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Sample records for active site finally

  1. Active sites in char gasification: Final technical report

    SciTech Connect

    Wojtowicz, M.; Lilly, W.D.; Perkins, M.T.; Hradil, G.; Calo, J.M.; Suuberg, E.M.

    1987-09-01

    Among the key variables in the design of gasifiers and combustors is the reactivity of the chars which must be gasified or combusted. Significant loss of unburned char is unacceptable in virtually any process; the provision of sufficient residence time for complete conversion is essential. A very wide range of reactivities are observed, depending upon the nature of the char in a process. The current work focuses on furthering the understanding of gasification reactivities of chars. It has been well established that the reactivity of char to gasification generally depends upon three principal factors: (1) the concentration of ''active sites'' in the char; (2) mass transfer within the char; and (3) the type and concentration of catalytic impurities in the char. The present study primarily addresses the first factor. The subject of this research is the origin, nature, and fate of active sites in chars derived from parent hydrocarbons with coal-like structure. The nature and number of the active sites and their reactivity towards oxygen are examined in ''model'' chars derived from phenol-formaldehyde type resins. How the active sites are lost by the process of thermal annealing during heat treatment of chars are studied, and actual rate for the annealing process is derived. Since intrinsic char reactivities are of primary interest in the present study, a fair amount of attention was given to the model char synthesis and handling so that the effect of catalytic impurities and oxygen-containing functional groups in the chemical structure of the material were minimized, if not completely eliminated. The project would not be considered complete without comparing characteristic features of synthetic chars with kinetic behavior exhibited by natural chars, including coal chars.

  2. Regulatory impact analysis of environmental standards for uranium mill tailings at active sites. Final report

    SciTech Connect

    Not Available

    1983-03-01

    The Environmental Protection Agency was directed by Congress, under PL 95-604, the Uranium Mill Tailings Radiation Control Act of 1978, to set standards of general application that provide protection from the hazards associated with uranium mill tailings. Title I of the Act pertains to tailings at inactive sites for which the Agency has developed standards as part of a separate rulemaking. Title II of the Act requires standards covering the processing and disposal of byproduct materials at mills which are currently licensed by the appropriate regulatory authorities. This Regulatory Impact Analysis (RIA) addresses the standards developed under Title II. There are two major parts of the standards for active mills: standards for control of releases from tailings during processing operations and prior to final disposal, and standards for protection of the public after the disposal of tailings. This report presents a detailed analysis of standards for disposal only, since the analysis required for the operations standards is very limited.

  3. Final Report - Independent Verification Survey Activities at the Seperations Process Research Unit Sites, Niskayuna, New York

    SciTech Connect

    Evan Harpenau

    2011-03-15

    The Separations Process Research Unit (SPRU) complex located on the Knolls Atomic Power Laboratory (KAPL) site in Niskayuna, New York, was constructed in the late 1940s to research the chemical separation of plutonium and uranium (Figure A-1). SPRU operated as a laboratory scale research facility between February 1950 and October 1953. The research activities ceased following the successful development of the reduction oxidation and plutonium/uranium extraction processes. The oxidation and extraction processes were subsequently developed for large scale use by the Hanford and Savannah River sites (aRc 2008a). Decommissioning of the SPRU facilities began in October 1953 and continued through the 1990s.

  4. Site activities of zeolite-support Ru for CO hydrogenation. Final report

    SciTech Connect

    Goodwin, J.G. Jr.

    1983-10-01

    The work supported by this grant can be grouped under three headings: a comprehensive study of RuY, Ru supported on zeolites having a range of Si/Al values, and alkali promotion of Ru. NaY-supported Ru catalysts have been prepared by incipient-wetness (I.W.) (using RuCl/sub 3/), ion-exchange (I.E.) (using Ru(NH/sub 3/)/sub 6/Cl/sub 3/), and vapor-impregnation (V.I.) (using Ru/sub 3/(CO)/sub 12/). The resulting catalysts were extensively studied by chemisorption, atomic absorption, IR, ESCA, and catalytic reaction (especially F-T). Significant differences were found depending on the method of preparation. These differences were exhibited in both the physical and chemical characteristics of the catalysts. By variation of the preparation method and Si/Al ratio of the zeolite it is possible to develop a better understanding of how metal particle size and location, metal-zeolite interactions, neutralizing cation type and concentration, and the presence of zeolite acid sites can influence the catalytic properties of the supported metal. Ten papers are included in this final report and are grouped under the following headings: (1) chemisorption characteristics; (2) electronic state of Ru; (3) hydrogenolysis properties of NaY-supported Ru; and (4) Fischer-Tropsch synthesis. All papers have been processed for inclusion in the Energy Data Base.

  5. Risk assessment for the Explosive Washout Lagoons (Site 4), Umatilla Depot Activity Hermiston, Oregon. Final report, Mar 91-Mar 92

    SciTech Connect

    Leinbach, A.; Enright, A.M.; Eaton, W.; Lemont, S.

    1992-03-01

    This document is the Risk Assessment (RA) for the Explosive Washout Lagoons (Site 4) at Umatilla Army Depot Activity (UMDA). The purpose of this RA is to address the potential future health risks posed by explosives-contaminated soil and groundwater associated with Site 4 in the absence of remediation, and to identify safe residual explosives concentrations (remedial action criteria) in soil if remediation is determined to be a requirement. This RA is not intended to address the remediation of contaminated groundwater; contaminated groundwater is addressed only to the extent that contaminants in Site 4 soil are affecting groundwater quality. The potential remediation of contaminated groundwater will be addressed in the installation-wide Baseline RA for UMDA. Based on the available data, explosives contamination appears to be widespread in soil near the lagoons and in groundwater at distances of over 650 yards from the lagoons. Three future land use scenarios-residential, light industrial, and military-and four potential future exposure pathways-soil ingestion, dust inhalation, dermal contact with soil, and groundwater ingestion-were evaluated in the RA to estimate potential future carcinogenic hazards. The results of RA indicate that remediation may be a requirement for soil at Site 4; therefore, remedial action criteria for soil were developed.

  6. Final vegetative cover for closed waste sites

    SciTech Connect

    Cook, J.R.; Salvo, S.K.

    1993-01-22

    Low-level, hazardous, and mixed waste disposal sites normally require some form of plant material to prevent erosion of the final closure cap. Waste disposal sites are closed and capped in a complex scientific manner to minimize water infiltration and percolation into and through the waste material. Turf type grasses are currently being used as an interim vegetative cover for most sites. This coverage allows for required monitoring of the closure cap for settlement and maintenance activities. The purpose of this five year study was to evaluate plant materials for use on wastes sites after the post-closure care period that are quickly and easily established and economically maintained, retard water infiltration, provide maximum year-round evapotranspiration, are ecologically acceptable and do not harm the closure cap. The results of the study suggest that two species of bamboo (Phyllostachys (P.) bissetii and P. rubromarginata) can be utilized to provide long lived, low maintenance, climax vegetation for the waste sites after surveillance and maintenance requirements have ceased.

  7. Preliminary site characterization - final report

    SciTech Connect

    Clark, D.; Smith, L.B.

    1993-12-01

    This report summarizes the ecological unit reconnaissance conducted at the F-Area Burning/Rubble Pit(s) RCRA/CERCLA Unit (F-Area BRP) on August 30 and 31, 1993 as part of the RFI/RI baseline risk assessment for the waste unit The baseline risk assessment will assess the potential endangerment to human health and the environment associated with the unit and will be used to evaluate remediation criteria, if needed. The information presented in this report will be used in subsequent stages of the ecological risk assessment to refine the conceptual site model, assist in the selection of contaminants of concern, identify potential ecological receptors, and evaluate trophic relationships and other exposure pathways. The unit reconnaissance survey was conducted in accordance with Specification No. E-18272, Rev. 1 dated August 5, 1993, and the Draft {open_quotes}Ecological Risk Assessment Program Plan for Evaluation of Waste Sites on the Savannah River Site{close_quotes}. The objectives of the site reconnaissance were to: Assess the general characteristics of on-unit biological communities including mammals, birds, reptiles, amphibians, and any aquatic communities present. Determine the location, extent, and characteristics of on-unit ecological resources, such as forested areas and wetlands, that could serve as important wildlife habitat or provide other ecological functions. Identify any overt effects of contamination on biological communities. The field investigations included mapping and describing all wetland and terrestrial habitats; recording wildlife observations of birds, mammals, and reptiles; and investigating ecological resources in nearby downgradient and downstream areas which could be affected by mobile contaminants or future remedial actions. In preparation for the field investigation, existing unit information including aerial photographs and reports were reviewed to help identify and describe ecological resources at the waste unit.

  8. Final Environmental Assessment and Finding of No Significant Impact: Waste Disposition Activities at the Paducah Site Paducah, Kentucky

    SciTech Connect

    N /A

    2002-11-05

    The U.S. Department of Energy (DOE) has completed an environmental assessment (DOE/EA-1339), which is incorporated herein by reference, for proposed disposition of polychlorinated biphenyl (PCB) wastes, low-level radioactive waste (LLW), mixed low-level radioactive waste (MLLW), and transuranic (TRU) waste from the Paducah Gaseous Diffusion Plant Site (Paducah Site) in Paducah, Kentucky. All of the wastes would be transported for disposal at various locations in the United States. Based on the results of the impact analysis reported in the EA, DOE has determined that the proposed action is not a major federal action that would significantly affect the quality of the human environment with in the context of the National Environmental Policy Act of 1969 (NEPA). Therefore, preparation of an environmental impact statement is not necessary, and DOE is issuing this Finding of No Significant Impact (FONSI).

  9. Characterization of the geochemical and physical properties of wetland soils on the Savannah River Site: Field sampling activities. Final report

    SciTech Connect

    Dixon, K.L.

    1992-11-01

    There are 36,000 acres of wetlands on the Savannah River Site (SRS) and an additional 5,000 acres of floodplain. Recent studies of wetland soils near various waste sites at SRS have shown that some wetlands have been contaminated with pollutants resulting from SRS operations. In general, releases of contaminants to wetland areas have been indirect. These releases may have originated at disposal lagoons or waste facilities located in the vicinity of the wetland areas. Transport mechanisms such as surface runoff, soil erosion, sediment transport, and groundwater seepage into downgradient wetland areas are responsible for the indirect discharges to the wetland areas. The SRS determined that a database of background geochemical and physical properties for wetland soils on the SRS was needed to facilitate future remedial investigations, human health and ecological risk assessments, treatability studies, and feasibility studies for the wetland areas. These data are needed for comparison to contaminant data collected from wetland soils that have been affected by contamination from SRS operations. This report describes the efforts associated with the collection of soil cores, preparation of a lithologic log for each core, and the processing and packaging of individual soil samples for shipment to analytical laboratory facilities.

  10. Umatilla Satellite and Release Sites Project : Final Siting Report.

    SciTech Connect

    Montgomery, James M.

    1992-04-01

    This report presents the results of site analysis for the Umatilla Satellite and Release Sites Project. The purpose of this project is to provide engineering services for the siting and conceptual design of satellite and release facilities for the Umatilla Basin hatchery program. The Umatilla Basin hatchery program consists of artificial production facilities for salmon and steelhead to enhance production in the Umatilla River as defined in the Umatilla master plan approved in 1989 by the Northwest Power Planning Council. Facilities identified in the master plan include adult salmon broodstock holding and spawning facilities, facilities for recovery, acclimation, and/or extended rearing of salmon juveniles, and development of river sites for release of hatchery salmon and steelhead. The historic and current distribution of fall chinook, summer chinook, and coho salmon and steelhead trout was summarized for the Umatilla River basin. Current and future production and release objectives were reviewed. Twenty seven sites were evaluated for the potential and development of facilities. Engineering and environmental attributes of the sites were evaluated and compared to facility requirements for water and space. Site screening was conducted to identify the sites with the most potential for facility development. Alternative sites were selected for conceptual design of each facility type. A proposed program for adult holding facilities, final rearing/acclimation, and direct release facilities was developed.

  11. Northeast Oregon Hatchery Project, Final Siting Report.

    SciTech Connect

    Watson, Montgomery

    1995-03-01

    This report presents the results of site analysis for the Bonneville Power Administration Northeast Oregon Hatchery Project. The purpose of this project is to provide engineering services for the siting and conceptual design of hatchery facilities for the Bonneville Power Administration. The hatchery project consists of artificial production facilities for salmon and steelhead to enhance production in three adjacent tributaries to the Columbia River in northeast Oregon: the Grande Ronde, Walla Walla, and Imnaha River drainage basins. Facilities identified in the master plan include adult capture and holding facilities; spawning incubation, and early rearing facilities; full-term rearing facilities; and direct release or acclimation facilities. The evaluation includes consideration of a main production facility for one or more of the basins or several smaller satellite production facilities to be located within major subbasins. The historic and current distribution of spring and fall chinook salmon and steelhead was summarized for the Columbia River tributaries. Current and future production and release objectives were reviewed. Among the three tributaries, forty seven sites were evaluated and compared to facility requirements for water and space. Site screening was conducted to identify the sites with the most potential for facility development. Alternative sites were selected for conceptual design of each facility type. A proposed program for adult holding facilities, final rearing/acclimation, and direct release facilities was developed.

  12. Western Maryland power plant siting study: biological characterization of candidate sites. Final assessment. Final report

    SciTech Connect

    Jacobs, F.; Himel, J.; Cummins, R.; Weisberg, S.

    1984-10-01

    Three locations in western Maryland are being considered as potential candidate sites for future construction of a 1200-1800 MWe coal-fired power plant. This report provides a detailed biological characterization of each site and assesses potential terrestrial and aquatic impacts associated with plant construction and operation. This assessment considers possible impacts on geomorphology, vegetation, wildlife, water quality, and nearby aquatic biota. Relevant information contained in a Phase I document produced earlier under this contract, was incorporated into this final report.

  13. REVISED FINAL REPORT – INDEPENDENT VERIFICATION SURVEY ACTIVITIES AT THE SEPARATIONS PROCESS RESEARCH UNIT SITES, NISKAYUNA, NEW YORK – DCN 0496-SR-06-1

    SciTech Connect

    Evan Harpenau

    2011-10-10

    The Separations Process Research Unit (SPRU) complex located on the Knolls Atomic Power Laboratory (KAPL) site in Niskayuna, New York, was constructed in the late 1940s to research the chemical separation of plutonium and uranium (Figure A-1). SPRU operated as a laboratory scale research facility between February 1950 and October 1953. The research activities ceased following the successful development of the reduction oxidation and plutonium/uranium extraction processes. The oxidation and extraction processes were subsequently developed for large scale use by the Hanford and Savannah River sites (aRc 2008a). Decommissioning of the SPRU facilities began in October 1953 and continued through the 1990s.

  14. ExoMars 2018: the four final candidate Landing Sites

    NASA Astrophysics Data System (ADS)

    Loizeau, Damien; Flahaut, Jessica; Vago, Jorge L.; Hauber, Ernst; Bridges, John C.

    2015-04-01

    December 2014. The Aram Dorsum site comprises Noachian layered sedimentary rocks with a prominent inverted channel system (>80 km long). Potential targets include the inverted channel, the channel margins, a channel transition unit, and pits present within the floodplain. The Hypanis Vallis site lies near two fluvial fan/deltaic systems at the termination of Hypanis and Sabrina Valles. Potential targets include mainly outcrops of expected fine-grained sediments on the smooth transition unit that surrounds the delta/fan, and units around the rim of Magong crater. The Mawrth Vallis site contains one of the largest exposures of phyllosilicates detected on the Martian surface, in Noachian terrain [8]. Potential targets include the mineralogically diverse clay-rich outcrops and ancient channels. The Oxia Planum site lies on Fe/Mg phyllosilicates-rich exposures associated to layered rocks that may be related to the Mawrth Vallis sequence. Potential targets include the clay-rich outcrops as well as channels and inverted channels and delta-fan deposits. New data are being actively acquired by the HiRISE, CRISM and HRSC teams to support the ExoMars 2018 landing site selection process. The ellipses are large and new data are important for characterizing the potential targets and evaluating the safety of the sites. The proposing teams, the ExoMars project team and the LSSWG will continue their analysis and comparison of the sites, aiming to complete the certification of at least one site by September 2016 -- in time for the start of the mission's Critical Design Review (CDR). The final selection of the landing site is expected within 2017. References: [1] http://exploration.esa.int/mars/48088-mission-overview/ [2] http://exploration.esa.int/mars/53462-call-for-exo mars-2018-landing-site-selection/ [3] ExoMars 2018 LSSWG recommendation: http://exploration.esa.int/mars/54707-recommendation-for-the-narrowing-of-exomars-2018-landing-sites/

  15. Final vegetative cover for closed waste sites. Revision 1

    SciTech Connect

    Cook, J.R.; Salvo, S.K.

    1993-01-22

    Low-level, hazardous, and mixed waste disposal sites normally require some form of plant material to prevent erosion of the final closure cap. Waste disposal sites are closed and capped in a complex scientific manner to minimize water infiltration and percolation into and through the waste material. Turf type grasses are currently being used as an interim vegetative cover for most sites. This coverage allows for required monitoring of the closure cap for settlement and maintenance activities. The purpose of this five year study was to evaluate plant materials for use on wastes sites after the post-closure care period that are quickly and easily established and economically maintained, retard water infiltration, provide maximum year-round evapotranspiration, are ecologically acceptable and do not harm the closure cap. The results of the study suggest that two species of bamboo (Phyllostachys (P.) bissetii and P. rubromarginata) can be utilized to provide long lived, low maintenance, climax vegetation for the waste sites after surveillance and maintenance requirements have ceased.

  16. The Interactions in the Carboxyl Terminus of Human 4-Hydroxyphenylpyruvate Dioxygenase Are Critical to Mediate the Conformation of the Final Helix and the Tail to Shield the Active Site for Catalysis

    PubMed Central

    Chang, Tsu-Chung; Chang, Ni-Yuan; Chang, Chiung-Wen; Shen, Chia-Pei; Lee, Hwei-Jen

    2013-01-01

    4-Hydroxylphenylpyruvate dioxygenase (4-HPPD) is an important enzyme for tyrosine catabolism, which catalyzes the conversion of 4-hydroxylphenylpyruvate (4-HPP) to homogentisate. In the present study, human 4-HPPD was cloned and expressed in E. coli. The kinetic parameters for 4-HPP conversion were: kcat = 2.2±0.1 s−1; and Km = 0.08±0.02 mM. Sequence alignments show that human 4-HPPD possesses an extended C-terminus compared to other 4-HPPD enzymes. Successive truncation of the disordered tail which follows the final α-helix resulted in no changes in the Km value for 4-HPP substrate but the kcat values were significantly reduced. The results suggest that this disordered C-terminal tail plays an important role in catalysis. For inspection the effect of terminal truncation on protein structure, mutant models were built. These models suggest that the different conformation of E254, R378 and Q375 in the final helix might be the cause of the activity loss. In the structure E254 interacts with R378, the end residue in the final helix; mutation of either one of these residues causes a ca. 95% reductions in kcat values. Q375 provides bifurcate interactions to fix the tail and the final helix in position. The model of the Q375N mutant shows that a solvent accessible channel opens to the putative substrate binding site, suggesting this is responsible for the complete loss of activity. These results highlight the critical role of Q375 in orientating the tail and ensuring the conformation of the terminal α-helix to maintain the integrity of the active site for catalysis. PMID:23950902

  17. Radiological surveillance of Remedial Action activities at the processing site, Ambrosia Lake, New Mexico, April 12--16, 1993. Final report

    SciTech Connect

    1993-04-01

    The Uranium Mill Tailings Remedial Action (UMTRA) Project`s Technical Assistance Contractor (TAC) performed a radiological surveillance of the Remedial Action Contractor (RAC), MK-Ferguson and CWM Federal Environmental Services, Inc., at the processing site in Ambrosia Lake, New Mexico. The requirements and attributes examined during the audit were developed from reviewing working-level procedures developed by the RAC. Objective evidence, comments, and observations were verified based on investigating procedures, documentation, records located at the site, personal interviews, and tours of the site. No findings were identified during this audit. Ten site-specific observations, three good practice observations, and five programmatic observations are presented in this report. The overall conclusion from the surveillance is that the radiological aspects of the Ambrosia Lake, New Mexico, remedial action program are performed adequately. The results of the good practice observations indicate that the site health physics (HP) staff is taking the initiative to address and resolve potential issues, and implement suggestions useful to the UMTRA Project. However, potential exists for improving designated storage areas for general items, and the RAC Project Office should consider resolving site-specific and procedural inconsistencies.

  18. Final Land Configuration for the Rocky Flats Environmental Technology Site

    SciTech Connect

    Stegen, R. L.; Kapinos, J. M.; Wehner, J. P.; Snyder, B.; Davis, R. W.

    2006-07-01

    Closure of the Rocky Flats Environmental Technology Site (RFETS) has been completed. The future land use of the site is designated as a National Wildlife Refuge. A joint effort between Kaiser-Hill, Department of Energy, U.S. Fish and Wildlife Service, Environmental Protection Agency, State of Colorado, and other stakeholders was initiated to provide direction for developing the final land configuration. Through early identification of issues and developing mutually agreeable solutions, the final land configuration of the site was successfully completed. (authors)

  19. Salt site performance assessment activities

    SciTech Connect

    Kircher, J.F.; Gupta, S.K.

