 2] alkyne–azide cycloaddition reaction. Importantly, labeling does not influence VLP production and allows for construction of functionalized VLPs without deleterious effects on their biological function. Refined discrimination and separation between VLP and baculovirus, the major impurity of the process, is achieved when this technique is combined with flow cytometry analysis, as demonstrated by atomic force microscopy. TagE-VLPs is a versatile tool broadly applicable to the production, monitoring, and purification of functionalized enveloped VLPs for vaccine design trial runs, targeted drug delivery, and molecular imaging. PMID:27652605

  10. Site-specific parameter values for the Nuclear Regulatory Commission's food pathway dose model.

    PubMed

    Hamby, D M

    1992-02-01

    Routine operations at the Savannah River Site (SRS) in Western South Carolina result in radionuclide releases to the atmosphere and to the Savannah River. The resulting radiation doses to the off-site maximum individual and the off-site population within 80 km of the SRS are estimated on a yearly basis. These estimates are currently generated using dose models prescribed for the commercial nuclear power industry by the Nuclear Regulatory Commission (NRC). The NRC provides default values for dose-model parameters for facilities without resources to develop site-specific values. A survey of land- and water-use characteristics for the Savannah River area has been conducted to determine site-specific values for water recreation, consumption, and agricultural parameters used in the NRC Regulatory Guide 1.109 (1977) dosimetric models. These site parameters include local characteristics of meat, milk, and vegetable production; recreational and commercial activities on the Savannah River; and meat, milk, vegetable, and seafood consumption rates. This paper describes how parameter data were obtained at the Savannah River Site and the impacts of such data on off-site dose. Dose estimates using site-specific parameter values are compared to estimates using the NRC default values. PMID:1730555

  11. Estimating peak flow characteristics at ungaged sites by ridge regression

    USGS Publications Warehouse

    Tasker, Gary D.

    1982-01-01

    A regression simulation model, is combined with a multisite streamflow generator to simulate a regional regression of 50-year peak discharge against a set of basin characteristics. Monte Carlo experiments are used to compare the unbiased ordinary lease squares parameter estimator with Hoerl and Kennard's (1970a) ridge estimator in which the biasing parameter is that proposed by Hoerl, Kennard, and Baldwin (1975). The simulation results indicate a substantial improvement in parameter estimation using ridge regression when the correlation between basin characteristics is more than about 0.90. In addition, results indicate a strong potential for improving the mean square error of prediction of a peak-flow characteristic versus basin characteristics regression model when the basin characteristics are approximately colinear. The simulation covers a range of regression parameters, streamflow statistics, and basin characteristics commonly found in regional regression studies.

  12. Species- and site-specific impacts of an invasive herbivore on tree survival in mixed forests.

    PubMed

    Holland, E Penelope; Gormley, Andrew M; Pech, Roger P

    2016-04-01

    Invasive herbivores are often managed to limit their negative impact on plant populations, but herbivore density - plant damage relationships are notoriously spatially and temporally variable. Site and species characteristics (both plant and herbivore) must be considered when assessing the potential for herbivore damage, making it difficult to set thresholds for efficient management. Using the invasive brushtail possum Trichosurus vulpecula in New Zealand as a case study, we parameterized a generic model to predict annual probability of browse-induced mortality of five tree species at 12 sites. We compared predicted and observed tree mortality for each species + site combination to establish herbivore abundance - tree mortality thresholds for each site on a single and combined tree species basis. Model results indicated it is likely that possum browse was the primary cause of all tree mortality at nine of the 12 species-site combinations, allowing us to estimate site-specific thresholds below which possum population numbers should be reduced and maintained to keep tree mortality under a predetermined level, for example 0.5% per year. The browse model can be used to set site- and species-specific management action thresholds, and can be adapted easily for other plant or herbivore species. Results for multiple plant or herbivore species at a single site can be combined to create conservative, site-wide management strategies, and used to: determine which sites will be affected most by changes in herbivore abundance; quantify thresholds for herbivore management; and justify expenditure on herbivore control.

  13. Toward site-specific, homogeneous and highly stable fluorescent silver nanoclusters fabrication on triplex DNA scaffolds

    PubMed Central

    Feng, Lingyan; Huang, Zhenzhen; Ren, Jinsong; Qu, Xiaogang

    2012-01-01

    A new strategy to create site-specific, homogeneous, and bright silver nanoclusters (AgNCs) with high-stability was demonstrated by triplex DNA as template. By reasonable design of DNA sequence, homogeneous Ag2 cluster was obtained in the predefined position of CG.C+ site of triplex DNA. This strategy was also explored for controlled alignment of AgNCs on the DNA nanoscaffold. To the best of our knowledge, this was the first example to simultaneously answer the challenges of excellent site-specific nucleation and growth, homogeneity and stability against salt of DNA-templated AgNCs. PMID:22570417

  14. 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.

  15. A water framework directive (WFD) compliant determination of eologically acceptable flows in alpine rivers - a river type specific approach

    NASA Astrophysics Data System (ADS)

    Jäger, Paul; Zitek, Andreas

    2010-05-01

    Currently the EU-Water Framework Directive (WFD) represents the driving force behind the assessment for rehabilitation and conservation of aquatic resources throughout Europe. Hydropower production, often considered as "green energy", in the past has put significant pressures on river systems like fragmentation by weirs, impoundment, hydropeaking and water abstraction. Due to the limited availability of data for determining ecologically acceptable flow for rivers at water abstraction sites, a special monitoring program was conducted in the federal state of Salzburg in Austria from 2006 to 2009. Water abstraction sites at 19 hydropower plants, mostly within the trout region of the River Salzach catchment, were assessed in detail with regard to the effect of water abstraction on fish and macrozoobenthos. Based on a detailed assessment of the specific local hydro-morphological and biological situations, the validity of natural low flow criteria (Absolute Minimum Flow - AMF, the lowest daily average flow ever measured and Mean Annual Daily Low Flow - MADLF) as starting points for the determination of an ecologically acceptable flow was tested. It was assessed, if a good ecological status in accordance with the EU-WFD can be maintained at natural AMF. Additionally it was tested, if important habitat parameters describing connectivity, river type specific flow variability and river type specific habitats are maintained at this discharge. Habitat modelling was applied in some situations. Hydraulic results showed that at AMF the highest flow velocity classes were lost in most situations. When AMF was significantly undercut, flow velocities between 0,0 - 0,4 m/s became dominant, describing the loss of the river type specific flow character, leading to a loss of river type specific flow variability and habitats and increased sedimentation of fines. Furthermore limits for parameters describing connectivity for fish like maximum depth at the pessimum profile and minimum flow

  16. Site specific metals criteria as determined by Water Effect Ratio studies

    SciTech Connect

    Castle, C.J.; Neserke, G.

    1994-12-31

    Water Effect Ratios (WER) are being used to implement site-specific water quality criteria to address the variability of physical and chemical characteristics of site water and metals that may influence toxicity. A case in point, Coors Brewing Company in Golden, Colorado, has been granted site-specific criteria for the discharge of copper and zinc based on results of WER studies. Acute bioassays were conducted to determine seasonal WER values for copper, zinc and silver. The tests exposed Ceriodaphnia dubia and Pimephales promelas to graduated levels of metals in Clear Creek site water (below discharge mixing zone), reconstituted laboratory water and effluent. Final WER values, calculated by the ratio of LC50`s determined in site water and laboratory water, were multiplied by the standard metals criteria to develop the site specific values incorporated into the Coors Brewing Company permit to discharge. It is suggested that the high LC50 values for metals in site water is a factor of the effluent`s binding capacity that may reduce the bioavailability of metals in site water.

  17. n-Dodecyl β-D-maltoside specifically competes with general anesthetics for anesthetic binding sites.

    PubMed

    Xu, Longhe; Matsunaga, Felipe; Xi, Jin; Li, Min; Ma, Jingyuan; Liu, Renyu

    2014-01-01

    We recently demonstrated that the anionic detergent sodium dodecyl sulfate (SDS) specifically interacts with the anesthetic binding site in horse spleen apoferritin, a soluble protein which models anesthetic binding sites in receptors. This raises the possibility of other detergents similarly interacting with and occluding such sites from anesthetics, thereby preventing the proper identification of novel anesthetic binding sites. n-Dodecyl β-D-maltoside (DDM) is a non-ionic detergent commonly used during protein-anesthetic studies because of its mild and non-denaturing properties. In this study, we demonstrate that SDS and DDM occupy anesthetic binding sites in the model proteins human serum albumin (HSA) and horse spleen apoferritin and thereby inhibit the binding of the general anesthetics propofol and isoflurane. DDM specifically interacts with HSA (Kd = 40 μM) with a lower affinity than SDS (Kd = 2 μM). DDM exerts all these effects while not perturbing the native structures of either model protein. Computational calculations corroborated the experimental results by demonstrating that the binding sites for DDM and both anesthetics on the model proteins overlapped. Collectively, our results indicate that DDM and SDS specifically interact with anesthetic binding sites and may thus prevent the identification of novel anesthetic sites. Special precaution should be taken when undertaking and interpreting results from protein-anesthetic investigations utilizing detergents like SDS and DDM.

  18. Site-specific water quality guidelines: 1. Derivation approaches based on physicochemical, ecotoxicological and ecological data.

    PubMed

    van Dam, R A; Humphrey, C L; Harford, A J; Sinclair, A; Jones, D R; Davies, S; Storey, A W

    2014-01-01

    Generic water quality guidelines (WQGs) are developed by countries/regions as broad scale tools to assist with the protection of aquatic ecosystems from the impacts of toxicants. However, since generic WQGs cannot adequately account for the many environmental factors that may affect toxicity at a particular site, site-specific WQGs are often needed, especially for high environmental value ecosystems. The Australian and New Zealand Guidelines for Fresh and Marine Water Quality provide comprehensive guidance on methods for refining or deriving WQGs for site-specific purposes. This paper describes three such methods for deriving site-specific WQGs, namely: (1) using local reference water quality data, (2) using biological effects data from laboratory-based toxicity testing, and (3) using biological effects data from field surveys. Two case studies related to the assessment of impacts arising from mining operations in northern Australia are used to illustrate the application of these methods. Finally, the potential of several emerging methods designed to assess thresholds of ecological change from field data for deriving site-specific WQGs is discussed. Ideally, multiple lines of evidence approaches, integrating both laboratory and field data, are recommended for deriving site-specific WQGs. PMID:23846952

  19. Hetero-site-specific X-ray pump-probe spectroscopy for femtosecond intramolecular dynamics

    DOE PAGES

    Picón, A.; Lehmann, C. S.; Bostedt, C.; Rudenko, A.; Marinelli, A.; Osipov, T.; Rolles, D.; Berrah, N.; Bomme, C.; Bucher, M.; et al

    2016-05-23

    New capabilities at X-ray free-electron laser facilities allow the generation of two-colour femtosecond X-ray pulses, opening the possibility of performing ultrafast studies of X-ray-induced phenomena. Specifically, the experimental realization of hetero-site-specific X-ray-pump/X-ray-probe spectroscopy is of special interest, in which an X-ray pump pulse is absorbed at one site within a molecule and an X-ray probe pulse follows the X-ray-induced dynamics at another site within the same molecule. In this paper, we show experimental evidence of a hetero-site pump-probe signal. By using two-colour 10-fs X-ray pulses, we are able to observe the femtosecond time dependence for the formation of F ionsmore » during the fragmentation of XeF2 molecules following X-ray absorption at the Xe site.« less

  20. 76 FR 70120 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-10

    ... 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... Taos Highway 68, San Juan Pueblo, New Mexico 87566. FOR FURTHER INFORMATION CONTACT: Menice...

  1. 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...

  2. 75 FR 53280 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-31

    ... 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...

  3. 78 FR 23759 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-22

    ... 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... Drive, Santa Fe, NM 87501. FOR FURTHER INFORMATION CONTACT: Menice Santistevan, Northern New...

  4. 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'...

  5. 77 FR 47047 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-07

    ... 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... Road, Pojoaque, NM 87506. FOR FURTHER INFORMATION CONTACT: Menice Santistevan, Northern New...

  6. 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...

  7. 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...

  8. 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...

  9. Vika/vox, a novel efficient and specific Cre/loxP-like site-specific recombination system

    PubMed Central

    Karimova, Madina; Abi-Ghanem, Josephine; Berger, Nicolas; Surendranath, Vineeth; Pisabarro, Maria Teresa; Buchholz, Frank

    2013-01-01

    Targeted genome engineering has become an important research area for diverse disciplines, with site-specific recombinases (SSRs) being among the most popular genome engineering tools. Their ability to trigger excision, integration, inversion and translocation has made SSRs an invaluable tool to manipulate DNA in vitro and in vivo. However, sophisticated strategies that combine different SSR systems are ever increasing. Hence, the demand for additional precise and efficient recombinases is dictated by the increasing complexity of the genetic studies. Here, we describe a novel site-specific recombination system designated Vika/vox. Vika originates from a degenerate bacteriophage of Vibrio coralliilyticus and shares low sequence similarity to other tyrosine recombinases, but functionally carries out a similar type of reaction. We demonstrate that Vika is highly specific in catalyzing vox recombination without recombining target sites from other SSR systems. We also compare the recombination activity of Vika/vox with other SSR systems, providing a guideline for deciding on the most suitable enzyme for a particular application and demonstrate that Vika expression does not cause cytotoxicity in mammalian cells. Our results show that Vika/vox is a novel powerful and safe instrument in the ‘genetic toolbox’ that can be used alone or in combination with other SSRs in heterologous hosts. PMID:23143104

  10. Vika/vox, a novel efficient and specific Cre/loxP-like site-specific recombination system.

    PubMed

    Karimova, Madina; Abi-Ghanem, Josephine; Berger, Nicolas; Surendranath, Vineeth; Pisabarro, Maria Teresa; Buchholz, Frank

    2013-01-01

    Targeted genome engineering has become an important research area for diverse disciplines, with site-specific recombinases (SSRs) being among the most popular genome engineering tools. Their ability to trigger excision, integration, inversion and translocation has made SSRs an invaluable tool to manipulate DNA in vitro and in vivo. However, sophisticated strategies that combine different SSR systems are ever increasing. Hence, the demand for additional precise and efficient recombinases is dictated by the increasing complexity of the genetic studies. Here, we describe a novel site-specific recombination system designated Vika/vox. Vika originates from a degenerate bacteriophage of Vibrio coralliilyticus and shares low sequence similarity to other tyrosine recombinases, but functionally carries out a similar type of reaction. We demonstrate that Vika is highly specific in catalyzing vox recombination without recombining target sites from other SSR systems. We also compare the recombination activity of Vika/vox with other SSR systems, providing a guideline for deciding on the most suitable enzyme for a particular application and demonstrate that Vika expression does not cause cytotoxicity in mammalian cells. Our results show that Vika/vox is a novel powerful and safe instrument in the 'genetic toolbox' that can be used alone or in combination with other SSRs in heterologous hosts.

  11. 40 CFR 86.313-79 - Air flow measurement specifications; diesel engines.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...; diesel engines. 86.313-79 Section 86.313-79 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Emission Regulations for New Gasoline-Fueled and Diesel-Fueled Heavy-Duty Engines; Gaseous Exhaust Test Procedures § 86.313-79 Air flow measurement specifications; diesel engines. (a) The air flow...

  12. 40 CFR 86.313-79 - Air flow measurement specifications; diesel engines.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...; diesel engines. 86.313-79 Section 86.313-79 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Emission Regulations for New Gasoline-Fueled and Diesel-Fueled Heavy-Duty Engines; Gaseous Exhaust Test Procedures § 86.313-79 Air flow measurement specifications; diesel engines. (a) The air flow...

  13. 40 CFR 86.313-79 - Air flow measurement specifications; diesel engines.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...; diesel engines. 86.313-79 Section 86.313-79 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Emission Regulations for New Gasoline-Fueled and Diesel-Fueled Heavy-Duty Engines; Gaseous Exhaust Test Procedures § 86.313-79 Air flow measurement specifications; diesel engines. (a) The air flow...

  14. 40 CFR 86.313-79 - Air flow measurement specifications; diesel engines.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...; diesel engines. 86.313-79 Section 86.313-79 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Emission Regulations for New Gasoline-Fueled and Diesel-Fueled Heavy-Duty Engines; Gaseous Exhaust Test Procedures § 86.313-79 Air flow measurement specifications; diesel engines. (a) The air flow...

  15. On specific features of investigation of fluid flows by photometric techniques

    NASA Astrophysics Data System (ADS)

    Vologdin, V. A.; Davydov, V. V.; Velichko, E. N.

    2016-08-01

    Specific features of investigation of the fluid flow structure in a pipeline by photometric techniques are considered. The applicability of the photometric techniques based on the Doppler effect to such studies is discussed. A new method for detecting defects on inner walls of a pipeline that involves the use of the laser radiation scattered from particles in a flowing fluid is suggested.

  16. Determination of human health risk incorporating experimentally derived site-specific bioaccessibility of arsenic at an old abandoned smelter site.

    PubMed

    Yang, Kyung; Im, Jinwoo; Jeong, Seulki; Nam, Kyoungphile

    2015-02-01

    This study was conducted to investigate the contribution of a site-specific bioavailability of arsenic (As) to human health risk at an old abandoned smelter site in Korea. The site was contaminated with As for over 60 years with the same source (As2O3 in flue gas), but concentration and in vitro bioaccessibility (IVBA) of As differed by operable units (OU), which consequently resulted in difference in estimated risk. Soil samples collected from six OUs showed that aqua regia-extractable As concentrations ranged from 9.8 to 52.8mg/kg (average 34.1mg/kg) at OUs 1-5, which had been used as rice paddy field and farmland, and a forest region OU 6 showed much higher As concentrations (14.4-169.8mg/kg, average 85.9mg/kg). IVBA of As, determined from the ratio of Solubility/Bioavailability Research Consortium (SBRC)-extractable As to aqua regia-extractable As had a wide range of values (90th percentile values of 28.2-65.8%). Carcinogenic risk calculated with total soil As concentration was the highest (1.4×10(-4)) at OU 6 and the risk at the other OUs ranged from 3.8×10(-5) to 5.7×10(-5). In contrast, when site-specific relative bioavailability (i.e., IVBA values) was incorporated, the estimated risk was reduced by 29.5-62.0% and the decrease was the highest at OUs 1 and 5 with the lowest IVBA of 28.2%. The results demonstrate that the chemical forms of As may be different although the source of contamination is similar, and site-specific bioavailability affected by the chemical forms is an important factor in determining human health risk.

  17. Determination of human health risk incorporating experimentally derived site-specific bioaccessibility of arsenic at an old abandoned smelter site.

    PubMed

    Yang, Kyung; Im, Jinwoo; Jeong, Seulki; Nam, Kyoungphile

    2015-02-01

    This study was conducted to investigate the contribution of a site-specific bioavailability of arsenic (As) to human health risk at an old abandoned smelter site in Korea. The site was contaminated with As for over 60 years with the same source (As2O3 in flue gas), but concentration and in vitro bioaccessibility (IVBA) of As differed by operable units (OU), which consequently resulted in difference in estimated risk. Soil samples collected from six OUs showed that aqua regia-extractable As concentrations ranged from 9.8 to 52.8mg/kg (average 34.1mg/kg) at OUs 1-5, which had been used as rice paddy field and farmland, and a forest region OU 6 showed much higher As concentrations (14.4-169.8mg/kg, average 85.9mg/kg). IVBA of As, determined from the ratio of Solubility/Bioavailability Research Consortium (SBRC)-extractable As to aqua regia-extractable As had a wide range of values (90th percentile values of 28.2-65.8%). Carcinogenic risk calculated with total soil As concentration was the highest (1.4×10(-4)) at OU 6 and the risk at the other OUs ranged from 3.8×10(-5) to 5.7×10(-5). In contrast, when site-specific relative bioavailability (i.e., IVBA values) was incorporated, the estimated risk was reduced by 29.5-62.0% and the decrease was the highest at OUs 1 and 5 with the lowest IVBA of 28.2%. The results demonstrate that the chemical forms of As may be different although the source of contamination is similar, and site-specific bioavailability affected by the chemical forms is an important factor in determining human health risk. PMID:25490246

  18. Isolation and characterization of site-specific DNA-methyltransferases from Bacillus coagulans K.

    PubMed

    Svadbina, I V; Zelinskaya, N V; Kovalevskaya, N P; Zheleznaya, L A; Matvienko, N I

    2004-03-01

    Two site-specific DNA methyltransferases, M.BcoKIA and M.BcoKIB, were isolated from the thermophilic strain Bacillus coagulans K. Each of the methylases protects the recognition site 5'-CTCTTC-3'/5'-GAAGAG-3' from cleavage with the cognate restriction endonuclease BcoKI. It is shown that M.BcoKIB is an N6-adenine specific methylase and M.BcoKIA is an N4-cytosine specific methylase. According to bisulfite mapping, M.BcoKIA methylates the first cytosine in the sequence 5'-CTCTTC-3'. PMID:15061697

  19. Site-specific DNA-affinity chromatography of the lac repressor.

    PubMed Central

    Herrick, G

    1980-01-01

    To test the feasibility of site-specific DNA-affinity chromatography, E. coli lac repressor was bound to an operator-containing DNA column, and in parallel to a non-operator DNA column. Salt gradient elution shows: 1) elution from non-operator DNA was near 250mM KCl or NaCl; interpretation of this result suggests the usefulness of the procedure for studying salt-dependence of DNA-protein affinities; 2) elution from operator-containing DNA was delayed (average elution = 1000mM salt), demonstrating a feasibility of site-specific DNA-affinity chromatography, if one provides a sufficiently favorable ratio of specific to non-specific DNA binding sites; 3) repressor eluted from operator-containing DNA over a very broad salt range, which may represent chromatography-generated repressor heterogeneity. PMID:7001362

  20. Geographic origin determination of heroin and cocaine using site-specific isotopic ratio deuterium NMR

    PubMed

    Hays; Remaud; Jamin; Martin

    2000-05-01

    SNIF-NMR (Site-specific natural isotopic fractionation measured by deuterium NMR) was employed on 36 heroin samples from seven different known origins, and two cocaine samples from two different known origins. Heroin has two "synthetic" deuterium labeled sites (the two acetyls from acetic anhydride, each representing three equivalent nuclei) and 15 "natural" deuterium labeled sites (originating from the morphine produced in the opium plant). The "natural" sites have the potential for determining geographic location of the original opium plant, while the "synthetic" sites could assist in giving information about the commercial source of acetic anhydride used to convert morphine to heroin. Cocaine has 15 "natural" deuterium labeled sites. This study shows that SNIF-NMR has some use in determining the geographic origin of heroin and also has good potential for determining the geographical origin of cocaine.