    1983-01-01

    During this year the first selection of the tools (codes) for performance assessments of potential salt sites have been tentatively selected and documented; the emphasis has shifted from code development to applications. During this period prior to detailed characterization of a salt site, the focus is on bounding calculations, sensitivity and with the data available. The development and application of improved methods for sensitivity and uncertainty analysis is a focus for the coming years activities and the subject of a following paper in these proceedings. Although the assessments to date are preliminary and based on admittedly scant data, the results indicate that suitable salt sites can be identified and repository subsystems designed which will meet the established criteria for protecting the health and safety of the public. 36 references, 5 figures, 2 tables.

  20. Micro-mechanisms of corrosion fatigue using atomic force microscopy at active microstructural sites on 2024-T3 aluminum. Final report, May 1995-May 1996

    SciTech Connect

    Laird, C.; DeLuccia, J.J.

    1996-10-22

    This is a final report summarizing a one-year effort to define the micro-mechanisms of corrosion fatigue of 2024-T3 sheet aluminum alloy in low pH environments using in-situ and ex-situ instrumentation, e. g., atomic force microscopy (AFM), scanning electron microscopy, and Auger spectroscopy. Constant stress, flexure fatigue specimens cycled in a unique mechanically driven, environmentally controlled, deformation stage, are electrochemically polished to exhibit uniform quality metallographic surfaces. Pertinent surface microstructural features of crack nucleation were determined by AFM on specimens fatigued in air, .01 M and 0.1 M HCl. Imposed cathodic polarization potentials during corrosion fatigue indicate a hydrogen embrittlement contribution to the fatigue process at potentials not affording sufficient cathodic protection. Enhanced embrittlement (approx. 40% decreased in cycles to failure) was observed when 1.5 mg/ml of NaAsO2 was added to 0.1M HCl solution at open circuit voltages (freely corroding). Other results from the subject program previously reported in the open literature are referenced here, but not reported again.

  1. Umatilla Satellite and Release Sites Project : Final Conceptual Design Report.

    SciTech Connect

    Montgomery, James M.

    1992-03-01

    This report presents the results of site analysis for the Umatilla Satellite and Release Sites Project. The purpose of this project is to provide engineering services for the siting and conceptual design of satellite and release facilities for the Umatilla Basin hatchery program. The Umatilla Basin hatchery program consists of artificial production facilities for salmon and steelhead to enhance production in the Umatilla River as defined in the Umatilla master plan approved in 1989 by the Northwest Power Planning Council. Facilities identified in the master plan include adult salmon broodstock holding and spawning facilities, facilities for recovery, acclimation, and/or extended rearing of salmon juveniles, and development of river sites for release of hatchery salmon and steelhead. The historic and current distribution of fall chinook, summer chinook, and coho salmon and steelhead trout was summarized for the Umatilla River basin. Current and future production and release objectives were reviewed. Twenty seven sites were evaluated for the potential development of facilities. Engineering and environmental attributes of the sites were evaluated and compared to facility requirements for water and space. Site screening was conducted to identify the sites with the most potential for facility development. Alternative sites were selected for conceptual design of each facility type. A proposed program for adult holding facilities, final rearing/acclimation, and direct release facilities was developed.

  2. Technical planning activity: Final report

    SciTech Connect

    Not Available

    1987-01-01

    In April 1985, the US Department of Energy's (DOE's) Office of Fusion Energy commissioned the Technical Planning Activity (TPA). The purpose of this activity was to develop a technical planning methodology and prepare technical plans in support of the strategic and policy framework of the Magnetic Fusion Program Plan issued by DOE in February 1985. Although this report represents the views of only the US magnetic fusion community, it is international in scope in the sense that the technical plans contained herein describe the full scope of the tasks that are prerequisites for the commercialization of fusion energy. The TPA has developed a well-structured methodology that includes detailed definitions of technical issues, definitions of program areas and elements, statements of research and development objectives, identification of key decision points and milestones, and descriptions of facility requirements.

  3. Characterization of active sites in zeolite catalysts

    SciTech Connect

    Eckert, J.; Bug, A.; Nicol, J.M.

    1997-11-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). Atomic-level details of the interaction of adsorbed molecules with active sites in catalysts are urgently needed to facilitate development of more effective and/or environmentally benign catalysts. To this end the authors have carried out neutron scattering studies combined with theoretical calculations of the dynamics of small molecules inside the cavities of zeolite catalysts. The authors have developed the use of H{sub 2} as a probe of adsorption sites by observing the hindered rotations of the adsorbed H{sub 2} molecule, and they were able to show that an area near the four-rings is the most likely adsorption site for H{sub 2} in zeolite A while adsorption of H{sub 2} near cations located on six-ring sites decreases in strength as Ni {approximately} Co > Ca > Zn {approximately} Na. Vibrational and rotational motions of ethylene and cyclopropane adsorption complexes were used as a measure for zeolite-adsorbate interactions. Preliminary studies of the binding of water, ammonia, and methylamines were carried out in a number of related guest-host materials.

  4. FINAL CLOSURE PLAN SURFACE IMPOUNDMENTS CLOSURE, SITE 300

    SciTech Connect

    Lane, J E; Scott, J E; Mathews, S E

    2004-09-29

    Lawrence Livermore National Laboratory of the University of California (LLNL) operates two Class II surface impoundments that store wastewater that is discharged from a number of buildings located on the Site 300 Facility (Site 300). The wastewater is the by-product of explosives processing. Reduction in the volume of water discharged from these buildings over the past several years has significantly reduced the wastewater storage needs. In addition, the impoundments were constructed in 1984, and the high-density polyethylene (HDPE) geomembrane liners are nearing the end of their service life. The purpose of this project is to clean close the surface impoundments and provide new wastewater storage using portable, above ground storage tanks at six locations. The tanks will be installed prior to closure of the impoundments and will include heaters for allowing evaporation during relatively cool weather. Golder Associates (Golder) has prepared this Final Closure Plan (Closure Plan) on behalf of LLNL to address construction associated with the clean closure of the impoundments. This Closure Plan complies with State Water Resources Control Board (SWRCB) Section 21400 of the California Code of Regulations Title 27 (27 CCR {section}21400). As required by these regulations and guidance, this Plan provides the following information: (1) A site characterization, including the site location, history, current operations, and geology and hydrogeology; (2) The regulatory requirements relevant to clean closure of the impoundments; (3) The closure procedures; and, (4) The procedures for validation and documentation of clean closure.

  5. Establishing Final Cleanup Decisions for the Hanford Site River Corridor

    SciTech Connect

    Lerch, J.A.; Sands, J.P.

    2007-07-01

    A major challenge in the River Corridor Closure Contract is establishing final cleanup decisions for the source operable units in the Hanford Site river corridor. Cleanup actions in the river corridor began in 1994 and have been performed in accordance with a 'bias for action' approach adopted by the Tri-Parties - the U.S. Department of Energy, U.S. Environmental Protection Agency, and Washington State Department of Ecology. This approach enabled early application of cleanup dollars on actual remediation of contaminated waste sites. Consequently, the regulatory framework authorizing cleanup actions at source operable units in the river corridor consists largely of interim action records of decision, which were supported by qualitative risk assessments. Obtaining final cleanup decisions for the source operable units is necessary to determine whether past cleanup actions in the river corridor are protective of human health and the environment and to identify any course corrections that may be needed to ensure that ongoing and future cleanup actions are protective. Because the cleanup actions are ongoing, it is desirable to establish the final cleanup decisions as early as possible to minimize the impacts of any identified course corrections to the present cleanup approach. Development of a strategy to obtain final cleanup decisions for the source operable units in a manner that is responsive to desires for an integrated approach with the groundwater and Columbia River components while maintaining the ability to evaluate each component on its own merit represents a significant challenge. There are many different options for grouping final cleanup decisions, and each involved party or stakeholder brings slightly different interests that shape the approach. Regardless of the selected approach, there are several specific challenges and issues to be addressed before making final cleanup decisions. A multi-agency and contractor working group has been established to address

  6. Remedial action selection report Maybell, Colorado, site. Final report

    SciTech Connect

    1996-12-01

    The Maybell uranium mill tailings site is 25 miles (mi) (40 kilometers [km]) west of the town of Craig, Colorado, in Moffat County, in the northwestern part of the state. The unincorporated town of Maybell is 5 road mi (8 km) southwest of the site. The site is 2.5 mi (4 km) northeast of the Yampa River on relatively flat terrain broken by low, flat-topped mesas. U.S. Highway 40 runs east-west 2 mi (3.2 km) south of the site. The designated site covers approximately 110 acres (ac) (45 hectares [ha]) and consists of a concave-shaped tailings pile and rubble from the demolition of the mill buildings buried in the former mill area. The site is situated between Johnson Wash to the east and Rob Pit Mine to the west. Numerous reclaimed and unreclaimed mines are in the immediate vicinity. Aerial photographs (included at the end of this executive summary) show evidence of mining activity around the Maybell site. Contaminated materials at the Maybell processing site include the tailings pile, which has an average depth of 20 feet (ft) (6 meters [ml]) and contains 2.8 million cubic yards (yd{sup 3}) (2.1 million cubic meters [m{sup 3}]) of tailings. The former mill processing area is on the north side of the site and contains 20,000 yd 3 (15,000 m{sup 3}) of contaminated demolition debris. Off-pile contamination is present and includes areas adjacent to the tailings pile, as well as contamination dispersed by wind and surface water flow. The volume of off-pile contamination to be placed in the disposal cell is 550,000 yd{sup 3}(420,000 m{sup 3}). The total volume of contaminated materials to be disposed of as part of the remedial action is estimated to be 3.37 million yd{sup 3} (2.58 million m{sup 3}).

  7. Site Operator technical report. Final report (1992--1996)

    SciTech Connect

    1996-12-01

    The Southern California Edison Company (SCE) and the US Department of Energy (DOE) entered into cooperative agreement No. DE-FC07-91ID13077 on August 23, 1991, which expired on August 3, 1996. This cooperative agreement provided SCE with DOE cofunding for participation in the DOE`s Electric and Hybrid Vehicle Site Operator Program. In return, SCE provided the DOE with quarterly progress reports which include operating and maintenance data for the electric (EVs) vehicles in SCE`s fleet. Herein is SCE`s final report for the 1992 to 1996 agreement period. As of September 1, 1996 the SCE fleet had 65 electric vehicles in service. A total of 578,200 miles had been logged. During the agreement period, SCE sent the DOE a total of 19 technical reports (Appendix B). This report summarizes the technical achievements which took place during a long, productive and rewarding, relationship with the DOE.

  8. Final Reclamation Report: Basalt Waste Isolation Project exploratory shaft site

    SciTech Connect

    Brandt, C.A.; Rickard, W.H. Jr.

    1990-06-01

    The restoration of areas disturbed by activities of the Basalt Waste Isolation Project (BWIP) constitutes a unique operation at the US Department of Energy's (DOE) Hanford Site, both from the standpoint of restoration objectives and the time frame for accomplishing these objectives. The BWIP reclamation program comprises three separate projects: borehole reclamation, Near Surface Test Facility (NSTF) reclamation, and Exploratory Shaft Facility (ESF) reclamation. The main focus of this report is on determining the success of the revegetation effort 1 year after work was completed. This report also provides a brief overview of the ESF reclamation program. 21 refs., 7 figs., 14 tabs.

  9. Final Hanford Site Transuranic (TRU) Waste Characterization QA Project Plan

    SciTech Connect

    GREAGER, T.M.

    2000-12-06

    The Quality Assurance Project Plan (QAPjP) has been prepared for waste characterization activities to be conducted by the Transuranic (TRU) Project at the Hanford Site to meet requirements set forth in the Waste Isolation Pilot Plan (WIPP) Hazardous Waste Facility Permit, 4890139088-TSDF, Attachment B, including Attachments B1 through B6 (WAP) (DOE, 1999a). The QAPjP describes the waste characterization requirements and includes test methods, details of planned waste sampling and analysis, and a description of the waste characterization and verification process. In addition, the QAPjP includes a description of the quality assurance/quality control (QA/QC) requirements for the waste characterization program. Before TRU waste is shipped to the WIPP site by the TRU Project, all applicable requirements of the QAPjP shall be implemented. Additional requirements necessary for transportation to waste disposal at WIPP can be found in the ''Quality Assurance Program Document'' (DOE 1999b) and HNF-2600, ''Hanford Site Transuranic Waste Certification Plan.'' TRU mixed waste contains both TRU radioactive and hazardous components, as defined in the WLPP-WAP. The waste is designated and separately packaged as either contact-handled (CH) or remote-handled (RH), based on the radiological dose rate at the surface of the waste container. RH TRU wastes are not currently shipped to the WIPP facility.

  10. 3D reconstruction of the final PHILAE landing site: Abydos

    NASA Astrophysics Data System (ADS)

    Capanna, Claire; Jorda, Laurent; Lamy, Philippe; Gesquière, Gilles; Delmas, Cédric; Durand, Joëlle; Gaudon, Philippe; Jurado, Eric

    2015-11-01

    The Abydos region is the region of the final landing site of the PHILAE lander. The landing site has been potentially identified on images of this region acquired by the OSIRIS imaging system aboard the orbiter before (Oct 22, 2014) and after (Dec 6-13, 2014) the landing of PHILAE (Lamy et al., in prep.). Assuming that this identification is correct, we reconstructed the topography of Abydos in 3D using a method called ``multiresolution photoclinometry by deformation'' (MPCD, Capanna et al., The Visual Computer, 29(6-8): 825-835, 2013). The method works in two steps: (a) a DTM of this region is extracted from the global MPCD shape model, (b) the resulting triangular mesh is progressively deformed at increasing spatial resolution in order to match a set of 14 images of Abydos at pixel resolutions between 1 and 8 m. The method used to perform the image matching is the L-BFGS-b non-linear optimization (Morales et al., ACM Trans. Math. Softw., 38(1): 1-4, 2011).In spite of the very unfavourable illumination conditions, we achieve a vertical accuracy of about 3 m, while the horizontal sampling is 0.5 m. The accuracy is limited by high incidence angles on the images (about 60 deg on average) combined with a complex topography including numerous cliffs and a few overhangs. We also check the compatibility of the local DTM with the images obtained by the CIVA-P instrument aboard PHILAE. If the Lamy et al. identification is correct, our DTM shows that PHILAE landed in a cavity at the bottom of a small cliff of 8 m height.

  11. Catalysis: Elusive active site in focus

    NASA Astrophysics Data System (ADS)

    Labinger, Jay A.

    2016-08-01

    The identification of the active site of an iron-containing catalyst raises hopes of designing practically useful catalysts for the room-temperature conversion of methane to methanol, a potential fuel for vehicles. See Letter p.317

  12. Neutron activation of NIF Final Optics Assemblies

    NASA Astrophysics Data System (ADS)

    Sitaraman, S.; Dauffy, L.; Khater, H.; Brereton, S.

    2010-08-01

    Analyses were performed to characterize the radiation field in the vicinity of the Final Optics Assemblies (FOAs) at the National Ignition Facility (NIF) due to neutron activation following Deuterium-Deuterium (DD), Tritium-Hydrogen-Deuterium (THD), and Deuterium-Tritium (DT) shots associated with different phases of the NIF operations. The activation of the structural components of the FOAs produces one of the larger sources of gamma radiation and is a key factor in determining the stay out time between shots to ensure worker protection. This study provides estimates of effective dose rates in the vicinity of a single FOA and concludes that the DD and THD targets produce acceptable dose rates within10 minutes following a shot while about 6-days of stay out time is suggested following DT shots. Studies are ongoing to determine the combined effects of multiple FOAs and other components present in the Target Bay on stay-out time and worker dose.

  13. Final monitoring plan for site restoration at Murdock, Nebraska.

    SciTech Connect

    LaFreniere, L. M.; Environmental Science Division

    2006-02-28

    environmental impacts of carbon tetrachloride discharge to the surface waters of a tributary creek located immediately north of the town. (3) To permanently reduce carbon tetrachloride concentrations in the groundwater and surface water at Murdock and hence restore these resources for potential beneficial use. To evaluate the effectiveness of the selected remedy and its ability to achieve the objectives specified for this site, monitoring is required. This document outlines the proposed scope of a long-term program for monitoring of the removal action at Murdock. In this section the specific remedial objectives of the action are summarized, and a brief overview of the chosen remedy is provided. Section 2 summarizes the results of a baseline sampling event that documented the distribution of carbon tetrachloride contamination in selected media at the Murdock site immediately before cleanup activities began. Section 3 recommends a strategy for subsequent monitoring of the removal action at Murdock, as well as criteria for evaluating the performance of the remedial systems and the progress of the restoration effort.

  14. Final report : site reclassification investigation for Courtland, Kansas.

    SciTech Connect

    LaFreniere, L. M.; Dennis, C. B.; Environmental Science Division

    2006-01-31

    The Commodity Credit Corporation (CCC), an agency of the U.S. Department of Agriculture (USDA), formerly operated a grain storage facility in Courtland, Kansas. Prior to 1986, commercial grain fumigants containing carbon tetrachloride were commonly used by the CCC/USDA and the grain industry to preserve stored grain. In 1999, the Kansas Department of Health and Environment (KDHE) identified the former CCC/USDA operation as the likely source of carbon tetrachloride found in groundwater east of the former CCC/USDA facility in Courtland. Sampling by the KDHE in April 1998 had found carbon tetrachloride in the Garman residence lawn and garden well at a concentration of 2.1 {micro}g/L and in the Hoard residence lawn and garden well at a concentration of 0.5 {micro}g/L. Subsequent soil and groundwater sampling by the KDHE at the former CCC/USDA facility found no indication of a continuing source, and subsequent sampling of the affected wells showed generally declining contaminant levels. At the request of the KDHE and the CCC/USDA, Argonne National Laboratory prepared a Work Plan for Groundwater Sampling for Potential Site Reclassification, Courtland, Kansas (Argonne 2004). The objective of the proposed work was to conduct a single groundwater monitoring event and collect information necessary to update the status of the previously detected groundwater contamination, in support of an evaluation of appropriate actions for reclassification of the status of this site from active to resolved, under the Intergovernmental Agreement between the KDHE and the USDA's Farm Service Agency (FSA). The reclassification would be in accordance with the KDHE's Reclassification Plan (Policy No. BERRS-024, online at http://www.kdhe.state.ks.us/pdf/ber/scp/reclass.pdf). The KDHE approved the Work Plan on August 8, 2005. Sampling was conducted on September 7, 2005.

  15. Low dielectric response in enzyme active site

    PubMed Central

    Mertz, Edward L.; Krishtalik, Lev I.

    2000-01-01

    The kinetics of charge transfer depend crucially on the dielectric reorganization of the medium. In enzymatic reactions that involve charge transfer, atomic dielectric response of the active site and of its surroundings determines the efficiency of the protein as a catalyst. We report direct spectroscopic measurements of the reorganization energy associated with the dielectric response in the active site of α-chymotrypsin. A chromophoric inhibitor of the enzyme is used as a spectroscopic probe. We find that water strongly affects the dielectric reorganization in the active site of the enzyme in solution. The reorganization energy of the protein matrix in the vicinity of the active site is similar to that of low-polarity solvents. Surprisingly, water exhibits an anomalously high dielectric response that cannot be described in terms of the dielectric continuum theory. As a result, sequestering the active site from the aqueous environment inside low-dielectric enzyme body dramatically reduces the dielectric reorganization. This reduction is particularly important for controlling the rate of enzymatic reactions. PMID:10681440

  16. Near-Site Transportation Infrastructure Project. Final report

    SciTech Connect

    Viebrock, J.M.; Mote, N.

    1992-02-01

    There are 122 commercial nuclear facilities from which spent nuclear fuel will be accepted by the Federal Waste Management System (FWMS). Since some facilities share common sites and some facilities are on adjacent sites, 76 sites were identified for the Near-Site Transportation Infrastructure (NSTI) project. The objective of the NSTI project was to identify the options available for transportation of spent-fuel casks from each of these commercial nuclear facility sites to the main transportation routes -- interstate highways, commercial rail lines and navigable waterways available for commercial use. The near-site transportation infrastructure from each site was assessed, based on observation of technical features identified during a survey of the routes and facilities plus data collected from referenced information sources. The potential for refurbishment of transportation facilities which are not currently operational was also assessed, as was the potential for establishing new transportation facilities.

  17. Final work plan : environmental site investigation at Sylvan Grove, Kansas.

    SciTech Connect

    LaFreniere, L. M.