  1. PhiC31 integrase induces efficient site-specific recombination in the Capra hircus genome.

    PubMed

    Ma, Haiyan; Ma, Qingwen; Lu, Yao; Wang, Juan; Hu, Wei; Gong, Zhijuan; Cai, Linlin; Huang, Ying; Huang, Shu-Zhen; Zeng, Fanyi

    2014-08-01

    Streptomyces phage φC31 integrase induces efficient site-specific recombination capable of integrating exogenous genes at pseudo attP sites in human, mouse, rat, rabbit, sheep, Drosophila, and bovine genomes. However, the φC31-mediated recombination between attB and the corresponding pseudo attP sites has not been investigated in Capra hircus. Here, we identified eight pseudo attP sites located in the intron or intergenic regions of the C. hircus genome, and demonstrated different levels of foreign gene expression after φC31 integrase-mediated integration. These pseudo attP sites share similar sequences with each other and with pseudo attP sites in other mammalian genomes, and these are associated with a neighboring consensus motif found in other genomes. The application of the φC31 integrase system in C. hircus provides a new option for genetic engineering of this economically important goat species.

  2. Custom-Designed Molecular Scissors for Site-Specific Manipulation of the Plant and Mammalian Genomes

    NASA Astrophysics Data System (ADS)

    Kandavelou, Karthikeyan; Chandrasegaran, Srinivasan

    Zinc finger nucleases (ZFNs) are custom-designed molecular scissors, engineered to cut at specific DNA sequences. ZFNs combine the zinc finger proteins (ZFPs) with the nonspecific cleavage domain of the FokI restriction enzyme. The DNA-binding specificity of ZFNs can be easily altered experimentally. This easy manipulation of the ZFN recognition specificity enables one to deliver a targeted double-strand break (DSB) to a genome. The targeted DSB stimulates local gene targeting by several orders of magnitude at that specific cut site via homologous recombination (HR). Thus, ZFNs have become an important experimental tool to make site-specific and permanent alterations to genomes of not only plants and mammals but also of many other organisms. Engineering of custom ZFNs involves many steps. The first step is to identify a ZFN site at or near the chosen chromosomal target within the genome to which ZFNs will bind and cut. The second step is to design and/or select various ZFP combinations that will bind to the chosen target site with high specificity and affinity. The DNA coding sequence for the designed ZFPs are then assembled by polymerase chain reaction (PCR) using oligonucleotides. The third step is to fuse the ZFP constructs to the FokI cleavage domain. The ZFNs are then expressed as proteins by using the rabbit reticulocyte in vitro transcription/translation system and the protein products assayed for their DNA cleavage specificity.

  3. Custom-Designed Molecular Scissors for Site-Specific Manipulation of the Plant and Mammalian Genomes

    PubMed Central

    Kandavelou, Karthikeyan; Chandrasegaran, Srinivasan

    2010-01-01

    Summary Zinc finger nucleases (ZFNs) are custom-designed molecular scissors, engineered to cut at specific DNA sequences. ZFNs combine the zinc finger proteins (ZFPs) with the nonspecific cleavage domain of the FokI restriction enzyme. The DNA-binding specificity of ZFNs can be easily altered experimentally. This easy manipulation of the ZFN recognition specificity enables one to deliver a targeted double-strand break (DSB) to a genome. The targeted DSB stimulates local gene targeting by several orders of magnitude at that specific cut site via homologous recombination (HR). Thus, ZFNs have become an important experimental tool to make site-specific and permanent alterations to genomes of not only plants and mammals but also of many other organisms. Engineering of custom ZFNs involves many steps. The first step is to identify a ZFN site at or near the chosen chromosomal target within the genome to which ZFNs will bind and cut. The second step is to design and/or select various ZFP combinations that will bind to the chosen target site with high specificity and affinity. The DNA coding sequence for the designed ZFPs are then assembled by polymerase chain reaction (PCR) using oligonucleotides. The third step is to fuse the ZFP constructs to the FokI cleavage domain. The ZFNs are then expressed as proteins by using the rabbit reticulocyte in vitro transcription/translation system and the protein products assayed for their DNA cleavage specificity. PMID:19488728

  4. Water-Level Data Analysis for the Saturated Zone Site-Scale Flow and Transport Model

    SciTech Connect

    K. Rehfeldt

    2004-10-08

    This report is an updated analysis of water-level data performed to provide the ''Saturated Zone Site-Scale Flow Model'' (BSC 2004 [DIRS 170037]) (referred to as the saturated zone (SZ) site-scale flow model or site-scale SZ flow model in this report) with the configuration of the potentiometric surface, target water-level data, and hydraulic gradients for calibration of groundwater flow models. This report also contains an expanded discussion of uncertainty in the potentiometric-surface map. The analysis of the potentiometric data presented in Revision 00 of this report (USGS 2001 [DIRS 154625]) provides the configuration of the potentiometric surface, target heads, and hydraulic gradients for the calibration of the SZ site-scale flow model (BSC 2004 [DIRS 170037]). Revision 01 of this report (USGS 2004 [DIRS 168473]) used updated water-level data for selected wells through the year 2000 as the basis for estimating water-level altitudes and the potentiometric surface in the SZ site-scale flow and transport model domain based on an alternative interpretation of perched water conditions. That revision developed computer files containing: Water-level data within the model area (DTN: GS010908312332.002); A table of known vertical head differences (DTN: GS010908312332.003); and A potentiometric-surface map (DTN: GS010608312332.001) using an alternative concept from that presented by USGS (2001 [DIRS 154625]) for the area north of Yucca Mountain. The updated water-level data presented in USGS (2004 [DIRS 168473]) include data obtained from the Nye County Early Warning Drilling Program (EWDP) Phases I and II and data from Borehole USW WT-24. This document is based on Revision 01 (USGS 2004 [DIRS 168473]) and expands the discussion of uncertainty in the potentiometric-surface map. This uncertainty assessment includes an analysis of the impact of more recent water-level data and the impact of adding data from the EWDP Phases III and IV wells. In addition to being utilized

  5. DAFS study of site-specific local structure of Mn in manganese ferrite films.

    SciTech Connect

    Kravtsov, E.; Haskel, D.; Cady, A.; Yang, A.; Vittoria, C.; Zuo, X.; Harris, V. G.; X-Ray Science Division; Inst. of Metal Physics; Northeastern Univ.; Nankai Univ.

    2006-01-01

    Manganese ferrite (MnFe{sub 2}O{sub 4}) is a well-known magnetic material widely used in electronics for many years. It is well established that its magnetic behavior is strongly influenced by local structural properties of Mn ions, which are distributed between crystallographically inequivalent tetrahedral and octahedral sites in the unit cell. In order to understand and be able to tune properties of these structures, it is necessary to have detailed site-specific structural information on the system. Here we report on the application of diffraction-anomalous fine structure (DAFS) spectroscopy to resolve site-specific Mn local structures in manganese ferrite films. The DAFS measurements were done at undulator beamline 4-ID-D of the Advanced Photon Source at Argonne National Laboratory. The DAFS spectra (Fig. 1) were measured at several Bragg reflections in the vicinity of the Mn absorption K-edge, having probed separately contributions from tetrahedrally and octahedrally coordinated Mn sites. The DAFS data analysis done with an iterative Kramers-Kroenig algorithm made it possible to solve separately the local structure around different inequivalent Mn sites in the unit cell. The reliability of the data treatment was checked carefully, and it was showed that the site-specific structural parameters obtained with DAFS allow us to describe fluorescence EXAFS spectrum measured independently. Fig. 2 shows individual site contributions to the imaginary part of the resonant scattering amplitude obtained from the treatment of the data of Fig. 1. The analysis of the refined site-specific absorption spectra was done using EXAFS methods based on theoretical standards. We provided direct evidence for the tetrahedral Mn-O bond distance being increased relative to the corresponding Fe-O distance in bulk manganese ferrites. The first coordination shell number was found to be reduced significantly for Mn atoms at these sites. This finding is consistent with the well-known tendency

  6. Effects of site-specific level adjustments on speech recognition with cochlear implants

    PubMed Central

    Zhou, Ning; Pfingst, Bryan E.

    2013-01-01

    Objectives Modulation detection thresholds (MDTs) vary across stimulation sites in a cochlear implant electrode array in a manner that is subject and ear specific. Previous studies have demonstrated that speech recognition with a cochlear implant can be improved by site-selection strategies, where selected stimulation sites with poor modulation sensitivity are removed from a subject’s processor MAP1. Limitations of site-selection strategies are that they can compromise spectral resolution and distort frequency-place mapping since the frequencies assigned to the removed sites are usually reallocated to other sites and site bandwidths are broadened. The objective of the current study was to test an alternative approach for rehabilitation that aimed at improving the across-site mean (ASM) MDTs by adjusting stimulation parameters at the poorly-performing sites. Based on previous findings that modulation detection contributes to speech recognition and improves significantly with stimulus level, we hypothesized that modulation sensitivity at the poor sites can be improved by artificially increasing stimulation levels at those sites in the speech processor, which then leads to improved speech recognition. Design Nine postlingually deafened ears implanted with Nucleus cochlear implants were evaluated for MDTs, absolute-detection threshold levels (T levels) and the maximum loudness levels (C levels) on each of the available stimulation sites. For each ear, the minimum stimulation level settings in the speech processor MAP were raised by 5%, and alternatively by 10%, of the dynamic range (DR) from true thresholds on 5 stimulation sites with the poorest MDTs. For comparison, a 5% level raise was globally applied to all stimulation sites. The C levels were fixed during these level manipulations. MDTs at the 5 poorest stimulation sites were compared at 20% DR before and after the level adjustments. Speech reception thresholds (SRTs), i.e., signal to noise ratios (SNRs

  7. A dermal HOX transcriptional program regulates site-specific epidermal fate

    PubMed Central

    Rinn, John L.; Wang, Jordon K.; Allen, Nancy; Brugmann, Samantha A.; Mikels, Amanda J.; Liu, Helen; Ridky, Todd W.; Stadler, H. Scott; Nusse, Roel; Helms, Jill A.; Chang, Howard Y.

    2008-01-01

    Reciprocal epithelial–mesenchymal interactions shape site-specific development of skin. Here we show that site-specific HOX expression in fibroblasts is cell-autonomous and epigenetically maintained. The distal-specific gene HOXA13 is continually required to maintain the distal-specific transcriptional program in adult fibroblasts, including expression of WNT5A, a morphogen required for distal development. The ability of distal fibroblasts to induce epidermal keratin 9, a distal-specific gene, is abrogated by depletion of HOXA13, but rescued by addition of WNT5A. Thus, maintenance of appropriate HOX transcriptional program in adult fibroblasts may serve as a source of positional memory to differentially pattern the epithelia during homeostasis and regeneration. PMID:18245445

  8. A replicator-specific binding protein essential for site-specific initiation of DNA replication in mammalian cells

    PubMed Central

    Zhang, Ya; Huang, Liang; Fu, Haiqing; Smith, Owen K.; Lin, Chii Mei; Utani, Koichi; Rao, Mishal; Reinhold, William C.; Redon, Christophe E.; Ryan, Michael; Kim, RyangGuk; You, Yang; Hanna, Harlington; Boisclair, Yves; Long, Qiaoming; Aladjem, Mirit I.

    2016-01-01

    Mammalian chromosome replication starts from distinct sites; however, the principles governing initiation site selection are unclear because proteins essential for DNA replication do not exhibit sequence-specific DNA binding. Here we identify a replication-initiation determinant (RepID) protein that binds a subset of replication-initiation sites. A large fraction of RepID-binding sites share a common G-rich motif and exhibit elevated replication initiation. RepID is required for initiation of DNA replication from RepID-bound replication origins, including the origin at the human beta-globin (HBB) locus. At HBB, RepID is involved in an interaction between the replication origin (Rep-P) and the locus control region. RepID-depleted murine embryonic fibroblasts exhibit abnormal replication fork progression and fewer replication-initiation events. These observations are consistent with a model, suggesting that RepID facilitates replication initiation at a distinct group of human replication origins. PMID:27272143

  9. Recruiting Human Microbiome Shotgun Data to Site-Specific Reference Genomes

    PubMed Central

    Xie, Gary; Lo, Chien-Chi; Scholz, Matthew; Chain, Patrick S. G.

    2014-01-01

    The human body consists of innumerable multifaceted environments that predispose colonization by a number of distinct microbial communities, which play fundamental roles in human health and disease. In addition to community surveys and shotgun metagenomes that seek to explore the composition and diversity of these microbiomes, there are significant efforts to sequence reference microbial genomes from many body sites of healthy adults. To illustrate the utility of reference genomes when studying more complex metagenomes, we present a reference-based analysis of sequence reads generated from 55 shotgun metagenomes, selected from 5 major body sites, including 16 sub-sites. Interestingly, between 13% and 92% (62.3% average) of these shotgun reads were aligned to a then-complete list of 2780 reference genomes, including 1583 references for the human microbiome. However, no reference genome was universally found in all body sites. For any given metagenome, the body site-specific reference genomes, derived from the same body site as the sample, accounted for an average of 58.8% of the mapped reads. While different body sites did differ in abundant genera, proximal or symmetrical body sites were found to be most similar to one another. The extent of variation observed, both between individuals sampled within the same microenvironment, or at the same site within the same individual over time, calls into question comparative studies across individuals even if sampled at the same body site. This study illustrates the high utility of reference genomes and the need for further site-specific reference microbial genome sequencing, even within the already well-sampled human microbiome. PMID:24454771

  10. 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.

  11. Numerical modeling of geothermal heat pump system: evaluation of site specific groundwater thermal impact

    NASA Astrophysics Data System (ADS)

    Pedron, Roberto; Sottani, Andrea; Vettorello, Luca

    2014-05-01

    A pilot plant using a geothermal open-loop heat pump system has been realized in the city of Vicenza (Northern Italy), in order to meet the heating and cooling needs of the main monumental building in the historical center, the Palladian Basilica. The low enthalpy geothermal system consists of a pumping well and a reinjection well, both intercepting the same confined aquifer; three other monitoring wells have been drilled and then provided with water level and temperature dataloggers. After about 1 year and a half of activity, during a starting experimental period of three years, we have now the opportunity to analyze long term groundwater temperature data series and to evaluate the numerical modeling reliability about thermal impact prediction. The initial model, based on MODFLOW and SHEMAT finite difference codes, has been calibrated using pumping tests and other field investigations data, obtaining a valid and reliable groundwater flow simulation. But thermal parameters, such as thermal conductivity and volumetric heat capacity, didn't have a site specific direct estimation and therefore they have been assigned to model cells referring to bibliographic standards, usually derived from laboratory tests and barely representing real aquifer properties. Anyway preliminary heat transport results have been compared with observed temperature trends, showing an efficient representation of the thermal plume extension and shape. The ante operam simulation could not consider heat pump real utilization, that happened to be relevantly different from the expected project values; so the first numerical model could not properly simulate the groundwater temperature evolution. Consequently a second model has been implemented, in order to calibrate the mathematical simulation with monitored groundwater temperature datasets, trying to achieve higher levels of reliability in heat transport phenomena interpretation. This second step analysis focuses on aquifer thermal parameters

  12. Position specific variation in the rate of evolution intranscription factor binding sites

    SciTech Connect

    Moses, Alan M.; Chiang, Derek Y.; Kellis, Manolis; Lander, EricS.; Eisen, Michael B.

    2003-08-28

    The binding sites of sequence specific transcription factors are an important and relatively well-understood class of functional non-coding DNAs. Although a wide variety of experimental and computational methods have been developed to characterize transcription factor binding sites, they remain difficult to identify. Comparison of non-coding DNA from related species has shown considerable promise in identifying these functional non-coding sequences, even though relatively little is known about their evolution. Here we analyze the genome sequences of the budding yeasts Saccharomyces cerevisiae, S. bayanus, S. paradoxus and S. mikataeto study the evolution of transcription factor binding sites. As expected, we find that both experimentally characterized and computationally predicted binding sites evolve slower than surrounding sequence, consistent with the hypothesis that they are under purifying selection. We also observe position-specific variation in the rate of evolution within binding sites. We find that the position-specific rate of evolution is positively correlated with degeneracy among binding sites within S. cerevisiae. We test theoretical predictions for the rate of evolution at positions where the base frequencies deviate from background due to purifying selection and find reasonable agreement with the observed rates of evolution. Finally, we show how the evolutionary characteristics of real binding motifs can be used to distinguish them from artifacts of computational motif finding algorithms. As has been observed for protein sequences, the rate of evolution in transcription factor binding sites varies with position, suggesting that some regions are under stronger functional constraint than others. This variation likely reflects the varying importance of different positions in the formation of the protein-DNA complex. The characterization of the pattern of evolution in known binding sites will likely contribute to the effective use of comparative

  13. Simple nocturnal slope-flow data from the Rattlesnake Mountain site

    SciTech Connect

    Horst, T.W.; Doran, J.C.

    1982-10-01

    Detailed vertical profiles of the wind and temperture structure of nocturnal slope flows were measured at a site that is uniform in the cross-slope direction. The upper part of the slope closely approximates a simple, tilted plane. These measurements were made from three towers at different distances from the ridge crest, each of which extended through the local depth of the katabatic flow. The tower wind and temperature data from the four best cases of slope flow observed in 1980 and 1981 are listed, as well as ambient wind and temperature profiles to a height of 300m from a Tethersonde flown at the experimental site and surface winds from a network of stations surrounding the site.

  14. Groundwater flow near the Shoal Site, Sand Springs Range, Nevada: Impact of density-driven flow

    SciTech Connect

    Chapman, J.; Mihevc, T.; McKay, A.

    1994-09-01

    The nature of flow from a highland recharge area in a mountain range in north-central Nevada to discharge areas on either side of the range is evaluated to refine a conceptual model of contaminant transport from an underground nuclear test conducted beneath the range. The test, known as the Shoal event, was conducted in 1963 in granitic rocks of the Sand Springs Range. Sparse hydraulic head measurements from the early 1960s suggest flow from the shot location to the east to Fairview Valley, while hydrochemistry supports flow to salt pans in Fourmile Flat to the west. Chemical and isotopic data collected from water samples and during well-logging arc best explained by a reflux brine system on the west side of the Sand Springs Range, rather than a typical local flow system where all flow occurs from recharge areas in the highlands to a central discharge area in a playa. Instead, dense saline water from the playa is apparently being driven toward the range by density contrasts. The data collected between the range and Fourmile Flat suggest the groundwater is a mixture of younger, fresher recharge water with older brine. Chemical contrasts between groundwater in the east and west valleys reflect the absence of re-flux water in Fairview Valley because the regional discharge area is distant and thus there is no accumulation of salts. The refluxing hydraulic system probably developed after the end of the last pluvial period and differences between the location of the groundwater divide based on hydraulic and chemical indicators could reflect movement of the divide as the groundwater system adjusts to the new reflux condition.

  15. Propofol inhibits SIRT2 deacetylase through a conformation-specific, allosteric site.

    PubMed

    Weiser, Brian P; Eckenhoff, Roderic G

    2015-03-27

    meta-Azi-propofol (AziPm) is a photoactive analog of the general anesthetic propofol. We photolabeled a myelin-enriched fraction from rat brain with [(3)H]AziPm and identified the sirtuin deacetylase SIRT2 as a target of the anesthetic. AziPm photolabeled three SIRT2 residues (Tyr(139), Phe(190), and Met(206)) that are located in a single allosteric protein site, and propofol inhibited [(3)H]AziPm photolabeling of this site in myelin SIRT2. Structural modeling and in vitro experiments with recombinant human SIRT2 determined that propofol and [(3)H]AziPm only bind specifically and competitively to the enzyme when co-equilibrated with other substrates, which suggests that the anesthetic site is either created or stabilized in enzymatic conformations that are induced by substrate binding. In contrast to SIRT2, specific binding of [(3)H]AziPm or propofol to recombinant human SIRT1 was not observed. Residues that line the propofol binding site on SIRT2 contact the sirtuin co-substrate NAD(+) during enzymatic catalysis, and assays that measured SIRT2 deacetylation of acetylated α-tubulin revealed that propofol inhibits enzymatic function. We conclude that propofol inhibits the mammalian deacetylase SIRT2 through a conformation-specific, allosteric protein site that is unique from the previously described binding sites of other inhibitors. This suggests that propofol might influence cellular events that are regulated by protein acetylation state.

  16. Conversion of transuranic waste to low level waste by decontamination: a site specific update

    SciTech Connect

    Allen, R.P.; Hazelton, R.F.

    1985-09-01

    As a followup to an FY-1984 cost/benefit study, a program was conducted in FY-1985 to transfer to the relevant DOE sites the information and technology for the direct conversion of transuranic (TRU) waste to low-level waste (LLW) by decontamination. As part of this work, the economic evaluation of the various TRUW volume reduction and conversion options was updated and expanded to include site-specific factors. The results show, for the assumptions used, that size reduction, size reduction followed by decontamination, or in situ decontamination are cost effective compared with the no-processing option. The technology transfer activities included site presentations and discussions with operations and waste management personnel to identify application opportunities and site-specific considerations and constraints that could affect the implementation of TRU waste conversion principles. These discussions disclosed definite potential for the beneficial application of these principles at most of the sites, but also confirmed the existence of site-specific factors ranging from space limitations to LLW disposal restrictions that could preclude particular applications or diminish expected benefits. 8 refs., 2 figs., 4 tabs.

  17. Stereospecific suppression of active site mutants by methylphosphonate substituted substrates reveals the stereochemical course of site-specific DNA recombination.