    2012-07-15

    what future CCC/USDA actions may be necessary, with the ultimate goal of achieving classification of the Sylvan Grove site at no further action status. The proposed activities are to be performed on behalf of the CCC/USDA by the Environmental Science Division of Argonne National Laboratory, a nonprofit, multidisciplinary research center operated by the UChicago Argonne, LLC, for the U.S. Department of Energy. Argonne provides technical assistance to the CCC/USDA concerning environmental site characterization and remediation at former grain storage facilities. Argonne issued a Master Work Plan (Argonne 2002) that has been approved by the KDHE. The Master Work Plan describes the general scope of all investigations at former CCC/USDA facilities in Kansas and provides guidance for these investigations. That document should be consulted for the complete details of plans for work associated with the former CCC/USDA facility at Sylvan Grove.

  18. Siting guidelines for utility application of wind turbines. Final report

    SciTech Connect

    Pennell, W.T.

    1983-01-01

    Utility-oriented guidelines are described for identifying viable sites for wind turbines. Topics and procedures are also discussed that are important in carrying out a wind turbine siting program. These topics include: a description of the Department of Energy wind resource atlases; procedures for predicting wind turbine performance at potential sites; methods for analyzing wind turbine economics; procedures for estimating installation and maintenance costs; methods for anlayzing the distribution of wind resources over an area; and instrumentation for documenting wind behavior at potential sites. The procedure described is applicable to small and large utilities. Although the procedure was developed as a site-selection tool, it can also be used by a utility who wishes to estimate the potential for wind turbine penetration into its future generation mix.

  19. Minimally invasive three-dimensional site characterization system. Final report

    SciTech Connect

    Steedman, D.; Seusy, F.E.; Gibbons, J.; Bratton, J.L.

    1993-09-01

    This paper presents an improved for hazardous site characterization. The major components of the systems are: (1) an enhanced cone penetrometer test, (2) surface geophysical surveys and (3) a field database and visualization code. The objective of the effort was to develop a method of combining geophysical data with cone penetrometer data in the field to produce a synergistic effect. Various aspects of the method were tested at three sites. The results from each site are discussed and the data compared. This method allows the data to be interpreted more fully with greater certainty, is faster, cheaper and leads to a more accurate site characterization. Utilizing the cone penetrometer test rather than the standard drilling, sampling and laboratory testing reduces the workers exposure to hazardous materials and minimizes the hazardous material disposal problems. The technologies employed in this effort are, for the most part, state-of-the-art procedures. The approach of using data from various measurement systems to develop a synergistic effect was a unique contribution to environmental site characterization. The use of the cone penetrometer for providing ``ground truth`` data and as a platform for subsurface sensors in environmental site characterization represents a significant advancement in environmental site characterization.

  20. Final Hanford Site Transuranic (TRU) Waste Characterization QA Project Plan

    SciTech Connect

    GREAGER, T.M.

    1999-09-09

    The Transuranic Waste Characterization Quality Assurance Program Plan required each US Department of Energy (DOE) site that characterizes transuranic waste to be sent the Waste Isolation Pilot Plan that addresses applicable requirements specified in the QAPP.

  1. Industrial Sites Project Establishment of Final Action Levels, Rev. No.: 0

    SciTech Connect

    Boehlecke, Robert F.

    2006-02-01

    The U.S. Department of Energy, National Nuclear Security Administration Nevada Site Office (NNSA/NSO) oversees numerous sites on the Nevada Test Site (NTS) and other locations in the State of Nevada that have been impacted by activities related to the development and testing of nuclear devices and by other activities. NNSA/NSO is responsible for protecting members of the public, including site workers, from harmful exposure to both chemical and radiological contaminants at these sites as they remediate these sites. The Nevada Division of Environmental Protection (NDEP) is the primary state agency responsible for protection of human health and the environment with respect to chemical and radiological wastes. In 1996 the DOE, U.S. Department of Defense, and the State of Nevada entered into an agreement known as the ''Federal Facility Agreement and Consent Order'' (FFACO) (1996). Appendix VI to the FFACO describes the strategy employed to plan, implement, and complete environmental corrective action activities at NTS and other locations in the state of Nevada. One of the categories of corrective action units (CAUs) is Industrial Sites, which consists of approximately 1,150 locations that may require some level of investigation and corrective action. To evaluate the need for the extent of corrective action at a particular site, NNSA/NSO assesses the potential impacts to receptors by comparing measurements of contaminant concentrations to risk-based (chemical) and dose-based (radionuclide) standards (action levels). Preliminary action levels (PALs) are established as part of the data quality objective (DQO) process, and are presented in one or more FFACO documents generated as part of the corrective action process. This document formally defines and clarifies the NDEP-approved process NNSA/NSO Industrial Sites Project uses to fulfill the requirements of the FFACO and state regulations. This process establishes final action levels (FALs) based on the risk

  2. 40 CFR 228.15 - Dumping sites designated on a final basis.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... practicable alternatives (as defined in 40 CFR 227.16(b)) to open-water disposal in Long Island Sound and that...) Restrictions: See 40 CFR 228.15(b)(4)(vi). (c) Region I Final Other Wastes Sites. (1) No final sites. (2) (d... will be managed so as to reduce impacts within the PRA to acceptable levels in accordance with 40...

  3. Energy conserving site design case study: Shenandoah, Georgia. Final report

    SciTech Connect

    Not Available

    1980-01-01

    The case study examines the means by which energy conservation can be achieved at an aggregate community level by using proper planning and analytical techniques for a new town, Shenandoah, Georgia, located twenty-five miles southwest of Atlanta's Hartsfield International Airport. A potentially implementable energy conservation community plan is achieved by a study team examining the land use options, siting characteristics of each building type, alternate infrastructure plans, possible decentralized energy options, and central utility schemes to determine how community energy conservation can be achieved by use of pre-construction planning. The concept for the development of mixed land uses as a passively sited, energy conserving community is based on a plan (Level 1 Plan) that uses the natural site characteristics, maximizes on passive energy siting requirement, and allows flexibility for the changing needs of the developers. The Level 2 Plan is identical with Level 1 plan plus a series of decentraized systems that have been added to the residential units: the single-family detached, the apartments, and the townhouses. Level 3 Plan is similar to the Level 1 Plan except that higher density dwellings have been moved to areas adjacent to central site. The total energy savings for each plan relative to the conventional plan are indicated. (MCW)

  4. ARAC`s site workstation final design and deployment

    SciTech Connect

    Abriam, R.O.; Moore, R.M.

    1994-08-01

    The Atmospheric Release Advisory Capability (ARAC) Center located at Lawrence Livermore National Laboratory, provides real-time estimates of the environmental consequences of accidental releases of radioactivity or other hazardous materials into the atmosphere anywhere in the world. ARAC`s expertise includes integrating a suite of local, regional and global dispersion models into a highly automated system. Since 1979, on-site computers have provided the link between DOE and DOD facilities around the U.S. and the ARAC Center. Beginning in 1993, these facilities have been replacing their personal computers with UNIX workstations running ARAC`s Site Workstation Systems (SWS) software. The SWS consists of a collection of applications that help sites prepare for and respond to incidents involving an atmospheric release. The SWS can be used either as a real-time emergency-response tool or to make historical or hypothetical assessments of releases.

  5. Neutral Site Planning Project, Final Report. Volume IV: Facilities Analysis.

    ERIC Educational Resources Information Center

    Providence School Dept., RI.

    This report focuses on predicting the various physical impacts that proposed magnet school programs will have on potential magnet school sites in Providence, Rhode Island. Included are brief descriptions of the secondary schools in Providence being considered for the magnet programs and a listing of prevailing standards and building regulations…

  6. Active Sites Environmental Monitoring Program: Action levels

    SciTech Connect

    Ashwood, J.S.; Ashwood, T.L.

    1991-10-01

    The Active Sites Environmental Monitoring Program (ASEMP) was established at Oak Ridge National Laboratory to provide for early leak detection and to monitor performance of the active low-level waste disposal facilities in Solid Waste Storage Area (SWSA) 6 and the transuranic waste storage areas in SWSA 5 North. Early leak detection is accomplished by sampling runoff, groundwater, and perched water in burial trenches. Sample results are compared to action levels that represent background contamination by naturally occurring and fallout-derived radionuclides. 15 refs., 3 figs., 12 tabs.

  7. Nevada Test Site tortoise population monitoring study. Final report

    SciTech Connect

    Mueller, J.M.; Zander, K.K.

    1994-12-01

    A Tortoise Population Monitoring Study was initiated to determine and monitor the density of desert tortoises (Gopherus agassizii) on the Nevada Test Site. Quadrat sampling was conducted following methodology described in the Draft Desert Tortoise Recovery Plan (FWS, 1993). So few tortoises were found that densities could not be calculated. Based on estimates of capture probabilities and densities from other studies, it was determined that 1-km{sup 2} (0.4 mi{sup 2}) plots did not contain enough tortoises for estimating densities with the Recovery Plan methods. It was recommended that additional surveys on the Nevada Test Site using those methods not be conducted. Any future efforts to monitor desert tortoise densities should start by identifying other possible methods, determining their relative power to detect changes, and estimating their cost.

  8. 10 CFR 52.39 - Finality of early site permit determinations.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... proceeding: (i) The nuclear power reactor proposed to be built does not fit within one or more of the site... NUCLEAR POWER PLANTS Early Site Permits § 52.39 Finality of early site permit determinations. (a... approved an emergency plan (or major features thereof) that is in use by a licensee of a nuclear...

  9. 10 CFR 52.39 - Finality of early site permit determinations.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... proceeding: (i) The nuclear power reactor proposed to be built does not fit within one or more of the site... NUCLEAR POWER PLANTS Early Site Permits § 52.39 Finality of early site permit determinations. (a... approved an emergency plan (or major features thereof) that is in use by a licensee of a nuclear...

  10. 10 CFR 52.39 - Finality of early site permit determinations.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... proceeding: (i) The nuclear power reactor proposed to be built does not fit within one or more of the site... NUCLEAR POWER PLANTS Early Site Permits § 52.39 Finality of early site permit determinations. (a... approved an emergency plan (or major features thereof) that is in use by a licensee of a nuclear...

  11. 10 CFR 52.39 - Finality of early site permit determinations.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... proceeding: (i) The nuclear power reactor proposed to be built does not fit within one or more of the site... NUCLEAR POWER PLANTS Early Site Permits § 52.39 Finality of early site permit determinations. (a... approved an emergency plan (or major features thereof) that is in use by a licensee of a nuclear...

  12. 10 CFR 52.39 - Finality of early site permit determinations.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... proceeding: (i) The nuclear power reactor proposed to be built does not fit within one or more of the site... NUCLEAR POWER PLANTS Early Site Permits § 52.39 Finality of early site permit determinations. (a... approved an emergency plan (or major features thereof) that is in use by a licensee of a nuclear...

  13. [Paleoclimatology studies for Yucca Mountain site characterization]. Final report

    SciTech Connect

    1996-05-03

    This report consists of two separate papers: Fernley Basin studies; and Influence of sediment supply and climate change on late Quaternary eolian accumulation patterns in the Mojave Desert. The first study involved geologic mapping of late Quaternary sediments and lacustrine features combined with precise control of elevations and descriptions of sediments for each of the major sedimentary units. The second paper documents the response of a major eolian sediment transport system in the east-central Mojave Desert: that which feeds the Kelso Dune field. Information from geomorphic, stratigraphic, and sedimentologic studies of eolian deposits and landforms is combined with luminescence dating of these deposits to develop a chronology of periods of eolian deposition. Both studies are related to site characterization studies of Yucca Mountain and the forecasting of rainfall patterns possible for the high-level radioactive waste repository lifetime.

  14. Final audit report of remedial action construction at the UMTRA Project Mexican Hat, Utah -- Monument Valley, Arizona, sites

    SciTech Connect

    1995-10-01

    The final audit report for remedial action at the Mexican Hat, Utah, Monument Valley, Arizona, Uranium Mill Tailings Remedial Action (UMTRA) Project sites consists of a summary of the radiological surveillances/audits, quality assurance (QA) in-process surveillances, and QA remedial action close-out inspections performed by the US Department of Energy (DOE) and the Technical Assistance Contractor (TAC); on-site construction reviews (OSCR) performed by the US Nuclear Regulatory Commission (NRC); and a surveillance performed by the Navajo Nation. This report refers to remedial action activities performed at the Mexican Hat, Utah--Monument Valley, Arizona, Uranium Mill Tailings Remedial Action (UMTRA) Project sites.

  15. Hydrogeological-Geophysical Methods for Subsurface Site Characterization - Final Report

    SciTech Connect

    Rubin, Yoram

    2001-01-01

    The goal of this research project is to increase water savings and show better ecological control of natural vegetation by developing hydrogeological-geophysical methods for characterizing the permeability and content of water in soil. The ground penetrating radar (GPR) tool was developed and used as the surface geophysical method for monitoring water content. Initial results using the tool suggest that surface GPR is a viable technique for obtaining precision volumetric water content profile estimates, and that laboratory-derived petrophysical relationships could be applied to field-scale GPR data. A field-scale bacterial transport study was conducted within an uncontaminated sandy Pleistocene aquifer to evaluate the importance of heterogeneity in controlling the transport of bacteria. Geochemical, hydrological, geological, and geophysical data were collected to characterize the site prior to and after chemical and bacterial injection experiments. Study results shows that, even within the fairly uniform shallow marine deposits of the narrow channel focus area, heterogeneity existed that influenced the chemical tracer transport over lateral distances of a few meters and vertical distances of less than a half meter. The interpretation of data suggest that the incorporation of geophysical data with limited hydrological data may provide valuable information about the stratigraphy, log conductivity values, and the spatial correlation structure of log conductivity, which have traditionally been obtainable only by performing extensive and intrusive hydrological sampling.

  16. Assessing Risks to Populations at Superfund and Rcra Sites: Characterizing Effects on Populations (Final)

    EPA Science Inventory

    The Ecological Risk Assessment Support Center (ERASC) announced the release of the final document titled, Assessing Risks to Populations at Superfund and RCRA Sites: Characterizing Effects on Populations.

  17. Neutral Site Planning Project, Final Report. Volume I: Neutral Site Plan.

    ERIC Educational Resources Information Center

    Providence School Dept., RI.

    This report documents the process, findings, and support data of the Neutral Site Planning Project (NSPP) regarding a proposed magnet school program in Providence, Rhode Island. The need for a neutral site school that is accessible to a substantial number of students from different racial/ethnic backgrounds in Providence is discussed and an…

  18. Active site of ribulosebisphosphate carboxylase/oxygenase

    SciTech Connect

    Hartman, F.C.; Stringer, C.D.; Milanez, S.; Lee, E.H.

    1985-01-01

    Previous affinity labeling studies and comparative sequence analyses have identified two different lysines at the active site of ribulosebisphosphate carboxylase/oxygenase and have suggested their essentiality to function. The essential lysines occupy positions 166 and 329 in the Rhodospirillum rubrum enzyme and positions 175 and 334 in the spinach enzyme. Based on the pH-dependencies of inactivations of the two enzymes by trinitrobenzene sulfonate, Lys-166 (R. rubrum enzyme) exhibits a pK/sub a/ of 7.9 and Lys-334 (spinach enzyme) exhibits a pK/sub a/ of 9.0. These low pK/sub a/ values as well as the enhanced nucleophilicities of the lysyl residues argue that both are important to catalysis rather than to substrate binding. Lys-166 may correspond to the essential base that initiates catalysis and that displays a pK/sub a/ of 7.5 in the pH-curve for V/sub max//K/sub m/. Cross-linking experiments with 4,4'-diisothiocyano-2,2'-disulfonate stilbene demonstrate that the two active-site lysines are within 12 A. 50 refs., 7 figs., 1 tab.

  19. 40 CFR 228.15 - Dumping sites designated on a final basis.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... practicable alternatives (as defined in 40 CFR 227.16(b)) to open-water disposal in Long Island Sound and that...) Restrictions: See 40 CFR 228.15(b)(4)(vi). (c) Region I Final Other Wastes Sites. (1) No final sites. (2) (d... as to reduce impacts within the PRA to acceptable levels in accordance with 40 CFR 228.11(c). Use...

  20. 40 CFR 228.15 - Dumping sites designated on a final basis.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... practicable alternatives (as defined in 40 CFR 227.16(b)) to open-water disposal in Long Island Sound and that...) Restrictions: See 40 CFR 228.15(b)(4)(vi). (c) Region I Final Other Wastes Sites. (1) No final sites. (2) (d... as to reduce impacts within the PRA to acceptable levels in accordance with 40 CFR 228.11(c). Use...

  1. 40 CFR 228.15 - Dumping sites designated on a final basis.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... practicable alternatives (as defined in 40 CFR 227.16(b)) to open-water disposal in Long Island Sound and that...) Restrictions: See 40 CFR 228.15(b)(4)(vi). (c) Region I Final Other Wastes Sites. (1) No final sites. (2) (d... as to reduce impacts within the PRA to acceptable levels in accordance with 40 CFR 228.11(c). Use...

  2. 40 CFR 228.15 - Dumping sites designated on a final basis.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... practicable alternatives (as defined in 40 CFR 227.16(b)) to open-water disposal in Long Island Sound and that...) Restrictions: See 40 CFR 228.15(b)(4)(vi). (c) Region I Final Other Wastes Sites. (1) No final sites. (2) (d... as to reduce impacts within the PRA to acceptable levels in accordance with 40 CFR 228.11(c). Use...

  3. Active Sites Environmental Monitoring Program: Program plan

    SciTech Connect

    Ashwood, T.L.; Wickliff, D.S.; Morrissey, C.M.

    1992-02-01

    The Active Sites Environmental Monitoring Program (ASEMP), initiated in 1989, provides early detection and performance monitoring of transuranic (TRU) waste and active low-level waste (LLW) facilities at Oak Ridge National Laboratory (ORNL) in accordance with US Department of Energy (DOE) Order 5820.2A. Active LLW facilities in Solid Waste Storage Area (SWSA) 6 include Tumulus I and Tumulus II, the Interim Waste Management Facility (IWMF), LLW silos, high-range wells, asbestos silos, and fissile wells. The tumulus pads and IWMF are aboveground, high-strength concrete pads on which concrete vaults containing metal boxes of LLW are placed; the void space between the boxes and vaults is filled with grout. Eventually, these pads and vaults will be covered by an engineered multilayered cap. All other LLW facilities in SWSA 6 are below ground. In addition, this plan includes monitoring of the Hillcut Disposal Test Facility (HDTF) in SWSA 6, even though this facility was completed prior to the data of the DOE order. In SWSA 5 North, the TRU facilities include below-grade engineered caves, high-range wells, and unlined trenches. All samples from SWSA 6 are screened for alpha and beta activity, counted for gamma-emitting isotopes, and analyzed for tritium. In addition to these analytes, samples from SWSA 5 North are analyzed for specific transuranic elements.

  4. Use of the site characterization and analysis penetrometer system at Grandville, Michigan superfund site. Final report

    SciTech Connect

    Sharp, M.K.; Kala, R.; Powell, J.

    1992-12-01

    This report documents the results of an investigation at the Organic Chemical, Inc. site in Grandville, Michigan. This site is on the National Priority List for cleanup, and is being overseen by the Environmental Protection Agency, Chicago, Region V office. The site was investigated utilizing the Site Characterization and Analysis Penetrometer System, with a fiber optic fluorimeter sensor. This sensor allows the detection of hydrocarbon contaminants in the subsurface. A total of fifty pushes were completed at the site to an average depth of approximately 15 ft, covering approximately 80 acres. A hydrocarbon contaminant plume was located at the site extending from the OCI facility in a northerly direction. This matches the flow of the groundwater in the area as it moves toward the Grand River. The plume was successfully bounded on the North, South, and West sides. The plume boundary on the East side could not be established due to property constraints. The concentrations of contaminants in certain areas of the site exceeded 5000 ppm. Cone penetrometer, Geophysics, Fiber optic fluorescence.

  5. Final report : Hanover environmental site investigation, 2009-2010.

    SciTech Connect

    LaFreniere, L. M.

    2011-06-07

    associated with potential exposure to contaminated groundwater at Hanover. No drinking water wells are known to exist in Hanover, and the drinking water supply comes from RWD No.1 at Lanham, Kansas, located 6.5 mi north of Hanover. Limited potential risk was identified due to exposure to indoor air contaminated with carbon tetrachloride, but this risk has been mitigated, thereby removing this threat to human health. Radon is prevalent in the community, at concentrations exceeding the level at which the EPA recommends additional measures (testing and/or mitigation). The recommended testing and mitigation (if needed) are the responsibility of the homeowners. In the current condition in which no private wells are used for drinking water in the affected area, no unacceptable human health risk from carbon tetrachloride is associated with the identified impacted media at the Hanover site.

  6. Brownian aggregation rate of colloid particles with several active sites

    SciTech Connect

    Nekrasov, Vyacheslav M.; Yurkin, Maxim A.; Chernyshev, Andrei V.; Polshchitsin, Alexey A.; Yakovleva, Galina E.; Maltsev, Valeri P.