    PubMed

    Rowley, Paul A; Kachroo, Aashiq H; Ma, Chien-Hui; Maciaszek, Anna D; Guga, Piotr; Jayaram, Makkuni

    2015-07-13

    Tyrosine site-specific recombinases, which promote one class of biologically important phosphoryl transfer reactions in DNA, exemplify active site mechanisms for stabilizing the phosphate transition state. A highly conserved arginine duo (Arg-I; Arg-II) of the recombinase active site plays a crucial role in this function. Cre and Flp recombinase mutants lacking either arginine can be rescued by compensatory charge neutralization of the scissile phosphate via methylphosphonate (MeP) modification. The chemical chirality of MeP, in conjunction with mutant recombinases, reveals the stereochemical contributions of Arg-I and Arg-II. The SP preference of the native reaction is specified primarily by Arg-I. MeP reaction supported by Arg-II is nearly bias-free or RP-biased, depending on the Arg-I substituent. Positional conservation of the arginines does not translate into strict functional conservation. Charge reversal by glutamic acid substitution at Arg-I or Arg-II has opposite effects on Cre and Flp in MeP reactions. In Flp, the base immediately 5' to the scissile MeP strongly influences the choice between the catalytic tyrosine and water as the nucleophile for strand scission, thus between productive recombination and futile hydrolysis. The recombinase active site embodies the evolutionary optimization of interactions that not only favor the normal reaction but also proscribe antithetical side reactions. PMID:25999343

  18. Stereospecific suppression of active site mutants by methylphosphonate substituted substrates reveals the stereochemical course of site-specific DNA recombination.

    PubMed

    Rowley, Paul A; Kachroo, Aashiq H; Ma, Chien-Hui; Maciaszek, Anna D; Guga, Piotr; Jayaram, Makkuni

    2015-07-13

    Tyrosine site-specific recombinases, which promote one class of biologically important phosphoryl transfer reactions in DNA, exemplify active site mechanisms for stabilizing the phosphate transition state. A highly conserved arginine duo (Arg-I; Arg-II) of the recombinase active site plays a crucial role in this function. Cre and Flp recombinase mutants lacking either arginine can be rescued by compensatory charge neutralization of the scissile phosphate via methylphosphonate (MeP) modification. The chemical chirality of MeP, in conjunction with mutant recombinases, reveals the stereochemical contributions of Arg-I and Arg-II. The SP preference of the native reaction is specified primarily by Arg-I. MeP reaction supported by Arg-II is nearly bias-free or RP-biased, depending on the Arg-I substituent. Positional conservation of the arginines does not translate into strict functional conservation. Charge reversal by glutamic acid substitution at Arg-I or Arg-II has opposite effects on Cre and Flp in MeP reactions. In Flp, the base immediately 5' to the scissile MeP strongly influences the choice between the catalytic tyrosine and water as the nucleophile for strand scission, thus between productive recombination and futile hydrolysis. The recombinase active site embodies the evolutionary optimization of interactions that not only favor the normal reaction but also proscribe antithetical side reactions.

  19. Crossover-site sequence and DNA torsional stress control strand interchanges by the Bxb1 site-specific serine recombinase

    PubMed Central

    Keenholtz, Ross A.; Grindley, Nigel D.F.; Hatfull, Graham F.; Marko, John F.

    2016-01-01

    DNA segment exchange by site-specific serine recombinases (SRs) is thought to proceed by rigid-body rotation of the two halves of the synaptic complex, following the cleavages that create the two pairs of exchangeable ends. It remains unresolved how the amount of rotation occurring between cleavage and religation is controlled. We report single-DNA experiments for Bxb1 integrase, a model SR, where dynamics of individual synapses were observed, using relaxation of supercoiling to report on cleavage and rotation events. Relaxation events often consist of multiple rotations, with the number of rotations per relaxation event and rotation velocity sensitive to DNA sequence at the center of the recombination crossover site, torsional stress and salt concentration. Bulk and single-DNA experiments indicate that the thermodynamic stability of the annealed, but cleaved, crossover sites controls ligation efficiency of recombinant and parental synaptic complexes, regulating the number of rotations during a breakage-religation cycle. The outcome is consistent with a ‘controlled rotation’ model analogous to that observed for type IB topoisomerases, with religation probability varying in accord with DNA base-pairing free energies at the crossover site. Significantly, we find no evidence for a special regulatory mechanism favoring ligation and product release after a single 180° rotation. PMID:27550179

  20. 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

  1. Site-specific interaction of thrombin and inhibitors observed by fluorescence correlation spectroscopy.

    PubMed Central

    Klingler, J; Friedrich, T

    1997-01-01

    We report on the application of fluorescence correlation spectroscopy (FCS) to observe the interaction between thrombin and thrombin inhibitors. Two site-specific fluorescent labels were used to distinguish between inhibitors directed to the active site, the exosite, or both binding sites of thrombin. For several well-known inhibitors of thrombin, the binding sites observed by FCS correspond to previous studies. The interaction of the recently discovered thrombin inhibitor ornithodorin from the tick Ornithodorus moubata with thrombin was investigated. It was found that this inhibitor, like hirudin and rhodniin, binds to both the active site and exosite of thrombin simultaneously. This study shows the feasibility of FCS as a sensitive and selective method for observing protein-ligand interactions. As an additional technique, simultaneous labeling with both fluorescent labels was successfully demonstrated. Images FIGURE 1 PMID:9336216

  2. [Case study on health risk assessment based on site-specific conceptual model].

    PubMed

    Zhong, Mao-Sheng; Jiang, Lin; Yao, Jue-Jun; Xia, Tian-Xiang; Zhu, Xiao-Ying; Han, Dan; Zhang, Li-Na

    2013-02-01

    Site investigation was carried out on an area to be redeveloped as a subway station, which is right downstream of the groundwater of a former chemical plant. The results indicate the subsurface soil and groundwater in the area are both polluted heavily by 1,2-dichloroethane, which was caused by the chemical plant upstream with the highest concentration was 104.08 mg.kg-1 for soil sample at 8.6 m below ground and the highest concentration was 18500 microg.L-1 for groundwater. Further, a site-specific contamination conceptual model, giving consideration to the specific structure configuration of the station, was developed, and the corresponding risk calculation equation was derived. The carcinogenic risks calculated with models developed on the generic site conceptual model and derived herein on the site-specific conceptual model were compared. Both models indicate that the carcinogenic risk is significantly higher than the acceptable level which is 1 x 10(-6). The comparison result reveals that the risk calculated with the former models for soil and groundwater are higher than the one calculated with the latter models by 2 times and 1.5 times, respectively. The finding in this paper indicates that the generic risk assessment model may underestimate the risk if specific site conditions and structure configuration are not considered.

  3. Estimating peak-flow frequency statistics for selected gaged and ungaged sites in naturally flowing streams and rivers in Idaho

    USGS Publications Warehouse

    Wood, Molly S.; Fosness, Ryan L.; Skinner, Kenneth D.; Veilleux, Andrea G.

    2016-06-27

    The U.S. Geological Survey, in cooperation with the Idaho Transportation Department, updated regional regression equations to estimate peak-flow statistics at ungaged sites on Idaho streams using recent streamflow (flow) data and new statistical techniques. Peak-flow statistics with 80-, 67-, 50-, 43-, 20-, 10-, 4-, 2-, 1-, 0.5-, and 0.2-percent annual exceedance probabilities (1.25-, 1.50-, 2.00-, 2.33-, 5.00-, 10.0-, 25.0-, 50.0-, 100-, 200-, and 500-year recurrence intervals, respectively) were estimated for 192 streamgages in Idaho and bordering States with at least 10 years of annual peak-flow record through water year 2013. The streamgages were selected from drainage basins with little or no flow diversion or regulation. The peak-flow statistics were estimated by fitting a log-Pearson type III distribution to records of annual peak flows and applying two additional statistical methods: (1) the Expected Moments Algorithm to help describe uncertainty in annual peak flows and to better represent missing and historical record; and (2) the generalized Multiple Grubbs Beck Test to screen out potentially influential low outliers and to better fit the upper end of the peak-flow distribution. Additionally, a new regional skew was estimated for the Pacific Northwest and used to weight at-station skew at most streamgages. The streamgages were grouped into six regions (numbered 1_2, 3, 4, 5, 6_8, and 7, to maintain consistency in region numbering with a previous study), and the estimated peak-flow statistics were related to basin and climatic characteristics to develop regional regression equations using a generalized least squares procedure. Four out of 24 evaluated basin and climatic characteristics were selected for use in the final regional peak-flow regression equations.Overall, the standard error of prediction for the regional peak-flow regression equations ranged from 22 to 132 percent. Among all regions, regression model fit was best for region 4 in west

  4. Flow and radionuclide transport from rock to surface systems: characterization and modelling of potential repository sites in Sweden

    SciTech Connect

    Werner, Kent; Bosson, Emma; Berglund, Sten

    2007-07-01

    The safety assessments of potential geological repositories for spent nuclear fuel in Sweden are supported by modelling of groundwater flow in rock, to predict locations (exit points) where radionuclides from the deep repository may enter land, surface waters and associated ecosystems above the rock. This modelling includes detailed rock descriptions, but simplifies the upper part of the flow domain, including representations of meteorological processes and interactions with hydrological objects at the surface. Using the Laxemar candidate site as example, this paper investigates some potentially important consequences of these simplifications. Specifically, it compares particle tracking results obtained by a deep-rock groundwater flow model (CONNECTFLOW) and by MIKE SHE-MIKE 11, which contains detailed descriptions of near-surface/surface water flow. Overall, the models predict similar exit point patterns, occurring as clusters along streams in valleys, at a lake, and in sea bays. However, on a detailed level there are some prediction differences, which may be of importance for biosphere-focused safety assessments. CONNECTFLOW essentially predicts flow paths through the repository that follow fractures and deformation zones, outcropping in valleys. In comparison, MIKE SHE-MIKE 11 provides more detailed information on near-surface water flow paths, including the associated exit points and inputs to assessments of radionuclide retention. (authors)

  5. Estimation of the pore pressure distribution from three dimensional groundwater flow model at mine sites in Korea

    NASA Astrophysics Data System (ADS)

    Kang, Sangsoo; Jang, Myounghwan; Kim, Gyoungman; Kim, Donghui; Kim, Daehoon; Baek, Hwanjo

    2016-04-01

    Mining activities continually change the groundwater flow and associated pore pressure distributions within the rockmass around the mine openings or the open-pit bench during the operational periods. As the pore pressure distributions may substantially affect the mechanical behaviour or stability of the rockmass, it is important to monitor the variation of pore pressure incurred by mining operation. The pore pressure distributions within the rockmass can be derived using a two- or three-dimensional finite element groundwater flow model, adopted to simulate the groundwater flow. While the groundwater inflow at mines has generally been dealt with respect to the working environment, detailed case studies on the distribution of pore water pressure related to the stability analysis of mine openings have been relatively rare in Korea. Recently, however, as the health and safety problems are emerged for sustainable mining practice, these issues are of the major concerns for the mining industries. This study aims to establish a three dimensional groundwater flow model to estimate the pore pressure distributions in order to employ as an input parameter for numerical codes such as the FLAC 3D. Also, the groundwater flow simulated can be used for de-watering design at a mine site. The MINEDW code, a groundwater flow model code specifically developed to simulate the complicated hydro-geologic conditions related to mining, has mainly been used in this study. Based on the data collected from field surveys and literature reviews, a conceptual model was established and sensitivity analysis was performed.

  6. Multiple-regression equations for estimating low flows at ungaged stream sites in Ohio

    USGS Publications Warehouse

    Koltun, G.F.; Schwartz, R.R.

    1987-01-01

    This report presents multiple-regression equations for estimating selected low-flow characteristics for most unregulated Ohio streams at sites where little or no discharge data are available. The equations relate combinations of drainage area, main-channel length, main-channel slope, average basin elevation, forested area, average annual precipitation, and an index of infiltration to low flows with durations of 7 and 30 days and average recurrence intervals of 2 and 10 years. Data from 132 long-term continuous-record gaging stations and partial-record sites in Ohio were used in the analyses. Multiple-regression analyses were first performed by using data from all 132 sites in an attempt to develop equations that would be applicable statewide. Standard errors for the statewide equations were too high (111 to 189 percent) for them to be of practical use in estimating low streamflows. Data for the state were then subdivided into five regions, and multiple-regression equations were developed for each region. Standard errors for four of the five regions improved, and raged from 43 to 106 percent. Standard errors for region 5 remained high (74 to 129 percent). The multiple-regression equations presented in this report are not applicable to streams with significant low-flow regulation. The equations also are not applicable if (1) the site has been gaged and low-flow estimates have been developed from gaging-station records, (2) low flow can be estimated by the drainage-area transference method from data for a nearby gaged site, or (3) a sufficient number of partial-record measurements made at the site can be adquately correlated with concurrent base flows at a suitable index station.

  7. Versatile and Efficient Site-Specific Protein Functionalization by Tubulin Tyrosine Ligase.

    PubMed

    Schumacher, Dominik; Helma, Jonas; Mann, Florian A; Pichler, Garwin; Natale, Francesco; Krause, Eberhard; Cardoso, M Cristina; Hackenberger, Christian P R; Leonhardt, Heinrich

    2015-11-01

    A novel chemoenzymatic approach for simple and fast site-specific protein labeling is reported. Recombinant tubulin tyrosine ligase (TTL) was repurposed to attach various unnatural tyrosine derivatives as small bioorthogonal handles to proteins containing a short tubulin-derived recognition sequence (Tub-tag). This novel strategy enables a broad range of high-yielding and fast chemoselective C-terminal protein modifications on isolated proteins or in cell lysates for applications in biochemistry, cell biology, and beyond, as demonstrated by the site-specific labeling of nanobodies, GFP, and ubiquitin. PMID:26404067

  8. Site-Specific Fragmentation of Polystyrene Molecule Using Size-Selected Ar Gas Cluster Ion Beam

    NASA Astrophysics Data System (ADS)

    Moritani, Kousuke; Mukai, Gen; Hashinokuchi, Michihiro; Mochiji, Kozo

    2009-04-01

    The secondary ion mass spectrum (SIMS) of a polystyrene thin film was investigated using a size-selected Ar gas cluster ion beam (GCIB). The fragmentation in the SIM spectrum varied by kinetic energy per atom (Eatom); the Eatom dependence of the secondary ion intensity of the fragment species of polystyrene can be essentially classified into three types based on the relationship between Eatom and the dissociation energy of a specific bonding site in the molecule. These results indicate that adjusting Eatom of size-selected GCIB may realize site-specific bond breaking within a molecule.

  9. Dry Deposition Velocity Estimation for the Savannah River Site: Part 2 -- Parametric and Site-Specific Analysis

    SciTech Connect

    Napier, Bruce A.; Rishel, Jeremy P.; Cook, Kary M.

    2013-09-12

    Values for the dry deposition velocity of airborne particles were estimated with the GENII Version 2.10.1 computer code for the Savannah River site using assumptions about surface roughness parameters and particle size and density. Use of the GENII code is recommended by the U.S. Department of Energy for this purpose. Meteorological conditions evaluated include atmospheric stability classes D, E, and F and wind speeds of 0.5, 1.0, 1.5, and 2.0 m/s. Local surface roughness values ranging from 0.03 to 2 meters were evaluated. Particles with mass mean diameters of 1, 5, and 10 microns and densities of 1, 3, 4, and 5 g/cm3 were evaluated. Site specific meteorology was used to predict deposition velocity for Savannah River conditions for a range of distances from 670 to 11,500 meters.

  10. Programmable Site-Specific Nucleases for Targeted Genome Engineering in Higher Eukaryotes.

    PubMed

    Govindan, Ganesan; Ramalingam, Sivaprakash

    2016-11-01

    Recent advances in the targeted genome engineering enable molecular biologists to generate sequence specific modifications with greater efficiency and higher specificity in complex eukaryotic genomes. Programmable site-specific DNA cleavage reagents and cellular DNA repair mechanisms have made this possible. These reagents have become powerful tools for delivering a site-specific genomic double-strand break (DSB) at the desired chromosomal locus, which produces sequence alterations through error-prone non-homologous end joining (NHEJ) resulting in gene inactivations/knockouts. Alternatively, the DSB can be repaired through homology-directed repair (HDR) using a donor DNA template, which leads to the introduction of desired sequence modifications at the predetermined site. Here, we summarize the role of three classes of nucleases; zinc finger nucleases (ZFNs), transcription activator like effector nucleases (TALENs), and clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) system in achieving targeted genome modifications. Further, we discuss the progress towards the applications of programmable site-specific nucleases (SSNs) in treating human diseases and other biological applications in economically important higher eukaryotic organisms such as plants and livestock. J. Cell. Physiol. 231: 2380-2392, 2016. © 2016 Wiley Periodicals, Inc. PMID:26945523

  11. 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

  12. SPEER-SERVER: a web server for prediction of protein specificity determining sites.

    PubMed

    Chakraborty, Abhijit; Mandloi, Sapan; Lanczycki, Christopher J; Panchenko, Anna R; Chakrabarti, Saikat

    2012-07-01

    Sites that show specific conservation patterns within subsets of proteins in a protein family are likely to be involved in the development of functional specificity. These sites, generally termed specificity determining sites (SDS), might play a crucial role in binding to a specific substrate or proteins. Identification of SDS through experimental techniques is a slow, difficult and tedious job. Hence, it is very important to develop efficient computational methods that can more expediently identify SDS. Herein, we present Specificity prediction using amino acids' Properties, Entropy and Evolution Rate (SPEER)-SERVER, a web server that predicts SDS by analyzing quantitative measures of the conservation patterns of protein sites based on their physico-chemical properties and the heterogeneity of evolutionary changes between and within the protein subfamilies. This web server provides an improved representation of results, adds useful input and output options and integrates a wide range of analysis and data visualization tools when compared with the original standalone version of the SPEER algorithm. Extensive benchmarking finds that SPEER-SERVER exhibits sensitivity and precision performance that, on average, meets or exceeds that of other currently available methods. SPEER-SERVER is available at http://www.hpppi.iicb.res.in/ss/.

  13. From regional to site specific SPTHA through inundation simulations: a case study for three test sites in Central Mediterranean

    NASA Astrophysics Data System (ADS)

    Selva, Jacopo; Tonini, Roberto; Romano, Fabrizio; Volpe, Manuela; Brizuela, Beatriz; Piatanesi, Alessio; Basili, Roberto; Lorito, Stefano

    2016-04-01

    We propose a procedure that enables the quantification of tsunami hazard at specific target sites through numerical simulations, accounting for the full variability of potential seismic sources. To this end, we developed a method that reduces the computational effort required by a very large number of detailed inundation simulations by adopting the offshore tsunami propagation patterns used for regional Seismic PTHA (SPTHA) as a proxy for the subsequent hazard estimate. The reduction of the computational effort is based on a two steps filtering procedure of the offshore SPTHA, through which a reduced number of scenarios to be modelled for inundation is selected. Each scenario represents a larger set of sources that form a cluster of potential tsunamis with similar impact on the target area. This filtering procedure is completely based on the tsunami profiles offshore, and it represents a generalization of the method proposed in Lorito et al. (2015) allowing i) to consider a much larger set of input linear simulations, and ii) to control the within-cluster variance of each selected cluster of seismic sources (thence, indirectly the artificial uncertainty introduced in probabilistic inundation maps by this filtering process). Here we present the preliminary results obtained for three test sites in central Mediterranean (Milazzo and Siracusa, Southern Italy, and Thessaloniki, Northern Greece). We preliminary perform a regional SPTHA covering the whole Mediterranean, in which the aleatory variability is quantified considering about 2 × 107 different seismic sources, and epistemic uncertainty is explored through an ensemble model based on more than ×105 alternative model implementations. For each site, separately, few hundreds of "representative scenarios" are filtered out of all the potential seismic sources. Then, the inundations caused by such scenarios is explicitly modelled and the site-specific SPTHA obtained, allowing a complete characterization of the tsunami

  14. PIV measurement of internal flow characteristics of very low specific speed semi-open impeller

    NASA Astrophysics Data System (ADS)

    Choi, Y.-D.; Nishino, K.; Kurokawa, J.; Matsui, J.

    2004-11-01

    Detailed particle-image velocimetry (PIV) measurements of flow fields inside semi-open impellers have been performed to understand better the internal flow patterns that are responsible for the unique performance of these centrifugal pumps operated in the range of very low specific speed. Two impellers, one equipped with six radial blades (impeller A) and the other with four conventional backward-swept blades (impeller B), are tested in a centrifugal pump designed to be operated at a non-dimensional specific speed of ns=0.24. Complex flow patterns captured by PIV are discussed in conjunction with the overall pump performance measured separately. It is revealed that impeller A achieves higher effective head than impeller B even though the flow patterns in impeller A are more complex, exhibiting secondary flows and reverse flows in the impeller passage. It is shown that both the localized strong outward flow at the pressure side of each blade outlet and the strong outward through-flow along the suction side of each blade are responsible for the better head performance of impeller A.

  15. Mechanisms regulating phosphatase specificity and the removal of individual phosphorylation sites during mitotic exit.

    PubMed

    Rogers, Samuel; McCloy, Rachael; Watkins, D Neil; Burgess, Andrew

    2016-07-01

    Entry into mitosis is driven by the activity of kinases, which phosphorylate over 7000 proteins on multiple sites. For cells to exit mitosis and segregate their genome correctly, these phosphorylations must be removed in a specific temporal order. This raises a critical and important question: how are specific phosphorylation sites on an individual protein removed? Traditionally, the temporal order of dephosphorylation was attributed to decreasing kinase activity. However, recent evidence in human cells has identified unique patterns of dephosphorylation during mammalian mitotic exit that cannot be fully explained by the loss of kinase activity. This suggests that specificity is determined in part by phosphatases. In this review, we explore how the physicochemical properties of an individual phosphosite and its surrounding amino acids can affect interactions with a phosphatase. These positive and negative interactions in turn help determine the specific pattern of dephosphorylation required for correct mitotic exit. PMID:27417119

  16. Comparison of on-site and laboratory toxicity tests: derivation of site-specific criteria for un-ionized ammonia in a Colorado transitional stream

    USGS Publications Warehouse

    Nimmo, Del Wayne R.; Link, Denise; Parrish, Loys P.; Rodriguez, Glenn J.; Wuerthele, William; Davies, Patrick H.