    2014-08-14

    We theoretically analyze the aggregation kinetics of colloid particles with several active sites. Such particles (so-called “patchy particles”) are well known as chemically anisotropic reactants, but the corresponding rate constant of their aggregation has not yet been established in a convenient analytical form. Using kinematic approximation for the diffusion problem, we derived an analytical formula for the diffusion-controlled reaction rate constant between two colloid particles (or clusters) with several small active sites under the following assumptions: the relative translational motion is Brownian diffusion, and the isotropic stochastic reorientation of each particle is Markovian and arbitrarily correlated. This formula was shown to produce accurate results in comparison with more sophisticated approaches. Also, to account for the case of a low number of active sites per particle we used Monte Carlo stochastic algorithm based on Gillespie method. Simulations showed that such discrete model is required when this number is less than 10. Finally, we applied the developed approach to the simulation of immunoagglutination, assuming that the formed clusters have fractal structure.

  7. 10 CFR 52.83 - Finality of referenced NRC approvals; partial initial decision on site suitability.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... decision on site suitability. 52.83 Section 52.83 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSES, CERTIFICATIONS, AND APPROVALS FOR NUCLEAR POWER PLANTS Combined Licenses § 52.83 Finality of referenced NRC....145, and 52.171. (b) While a partial decision on site suitability is in effect under 10 CFR...

  8. 10 CFR 52.83 - Finality of referenced NRC approvals; partial initial decision on site suitability.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... decision on site suitability. 52.83 Section 52.83 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSES, CERTIFICATIONS, AND APPROVALS FOR NUCLEAR POWER PLANTS Combined Licenses § 52.83 Finality of referenced NRC....145, and 52.171. (b) While a partial decision on site suitability is in effect under 10 CFR...

  9. 10 CFR 52.83 - Finality of referenced NRC approvals; partial initial decision on site suitability.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... decision on site suitability. 52.83 Section 52.83 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSES, CERTIFICATIONS, AND APPROVALS FOR NUCLEAR POWER PLANTS Combined Licenses § 52.83 Finality of referenced NRC....145, and 52.171. (b) While a partial decision on site suitability is in effect under 10 CFR...

  10. 10 CFR 52.83 - Finality of referenced NRC approvals; partial initial decision on site suitability.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... decision on site suitability. 52.83 Section 52.83 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSES, CERTIFICATIONS, AND APPROVALS FOR NUCLEAR POWER PLANTS Combined Licenses § 52.83 Finality of referenced NRC....145, and 52.171. (b) While a partial decision on site suitability is in effect under 10 CFR...

  11. 10 CFR 52.83 - Finality of referenced NRC approvals; partial initial decision on site suitability.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... decision on site suitability. 52.83 Section 52.83 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSES, CERTIFICATIONS, AND APPROVALS FOR NUCLEAR POWER PLANTS Combined Licenses § 52.83 Finality of referenced NRC....145, and 52.171. (b) While a partial decision on site suitability is in effect under 10 CFR...

  12. 77 FR 3460 - Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-24

    ... published a final rule under 10 CFR Part 765 in the Federal Register on May 23, 1994, (59 FR 26714) to carry... for reimbursement. DOE amended the final rule on June 3, 2003, (68 FR 32955) to adopt several... Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites AGENCY: Department...

  13. 75 FR 71677 - Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-24

    ... published a final rule under 10 CFR Part 765 in the Federal Register on May 23, 1994, (59 FR 26714) to carry... for reimbursement. DOE amended the final rule on June 3, 2003, (68 FR 32955) to adopt several... Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites AGENCY: Department...

  14. Catawba Science Center solar activities. Final report

    SciTech Connect

    1983-01-01

    Two demonstration solar water heaters were built. One was to be used at the Science Center and the other with traveling programs. This was completed and both units are being used for these programs which continue. We were able to build a library of 99 solar energy books and booklets that are available to the public for reference. We also conducted programs for 683 students of all ages. The culminating activity was the planned Energy Awareness Festival. This was held on September 26, 1981 and attracted 450 area citizens. We offered free exhibit space and hosted 17 exhibitors.

  15. Druggability analysis and classification of protein tyrosine phosphatase active sites

    PubMed Central

    Ghattas, Mohammad A; Raslan, Noor; Sadeq, Asil; Al Sorkhy, Mohammad; Atatreh, Noor

    2016-01-01

    Protein tyrosine phosphatases (PTP) play important roles in the pathogenesis of many diseases. The fact that no PTP inhibitors have reached the market so far has raised many questions about their druggability. In this study, the active sites of 17 PTPs were characterized and assessed for its ability to bind drug-like molecules. Consequently, PTPs were classified according to their druggability scores into four main categories. Only four members showed intermediate to very druggable pocket; interestingly, the rest of them exhibited poor druggability. Particularly focusing on PTP1B, we also demonstrated the influence of several factors on the druggability of PTP active site. For instance, the open conformation showed better druggability than the closed conformation, while the tight-bound water molecules appeared to have minimal effect on the PTP1B druggability. Finally, the allosteric site of PTP1B was found to exhibit superior druggability compared to the catalytic pocket. This analysis can prove useful in the discovery of new PTP inhibitors by assisting researchers in predicting hit rates from high throughput or virtual screening and saving unnecessary cost, time, and efforts via prioritizing PTP targets according to their predicted druggability. PMID:27757011

  16. Preliminary siting activities for new waste handling facilities at the Idaho National Engineering Laboratory

    SciTech Connect

    Taylor, D.D.; Hoskinson, R.L.; Kingsford, C.O.; Ball, L.W.

    1994-09-01

    The Idaho Waste Processing Facility, the Mixed and Low-Level Waste Treatment Facility, and the Mixed and Low-Level Waste Disposal Facility are new waste treatment, storage, and disposal facilities that have been proposed at the Idaho National Engineering Laboratory (INEL). A prime consideration in planning for such facilities is the selection of a site. Since spring of 1992, waste management personnel at the INEL have been involved in activities directed to this end. These activities have resulted in the (a) identification of generic siting criteria, considered applicable to either treatment or disposal facilities for the purpose of preliminary site evaluations and comparisons, (b) selection of six candidate locations for siting,and (c) site-specific characterization of candidate sites relative to selected siting criteria. This report describes the information gathered in the above three categories for the six candidate sites. However, a single, preferred site has not yet been identified. Such a determination requires an overall, composite ranking of the candidate sites, which accounts for the fact that the sites under consideration have different advantages and disadvantages, that no single site is superior to all the others in all the siting criteria, and that the criteria should be assigned different weighing factors depending on whether a site is to host a treatment or a disposal facility. Stakeholder input should now be solicited to help guide the final selection. This input will include (a) siting issues not already identified in the siting, work to date, and (b) relative importances of the individual siting criteria. Final site selection will not be completed until stakeholder input (from the State of Idaho, regulatory agencies, the public, etc.) in the above areas has been obtained and a strategy has been developed to make a composite ranking of all candidate sites that accounts for all the siting criteria.

  17. Control of active sites in flocculation: Concept of equivalent active sites''

    SciTech Connect

    Behl, S.; Moudgil, B.M. . Dept. of Materials Science and Engineering)

    1993-12-01

    Flocculation and dispersion of solids are strong functions of the amount and conformation of the adsorbed polymer. Regions of dispersion and flocculation of solids with particular polymer molecules may be deduced from saturation adsorption data. The concept of equivalent active sites'' is proposed to explain flocculation and dispersion behavior irrespective of the amount or conformation of the adsorbed polymer. The concept has been further extended to study the selective flocculation process.

  18. Selection and cultivation of final vegetative cover for closed waste sites at the Savannah River Site, SC

    SciTech Connect

    Cook, J.R. ); Salvo, S.K. )

    1992-01-01

    Low-level, hazardous, and mixed waste disposal sites normally require some form of plant material to prevent erosion of the final closure cap. Waste disposal sites are closed and capped in a complex scientific manner to minimize water infiltration and percolation into and through the waste material. Turf type grasses are currently being used as a vegetative cover for most sites. Consequently, the sites require periodic mowing and other expensive annual maintenance practices. The purpose of this five year study was to evaluate alternative plant material for use on wastes sites that is quickly and easily established and economically maintained, retards water infiltration, provides maximum year-round evapotranspiration, is ecologically acceptable and does not harm the closure cap. The results of the study are described in this report and suggest that two species of bamboo (Phyllostachys bissetii and P. rubromarainata) can be utilized to provide long lived, low maintenance, climax vegetation for the waste sites. These large species of bamboo will also reduce the probability of intrusion by humans, animals and deeply rooted plant species.

  19. Selection and cultivation of final vegetative cover for closed waste sites at the Savannah River Site, SC

    SciTech Connect

    Cook, J.R.; Salvo, S.K.

    1992-12-31

    Low-level, hazardous, and mixed waste disposal sites normally require some form of plant material to prevent erosion of the final closure cap. Waste disposal sites are closed and capped in a complex scientific manner to minimize water infiltration and percolation into and through the waste material. Turf type grasses are currently being used as a vegetative cover for most sites. Consequently, the sites require periodic mowing and other expensive annual maintenance practices. The purpose of this five year study was to evaluate alternative plant material for use on wastes sites that is quickly and easily established and economically maintained, retards water infiltration, provides maximum year-round evapotranspiration, is ecologically acceptable and does not harm the closure cap. The results of the study are described in this report and suggest that two species of bamboo (Phyllostachys bissetii and P. rubromarainata) can be utilized to provide long lived, low maintenance, climax vegetation for the waste sites. These large species of bamboo will also reduce the probability of intrusion by humans, animals and deeply rooted plant species.

  20. Final Hanford Comprehensive Land-Use Plan Environmental Impact Statement, Hanford Site, Richland, Washington

    SciTech Connect

    N /A

    1999-10-01

    This Final ''Hanford Comprehensive Land-Use Plan Environmental Impact Statement'' (HCP EIS) is being used by the Department of Energy (DOE) and its nine cooperating and consulting agencies to develop a comprehensive land-use plan (CLUP) for the Hanford Site. The DOE will use the Final HCP EIS as a basis for a Record of Decision (ROD) on a CLUP for the Hanford Site. While development of the CLUP will be complete with release of the HCP EIS ROD, full implementation of the CLUP is expected to take at least 50 years. Implementation of the CLUP would begin a more detailed planning process for land-use and facility-use decisions at the Hanford Site. The DOE would use the CLUP to screen proposals. Eventually, management of Hanford Site areas would move toward the CLUP land-use goals. This CLUP process could take more than 50 years to fully achieve the land-use goals.

  1. Characterize and explore potential sites and prepare research and development plan (site investigation study). Final draft. Task 2. Milestone report

    SciTech Connect

    1980-12-01

    Phase II of a 5-phase overall compressed air energy storage (CAES) development program was performed to characterize and explore potential CAES sites and to prepare a research and development plan. This volume for Phase II activities contains an evaluation of the suitability of seven selected sites to undergo field drilling and air injection testing; a bibliography; results of a literature search on the effects of air injection of aquifer-caprock well systems; reservoir data for the sites; cost estimates; and predicted potential risks from a CAES plant. (LCL)

  2. Ground-water protection standards for inactive uranium tailings sites (40 CFR 192): Background information for final rule. Final report

    SciTech Connect

    Not Available

    1989-03-01

    The Final Background Information Document summarizes the information and data considered by the Agency in developing the ground-water protection standards. The report presents a brief description of the Title II ground water standard and how it can be used to develop the Title I rulemaking. A description of the 24 designated uranium-tailings sites and their current status in the DOE remedial-action program is included as well as a detailed analysis of the available data on the ground water in the vicinity of 14 of the 24 sites. It also describes different methods that can be used for the restoration of ground water and the costs of using these restoration methods.

  3. Promoting Learning through Active Interaction. Project PLAI. Final Report.

    ERIC Educational Resources Information Center

    Chen, Deborah; Haney, Michele

    This final report describes the activities and outcomes of Promoting Learning through Active Interactions, a research-to-practice 4-year project that developed, implemented, and validated a five-module curriculum with 25 infants (ages 6-30 months) who are deaf-blind, their parents, and early interventionists. The project had the following…

  4. Stressor Identification (Si) at Contaminated Sites: Upper Arkansas River, Colorado (Final)

    EPA Science Inventory

    sites/production/files/2015-07/ca_gulch_cover.jpg" vspace = "5" hspace="5" width = "218" height = "286" align="right" border="1" alt="Cover of the CADDIS Arkansas River, CO Case Study Final Report "> This report describes a causal assessment for...

  5. 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.

  6. Dissecting the active site of a photoreceptor protein

    NASA Astrophysics Data System (ADS)

    Hoff, Wouter; Hara, Miwa; Ren, Jie; Moghadam, Farzaneh; Xie, Aihua; Kumauchi, Masato

    While enzymes are quite large molecules, functionally important chemical events are often limited to a small region of the protein: the active site. The physical and chemical properties of residues at such active sites are often strongly altered compared to the same groups dissolved in water. Understanding such effects is important for unraveling the mechanisms underlying protein function and for protein engineering, but has proven challenging. Here we report on our ongoing efforts on using photoactive yellow protein (PYP), a bacterial photoreceptor, as a model system for such effects. We will report on the following questions: How many residues affect active site properties? Are these residues in direct physical contact with the active site? Can functionally important residues be recognized in the crystal structure of a protein? What structural resolution is needed to understand active sites? What spectroscopic techniques are most informative? Which weak interactions dominate active site properties?

  7. Nesting habitat and nest site selection by the bald eagle in Maryland. Final report

    SciTech Connect

    Mosher, J.A.; Andrew, J.M.

    1981-07-01

    Habitat at 70 bald eagle (Haliaeetus leucocephalus) nest sites was quantified and compared with evaluations at 139 random habitat plots located in the Chesapeake Bay region of Maryland. Bald eagles selected vegetationally open habitats near water and away from selected human activities relative to random habitat plots. Successful nest sites were located in denser forest stands farther from water and unoccupied structures than unsuccessful nest sites.

  8. Mars Surveyor Project Landing Site Activities

    NASA Technical Reports Server (NTRS)

    Gulick, Virginia C.; Briggs, Geoffrey; Saunders, R. Stephen; Gilmore, Martha; Soderblom, Larry

    1999-01-01

    The Mars Surveyor Program --now a cooperative program led by NASA and CNES along with other international partners -- is underway. It has the primary science objective of furthering our understanding of the biological potential and possible biological history of Mars and has the complementary objective of improving our understanding of martian climate evolution and planetary history The missions will develop technology and acquire data necessary for eventual human Exploration. Launches of orbiters, landers and rovers will take place in 2001 and in 2003; in 2005 a complete system will be launched capable of returning samples to Earth by 2008. A key aspect of the program is the selection of landing sites. This abstract 1) reports on the status of the landing site selection process that begins with the 2001 lander mission and 2) outlines be opportunities for the Mars community to provide input into the landing site selection process.

  9. Mars Surveyor Project Landing Site Activities

    NASA Technical Reports Server (NTRS)

    Gulick, V. C.; Briggs, Geoffrey; Saunders, R. Stephen; Gilmore, Martha; Soderblom, Larry

    1999-01-01

    The Mars Surveyor Program -- now a cooperative program led by NASA and CNES along with other international partners -- is underway. It has the primary science objective of furthering our understanding of the biological potential and possible biological history of Mars and has the complementary objective of improving our understanding of martian climate evolution and planetary history. The missions will develop technology and acquire data necessary for eventual human exploration. Launches of orbiters, landers and rovers will take place in 2001 and in 2003; in 2005 a complete system will be launched capable of returning samples to Earth by 2008. A key aspect of the program is the selection of landing sites. This abstract 1) reports on the status of the landing site selection process that begins with the 2001 lander mission and 2) outlines the opportunities for the Mars community to provide input into the landing site selection process.

  10. Treatability of Ninth Avenue Superfund Site ground-water. Final report

    SciTech Connect

    Zappi, M.E.; Teeter, C.; Fleming, E.; Francingues, N.R.

    1991-03-01

    The Ninth Avenue Superfund Site is located in Gary, IN, and has been listed on the US Environmental Protection Agency's National Priorities List since 1973. The site is a 17-acre (68,800-sq m) inactive chemical disposal area within a relatively undeveloped, low-lying area. Past disposal activities resulted in the contamination of the underlying groundwater, predominantly with ketones, benzenes, phenols, and chlorinated aliphatic compounds. Four technologies were evaluated on the bench scale for their ability to remove organic contaminants from a composite of groundwater samples collected from six site observation wells. These technologies were activated sludge (aerobic biotreatment), activated sludge with powdered activated carbon (PAC) addition, air stripping, and activated carbon. The results indicate that activated carbon does not have a high sorptive capacity for the site contaminants. Air stripping did not exhibit a high potential for efficiently removing the contaminants from the composite sample. However, activated sludge indicated potential for removing the site contaminants. The addition of PAC improved contaminant removal. Increased removals of chemical oxygen demand and total organic carbon from the composite sample with increased PAC dose were observed. Activated sludge and PAC/activated carbon were capable of removing all priority pollutants to concentrations at or below detection limits.

  11. Activation of Inhibitors by Sortase Triggers Irreversible Modification of the Active Site*S

    PubMed Central

    Maresso, Anthony W.; Wu, Ruiying; Kern, Justin W.; Zhang, Rongguang; Janik, Dorota; Missiakas, Dominique M.; Duban, Mark-Eugene; Joachimiak, Andrzej; Schneewind, Olaf

    2011-01-01

    Sortases anchor surface proteins to the cell wall of Gram-positive pathogens through recognition of specific motif sequences. Loss of sortase leads to large reductions in virulence, which identifies sortase as a target for the development of antibacterials. By screening 135,625 small molecules for inhibition, we report here that aryl (β-amino)ethyl ketones inhibit sortase enzymes from staphylococci and bacilli. Inhibition of sortases occurs through an irreversible, covalent modification of their active site cysteine. Sortases specifically activate this class of molecules via β-elimination, generating a reactive olefin intermediate that covalently modifies the cysteine thiol. Analysis of the three-dimensional structure of Bacillus anthracis sortase B with and without inhibitor provides insights into the mechanism of inhibition and reveals binding pockets that can be exploited for drug discovery. PMID:17545669

  12. The bifunctional active site of s-adenosylmethionine synthetase. Roles of the active site aspartates.

    PubMed

    Taylor, J C; Markham, G D

    1999-11-12

    S-Adenosylmethionine (AdoMet) synthetase catalyzes the biosynthesis of AdoMet in a unique enzymatic reaction. Initially the sulfur of methionine displaces the intact tripolyphosphate chain (PPP(i)) from ATP, and subsequently PPP(i) is hydrolyzed to PP(i) and P(i) before product release. The crystal structure of Escherichia coli AdoMet synthetase shows that the active site contains four aspartate residues. Aspartate residues Asp-16* and Asp-271 individually provide the sole protein ligand to one of the two required Mg(2+) ions (* denotes a residue from a second subunit); aspartates Asp-118 and Asp-238* are proposed to interact with methionine. Each aspartate has been changed to an uncharged asparagine, and the metal binding residues were also changed to alanine, to assess the roles of charge and ligation ability on catalytic efficiency. The resultant enzyme variants all structurally resemble the wild type enzyme as indicated by circular dichroism spectra and are tetramers. However, all have k(cat) reductions of approximately 10(3)-fold in AdoMet synthesis, whereas the MgATP and methionine K(m) values change by less than 3- and 8-fold, respectively. In the partial reaction of PPP(i) hydrolysis, mutants of the Mg(2+) binding residues have >700-fold reduced catalytic efficiency (k(cat)/K(m)), whereas the D118N and D238*N mutants are impaired less than 35-fold. The catalytic efficiency for PPP(i) hydrolysis by Mg(2+) site mutants is improved by AdoMet, like the wild type enzyme. In contrast AdoMet reduces the catalytic efficiency for PPP(i) hydrolysis by the D118N and D238*N mutants, indicating that the events involved in AdoMet activation are hindered in these methionyl binding site mutants. Ca(2+) uniquely activates the D271A mutant enzyme to 15% of the level of Mg(2+), in contrast to the approximately 1% Ca(2+) activation of the wild type enzyme. This indicates that the Asp-271 side chain size is a discriminator between the activating ability of Ca(2+) and the

  13. Using catalytic atom maps to predict the catalytic functions present in enzyme active sites.

    PubMed

    Nosrati, Geoffrey R; Houk, K N

    2012-09-18

    Catalytic atom maps (CAMs) are minimal models of enzyme active sites. The structures in the Protein Data Bank (PDB) were examined to determine if proteins with CAM-like geometries in their active sites all share the same catalytic function. We combined the CAM-based search protocol with a filter based on the weighted contact number (WCN) of the catalytic residues, a measure of the "crowdedness" of the microenvironment around a protein residue. Using this technique, a CAM based on the Ser-His-Asp catalytic triad of trypsin was able to correctly identify catalytic triads in other enzymes within 0.5 Å rmsd of the CAM with 96% accuracy. A CAM based on the Cys-Arg-(Asp/Glu) active site residues from the tyrosine phosphatase active site achieved 89% accuracy in identifying this type of catalytic functionality. Both of these CAMs were able to identify active sites across different fold types. Finally, the PDB was searched to locate proteins with catalytic functionality similar to that present in the active site of orotidine 5'-monophosphate decarboxylase (ODCase), whose mechanism is not known with certainty. A CAM, based on the conserved Lys-Asp-Lys-Asp tetrad in the ODCase active site, was used to search the PDB for enzymes with similar active sites. The ODCase active site has a geometry similar to that of Schiff base-forming Class I aldolases, with lowest aldolase rmsd to the ODCase CAM at 0.48 Å. The similarity between this CAM and the aldolase active site suggests that ODCase has the correct catalytic functionality present in its active site for the generation of a nucleophilic lysine. PMID:22909276

  14. Using Catalytic Atom Maps to Predict the Catalytic Functions Present in Enzyme Active Sites

    PubMed Central

    Nosrati, Geoffrey R.; Houk, K. N.