    1989-01-01

    Acute tests with fathead minnows (Pimephales prornelas Rafinesque), johnny darters (Etheostoma nigrum Rafinesque), white suckers (Catostomus commersoni Lacépède) and acute and chronic tests with Ceriodaphnia dubia were conducted to evaluate whether characteristics of the St. Vrain River in Colorado would ameliorate or enhance toxicity of un-ionized ammonia compared to laboratory (well) water and LC50 values found in the literature. Concurrently, tests were conducted on dilutions of Longmont, Colorado, wastewater to evaluate its toxicity in differing ammonia concentrations. Tests were conducted at two temperatures (approximately 6 and 20°C) to simulate seasonal differences. LC50s for fishes in the St. Vrain River water were similar to LC50s in laboratory water, indicating there was no site water effect. LC50s derived for fishes tested in warm conditions were within a factor of about two or three of literature values. However, the constituents in or characteristics of the wastewater appeared to enhance ammonia toxicity. Literature values (LC50s) for resident aquatic organisms and the new LC50 value for johnny darters tested on-site were used to derive site-specific criteria for un-ionized ammonia. Greater sensitivities of species to ammonia at cold versus warm temperatures suggests that colder, low-flow conditions may be a critical period for warm-water aquatic communities with regard to ammonia toxicity.

  17. Estimated flow-duration curves for selected ungaged sites in Kansas

    USGS Publications Warehouse

    Studley, S.E.

    2001-01-01

    Flow-duration curves for 1968-98 were estimated for 32 ungaged sites in the Missouri, Smoky Hill-Saline, Solomon, Marais des Cygnes, Walnut, Verdigris, and Neosho River Basins in Kansas. Also included from a previous report are estimated flow-duration curves for 16 ungaged sites in the Cimarron and lower Arkansas River Basins in Kansas. The method of estimation used six unique factors of flow duration: (1) mean streamflow and percentage duration of mean streamflow, (2) ratio of 1-percent-duration streamflow to mean streamflow, (3) ratio of 0.1-percent-duration streamflow to 1-percent-duration streamflow, (4) ratio of 50-percent-duration streamflow to mean streamflow, (5) percentage duration of appreciable streamflow (0.10 cubic foot per second), and (6) average slope of the flow-duration curve. These factors were previously developed from a regionalized study of flow-duration curves using streamflow data for 1921-76 from streamflow-gaging stations with drainage areas of 100 to 3,000 square miles. The method was tested on a currently (2001) measured, continuous-record streamflow-gaging station on Salt Creek near Lyndon, Kansas, with a drainage area of 111 square miles and was found to adequately estimate the computed flow-duration curve for the station. The method also was tested on a currently (2001) measured, continuous-record, streamflow-gaging station on Soldier Creek near Circleville, Kansas, with a drainage area of 49.3 square miles. The results of the test on Soldier Creek near Circleville indicated that the method could adequately estimate flow-duration curves for sites with drainage areas of less than 100 square miles. The low-flow parts of the estimated flow-duration curves were verified or revised using 137 base-flow discharge measurements made during 1999-2000 at the 32 ungaged sites that were correlated with base-flow measurements and flow-duration analyses performed at nearby, long-term, continuous-record, streamflow-gaging stations (index stations

  18. 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

  19. A case for protein-level and site-level specificity in glycoproteomic studies of disease.

    PubMed

    Schumacher, Katherine N; Dodds, Eric D

    2016-06-01

    Abnormal glycosylation of proteins is known to be either resultant or causative of a variety of diseases. This makes glycoproteins appealing targets as potential biomarkers and focal points of molecular studies on the development and progression of human ailment. To date, a majority of efforts in disease glycoproteomics have tended to center on either determining the concentration of a given glycoprotein, or on profiling the total population of glycans released from a mixture of glycoproteins. While these approaches have demonstrated some diagnostic potential, they are inherently insensitive to the fine molecular detail which distinguishes unique and possibly disease relevant glycoforms of specific proteins. As a consequence, such analyses can be of limited sensitivity, specificity, and accuracy because they do not comprehensively consider the glycosylation status of any particular glycoprotein, or of any particular glycosylation site. Therefore, significant opportunities exist to improve glycoproteomic inquiry into disease by engaging in these studies at the level of individual glycoproteins and their exact loci of glycosylation. In this concise review, the rationale for glycoprotein and glycosylation site specificity is developed in the context of human disease glycoproteomics with an emphasis on N-glycosylation. Recent examples highlighting disease-related perturbations in glycosylation will be presented, including those involving alterations in the overall glycosylation of a specific protein, alterations in the occupancy of a given glycosylation site, and alterations in the compositional heterogeneity of glycans occurring at a given glycosylation site. Each will be discussed with particular emphasis on how protein-specific and site-specific approaches can contribute to improved discrimination between glycoproteomes and glycoproteins associated with healthy and unhealthy states.

  20. Site-Specifically Labeled Immunoconjugates for Molecular Imaging--Part 1: Cysteine Residues and Glycans.

    PubMed

    Adumeau, Pierre; Sharma, Sai Kiran; Brent, Colleen; Zeglis, Brian M

    2016-02-01

    Due to their remarkable selectivity and specificity for cancer biomarkers, immunoconjugates have emerged as extremely promising vectors for the delivery of diagnostic radioisotopes and fluorophores to malignant tissues. Paradoxically, however, these tools for precision medicine are synthesized in a remarkably imprecise way. Indeed, the vast majority of immunoconjugates are created via the random conjugation of bifunctional probes (e.g., DOTA-NCS) to amino acids within the antibody (e.g., lysines). Yet antibodies have multiple copies of these residues throughout their macromolecular structure, making control over the location of the conjugation reaction impossible. This lack of site specificity can lead to the formation of poorly defined, heterogeneous immunoconjugates with suboptimal in vivo behavior. Over the past decade, interest in the synthesis and development of site-specifically labeled immunoconjugates--both antibody-drug conjugates as well as constructs for in vivo imaging--has increased dramatically, and a number of reports have suggested that these better defined, more homogeneous constructs exhibit improved performance in vivo compared to their randomly modified cousins. In this two-part review, we seek to provide an overview of the various methods that have been developed to create site-specifically modified immunoconjugates for positron emission tomography, single photon emission computed tomography, and fluorescence imaging. We will begin with an introduction to the structure of antibodies and antibody fragments. This is followed by the core of the work: sections detailing the four different approaches to site-specific modification strategies based on cysteine residues, glycans, peptide tags, and unnatural amino acids. These discussions will be divided into two installments: cysteine residues and glycans will be detailed in Part 1 of the review, while peptide tags and unnatural amino acids will be addressed in Part 2. Ultimately, we sincerely hope

  1. In vitro investigation of contrast flow jet timing in patient-specific intracranial aneurysms

    PubMed Central

    Desai, Virendra R.; Britz, Garvin W.

    2016-01-01

    Background The direction and magnitude of intra-aneurysmal flow jet are significant risk factors of subarachnoid hemorrhage, and the change of flow jet during an endovascular procedure has been used for prediction of aneurysm occlusion or whether an additional flow diverter (FD) is warranted. However, evaluation of flow jets is often unreliable due to a large variation of flow jet on the digital subtraction angiograms, and this flow pattern variation may result in incorrect clinical diagnosis Therefore, factors contributing to the variation in flow jet are examined at an in vitro setting, and the findings can help us to understand the nature of flow jet and devise a better plan to quantify the aneurysmal hemodynamics accurately. Methods Intra-aneurysmal flows in three patient-specific aneurysms between 11 and 25 mm were investigated in vitro, and a FD was deployed in each aneurysm model. X-ray imaging of these models were performed at injection rates between 0.2 and 2 mL/s. Pulsatile blood pump and aneurysm model were imaged together to determine the timing of flow jet. Results The contrast bolus arrives at the aneurysm early at high contrast injection rates. The flow patterns with slow injection rates exhibit strong inertia that is associated with the systole flow. Flow jets arrive at the aneurysms at the peak systole when the bolus is injected at 0.2 mL/s. The contrast-to-signal ratio is the highest at the injection rate of 0.5 mL/s. Effect of flow diversion can only be assessed at an injection rate greater than 0.5 mL/s. Conclusions Intra-aneurysmal flow jet is highly dependent on the injection rate of the contrast agent. For the internal carotid artery (ICA) aneurysms, the systolic flows can be visualized at slow injection rates (<0.5 mL/s), while the diastolic flow jets are visible at higher injection rates (>1 mL/s). Dependence of flow jet on the contrast injection rate has serious clinical implications and needs to be considered during diagnostic procedures

  2. Site-specific identification of heparan and chondroitin sulfate glycosaminoglycans in hybrid proteoglycans

    PubMed Central

    Noborn, Fredrik; Gomez Toledo, Alejandro; Green, Anders; Nasir, Waqas; Sihlbom, Carina; Nilsson, Jonas; Larson, Göran

    2016-01-01

    Heparan sulfate (HS) and chondroitin sulfate (CS) are complex polysaccharides that regulate important biological pathways in virtually all metazoan organisms. The polysaccharides often display opposite effects on cell functions with HS and CS structural motifs presenting unique binding sites for specific ligands. Still, the mechanisms by which glycan biosynthesis generates complex HS and CS polysaccharides required for the regulation of mammalian physiology remain elusive. Here we present a glycoproteomic approach that identifies and differentiates between HS and CS attachment sites and provides identity to the core proteins. Glycopeptides were prepared from perlecan, a complex proteoglycan known to be substituted with both HS and CS chains, further digested with heparinase or chondroitinase ABC to reduce the HS and CS chain lengths respectively, and thereafter analyzed by nLC-MS/MS. This protocol enabled the identification of three consensus HS sites and one hybrid site, carrying either a HS or a CS chain. Inspection of the amino acid sequence at the hybrid attachment locus indicates that certain peptide motifs may encode for the chain type selection process. This analytical approach will become useful when addressing fundamental questions in basic biology specifically in elucidating the functional roles of site-specific glycosylations of proteoglycans. PMID:27694851

  3. Site-specific investigations of aquifer thermal energy storage for space and process cooling

    SciTech Connect

    Brown, D R; Hattrup, M P; Watts, R L

    1991-08-01

    The Pacific Northwest Laboratory (PNL) has completed three preliminary site-specific feasibility studies that investigated using aquifer thermal energy storage (ATES) to reduce space and process cooling costs. Chilled water stored in an ATES system could be used to meet all or part of the process and/or space cooling loads at the three facilities investigated. The work was sponsored by the US Department of Energy's (DOE) Office of Energy Management. The ultimate goal of DOE's Thermal Energy Storage Program is to successfully transfer ATES technology to industrial and commercial sectors. The primary objective of this study was to identify prospective sites and determine the technical and economic feasibility of implementing chill ATES technology. A secondary objective was to identify site-specific factors promoting or inhibiting the application of chill ATES technology so that other potentially attractive sites could be more easily identified and evaluated. A preliminary investigation of the feasibility of commercializing chill ATES in automotive assembly facilities was completed. The results suggested that automotive assembly facilities was completed. The results suggested that automotive assembly facilities represent a good entry market for chill ATES, if the system is cost-effective. As a result, this study was undertaken to identify and evaluate prospective chill ATES applications in the automotive industry. The balance of the report contains two main sections. Section 2.0 describes the site identification process. Site feasibility is addressed in Section 3.0. Overall study conclusions and recommendations are than presented in Section 4.0.

  4. Integrated decision support, sensor networks and adaptive control for wireless site-specific sprinkler irrigation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The development of site-specific sprinkler irrigation water management systems will be a major factor in future efforts to improve the various efficiencies of water-use and to support a sustainable irrigated environment. The challenge is to develop fully integrated management systems with supporting...