    2012-01-01

    Catalytic Atom Maps (CAMs) are minimal models of enzyme active sites. The structures in the Protein Data Bank (PDB) were examined to determine if proteins with CAM-like geometries in their active sites all share the same catalytic function. We combined the CAM-based search protocol with a filter based on the weighted contact number (WCN) of the catalytic residues, a measure of the “crowdedness” of the microenvironment around a protein residue. Using this technique, a CAM based on the Ser-His-Asp catalytic triad of trypsin was able to correctly identify catalytic triads in other enzymes within 0.5 Å RMSD of the Catalytic Atom Map with 96% accuracy. A CAM based on the Cys-Arg-(Asp/Glu) active site residues from the tyrosine phosphatase active site achieved 89% accuracy in identifying this type of catalytic functionality. Both of these Catalytic Atom Maps were able to identify active sites across different fold types. Finally, the PDB was searched to locate proteins with catalytic functionality similar to that present in the active site of orotidine 5′-monophosphate decarboxylase (ODCase), whose mechanism is not known with certainty. A CAM, based on the conserved Lys-Asp-Lys-Asp tetrad in the ODCase active site, was used to search the PDB for enzymes with similar active sites. The ODCase active site has a geometry similar to that of Schiff base-forming Class I aldolases, with lowest aldolase RMSD to the ODCase CAM at 0.48 Å. The similarity between this CAM and the aldolase active site suggests that ODCase has the correct catalytic functionality present in its active site for the generation of a nucleophilic lysine. PMID:22909276

  15. MARSSIM vs. DOE Order 5400.5: the Final Status Survey plan at the Rocky Flats Environmental Technology Site.

    PubMed

    Roberts, Sarah J; Stevens, Jeff

    2003-06-01

    A challenge unique to the decommissioning of Department of Energy (DOE) facilities involves the compromise between the existing and newly recommended standards for the unrestricted release of property and materials. The Rocky Flats Environmental Technology Site (RFETS) is currently decommissioning numerous plutonium contaminated facilities. The default DOE standard for unrestricted release, Order 5400.5, defines surface activity guidelines as averaged over a 1-square-meter area with a maximum value defined for any given 100-square-centimeter area. While the Order was initially developed to release property and materials from an operating site, it is restrictive in its use when performing Final Status Survey and, to date, no new complex wide standard has been developed. However, the RFETS stakeholders selected the MARSSIM, which provides a progressive method to demonstrate compliance with the defined "dose-based" limits for a specific site, as the governing document in developing a final survey method. The end result is a hybrid final status survey plan that incorporates the requirements of both documents. This plan represents several years of development and negotiation between the contractor, the DOE, the Colorado Department of Public Health and Environment, the Rocky Flats stakeholders, and other interested parties. PMID:12792399

  16. Final long-term surveillance plan for the Spook, Wyoming, disposal site

    SciTech Connect

    1993-01-01

    A general license for the custody and long-term care of DOE Uranium Mill Tailings Remedial Action (UMTRA) Project permanent disposal sites was issued by the US Nuclear Regulatory Commission (NRC), and became effective on November 29, 1990. The general license will be in effect for a specific disposal site when the NRC accepts the disposal site`s long-term surveillance plan (LTSP) and concurs that remedial action is complete at that site. This document describes in detail the long-term surveillance activities for the Spook, Wyoming, disposal site, including monitoring, maintenance, and emergency measures necessary to fulfill the conditions of the general license, and to ensure that the disposal cell continues to comply with the UMTRA design standards.

  17. The active site of ribulose-bisphosphate carboxylase/oxygenase

    SciTech Connect

    Hartman, F.C.

    1991-01-01

    The active site of ribulose-bisphosphate carboxylase/oxygenase requires interacting domains of adjacent, identical subunits. Most active-site residues are located within the loop regions of an eight-stranded {beta}/{alpha}-barrel which constitutes the larger C-terminal domain; additional key residues are located within a segment of the smaller N-terminal domain which partially covers the mouth of the barrel. Site-directed mutagenesis of the gene encoding the enzyme from Rhodospirillum rubrum has been used to delineate functions of active-site residues. 6 refs., 2 figs.

  18. The final steps of integrin activation: the end game

    PubMed Central

    Shattil, Sanford J.; Kim, Chungho; Ginsberg, Mark H.

    2014-01-01

    Cell-directed changes in the ligand-binding affinity (‘activation’) of integrins regulate cell adhesion and migration, extracellular matrix assembly and mechanotransduction, thereby contributing to embryonic development and diseases such as atherothrombosis and cancer. Integrin activation comprises triggering events, intermediate signalling events and, finally, the interaction of integrins with cytoplasmic regulators, which changes an integrin’s affinity for its ligands. The first two events involve diverse interacting signalling pathways, whereas the final steps are immediately proximal to integrins, thus enabling integrin-focused therapeutic strategies. Recent progress provides insight into the structure of integrin transmembrane domains, and reveals how the final steps of integrin activation are mediated by integrin-binding proteins such as talins and kindlins. PMID:20308986

  19. Savannah River Site prioritization of transition activities

    SciTech Connect

    Finley, R.H.

    1993-11-01

    Effective management of SRS conversion from primarily a production facility to other missions (or Decontamination and Decommissioning (D&D)) requires a systematic and consistent method of prioritizing the transition activities. This report discusses the design of a prioritizing method developed to achieve systematic and consistent methods of prioritizing these activities.

  20. DOE site performance assessment activities. Radioactive Waste Technical Support Program

    SciTech Connect

    Not Available

    1990-07-01

    Information on performance assessment capabilities and activities was collected from eight DOE sites. All eight sites either currently dispose of low-level radioactive waste (LLW) or plan to dispose of LLW in the near future. A survey questionnaire was developed and sent to key individuals involved in DOE Order 5820.2A performance assessment activities at each site. The sites surveyed included: Hanford Site (Hanford), Idaho National Engineering Laboratory (INEL), Los Alamos National Laboratory (LANL), Nevada Test Site (NTS), Oak Ridge National Laboratory (ORNL), Paducah Gaseous Diffusion Plant (Paducah), Portsmouth Gaseous Diffusion Plant (Portsmouth), and Savannah River Site (SRS). The questionnaire addressed all aspects of the performance assessment process; from waste source term to dose conversion factors. This report presents the information developed from the site questionnaire and provides a comparison of site-specific performance assessment approaches, data needs, and ongoing and planned activities. All sites are engaged in completing the radioactive waste disposal facility performance assessment required by DOE Order 5820.2A. Each site has achieved various degrees of progress and have identified a set of critical needs. Within several areas, however, the sites identified common needs and questions.

  1. Safety Oversight of Decommissioning Activities at DOE Nuclear Sites

    SciTech Connect

    Zull, Lawrence M.; Yeniscavich, William

    2008-01-15

    The Defense Nuclear Facilities Safety Board (Board) is an independent federal agency established by Congress in 1988 to provide nuclear safety oversight of activities at U.S. Department of Energy (DOE) defense nuclear facilities. The activities under the Board's jurisdiction include the design, construction, startup, operation, and decommissioning of defense nuclear facilities at DOE sites. This paper reviews the Board's safety oversight of decommissioning activities at DOE sites, identifies the safety problems observed, and discusses Board initiatives to improve the safety of decommissioning activities at DOE sites. The decommissioning of former defense nuclear facilities has reduced the risk of radioactive material contamination and exposure to the public and site workers. In general, efforts to perform decommissioning work at DOE defense nuclear sites have been successful, and contractors performing decommissioning work have a good safety record. Decommissioning activities have recently been completed at sites identified for closure, including the Rocky Flats Environmental Technology Site, the Fernald Closure Project, and the Miamisburg Closure Project (the Mound site). The Rocky Flats and Fernald sites, which produced plutonium parts and uranium materials for defense needs (respectively), have been turned into wildlife refuges. The Mound site, which performed R and D activities on nuclear materials, has been converted into an industrial and technology park called the Mound Advanced Technology Center. The DOE Office of Legacy Management is responsible for the long term stewardship of these former EM sites. The Board has reviewed many decommissioning activities, and noted that there are valuable lessons learned that can benefit both DOE and the contractor. As part of its ongoing safety oversight responsibilities, the Board and its staff will continue to review the safety of DOE and contractor decommissioning activities at DOE defense nuclear sites.

  2. Mutations of fumarase that distinguish between the active site and a nearby dicarboxylic acid binding site.

    PubMed Central

    Weaver, T.; Lees, M.; Banaszak, L.

    1997-01-01

    Two mutant forms of fumarase C from E. coli have been made using PCR and recombinant DNA. The recombinant form of the protein included a histidine arm on the C-terminal facilitating purification. Based on earlier studies, two different carboxylic acid binding sites, labeled A- and B-, were observed in crystal structures of the wild type and inhibited forms of the enzyme. A histidine at each of the sites was mutated to an asparagine. H188N at the A-site resulted in a large decrease in specific activity, while the H129N mutation at the B-site had essentially no effect. From the results, we conclude that the A-site is indeed the active site, and a dual role for H188 as a potential catalytic base is proposed. Crystal structures of the two mutant proteins produced some unexpected results. Both mutations reduced the affinity for the carboxylic acids at their respective sites. The H129N mutant should be particularly useful in future kinetic studies because it sterically blocks the B-site with the carboxyamide of asparagine assuming the position of the ligand's carboxylate. In the H188N mutation at the active site, the new asparagine side chain still interacts with an active site water that appears to have moved slightly as a result of the mutation. PMID:9098893

  3. Comment and response document for the final remedial action plan and site design for stabilization of the inactive uranium mill tailings sites at Slick Rock, Colorado. Revision 2

    SciTech Connect

    1996-05-01

    This document for the final remedial action plan and site design has been prepared for US Department of Energy Environmental Restoration Division as part of the Uranium Mill Tailings Remedial Action plan. Comments and responses are included for the site design for stabilization of the inactive uranium mill tailings sites at Slick Rock, Colorado.

  4. Challenges with Final Status Surveys at a Large Decommissioning Site - 13417

    SciTech Connect

    Downey, Heath; Collopy, Peter; Shephard, Eugene; Walter, Nelson; Conant, John

    2013-07-01

    As part of decommissioning a former nuclear fuel manufacturing site, one of the crucial final steps is to conduct Final Status Surveys (FSS) in order to demonstrate compliance with the release criteria. At this decommissioning site, the area for FSS was about 100 hectares (248 acres) and included varying terrain, wooded areas, ponds, excavations, buildings and a brook. The challenges in performing the FSS included determining location, identifying FSS units, logging gamma walkover survey data, determining sample locations, managing water in excavations, and diverting water in the brook. The approaches taken to overcome these challenges will be presented in the paper. The paper will present and discuss lessons learned that will aid others in the FSS process. (authors)

  5. Ionizable Side Chains at Catalytic Active Sites of Enzymes

    PubMed Central

    Jimenez-Morales, David; Liang, Jie

    2012-01-01

    Catalytic active sites of enzymes of known structure can be well defined by a modern program of computational geometry. The CASTp program was used to define and measure the volume of the catalytic active sites of 573 enzymes in the Catalytic Site Atlas database. The active sites are identified as catalytic because the amino acids they contain are known to participate in the chemical reaction catalyzed by the enzyme. Acid and base side chains are reliable markers of catalytic active sites. The catalytic active sites have 4 acid and 5 base side chains, in an average volume of 1072 Å3. The number density of acid side chains is 8.3 M (in chemical units); the number density of basic side chains is 10.6 M. The catalytic active site of these enzymes is an unusual electrostatic and steric environment in which side chains and reactants are crowded together in a mixture more like an ionic liquid than an ideal infinitely dilute solution. The electrostatics and crowding of reactants and side chains seems likely to be important for catalytic function. In three types of analogous ion channels, simulation of crowded charges accounts for the main properties of selectivity measured in a wide range of solutions and concentrations. It seems wise to use mathematics designed to study interacting complex fluids when making models of the catalytic active sites of enzymes. PMID:22484856

  6. Characterize and explore potential sites and prepare research and development plan (site investigation study). Final draft. Task 2. Milestone report

    SciTech Connect

    1980-12-01

    A specific research and development plan to investigate the behavior and suitability of aquifers as compressed air energy storage (CAES) sites is presented. The proposed effort will evaluate present uncertainties in the performance of the underground energy storage subsystem and its impact on above ground plant design and cost. The project is planned to provide the utility industry with a quantitative basis for confidence that financial commitment to a demonstration plant and subsequent expansion is justified and poses acceptable risks. Activities in Phase II of a 5-phase overall CAES development program are reported. Information is included on the development of field testing specifications and schedules; selection of specific site for the conceptual design; development plan and schedule for the media site; development of analytical models of aquifer airflow; and well drilling requirements. As a result of these studies 14 sites in Illinois and Indiana were evaluated, 7 were ranked for suitability for CAES, and 4 were selected for possible use in the field testing program. Test procedures, the mathematical models and drilling requirments were developed. (LCL)

  7. Final work plan: Expedited Site Characterization of the IES Industries, Inc., Site at Marshalltown, Iowa. Ames Expedited Site Characterization Project, Version 1.0

    SciTech Connect

    Not Available

    1994-04-04

    The overall goal of the Ames Laboratory Expedited Site Characterization (ESC) project is to evaluate and promote both innovative and state-of-the-practice site characterization and/or monitoring technologies. This will be accomplished by fielding both types of technologies together in the context of an expedited site characterization. The first site will be at a former manufactured gas plant (FMGP) in Marshalltown, Iowa. The project will field three areas of technology: geophysical, analytical, and data fusion. Geophysical technologies are designed to understand the subsurface geology to help predict fate and transport of the target contaminants. Analytical technologies/methods are designed to detect and quantify the target contaminants. Data fusion technology consists of software systems designed to rapidly integrate or fuse all site information into a conceptual site model that then becomes the decision making tool for the site team to plan subsequent sampling activity. Not all of the contaminants present can be located at the action level. Polynuclear aromatic hydrocarbons (PAHs) are the signature organics associated with the coal tar activities that took place at the site. As a result, PAHs were selected as the target compounds. Screening analytical instruments and nonintrusive geophysical techniques will be fielded to qualitatively map the spatial contaminant distribution. Soil gas surveys, immunoassay testing (IMA), innovative optical techniques, and passive organic sorbent sensors will be deployed along with the geophysical methods. Gas chromatography/mass spectrometry (GC/MS) instruments and a cone penetrometer system equipped with a laser-induced fluorescence (LIF) probe will quantitatively map the action level edges of the PAH plume(s). Samples will be taken both by the cone penetrometer test system (CPT) and the Geoprobe {reg_sign} sampler system.

  8. 76 FR 12103 - Notice of Availability of the Final Site-Wide Environmental Impact Statement for the Y-12...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-04

    ... Statement for the Y-12 National Security Complex AGENCY: National Nuclear Security Administration, U.S... the Final Site-Wide Environmental Impact Statement for the Y-12 National Security Complex (Final Y-12 SWEIS, DOE/EIS-0387). The Final Y-12 SWEIS analyzes the potential environmental impacts of ongoing...

  9. Nondiscrimination in Health Programs and Activities. Final rule.

    PubMed

    2016-05-18

    This final rule implements Section 1557 of the Affordable Care Act (ACA) (Section 1557). Section 1557 prohibits discrimination on the basis of race, color, national origin, sex, age, or disability in certain health programs and activities. The final rule clarifies and codifies existing nondiscrimination requirements and sets forth new standards to implement Section 1557, particularly with respect to the prohibition of discrimination on the basis of sex in health programs other than those provided by educational institutions and the prohibition of various forms of discrimination in health programs administered by the Department of Health and Human Services (HHS or the Department) and entities established under Title I of the ACA. In addition, the Secretary is authorized to prescribe the Department's governance, conduct, and performance of its business, including, here, how HHS will apply the standards of Section 1557 to HHS-administered health programs and activities.

  10. Nondiscrimination in Health Programs and Activities. Final rule.

    PubMed

    2016-05-18

    This final rule implements Section 1557 of the Affordable Care Act (ACA) (Section 1557). Section 1557 prohibits discrimination on the basis of race, color, national origin, sex, age, or disability in certain health programs and activities. The final rule clarifies and codifies existing nondiscrimination requirements and sets forth new standards to implement Section 1557, particularly with respect to the prohibition of discrimination on the basis of sex in health programs other than those provided by educational institutions and the prohibition of various forms of discrimination in health programs administered by the Department of Health and Human Services (HHS or the Department) and entities established under Title I of the ACA. In addition, the Secretary is authorized to prescribe the Department's governance, conduct, and performance of its business, including, here, how HHS will apply the standards of Section 1557 to HHS-administered health programs and activities. PMID:27192742

  11. Final Report: Imaging of Buried Nanoscale Optically Active Materials

    SciTech Connect

    Appelbaum, Ian

    2011-07-05

    This is a final report covering work done at University of Maryland to develop a Ballistic Electron Emission Luminescence (BEEL) microscope. This technique was intended to examine the carrier transport and photon emission in deeply buried optically-active layers and thereby provide a means for materials science to unmask the detailed consequences of experimentally controllable growth parameters, such as quantum dot size, statistics and orientation, and defect density and charge recombination pathways.

  12. Active site - a site of binding of affinity inhibitors in baker's yeast inorganic pyrophosphatase

    SciTech Connect

    Svyato, I.E.; Sklyankina, V.A.; Avaeva, S.M.

    1986-03-20

    The interaction of the enzyme-substrate complex with methyl phosphate, O-phosphoethanolamine, O-phosphopropanolamine, N-acetylphosphoserine, and phosphoglyolic acid, as well as pyrophosphatase, modified by monoesters of phosphoric acid, with pyrophosphate and tripolyphosphate, was investigated. It was shown that the enzyme containing the substrate in the active site does not react with monophosphates, but modified pyrophosphatase entirely retains the ability to bind polyanions to the regulatory site. It is concluded that the inactivation of baker's yeast inorganic pyrophosphatase by monoesters of phosphoric acid, which are affinity inhibitors of it, is the result of modification of the active site of the enzyme.

  13. A novel approach to predict active sites of enzyme molecules.

    PubMed

    Chou, Kuo-Chen; Cai, Yu-dong

    2004-04-01

    Enzymes are critical in many cellular signaling cascades. With many enzyme structures being solved, there is an increasing need to develop an automated method for identifying their active sites. However, given the atomic coordinates of an enzyme molecule, how can we predict its active site? This is a vitally important problem because the core of an enzyme molecule is its active site from the viewpoints of both pure scientific research and industrial application. In this article, a topological entity was introduced to characterize the enzymatic active site. Based on such a concept, the covariant discriminant algorithm was formulated for identifying the active site. As a paradigm, the serine hydrolase family was demonstrated. The overall success rate by jackknife test for a data set of 88 enzyme molecules was 99.92%, and that for a data set of 50 independent enzyme molecules was 99.91%. Meanwhile, it was shown through an example that the prediction algorithm can also be used to find any typographic error of a PDB file in annotating the constituent amino acids of catalytic triad and to suggest a possible correction. The very high success rates are due to the introduction of a covariance matrix in the prediction algorithm that makes allowance for taking into account the coupling effects among the key constituent atoms of active site. It is anticipated that the novel approach is quite promising and may become a useful high throughput tool in enzymology, proteomics, and structural bioinformatics. PMID:14997541

  14. Final Review of Safety Assessment Issues at Savannah River Site, August 2011

    SciTech Connect

    Napier, Bruce A.; Rishel, Jeremy P.; Bixler, Nathan E.

    2011-12-15

    At the request of Savannah River Nuclear Solutions (SRNS) management, a review team composed of experts in atmospheric transport modeling for environmental radiation dose assessment convened at the Savannah River Site (SRS) on August 29-30, 2011. Though the meeting was prompted initially by suspected issues related to the treatment of surface roughness inherent in the SRS meteorological dataset and its treatment in the MELCOR Accident Consequence Code System Version 2 (MACCS2), various topical areas were discussed that are relevant to performing safety assessments at SRS; this final report addresses these topical areas.

  15. Growth exponents in surface models with non-active sites

    NASA Astrophysics Data System (ADS)

    Santos, M.; Figueiredo, W.; Aarão Reis, F. D. A.

    2006-11-01

    In this work, we studied the role played by the inactive sites present on the substrate of a growing surface. In our model, one particle sticks at the surface if the site where it falls is an active site. However, we allow the deposited particle to diffuse along the surface in accordance with some mechanism previously defined. Using Monte Carlo simulations, and some analytical results, we have investigated the model in (1+1) and (2+1) dimensions considering different relaxation mechanisms. We show that the consideration of non-active sites is a crucial point in the model. In fact, we have seen that the saturation regime is not observed for any value of the density of inactive sites. Besides, the growth exponent β turns to be one, at long times, whatever the mechanism of diffusion we consider in one and two dimensions.

  16. A small ribozyme with dual-site kinase activity

    PubMed Central

    Biondi, Elisa; Maxwell, Adam W.R.; Burke, Donald H.

    2012-01-01

    Phosphoryl transfer onto backbone hydroxyls is a recognized catalytic activity of nucleic acids. We find that kinase ribozyme K28 possesses an unusually complex active site that promotes (thio)phosphorylation of two residues widely separated in primary sequence. After allowing the ribozyme to radiolabel itself by phosphoryl transfer from [γ-32P]GTP, DNAzyme-mediated cleavage yielded two radiolabeled cleavage fragments, indicating phosphorylation sites within each of the two cleavage fragments. These sites were mapped by alkaline digestion and primer extension pausing. Enzymatic digestion and mutational analysis identified nucleotides important for activity and established the active structure as being a constrained pseudoknot with unusual connectivity that may juxtapose the two reactive sites. Nuclease sensitivities for nucleotides near the pseudoknot core were altered in the presence of GTPγS, indicating donor-induced folding. The 5′ target site was more strongly favored in full-length ribozyme K28 (128 nt) than in truncated RNAs (58 nt). Electrophoretic mobilities of self-thiophosphorylated products on organomercurial gels are distinct from the 5′ mono-thiophosphorylated product produced by reaction with polynucleotide kinase, potentially indicating simultaneous labeling of both sites within individual RNA strands. Our evidence supports a single, compact structure with local dynamics, rather than global rearrangement, as being responsible for dual-site phosphorylation. PMID:22618879

  17. Remedial action plan and site design for stabilization of the inactive uranium mill tailings sites at Rifle, Colorado. Volume 2, Appendices D and E: Final report

    SciTech Connect

    Not Available

    1992-02-01

    This appendix assesses the present conditions and data gathered about the two inactive uranium mill tailings sites near Rifle, Colorado, and the designated disposal site six miles north of Rifle in the area of Estes Gulch. It consolidates available engineering, radiological, geotechnical, hydrological, meteorological, and other information pertinent to the design of the Remedial Action Plan (RAP). The data characterize conditions at the mill, tailings, and disposal site so that the Remedial Action Contractor (RAC) may complete final designs for the remedial actions.

  18. Architecture and active site of particulate methane monooxygenase

    PubMed Central

    Culpepper, Megen A.; Rosenzweig, Amy C.

    2012-01-01

    Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria, organisms that live on methane gas as their sole carbon source. Understanding pMMO function has important implications for bioremediation applications and for the development of new, environmentally friendly catalysts for the direct conversion of methane to methanol. Crystal structures of pMMOs from three different methanotrophs reveal a trimeric architecture, consisting of three copies each of the pmoB, pmoA, and pmoC subunits. There are three distinct metal centers in each protomer of the trimer, mononuclear and dinuclear copper sites in the periplasmic regions of pmoB and a mononuclear site within the membrane that can be occupied by copper or zinc. Various models for the pMMO active site have been proposed within these structural constraints, including dicopper, tricopper, and diiron centers. Biochemical and spectroscopic data on pMMO and recombinant soluble fragments, denoted spmoB proteins, indicate that the active site involves copper and is located at the site of the dicopper center in the pmoB subunit. Initial spectroscopic evidence for O2 binding at this site has been obtained. Despite these findings, questions remain about the active site identity and nuclearity and will be the focus of future studies. PMID:22725967

  19. Methanopyrus kandleri topoisomerase V contains three distinct AP lyase active sites in addition to the topoisomerase active site.

    PubMed

    Rajan, Rakhi; Osterman, Amy; Mondragón, Alfonso

    2016-04-20

    Topoisomerase V (Topo-V) is the only topoisomerase with both topoisomerase and DNA repair activities. The topoisomerase activity is conferred by a small alpha-helical domain, whereas the AP lyase activity is found in a region formed by 12 tandem helix-hairpin-helix ((HhH)2) domains. Although it was known that Topo-V has multiple repair sites, only one had been mapped. Here, we show that Topo-V has three AP lyase sites. The atomic structure and Small Angle X-ray Scattering studies of a 97 kDa fragment spanning the topoisomerase and 10 (HhH)2 domains reveal that the (HhH)2 domains extend away from the topoisomerase domain. A combination of biochemical and structural observations allow the mapping of the second repair site to the junction of the 9th and 10th (HhH)2 domains. The second site is structurally similar to the first one and to the sites found in other AP lyases. The 3rd AP lyase site is located in the 12th (HhH)2 domain. The results show that Topo-V is an unusual protein: it is the only known protein with more than one (HhH)2 domain, the only known topoisomerase with dual activities and is also unique by having three AP lyase repair sites in the same polypeptide. PMID:26908655

  20. Methanopyrus kandleri topoisomerase V contains three distinct AP lyase active sites in addition to the topoisomerase active site

    PubMed Central

    Rajan, Rakhi; Osterman, Amy; Mondragón, Alfonso

    2016-01-01

    Topoisomerase V (Topo-V) is the only topoisomerase with both topoisomerase and DNA repair activities. The topoisomerase activity is conferred by a small alpha-helical domain, whereas the AP lyase activity is found in a region formed by 12 tandem helix-hairpin-helix ((HhH)2) domains. Although it was known that Topo-V has multiple repair sites, only one had been mapped. Here, we show that Topo-V has three AP lyase sites. The atomic structure and Small Angle X-ray Scattering studies of a 97 kDa fragment spanning the topoisomerase and 10 (HhH)2 domains reveal that the (HhH)2 domains extend away from the topoisomerase domain. A combination of biochemical and structural observations allow the mapping of the second repair site to the junction of the 9th and 10th (HhH)2 domains. The second site is structurally similar to the first one and to the sites found in other AP lyases. The 3rd AP lyase site is located in the 12th (HhH)2 domain. The results show that Topo-V is an unusual protein: it is the only known protein with more than one (HhH)2 domain, the only known topoisomerase with dual activities and is also unique by having three AP lyase repair sites in the same polypeptide. PMID:26908655

  1. Active Sites Environmental Monitoring Program: Mid-FY 1991 report

    SciTech Connect

    Ashwood, T.L.; Wickliff, D.S.; Morrissey, C.M.

    1991-10-01

    This report summarizes the activities of the Active Sites Environmental Monitoring Program (ASEMP) from October 1990 through March 1991. The ASEMP was established in 1989 by Solid Waste Operations and the Environmental Sciences Division to provide early detection and performance monitoring at active low-level radioactive waste (LLW) disposal sites in Solid Waste Storage Area (SWSA) 6 and transuranic (TRU) waste storage sites in SWSA 5 as required by chapters II and III of US Department of Energy Order 5820.2A. Monitoring results continue to demonstrate the no LLW is being leached from the storage vaults on the tumulus pads. Loading of vaults on Tumulus II began during this reporting period and 115 vaults had been loaded by the end of March 1991.

  2. Active chemisorption sites in functionalized ionic liquids for carbon capture.

    PubMed

    Cui, Guokai; Wang, Jianji; Zhang, Suojiang

    2016-07-25

    Development of novel technologies for the efficient and reversible capture of CO2 is highly desired. In the last decade, CO2 capture using ionic liquids has attracted intensive attention from both academia and industry, and has been recognized as a very promising technology. Recently, a new approach has been developed for highly efficient capture of CO2 by site-containing ionic liquids through chemical interaction. This perspective review focuses on the recent advances in the chemical absorption of CO2 using site-containing ionic liquids, such as amino-based ionic liquids, azolate ionic liquids, phenolate ionic liquids, dual-functionalized ionic liquids, pyridine-containing ionic liquids and so on. Other site-containing liquid absorbents such as amine-based solutions, switchable solvents, and functionalized ionic liquid-amine blends are also investigated. Strategies have been discussed for how to activate the existent reactive sites and develop novel reactive sites by physical and chemical methods to enhance CO2 absorption capacity and reduce absorption enthalpy. The carbon capture mechanisms of these site-containing liquid absorbents are also presented. Particular attention has been paid to the latest progress in CO2 capture in multiple-site interactions by amino-free anion-functionalized ionic liquids. In the last section, future directions and prospects for carbon capture by site-containing ionic liquids are outlined.

  3. Active chemisorption sites in functionalized ionic liquids for carbon capture.

    PubMed

    Cui, Guokai; Wang, Jianji; Zhang, Suojiang

    2016-07-25

    Development of novel technologies for the efficient and reversible capture of CO2 is highly desired. In the last decade, CO2 capture using ionic liquids has attracted intensive attention from both academia and industry, and has been recognized as a very promising technology. Recently, a new approach has been developed for highly efficient capture of CO2 by site-containing ionic liquids through chemical interaction. This perspective review focuses on the recent advances in the chemical absorption of CO2 using site-containing ionic liquids, such as amino-based ionic liquids, azolate ionic liquids, phenolate ionic liquids, dual-functionalized ionic liquids, pyridine-containing ionic liquids and so on. Other site-containing liquid absorbents such as amine-based solutions, switchable solvents, and functionalized ionic liquid-amine blends are also investigated. Strategies have been discussed for how to activate the existent reactive sites and develop novel reactive sites by physical and chemical methods to enhance CO2 absorption capacity and reduce absorption enthalpy. The carbon capture mechanisms of these site-containing liquid absorbents are also presented. Particular attention has been paid to the latest progress in CO2 capture in multiple-site interactions by amino-free anion-functionalized ionic liquids. In the last section, future directions and prospects for carbon capture by site-containing ionic liquids are outlined. PMID:27243042

  4. Studies on the active site of pig plasma amine oxidase.

    PubMed Central

    Collison, D; Knowles, P F; Mabbs, F E; Rius, F X; Singh, I; Dooley, D M; Cote, C E; McGuirl, M

    1989-01-01

    Amine oxidase from pig plasma (PPAO) has two bound Cu2+ ions and at least one pyrroloquinoline quinone (PQQ) moiety as cofactors. It is shown that recovery of activity by copper-depleted PPAO is linear with respect to added Cu2+ ions. Recovery of e.s.r. and optical spectral characteristics of active-site copper parallel the recovery of catalytic activity. These results are consistent with both Cu2+ ions contributing to catalysis. Further e.s.r. studies indicate that the two copper sites in PPAO, unlike those in amine oxidases from other sources, are chemically distinct. These comparative studies establish that non-identity of the Cu2+ ions in PPAO is not a requirement for amine oxidase activity. It is shown through the use of a new assay procedure that there are two molecules of PQQ bound per molecule of protein in PPAO; only the more reactive of these PQQ moieties is required for activity. PMID:2559715

  5. Report on Lessons Learned from the NP 2010 Early Site Permit Program FINAL REPORT

    SciTech Connect

    2008-03-26

    guidance for developing and reviewing ESP applications, issues involving ESP plant parameters, and suggestions for future ESP applicants. The development, submittal, and issuance of these first ESPs under DOE’s NP 2010 program started the momentum to exercise NRC’s new 10 CFR Part 52 licensing process. Several key questions that define critical issues regarding the effectiveness of regulations pertaining to ESPs have been identified and summarized in this report. However, the final resolution of whether the ESP component of the Part 52 process significantly contributes to the predictability in nuclear power plant licensing requires more experience and time, such as the completion of the ongoing combined Construction and Operating License (COL) process for the North Anna and Grand Gulf sites. The three ESP project participants prepared and submitted to DOE lessons learned reports from their experience in developing, submitting, and receiving an ESP. This document summarizes these reports, which are appended hereto. The Nuclear Energy Institute (http://www.nei.org/) and NRC (http://www.nrc.gov/) have also prepared reports regarding their perspectives on lessons learned during the ESP process. Their documents can be accessed on their respective web sites. Following is a summary of the lessons learned from the NP 2010 ESP projects. Effectiveness of the ESP Process: In general, the ESP process is expected (subject to demonstration of the ESP finality provisions in the North Anna and Grand Gulf ESPs) to provide high value for applicants as a site banking and risk mitigation strategy. However, several aspects of the initial process, such as NRC hearings and determining an acceptable approach to the NRC’s Emergency Planning requirements, proved challenging for the applicants. Project Execution: Initial regulatory and industry guidance for planning and executing an ESP application program proved to be insufficient to address NRC’s document review expectations. However

  6. Superfund Record of Decision (EPA Region 3): Moyer Landfill Site, Collegeville, Pennsylvania, September 1985. Final report

    SciTech Connect

    Not Available

    1985-09-30

    The Moyer Landfill is an inactive privately owned landfill located in Lower Providence Township in Montgomery County, Pennsylvania. The site was operated as a municipal landfill from the 1940's until April 1981, during which time it received municipal refuse and sewage sludges. According to local Federal Bureau of Investigation (FBI) officials, the landfill accepted a variety of solid and liquid hazardous wastes, including polychlorinated biphenyls (PCBs), solvents, paints, low-level radioactive wastes, and incinerated materials in bulk form and/or containerized in drums. In 1972, when the Pennsylvania Dept. of Environmental Resources (PADER) rules and regulations became more restrictive, this landfill was cited, and finally in 1981, it was closed and brought into receivership of the U.S. District Court.

  7. Final report on the radiological surveys of designated DX firing sites at Los Alamos National Laboratory

    SciTech Connect

    1996-09-09

    CHEMRAD was contracted by Los Alamos National Laboratory to perform USRADS{reg_sign} (UltraSonic Ranging And Data System) radiation scanning surveys at designated DX Sites at the Los Alamos National Laboratory. The primary purpose of these scanning surveys was to identify the presence of Depleted Uranium (D-38) resulting from activities at the DX Firing Sites. This effort was conducted to update the most recent surveys of these areas. This current effort was initiated with site orientation on August 12, 1996. Surveys were completed in the field on September 4, 1996. This Executive Summary briefly presents the major findings of this work. The detail survey results are presented in the balance of this report and are organized by Technical Area and Site number in section 2. This organization is not in chronological order. USRADS and the related survey methods are described in section 3. Quality Control issues are addressed in section 4. Surveys were conducted with an array of radiation detectors either mounted on a backpack frame for man-carried use (Manual mode) or on a tricycle cart (RadCart mode). The array included radiation detectors for gamma and beta surface near surface contamination as well as dose rate at 1 meter above grade. The radiation detectors were interfaced directly to an USRADS 2100 Data Pack.

  8. Computer simulation of the active site of human serum cholinesterase

    SciTech Connect

    Kefang Jiao; Song Li; Zhengzheng Lu

    1996-12-31

    The first 3D-structure of acetylchelinesterase from Torpedo California electric organ (T.AChE) was published by JL. Sussman in 1991. We have simulated 3D-structure of human serum cholinesterase (H.BuChE) and the active site of H.BuChE. It is discovered by experiment that the residue of H.BuChE is still active site after a part of H.BuChE is cut. For example, the part of 21KD + 20KD is active site of H.BuChE. The 20KD as it is. Studies on these peptides by Hemelogy indicate that two active peptides have same negative electrostatic potential maps diagram. These negative electrostatic areas attached by acetyl choline with positive electrostatic potency. We predict that 147...236 peptide of AChE could be active site because it was as 20KD as with negative electrostatic potential maps. We look forward to proving from other ones.

  9. Resonant active sites in catalytic ammonia synthesis: A structural model

    NASA Astrophysics Data System (ADS)

    Cholach, Alexander R.; Bryliakova, Anna A.; Matveev, Andrey V.; Bulgakov, Nikolai N.

    2016-03-01

    Adsorption sites Mn consisted of n adjacent atoms M, each bound to the adsorbed species, are considered within a realistic model. The sum of bonds Σ lost by atoms in a site in comparison with the bulk atoms was used for evaluation of the local surface imperfection, while the reaction enthalpy at that site was used as a measure of activity. The comparative study of Mn sites (n = 1-5) at basal planes of Pt, Rh, Ir, Fe, Re and Ru with respect to heat of N2 dissociative adsorption QN and heat of Nad + Had → NHad reaction QNH was performed using semi-empirical calculations. Linear QN(Σ) increase and QNH(Σ) decrease allowed to specify the resonant Σ for each surface in catalytic ammonia synthesis at equilibrium Nad coverage. Optimal Σ are realizable for Ru2, Re2 and Ir4 only, whereas other centers meet steric inhibition or unreal crystal structure. Relative activity of the most active sites in proportion 5.0 × 10- 5: 4.5 × 10- 3: 1: 2.5: 3.0: 1080: 2270 for a sequence of Pt4, Rh4, Fe4(fcc), Ir4, Fe2-5(bcc), Ru2, Re2, respectively, is in agreement with relevant experimental data. Similar approach can be applied to other adsorption or catalytic processes exhibiting structure sensitivity.

  10. Multi-site Phosphorylation Regulates Bim Stability and Apoptotic Activity

    PubMed Central

    Hübner, Anette; Barrett, Tamera; Flavell, Richard A.; Davis, Roger J.

    2008-01-01

    The pro-apoptotic BH3-only protein Bim is established to be an important mediator of signaling pathways that induce cell death. Multi-site phosphorylation of Bim by several members of the MAP kinase group is implicated as a regulatory mechanism that controls the apoptotic activity of Bim. To test the role of Bim phosphorylation in vivo, we constructed mice with a series of mutant alleles that express phosphorylation-defective Bim proteins. We show that mutation of the phosphorylation site Thr-112 causes decreased binding of Bim to the anti-apoptotic protein Bcl2 and can increase cell survival. In contrast, mutation of the phosphorylation sites Ser-55, Ser-65, and Ser-73 can cause increased apoptosis because of reduced proteasomal degradation of Bim. Together, these data indicate that phosphorylation can regulate Bim by multiple mechanisms and that the phosphorylation of Bim on different sites can contribute to the sensitivity of cellular apoptotic responses. PMID:18498746

  11. Mineral abundances at the final four curiosity study sites and implications for their formation

    NASA Astrophysics Data System (ADS)

    Poulet, F.; Carter, J.; Bishop, J. L.; Loizeau, D.; Murchie, S. M.

    2014-03-01

    A component of the landing site selection process for the Mars Science Laboratory (MSL) involved the presence of phyllosilicates as the main astrobiological targets. Gale crater was selected as the MSL landing site from among 4 down selected study sites (Gale, Eberswalde and Holden craters, Mawrth Vallis) that addressed the primary scientific goal of assessing the past habitability of Mars. A key constraint on the formation process of these phyllosilicate-bearing deposits is in the precise mineralogical composition. We present a reassessment of the mineralogy of the sites combined with a determination of the modal mineralogy of the major phyllosilicate-bearing deposits of the four final study sites from the modeling of near-infrared spectra using a radiative transfer model. The largest abundance of phyllosilicates (30-70%) is found in Mawrth Vallis, the lowest one in Eberswalde (<25%). Except for Mawrth Vallis, the anhydrous phases (plagioclase, pyroxenes and martian dust) are the dominant phases, suggesting formation conditions with a lower alteration grade and/or a post-formation mixing with anhydrous phases. The composition of Holden layered deposits (mixture of saponite and micas with a total abundance in the range of 25-45%) suggests transport and deposition of altered basalts of the Noachian crust without major chemical transformation. For Eberswalde, the modal mineralogy is also consistent with detrital clays, but the presence of opaline silica indicates that an authigenic formation occurred during the deposition. The overall composition including approximately 20-30% smectite detected by MSL in the rocks of Yellow-knife Bay area interpreted to be material deposited on the floor of Gale crater by channels (http://www.nasa.gov/mission_pages/msl/news/msl20130312.html) is consistent with the compositions modeled for the Eberswalde and Holden deltaic rocks. At Gale, the paucity, the small diversity and the low abundance of nontronite do not favor a complex and

  12. Water in the Active Site of Ketosteroid Isomerase

    PubMed Central

    Hanoian, Philip; Hammes-Schiffer, Sharon

    2011-01-01

    Classical molecular dynamics simulations were utilized to investigate the structural and dynamical properties of water in the active site of ketosteroid isomerase (KSI) to provide insight into the role of these water molecules in the enzyme-catalyzed reaction. This reaction is thought to proceed via a dienolate intermediate that is stabilized by hydrogen bonding with residues Tyr16 and Asp103. A comparative study was performed for the wild-type (WT) KSI and the Y16F, Y16S, and Y16F/Y32F/Y57F (FFF) mutants. These systems were studied with three different bound ligands: equilenin, which is an intermediate analog, and the intermediate states of two steroid substrates. Several distinct water occupation sites were identified in the active site of KSI for the WT and mutant systems. Three additional sites were identified in the Y16S mutant that were not occupied in WT KSI or the other mutants studied. The number of water molecules directly hydrogen bonded to the ligand oxygen was approximately two waters in the Y16S mutant, one water in the Y16F and FFF mutants, and intermittent hydrogen bonding of one water molecule in WT KSI. The molecular dynamics trajectories of the Y16F and FFF mutants reproduced the small conformational changes of residue 16 observed in the crystal structures of these two mutants. Quantum mechanical/molecular mechanical calculations of 1H NMR chemical shifts of the protons in the active site hydrogen-bonding network suggest that the presence of water in the active site does not prevent the formation of short hydrogen bonds with far-downfield chemical shifts. The molecular dynamics simulations indicate that the active site water molecules exchange much more frequently for WT KSI and the FFF mutant than for the Y16F and Y16S mutants. This difference is most likely due to the hydrogen-bonding interaction between Tyr57 and an active site water molecule that is persistent in the Y16F and Y16S mutants but absent in the FFF mutant and significantly less

  13. Activation of phenylalanine hydroxylase by phenylalanine does not require binding in the active site.

    PubMed

    Roberts, Kenneth M; Khan, Crystal A; Hinck, Cynthia S; Fitzpatrick, Paul F

    2014-12-16

    Phenylalanine hydroxylase (PheH), a liver enzyme that catalyzes the hydroxylation of excess phenylalanine in the diet to tyrosine, is activated by phenylalanine. The lack of activity at low levels of phenylalanine has been attributed to the N-terminus of the protein's regulatory domain acting as an inhibitory peptide by blocking substrate access to the active site. The location of the site at which phenylalanine binds to activate the enzyme is unknown, and both the active site in the catalytic domain and a separate site in the N-terminal regulatory domain have been proposed. Binding of catecholamines to the active-site iron was used to probe the accessibility of the active site. Removal of the regulatory domain increases the rate constants for association of several catecholamines with the wild-type enzyme by ∼2-fold. Binding of phenylalanine in the active site is effectively abolished by mutating the active-site residue Arg270 to lysine. The k(cat)/K(phe) value is down 10⁴ for the mutant enzyme, and the K(m) value for phenylalanine for the mutant enzyme is >0.5 M. Incubation of the R270K enzyme with phenylalanine also results in a 2-fold increase in the rate constants for catecholamine binding. The change in the tryptophan fluorescence emission spectrum seen in the wild-type enzyme upon activation by phenylalanine is also seen with the R270K mutant enzyme in the presence of phenylalanine. Both results establish that activation of PheH by phenylalanine does not require binding of the amino acid in the active site. This is consistent with a separate allosteric site, likely in the regulatory domain.