  5. Integrated Decision Support, Sensor Networks and Adaptive Control for Wireless Site-specific Sprinkler Irrigation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The development of site-specific sprinkler irrigation water management systems will be a major factor in future efforts to improve the various efficiencies of water-use and to support a sustainable irrigated environment. The challenge is to develop fully integrated management systems with supporting...

  6. 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...

  7. A readily synthesized cyclic pyrrolysine analogue for site-specific protein "click" labeling.

    PubMed

    Hao, Ziyang; Song, Yanqun; Lin, Shixian; Yang, Maiyun; Liang, Yujie; Wang, Jing; Chen, Peng R

    2011-04-21

    A concise route was developed for the facile synthesis of a cyclic pyrrolysine analogue bearing an azide handle. Directed evolution enabled the encoding of this non-natural amino acid in both prokaryotic and eukaryotic cells, which offers a highly efficient approach for the site-specific protein labeling using click chemistry.

  8. 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 §...

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

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 36 Parks, Forests, and Public Property 2 2011-07-01 2011-07-01 false Appeals of site-specific decisions. 219.33 Section 219.33 Parks, Forests, and Public Property FOREST SERVICE, DEPARTMENT OF AGRICULTURE PLANNING National Forest System Land and Resource Management Planning Objections and Appeals §...

  10. 78 FR 20311 - Environmental Management Site-Specific Advisory Board Chairs

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-04

    ... Open Webinar. SUMMARY: This notice announces a webinar of the Environmental Management Site-Specific... that public notice of this webinar be announced in the Federal Register. DATES: Thursday, April 25... Update Waste Disposition Strategies EM SSAB Cross-Cutting Issues Public Participation: The webinar...

  11. 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 ...

  12. 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...

  13. 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-...

  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. 40 CFR 258.62 - Approval of site-specific flexibility requests in Indian country.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 5 U.S.C. 552(a) and 1 CFR part 51. You may inspect or obtain a copy at the Environmental Protection... other applicable provisions of 40 CFR part 258 remain in effect. ... 40 Protection of Environment 25 2014-07-01 2014-07-01 false Approval of site-specific...

  16. 76 FR 51361 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-18

    ... Environmental Management Site-Specific Advisory Board, Northern New Mexico AGENCY: Department of Energy (DoE). ACTION: Notice of Open Meeting. SUMMARY: This notice announces a meeting of the Environmental Management... the areas of environmental restoration, waste management, and related activities. Tentative Agenda 1...

  17. 75 FR 11872 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-12

    ..., Idaho National Laboratory to be held on March 16, 2010 75 FR 9590. In that notice, the meeting address... 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...

  18. 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

  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. 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 ...

  1. 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...

  2. 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...

  3. 40 CFR 60.3019 - What site-specific documentation is required?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... procedures. (8) The waste management plan required under §§ 60.3010 through 60.3012. (9) Procedures for... Times for Other Solid Waste Incineration Units That Commenced Construction On or Before December 9, 2004 Model Rule-Operator Training and Qualification § 60.3019 What site-specific documentation is...

  4. 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...

  5. Site-specific unfolding thermodynamics of a helix-turn-helix protein.

    PubMed

    Amunson, Krista E; Ackels, Loren; Kubelka, Jan

    2008-07-01

    The thermal unfolding of a 40-residue helix-turn-helix subdomain of the P22 viral coat protein was investigated using circular dichroism (CD) and Fourier transform infrared spectroscopy (FTIR) with site-specific 13C isotopic labeling. Helix-turn-helix is the simplest alpha-helical structural motif that combines both secondary and tertiary structural elements. The CD of individual helical fragments reveals that the P22 subdomain is stabilized by tertiary interhelical interactions. Overall the temperature-dependent CD and FTIR data can be described by a three-state process with a partially folded intermediate. However, the analysis of the site-specific 13C IR signals reveals distinct unfolding thermodynamics for each of the labeled sites. The thermodynamic parameters of the thermal unfolding of each of the labeled segments were obtained using singular value decomposition in combination with target transformation and global fitting. The P22 subdomain unfolds from the N-terminus toward the helical segments near the turn. Our results show that as few as two 13C labeled residues can be detected in a 40 residue protein and provide local, site-specific structural information about protein unfolding, which is not resolved by standard, nonsite-specific spectroscopic probes.

  6. Chemoenzymatic bio-orthogonal chemistry for site-specific double modification of recombinant thrombomodulin.

    PubMed

    Jiang, Rui; Wang, Lin; Weingart, Jacob; Sun, Xue-Long

    2014-01-01

    Best of both worlds: A one-pot strategy for site-specific PEGylation through strain-promoted alkyne-azide cycloaddition (SPAAC) and fluorescent labeling through sortase A-mediated ligation (SML) of recombinant thrombomodulin without prior chemical modification and without diminishing the protein activity has been developed. PMID:24357004

  7. CRISPR Outsourcing: Commissioning IHF for Site-Specific Integration of Foreign DNA at the CRISPR Array.

    PubMed

    Wei, Yunzhou; Terns, Michael P

    2016-06-16

    In this issue of Molecular Cell, Nuñez et al. (2016) report that site-specific integration of foreign DNA into CRISPR loci by the Cas1-Cas2 integrase complex is promoted by a host factor, IHF (integration host factor), that binds and bends CRISPR leader DNA. PMID:27315553

  8. 75 FR 82003 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-29

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION... Officer, Department of Energy Portsmouth/Paducah Project Office, Post Office Box 700, Piketon, Ohio...

  9. 75 FR 82004 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-29

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of.... FOR FURTHER INFORMATION CONTACT: Denise Rupp, Board Administrator, 232 Energy Way, M/S 505, North...

  10. 78 FR 53135 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-28

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of..., Nevada 89119. FOR FURTHER INFORMATION CONTACT: Barbara Ulmer, Board Administrator, 232 Energy Way,...

  11. 75 FR 65310 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-22

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of..., Nevada 89119. FOR FURTHER INFORMATION CONTACT: Denise Rupp, Board Administrator, 232 Energy Way, M/S...

  12. 76 FR 5365 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-31

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of.... FOR FURTHER INFORMATION CONTACT: Denise Rupp, Board Administrator, 232 Energy Way, M/S 505, North...

  13. 77 FR 4027 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-26

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of.... FOR FURTHER INFORMATION CONTACT: Denise Rupp, Board Administrator, 232 Energy Way, M/S 505, North...

  14. 75 FR 3455 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-21

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

  15. 76 FR 29229 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-20

    ... Agenda: 1. Recommendation Development: Greater-Than-Class C Draft Environmental Impact Statement (EIS) 2... number listed above. Written statements may be filed with the Board either before or after the meeting... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice...

  16. 76 FR 59393 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-26

    ... Impact Statement Public Participation: The EM SSAB, Nevada, welcomes the attendance of the public at its... least seven days in advance of the meeting at the phone number listed above. Written statements may be... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice...

  17. 75 FR 64719 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-20

    ...-Specific Advisory Board (EM SSAB), Northern New Mexico. The Federal Advisory Committee Act (Pub. L. 92-463...: Wednesday, November 17, 2010, 1 p.m.-7 p.m. ADDRESSES: The Lodge at Santa Fe, 750 North St. Francis Drive... purpose of the Board is to make recommendations to DOE-EM and site management in the areas...

  18. Site-specific fragmentation caused by core-level photoionization: Effect of chemisorption

    NASA Astrophysics Data System (ADS)

    Nagaoka, Shin-ichi; Mase, Kazuhiko; Nakamura, Arinobu; Nagao, Masashi; Yoshinobu, Jun; Tanaka, Shin-ichiro

    2002-08-01

    We used the energy-selected-photoelectron photoion coincidence (ESPEPICO) method to study site-specific fragmentation caused by C:1s photoionization of 1,1,1-trifluoro-2-propanol-d1 [CF3)CD(OHCH3, TFIP-d1] on a Si(100) surface. High-resolution electron energy loss spectroscopy showed that TFIP-d1 is dissociatively chemisorbed like (CF3)(CH3))CDO-Si(100, and different chemical shifts at the three carbon sites were observed by photoelectron spectroscopy. The site-specific fragmentation evident in the ESPEPICO spectra of the sub-monolayer at room temperature indicates that the TFIP-d1 there has an O-Si bond oriented in the trans position with respect to the C-CF3 bond. Here we discuss the fragmentation processes in light of the results obtained with the ESPEPICO method and the Auger-electron photoion coincidence method.

  19. Distinct specificity for corticosteroid binding sites in amphibian cytosol, neuronal membranes, and plasma.

    PubMed

    Orchinik, M; Matthews, L; Gasser, P J

    2000-05-01

    To address mechanisms of corticosteroid action, one needs tools for distinguishing between the major classes of corticosteroid binding sites: neuronal membrane-associated receptors, intracellular ligand-activated transcription factors, and corticosteroid binding globulins (CBG) in plasma. We characterized the binding parameters for three classes of binding sites in an amphibian, Ambystoma tigrinum, and found that each class had a distinct pharmacological specificity. Equilibrium saturation and kinetic experiments indicated that [3H]corticosterone binds to neuronal membranes with high affinity (Kd approximately 0.37 nM). Aldosterone and two synthetic ligands for mammalian intracellular receptors, dexamethasone and RU486, displayed low affinity for brain membrane sites. In cytosol prepared from brain and liver, [3H]corticosterone bound to a single class of receptors with high affinity (Kd approximately 0.75 and 4.69 nM, respectively) and the rank order potencies for steroid inhibition of [3H]corticosterone binding was RU486 > dexamethasone approximately = corticosterone > aldosterone. In kidney and skin cytosol, [3H]corticosterone binding was best fit with a model having a high-affinity and a lower-affinity site; these sites are not consistent with the pharmacology of mammalian Type I (MR) and Type II (GR) receptors. [3H]Corticosterone also bound to presumed CBG in plasma with high affinity (Kd approximately 2.7 nM), but dexamethasone and androgens bound to plasma CBG with equivalently high affinity. These data demonstrate that pharmacological specificity can be a useful tool for distinguishing corticosteroid binding to different classes of binding sites. These data also indicate that there may be marked species differences in the specificity of corticosteroid binding sites.

  20. Uncovering Global SUMOylation Signaling Networks in a Site-Specific Manner

    PubMed Central

    Hendriks, Ivo A.; D’Souza, Rochelle C.J.; Yang, Bing; Verlaan-de Vries, Matty; Mann, Matthias; Vertegaal, Alfred C.O.

    2014-01-01

    SUMOylation is a reversible post-translational modification essential for genome stability. Using high-resolution mass spectrometry, we have studied global SUMOylation in human cells and in a site-specific manner, identifying a total of over 4,300 SUMOylation sites in over 1,600 proteins. Moreover, for the first time in excess of 1,000 SUMOylation sites were identified under standard growth conditions. SUMOylation dynamics were quantitatively studied in response to SUMO protease inhibition, proteasome inhibition and heat shock. A considerable amount of SUMOylated lysines have previously been reported to be ubiquitylated, acetylated or methylated, indicating crosstalk between SUMO and other post-translational modifications. We identified 70 phosphorylation and 4 acetylation events in close proximity to SUMOylation sites, and provide evidence for acetylation-dependent SUMOylation of endogenous histone H3. SUMOylation regulates target proteins involved in all nuclear processes including transcription, DNA repair, chromatin remodeling, pre-mRNA splicing and ribosome assembly. PMID:25218447