  14. Chemical Modification of Papain and Subtilisin: An Active Site Comparison

    ERIC Educational Resources Information Center

    St-Vincent, Mireille; Dickman, Michael

    2004-01-01

    An experiment using methyle methanethiosulfonate (MMTS) and phenylmethylsulfonyl flouride (PMSF) to specifically modify the cysteine and serine residues in the active sites of papain and subtilism respectively is demonstrated. The covalent modification of these enzymes and subsequent rescue of papain shows the beginning biochemist that proteins…

  15. Energy transfer at the active sites of heme proteins

    SciTech Connect

    Dlott, D.D.; Hill, J.R.

    1995-12-31

    Experiments using a picosecond pump-probe apparatus at the Picosecond Free-electron Laser Center at Stanford University, were performed to investigate the relaxation of carbon monoxide bound to the active sites of heme proteins. The significance of these experiments is two-fold: (1) they provide detailed information about molecular dynamics occurring at the active sites of proteins; and (2) they provide insight into the nature of vibrational relaxation processes in condensed matter. Molecular engineering is used to construct various molecular systems which are studied with the FEL. We have studied native proteins, mainly myoglobin obtained from different species, mutant proteins produced by genetic engineering using recombinant DNA techniques, and a variety of model systems which mimic the structures of the active sites of native proteins, which are produced using molecular synthesis. Use of these different systems permits us to investigate how specific molecular structural changes affect dynamical processes occurring at the active sites. This research provides insight into the problems of how different species needs are fulfilled by heme proteins which have greatly different functionality, which is induced by rather small structural changes.

  16. Remedial Action Plan and site design for stabilization of the inactive uranium mill tailings site at Mexican Hat, Utah: Appendix D. Final report

    SciTech Connect

    1988-07-01

    This appendix is an assessment of the present conditions of the inactive uranium mill site near Mexican Hat, Utah. It consolidates available engineering, radiological, geotechnical, hydrological, meteorological, and other information pertinent to the design of the Remedial Action Plan. Plan is to characterize the conditions at the mill and tailings site so that the Remedial Action Contractor may complete final designs of the remedial action.

  17. Mapping Topoisomerase IV Binding and Activity Sites on the E. coli Genome

    PubMed Central

    Lebailly, Elise; Pages, Carine; Cornet, Francois; Cosentino Lagomarsino, Marco

    2016-01-01

    Catenation links between sister chromatids are formed progressively during DNA replication and are involved in the establishment of sister chromatid cohesion. Topo IV is a bacterial type II topoisomerase involved in the removal of catenation links both behind replication forks and after replication during the final separation of sister chromosomes. We have investigated the global DNA-binding and catalytic activity of Topo IV in E. coli using genomic and molecular biology approaches. ChIP-seq revealed that Topo IV interaction with the E. coli chromosome is controlled by DNA replication. During replication, Topo IV has access to most of the genome but only selects a few hundred specific sites for its activity. Local chromatin and gene expression context influence site selection. Moreover strong DNA-binding and catalytic activities are found at the chromosome dimer resolution site, dif, located opposite the origin of replication. We reveal a physical and functional interaction between Topo IV and the XerCD recombinases acting at the dif site. This interaction is modulated by MatP, a protein involved in the organization of the Ter macrodomain. These results show that Topo IV, XerCD/dif and MatP are part of a network dedicated to the final step of chromosome management during the cell cycle. PMID:27171414

  18. Changes in active site histidine hydrogen bonding trigger cryptochrome activation.

    PubMed

    Ganguly, Abir; Manahan, Craig C; Top, Deniz; Yee, Estella F; Lin, Changfan; Young, Michael W; Thiel, Walter; Crane, Brian R

    2016-09-01

    Cryptochrome (CRY) is the principal light sensor of the insect circadian clock. Photoreduction of the Drosophila CRY (dCRY) flavin cofactor to the anionic semiquinone (ASQ) restructures a C-terminal tail helix (CTT) that otherwise inhibits interactions with targets that include the clock protein Timeless (TIM). All-atom molecular dynamics (MD) simulations indicate that flavin reduction destabilizes the CTT, which undergoes large-scale conformational changes (the CTT release) on short (25 ns) timescales. The CTT release correlates with the conformation and protonation state of conserved His378, which resides between the CTT and the flavin cofactor. Poisson-Boltzmann calculations indicate that flavin reduction substantially increases the His378 pKa Consistent with coupling between ASQ formation and His378 protonation, dCRY displays reduced photoreduction rates with increasing pH; however, His378Asn/Arg variants show no such pH dependence. Replica-exchange MD simulations also support CTT release mediated by changes in His378 hydrogen bonding and verify other responsive regions of the protein previously identified by proteolytic sensitivity assays. His378 dCRY variants show varying abilities to light-activate TIM and undergo self-degradation in cellular assays. Surprisingly, His378Arg/Lys variants do not degrade in light despite maintaining reactivity toward TIM, thereby implicating different conformational responses in these two functions. Thus, the dCRY photosensory mechanism involves flavin photoreduction coupled to protonation of His378, whose perturbed hydrogen-bonding pattern alters the CTT and surrounding regions. PMID:27551082

  19. Conformational Transitions in Human AP Endonuclease 1 and Its Active Site Mutant during Abasic Site Repair†

    PubMed Central

    Kanazhevskaya, Lyubov Yu.; Koval, Vladimir V.; Zharkov, Dmitry O.; Strauss, Phyllis R.; Fedorova, Olga S.

    2010-01-01

    AP endonuclease 1 (APE 1) is a crucial enzyme of the base excision repair pathway (BER) in human cells. APE1 recognizes apurinic/apyrimidinic (AP) sites and makes a nick in the phosphodiester backbone 5′ to them. The conformational dynamics and presteady-state kinetics of wild-type APE1 and its active site mutant, Y171F-P173L-N174K, have been studied. To observe conformational transitions occurring in the APE1 molecule during the catalytic cycle, we detected intrinsic tryptophan fluorescence of the enzyme under single turnover conditions. DNA duplexes containing a natural AP site, its tetrahydrofuran analogue, or a 2′-deoxyguanosine residue in the same position were used as specific substrates or ligands. The stopped-flow experiments have revealed high flexibility of the APE1 molecule and the complexity of the catalytic process. The fluorescent traces indicate that wild-type APE1 undergoes at least four conformational transitions during the processing of abasic sites in DNA. In contrast, nonspecific interactions of APE1 with undamaged DNA can be described by a two-step kinetic scheme. Rate and equilibrium constants were extracted from the stopped-flow and fluorescence titration data for all substrates, ligands, and products. A replacement of three residues at the enzymatic active site including the replacement of tyrosine 171 with phenylalanine in the enzyme active site resulted in a 2 × 104-fold decrease in the reaction rate and reduced binding affinity. Our data indicate the important role of conformational changes in APE1 for substrate recognition and catalysis. PMID:20575528

  20. N-methyl-D-aspartate recognition site ligands modulate activity at the coupled glycine recognition site.

    PubMed

    Hood, W F; Compton, R P; Monahan, J B

    1990-03-01

    In synaptic plasma membranes from rat forebrain, the potencies of glycine recognition site agonists and antagonists for modulating [3H]1-[1-(2-thienyl)cyclohexyl]piperidine ([3H]TCP) binding and for displacing strychnine-insensitive [3H]glycine binding are altered in the presence of N-methyl-D-aspartate (NMDA) recognition site ligands. The NMDA competitive antagonist, cis-4-phosphonomethyl-2-piperidine carboxylate (CGS 19755), reduces [3H]glycine binding, and the reduction can be fully reversed by the NMDA recognition site agonist, L-glutamate. Scatchard analysis of [3H]glycine binding shows that in the presence of CGS 19755 there is no change in Bmax (8.81 vs. 8.79 pmol/mg of protein), but rather a decrease in the affinity of glycine (KD of 0.202 microM vs. 0.129 microM). Similar decreases in affinity are observed for the glycine site agonists, D-serine and 1-aminocyclopropane-1-carboxylate, in the presence of CGS 19755. In contrast, the affinity of glycine antagonists, 1-hydroxy-3-amino-2-pyrrolidone and 1-aminocyclobutane-1-carboxylate, at this [3H]glycine recognition site increases in the presence of CGS 19755. The functional consequence of this change in affinity was addressed using the modulation of [3H]TCP binding. In the presence of L-glutamate, the potency of glycine agonists for the stimulation of [3H]TCP binding increases, whereas the potency of glycine antagonists decreases. These data are consistent with NMDA recognition site ligands, through their interactions at the NMDA recognition site, modulating activity at the associated glycine recognition site.

  1. Site operator program final report for fiscal years 1992 through 1996

    SciTech Connect

    Francfort, J.E.; Bassett, R.R.; Birasco, S.

    1998-01-01

    The Site Operator Program was an electric vehicle testing and evaluation program sponsored by US Department of Energy and managed at the Idaho National Engineering and Environmental Laboratory. The Program`s goals included the field evaluation of electric vehicles in real-world applications and environments; the support of electric vehicle technology advancement; the development of infrastructure elements necessary to support significant electric vehicle use; and increasing the awareness and acceptance of electric vehicles. This report covers Program activities from 1992 to 1996. The Site Operator Program ended in September 1996, when it was superseded by the Field Operations Program. Electric vehicle testing included baseline performance testing, which was performed in conjunction with EV America. The baseline performance parameters included acceleration, braking, range, energy efficiency, and charging time. The Program collected fleet operations data on electric vehicles operated by the Program`s thirteen partners, comprising electric utilities, universities, and federal agencies. The Program`s partners had over 250 electric vehicles, from vehicle converters and original equipment manufacturers, in their operating fleets. Test results are available via the World Wide Web site at http://ev.inel.gov/sop.

  2. Site 1 field testing for cooling-water treatment. Final report

    SciTech Connect

    Litherland, S.T.; Owen, M.L.; Scholl, F.A.; Kamas, J.W.; Nassos, P.A.

    1985-06-01

    The Electric Power Research Institute is sponsoring a three phase research project to develop a design and operating methodology for recirculating cooling water systems at high concentration factors. To expand the available data base for cooling water systems at high concentration factors, a portable field test unit (FTU) has been designed and fabricated for operation at sites with different makeup water qualities. For a ten month period during 1981, the FTU was operated at the first site, Comanche Generating Station in Pueblo, Colorado. During the field testing, several cooling water treatment options were used to increase the concentration factor for operating the FTU. These water treatment options included: (1) sulfuric acid addition for alkalinity control; (2) lime-soda makeup softening; (3) lime-soda sidestream softening; (4) combined lime-soda makeup and sidestream softening; and (5) inhibitor addition for gypsum scale control. The purpose of this report is to present a detailed discussion of all Site 1 field test activities, including FTU operation and data interpretation and analyses. 11 refs., 68 figs., 70 tabs.

  3. Remedial action plan and site conceptual design for stabilization of the inactive uranium mill tailings sites at Rifle, Colorado. Appendix D, Final report

    SciTech Connect

    1992-02-01

    This appendix assesses the present conditions and data gathered about the two designated inactive uranium mill tailings sites near Rifle, Colorado, and the proposed disposal site six miles north of Rifle in the area of Estes Gulch. It consolidates available engineering, radiological, geotechnical, hydrological, meteorological, and other information pertinent to the design of the Remedial Action Plan (RAP). The data characterize conditions at the mill, tailings, and disposal site so that the Remedial Action Contractor (RAC) may complete final designs for the remedial actions.

  4. Control of active sites in selective flocculation: I -- Mathematical model

    SciTech Connect

    Behl, S.; Moudgil, B.M.; Prakash, T.S. . Dept. of Materials Science and Engineering)

    1993-12-01

    Heteroflocculation has been determined to be another major reason for loss in selectivity for flocculation process. In a mathematical model developed earlier, conditions for controlling heteroflocculation were discussed. Blocking active sites to control selective adsorption of a flocculant oil a desirable solid surface is discussed. It has been demonstrated that the lower molecular weight fraction of a flocculant which is incapable of flocculating the particles is an efficient site blocking agent. The major application of selective flocculation has been in mineral processing but many potential uses exist in biological and other colloidal systems. These include purification of ceramic powders, separating hazardous solids from chemical waste, and removal of deleterious components from paper pulp.

  5. The site of activation of factor X by cancer procoagulant.

    PubMed

    Gordon, S G; Mourad, A M

    1991-12-01

    Cancer procoagulant (CP) is a cysteine proteinase found in a variety of malignant cells and tissues and in human amnion-chorion tissue. It initiates coagulation by activating factor X. However, the amino acid sequence of the substrate protein that determines the cleavage site of cysteine proteinases is different from that of the serine proteinases that normally activate factor X, such as factor IXa, VIIa and Russell's Viper Venom (RVV). Therefore, it was of interest to determine the site of cleavage of human factor X by CP. Purified CP was incubated with purified factor X and the reaction mixture was electrophoresed on a 10% Tris-tricine SDS-PAGE gel. The proteins were electroeluted on to a polyvinylidene difluoride (PVDF) membrane, and stained with Coomassie blue. The heavy chain of activated factor X was cut out of the PVDF membrane and sequenced with an Applied Biosystems 477A with on-line HPLC. The primary cleavage sequence was Asp-Ala-Ala-Asp-Leu-Asp-Pro-; two other secondary sequences Ser-Ile-Thr-Trp-Lys-Pro- and Glu-Asn-Pro-Phe-Asp-Leu were found. The penultimate amino acid on the carbonyl side of the hydrolysed amide bond plays a critical role for the recognition of the cleavage site of cysteine proteinases. These data indicate that the penultimate amino acid for the primary cleavage site of factor X by CP is proline-20 and for the secondary sites, proline-13 and proline-28. This is in contrast to arginine-52 that determines the specificity of the cleavage by normal serine proteinase activation.(ABSTRACT TRUNCATED AT 250 WORDS)

  6. Identification of ice nucleation active sites on feldspar dust particles.

    PubMed

    Zolles, Tobias; Burkart, Julia; Häusler, Thomas; Pummer, Bernhard; Hitzenberger, Regina; Grothe, Hinrich

    2015-03-19

    Mineral dusts originating from Earth's crust are known to be important atmospheric ice nuclei. In agreement with earlier studies, feldspar was found as the most active of the tested natural mineral dusts. Here we investigated in closer detail the reasons for its activity and the difference in the activity of the different feldspars. Conclusions are drawn from scanning electron microscopy, X-ray powder diffraction, infrared spectroscopy, and oil-immersion freezing experiments. K-feldspar showed by far the highest ice nucleation activity. Finally, we give a potential explanation of this effect, finding alkali-metal ions having different hydration shells and thus an influence on the ice nucleation activity of feldspar surfaces. PMID:25584435

  7. Identification of Ice Nucleation Active Sites on Feldspar Dust Particles

    PubMed Central

    2015-01-01

    Mineral dusts originating from Earth’s crust are known to be important atmospheric ice nuclei. In agreement with earlier studies, feldspar was found as the most active of the tested natural mineral dusts. Here we investigated in closer detail the reasons for its activity and the difference in the activity of the different feldspars. Conclusions are drawn from scanning electron microscopy, X-ray powder diffraction, infrared spectroscopy, and oil-immersion freezing experiments. K-feldspar showed by far the highest ice nucleation activity. Finally, we give a potential explanation of this effect, finding alkali-metal ions having different hydration shells and thus an influence on the ice nucleation activity of feldspar surfaces. PMID:25584435

  8. Final report for the geothermal well site restoration and plug and abandonment of wells: DOE Pleasant Bayou test site, Brazoria County, Texas

    SciTech Connect

    Rinehart, Ben N.; Seigel, Ben H.

    1994-03-13

    For a variety of reasons, thousands of oil and gas wells have been abandoned in the Gulf Coast Region of the United States. Many of these wells penetrated geopressured zones whose resource potential for power generation was undervalued or ignored. The U.S. Department of Energy (DOE) Geopressured-Geothermal Research Program was chartered to improve geothermal technology to the point where electricity could be commercially produced from a substantial number of geopressured resource sites. This research program focused on relatively narrow technical issues that are unique to geopressured resources such as the ability to predict reservoir production capacity based on preliminary flow tests. Three well sites were selected for the research program. These are the Willis Hulin and Gladys McCall sites in Louisiana, and the Pleasant Bayou site in Texas. The final phase of this research project consists of plug and abandonment (P&A) of the wells and site restoration.

  9. Final Status Survey Report for Corrective Action Unit 117 - Pluto Disassembly Facility, Building 2201, Nevada National Security Site, Nevada

    SciTech Connect

    Jeremy Gwin and Douglas Frenette

    2010-09-30

    This document contains the process knowledge, radiological data and subsequent statistical methodology and analysis to support approval for the radiological release of Corrective Action Unit (CAU) 117 – Pluto Disassembly Facility, Building 2201 located in Area 26 of the Nevada National Security Site (NNSS). Preparations for release of the building began in 2009 and followed the methodology described in the Multi-Agency Radiation Survey and Site Investigation Manual (MARSSIM). MARSSIM is the DOE approved process for release of Real Property (buildings and landmasses) to a set of established criteria or authorized limits. The pre-approved authorized limits for surface contamination values and corresponding assumptions were established by DOE O 5400.5. The release criteria coincide with the acceptance criteria of the U10C landfill permit. The U10C landfill is the proposed location to dispose of the radiologically non-impacted, or “clean,” building rubble following demolition. However, other disposition options that include the building and/or waste remaining at the NNSS may be considered providing that the same release limits apply. The Final Status Survey was designed following MARSSIM guidance by reviewing historical documentation and radiological survey data. Following this review a formal radiological characterization survey was performed in two phases. The characterization revealed multiple areas of residual radioactivity above the release criteria. These locations were remediated (decontaminated) and then the surface activity was verified to be less than the release criteria. Once remediation efforts had been successfully completed, a Final Status Survey Plan (10-015, “Final Status Survey Plan for Corrective Action Unit 117 – Pluto Disassembly Facility, Building 2201”) was developed and implemented to complete the final step in the MARSSIM process, the Final Status Survey. The Final Status Survey Plan consisted of categorizing each individual room

  10. Active-Site-Accessible, Porphyrinic Metal;#8722;Organic Framework Materials

    SciTech Connect

    Farha, Omar K.; Shultz, Abraham M.; Sarjeant, Amy A.; Nguyen, SonBinh T.; Hupp, Joseph T.

    2012-02-06

    On account of their structural similarity to cofactors found in many metallo-enzymes, metalloporphyrins are obvious potential building blocks for catalytically active, metal-organic framework (MOF) materials. While numerous porphyrin-based MOFs have already been described, versions featuring highly accessible active sites and permanent microporosity are remarkably scarce. Indeed, of the more than 70 previously reported porphyrinic MOFs, only one has been shown to be both permanently microporous and contain internally accessible active sites for chemical catalysis. Attempts to generalize the design approach used in this single successful case have failed. Reported here, however, is the synthesis of an extended family of MOFs that directly incorporate a variety of metalloporphyrins (specifically Al{sup 3+}, Zn{sup 2+}, Pd{sup 2+}, Mn{sup 3+}, and Fe{sup 3+} complexes). These robust porphyrinic materials (RPMs) feature large channels and readily accessible active sites. As an illustrative example, one of the manganese-containing RPMs is shown to be catalytically competent for the oxidation of alkenes and alkanes.

  11. Extreme 3D reconstruction of the final ROSETTA/PHILAE landing site

    NASA Astrophysics Data System (ADS)

    Capanna, Claire; Jorda, Laurent; Lamy, Philippe; Gesquiere, Gilles; Delmas, Cédric; Durand, Joelle; Garmier, Romain; Gaudon, Philippe; Jurado, Eric

    2016-04-01

    The Philae lander aboard the Rosetta spacecraft successfully landed at the surface of comet 67P/Churyumov-Gerasimenko (hereafter 67P/C-G) after two rebounds on November 12, 2014. The final landing site, now known as « Abydos », has been identified on images acquired by the OSIRIS imaging system onboard the Rosetta orbiter[1]. The available images of Abydos are very limited in number and reveal a very extreme topography containing cliffs and overhangs. Furthermore, the surface is only observed under very high incidence angles of 60° on average, which implies that the images also exhibit lots of cast shadows. This makes it very difficult to reconstruct the 3D topography with standard methods such as photogrammetry or standard clinometry. We apply a new method called ''Multiresolution PhotoClinometry by Deformation'' (MPCD, [2]) to retrieve the 3D topography of the area around Abydos. The method works in two main steps: (i) a DTM of this region is extracted from a low resolution MPCD global shape model of comet 67P/C-G, and (ii) the resulting triangular mesh is progressively deformed at increasing spatial sampling down to 0.25 m in order to match a set of 14 images of Abydos with projected pixel scales between 1 and 8 m. The method used to perform the image matching is a quasi-Newton non-linear optimization method called L-BFGS-b[3] especially suited to large-scale problems. Finally, we also checked the compatibility of the final MPCD digital terrain model with a set of five panoramic images obtained by the CIVA-P instrument aboard Philae[4]. [1] Lamy et al., 2016, submitted. [2] Capanna et al., Three dimensional reconstruction using multiresoluton photoclinometry by deformation, The visual Computer, v. 29(6-8) pp. 825-835, 2013. [3] Morales et al., Remark on "Algorithm 778: L-BFGS-B: Fortran subroutines for large-scale bound constrained optimization", v.38(1) pp.1-4, ACM Trans. Math. Softw., 2011 [4] Bibring et al., 67P/Churyumov-Gerasimenko surface properties as

  12. Functional constituents of the active site of human neutrophil collagenase.

    PubMed

    Mookhtiar, K A; Wang, F; Van Wart, H E

    1986-05-01

    A series of chemical modification reactions has been carried out to identify functional constituents of the active site of human neutrophil collagenase. The enzyme is reversibly inhibited by the transition metal chelating agent 1,10-phenanthroline, and inhibition is fully reversed by zinc. Removal of weakly bound metal ions by gel filtration inactivates collagenase, and activity is fully restored on immediate readdition of calcium. The enzyme is unaffected by reagents that modify serine, cysteine, and arginine residues. However, reaction with the carboxyl reagents cyclohexylmorpholinocarbodiimide and Woodward's Reagent K lowers the activity of the enzyme substantially. Acetylimidazole inactivates the enzyme, but activity is completely restored on addition of hydroxylamine. The enzyme is also inactivated by tetranitromethane, indicating that it contains an essential tyrosine residue. Acylation of collagenase with diethyl pyrocarbonate, diketene, acetic anhydride, or trinitrobenzenesulfonate inactivates the enzyme, and activity is not restored on addition of hydroxylamine, indicating the presence of an essential lysine residue.

  13. Nest predation increases with parental activity: Separating nest site and parental activity effects

    USGS Publications Warehouse

    Martin, T.E.; Scott, J.; Menge, C.

    2000-01-01

    Alexander Skutch hypothesized that increased parental activity can increase the risk of nest predation. We tested this hypothesis using ten open-nesting bird species in Arizona, USA. Parental activity was greater during the nestling than incubation stage because parents visited the nest frequently to feed their young during the nestling stage. However, nest predation did not generally increase with parental activity between nesting stages across the ten study species. Previous investigators have found similar results. We tested whether nest site effects might yield higher predation during incubation because the most obvious sites are depredated most rapidly. We conducted experiments using nest sites from the previous year to remove parental activity. Our results showed that nest sites have highly repeatable effects on nest predation risk; poor nest sites incurred rapid predation and caused predation rates to be greater during the incubation than nestling stage. This pattern also was exhibited in a bird species with similar (i.e. controlled) parental activity between nesting stages. Once nest site effects are taken into account, nest predation shows a strong proximate increase with parental activity during the nestling stage within and across species. Parental activity and nest sites exert antagonistic influences on current estimates of nest predation between nesting stages and both must be considered in order to understand current patterns of nest predation, which is an important source of natural selection.

  14. CO Oxidation on Au/TiO2: Condition-Dependent Active Sites and Mechanistic Pathways.

    PubMed

    Wang, Yang-Gang; Cantu, David C; Lee, Mal-Soon; Li, Jun; Glezakou, Vassiliki-Alexandra; Rousseau, Roger

    2016-08-24

    We present results of ab initio electronic structure and molecular dynamics simulations (AIMD), as well as a microkinetic model of CO oxidation catalyzed by TiO2 supported Au nanocatalysts. A coverage-dependent microkinetic analysis, based on energetics obtained with density functional methods, shows that the dominant kinetic pathway, activated oxygen species, and catalytic active sites are all strongly depended on both temperature and oxygen partial pressure. Under oxidizing conditions and T < 400 K, the prevalent pathway involves a dynamic single atom catalytic mechanism. This reaction is catalyzed by a transient Au-CO species that migrates from the Au-cluster onto a surface oxygen adatom. It subsequently reacts with the TiO2 support via a Mars van Krevelen mechanism to form CO2 and finally the Au atom reintegrates back into the gold cluster to complete the catalytic cycle. At 300 ≤ T ≤ 600 K, oxygen-bound single Oad-Au(+)-CO sites and the perimeter Au-sites of the nanoparticle work in tandem to optimally catalyze the reaction. Above 600 K, a variety of alternate pathways associated with both single-atom and the perimeter sites of the Au nanoparticle are found to be active. Under low oxygen pressures, Oad-Au(+)-CO species can be a source of catalyst deactivation and the dominant pathway involves only Au-perimeter sites. A detailed comparison of the current model and the existing literature resolves many apparent inconsistencies in the mechanistic interpretations. PMID:27480512

  15. Post-Injection Geophysical Evaluation of the Winding Ridge Site CRADA 98-F012, Final Report

    SciTech Connect

    Connie Lyons; Richard Current; Terry Ackman

    1998-09-16

    Acid mine drainage (AMD) from underground mines is a major environmental problem. The disposal of coal combustion by-products (CCB) is also a major national problem due to the large volumes produced annually and the economics associated with transportation and environmentally safe disposal. The concept of returning large volumes of the CCB to their point of origin, underground mines, and using the typically alkaline and pozzolanic attributes of the waste material for the remediation of AMD has been researched rather diligently during the past few years by various federal and state agencies and universities. As the result, the State of Maryland initiated a full-scale demonstration of this concept in a small, 5-acre, unmapped underground mine located near Friendsville, MD. Through a cooperative agreement between the State of Maryland and the U.S. Department of Energy, several geophysical techniques were evaluated as potential tools for the post-injection evaluation of the underground mine site. Three non-intrusive geophysical surveys, two electromagnetic (EM) techniques and magnetometry, were conducted over the Frazee Mine, which is located on Winding Ridge near Friendsville, MD. The EM surveys were conducted to locate ground water in both mine void and overburden. The presence of magnetite, which is naturally inherent to CCB'S due to the combustion process and essentially transparent in sedimentary rock, provided the reason for using magnetometry to locate the final resting place of the CCB grout.

  16. Active Sites Environmental Monitoring Program: FY 1991 report

    SciTech Connect

    Ashwood, T.L.; Hicks, D.S.; Morrissey, C.M.

    1992-11-01

    This report summarizes the activities of the Active Sites Environmental Monitoring Program (ASEMP) from April 1991 through September 1991. The ASEMP was established in 1989 by Solid Waste Operations (SWO) and the Environmental Sciences Division, both of Oak Ridge National Laboratory, to provide early detection and performance monitoring at active low-level (radioactive) waste (LLW) disposal sites in Solid Waste Storage Area (SWSA) 6 and transuranic (TRU) waste storage sites in SWSA 5 as required by chapters II and III of US Department of Energy Order 5820.2A. A new set of action levels was developed on the basis of a statistical analysis of background contamination. These new action levels have been used to evaluate results in this report. Results of ASEMP monitoring continue to demonstrate that no LLW (except [sup 3]H) is being leached from the storage vaults on the tumulus pads. Loading of vaults on Tumulus II, which began in early FY 1991, was >90% complete at the end of September 1991. Results of sampling of groundwater and surface waters is presented.

  17. Inhibition and active-site modelling of prolidase.

    PubMed

    King, G F; Crossley, M J; Kuchel, P W

    1989-03-15

    Consideration of the active-site model of prolidase led us to examine azetidine, pyrrolidine and piperidine substrate analogs as potential in vivo inhibitors of the enzyme. One of these, N-benzyloxycarbonyl-L-proline, was shown to be a potent competitive inhibitor of porcine kidney prolidase (Ki = 90 microM); its rapid protein-mediated permeation of human and sheep erythrocytes suggests that it may be effective in vivo. The higher homolog, N-benzyloxycarbonyl-L-pipecolic acid, was also a potent inhibitor of the enzyme while the antihypertensive drugs, captopril and enalaprilat, were shown to have mild and no inhibitory effects, respectively. Analysis of inhibitor action and consideration of X-ray crystallographic data of relevant Mn2+ complexes allowed the active-site model of prolidase to be further refined; a new model is presented in which the substrate acts as a bidentate ligand towards the active-site manganous ion. Various aspects of the new model help to explain why Mn2+ has been 'chosen' by the enzyme in preference to other biologically available metal ions. PMID:2924773

  18. Redd Site Selection and Spawning Habitat Use by Fall Chinook Salmon, Hanford Reach, Columbia River : Final Report 1995 - 1998.

    SciTech Connect

    Geist, David R.

    1999-05-01

    This report summarizes results of research activities conducted from 1995 through 1998 on identifying the spawning habitat requirements of fall chinook salmon (Oncorhynchus tshawytscha) in the Hanford Reach of the Columbia River. The project investigated whether traditional spawning habitat models could be improved in order to make better predictions of available habitat for fall chinook salmon in the Snake River. Results suggest models could be improved if they used spawning area-specific, rather than river-specific, spawning characteristics; incorporated hyporheic discharge measurements; and gave further consideration to the geomorphic features that are present in the unconstrained segments of large alluvial rivers. Ultimately the recovery of endangered fall chinook salmon will depend on how well we are able to recreate the characteristics once common in alluvial floodplains of large rivers. The results from this research can be used to better define the relationship between these physical habitat characteristics and fall chinook salmon spawning site selection, and provide more efficient use of limited recovery resources. This report is divided into four chapters which were presented in the author's doctoral dissertation which he completed through the Department of Fisheries and Wildlife at Oregon State University. Each of the chapters has been published in peer reviewed journals or is currently under review. Chapter one is a conceptual spawning habitat model that describes how geomorphic features of river channels create hydraulic processes, including hyporheic flows, that influence where salmon spawn in unconstrained reaches of large mainstem alluvial rivers. Chapter two describes the comparison of the physical factors associated with fall chinook salmon redd clusters located at two sites within the Reach. Spatial point pattern analysis of redds showed that redd clusters averaged approximately 10 hectares in area and their locations were consistent from year to

  19. Novel active comb-shaped dry electrode for EEG measurement in hairy site.

    PubMed

    Huang, Yan-Jun; Wu, Chung-Yu; Wong, Alice May-Kuen; Lin, Bor-Shyh

    2015-01-01

    Electroencephalography (EEG) is an important biopotential, and has been widely applied in clinical applications. The conventional EEG electrode with conductive gels is usually used for measuring EEG. However, the use of conductive gel also encounters with the issue of drying and hardening. Recently, many dry EEG electrodes based on different conductive materials and techniques were proposed to solve the previous issue. However, measuring EEG in the hairy site is still a difficult challenge. In this study, a novel active comb-shaped dry electrode was proposed to measure EEG in hairy site. Different form other comb-shaped or spike-shaped dry electrodes, it can provide more excellent performance of avoiding the signal attenuation, phase distortion, and the reduction of common mode rejection ratio. Even under walking motion, it can effectively acquire EEG in hairy site. Finally, the experiments for alpha rhythm and steady-state visually evoked potential were also tested to validate the proposed electrode.

  20. Final Phase II report : QuickSite(R) investigation, Everest, Kansas.

    SciTech Connect

    LaFreniere, L. M.

    2003-11-01

    field work at Everest. The main session of field work for the Phase II QuickSite{reg_sign} investigation of the Everest site began on March 6, 2001. Work was suspended at the site on April 6, 2001, (1) because of access limitations to key properties, located north and west of the former CCC/USDA facility, imposed by the private owners at the onset of the spring planting season and (2) to permit further documentation by Argonne, at the request of the CCC/USDA, of the land use and ownership history of the Nigh property as a precursor to completion of the field work. This period is termed the second session of Phase II field work at Everest. Investigation of the Nigh property history was prompted by groundwater contamination evidence obtained during the second session of Phase II field activities (discussed in Section 3.7).

  1. Evaluation of Final Radiological Conditions at Areas of the Niagara Falls Storage Site Remediated under the Formerly Utilized Sites Remedial Action Program -12184

    SciTech Connect

    Clayton, Christopher; Kothari, Vijendra; Starr, Ken; Widdop, Michael; Gillespie, Joey

    2012-02-26

    The U. S. Department of Energy (DOE) methods and protocols allow evaluation of remediation and final site conditions to determine if remediated sites remain protective. Two case studies are presented that involve the Niagara Falls Storage Site (NFSS) and associated vicinity properties (VPs), which are being remediated under the Formerly Utilized Sites Remedial Action Program (FUSRAP). These properties are a part of the former Lake Ontario Ordnance Works (LOOW). In response to stakeholders concerns about whether certain remediated NFSS VPs were putting them at risk, DOE met with stakeholders and agreed to evaluate protectiveness. Documentation in the DOE records collection adequately described assessed and final radiological conditions at the completed VPs. All FUSRAP wastes at the completed sites were cleaned up to meet DOE guidelines for unrestricted use. DOE compiled the results of the investigation in a report that was released for public comment. In conducting the review of site conditions, DOE found that stakeholders were also concerned about waste from the Separations Process Research Unit (SPRU) at the Knolls Atomic Power Laboratory (KAPL) that was handled at LOOW. DOE agreed to determine if SPRU waste remained at that needed to be remediated. DOE reviewed records of waste characterization, historical handling locations and methods, and assessment and remediation data. DOE concluded that the SPRU waste was remediated on the LOOW to levels that pose no unacceptable risk and allow unrestricted use and unlimited exposure. This work confirms the following points as tenets of an effective long-term surveillance and maintenance (LTS&M) program: Stakeholder interaction must be open and transparent, and DOE must respond promptly to stakeholder concerns. DOE, as the long-term custodian, must collect and preserve site records in order to demonstrate that remediated sites pose no unacceptable risk. DOE must continue to maintain constructive relationships with the U

  2. The two active sites in human branched-chain alpha-keto acid dehydrogenase operate independently without an obligatory alternating-site mechanism.

    PubMed

    Li, Jun; Machius, Mischa; Chuang, Jacinta L; Wynn, R Max; Chuang, David T

    2007-04-20

    A long standing controversy is whether an alternating activesite mechanism occurs during catalysis in thiamine diphosphate (ThDP)-dependent enzymes. We address this question by investigating the ThDP-dependent decarboxylase/dehydrogenase (E1b) component of the mitochondrial branched-chain alpha-keto acid dehydrogenase complex (BCKDC). Our crystal structure reveals that conformations of the two active sites in the human E1b heterotetramer harboring the reaction intermediate are identical. Acidic residues in the core of the E1b heterotetramer, which align with the proton-wire residues proposed to participate in active-site communication in the related pyruvate dehydrogenase from Bacillus stearothermophilus, are mutated. Enzyme kinetic data show that, except in a few cases because of protein misfolding, these alterations are largely without effect on overall activity of BCKDC, ruling out the requirement of a proton-relay mechanism in E1b. BCKDC overall activity is nullified at 50% phosphorylation of E1b, but it is restored to nearly half of the pre-phosphorylation level after dissociation and reconstitution of BCKDC with the same phosphorylated E1b. The results suggest that the abolition of overall activity likely results from the specific geometry of the half-phosphorylated E1b in the BCKDC assembly and not due to a disruption of the alternating active-site mechanism. Finally, we show that a mutant E1b containing only one functional active site exhibits half of the wild-type BCKDC activity, which directly argues against the obligatory communication between active sites. The above results provide evidence that the two active sites in the E1b heterotetramer operate independently during the ThDP-dependent decarboxylation reaction. PMID:17329260

  3. Final Phase II Report : QuickSite{reg_sign} investigation, Centralia, Kansas.

    SciTech Connect

    LaFreniere, L.

    2004-04-01

    District No.3. Therefore, local residents are not drinking or using the contaminated groundwater detected at the former facility. The Environmental Research Division of Argonne National Laboratory is performing the investigation at Centralia on behalf of the CCC/USDA. Argonne is a nonprofit, multidisciplinary research center operated by the University of Chicago for the U.S. Department of Energy (DOE). The CCC/USDA has entered into an interagency agreement with DOE, under which Argonne provides technical assistance to the CCC/USDA with environmental site characterization and remediation at its former grain storage facilities. At these former facilities, Argonne is applying its QuickSite{reg_sign} environmental site characterization methodology. QuickSite is Argonne's proprietary implementation system for the expedited site characterization process. This methodology has been applied successfully at a number of former CCC/USDA facilities in Nebraska and Kansas and has been adopted by the American Society for Testing and Materials (ASTM 1998) as standard practice for environmental site characterization. Argonne's investigations are conducted with a phased approach. Phase I focuses primarily on the investigation and evaluation of geology, hydrogeology, and hydrogeochemistry to identify potential contaminant pathways at a site. Phase II focuses on delineating the contamination present in both soil and aquifers along the potential migration pathways. Phase I of Argonne's investigation was conducted in March-April 2002. The results and findings of the Phase I investigation at Centralia were reported previously (Argonne 2003). This report documents the findings of the Phase II activities at Centralia. Section 1 provides a brief history of the area, a review of the Phase I results and conclusions, technical objectives for the Phase II investigation, and a brief description of the sections contained in this report. Section 2 describes the investigative methods used during the Phase

  4. 10 CFR 2.629 - Finality of partial decision on site suitability issues in a combined license proceeding.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ...), the Director of the Office of New Reactors or the Director of the Office of Nuclear Reactor Regulation... a combined license proceeding. 2.629 Section 2.629 Energy NUCLEAR REGULATORY COMMISSION AGENCY RULES... Decisions on Site Suitability-Combined License Under 10 Cfr Part 52 § 2.629 Finality of partial decision...

  5. 10 CFR 2.629 - Finality of partial decision on site suitability issues in a combined license proceeding.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ...), the Director of the Office of New Reactors or the Director of the Office of Nuclear Reactor Regulation... a combined license proceeding. 2.629 Section 2.629 Energy NUCLEAR REGULATORY COMMISSION AGENCY RULES... Decisions on Site Suitability-Combined License Under 10 Cfr Part 52 § 2.629 Finality of partial decision...

  6. Fibromodulin Interacts with Collagen Cross-linking Sites and Activates Lysyl Oxidase*

    PubMed Central

    Bihan, Dominique; Bonna, Arkadiusz; Rubin, Kristofer; Farndale, Richard W.

    2016-01-01

    The hallmark of fibrotic disorders is a highly cross-linked and dense collagen matrix, a property driven by the oxidative action of lysyl oxidase. Other fibrosis-associated proteins also contribute to the final collagen matrix properties, one of which is fibromodulin. Its interactions with collagen affect collagen cross-linking, packing, and fibril diameter. We investigated the possibility that a specific relationship exists between fibromodulin and lysyl oxidase, potentially imparting a specific collagen matrix phenotype. We mapped the fibromodulin-collagen interaction sites using the collagen II and III Toolkit peptide libraries. Fibromodulin interacted with the peptides containing the known collagen cross-linking sites and the MMP-1 cleavage site in collagens I and II. Interestingly, the interaction sites are closely aligned within the quarter-staggered collagen fibril, suggesting a multivalent interaction between fibromodulin and several collagen helices. Furthermore, we detected an interaction between fibromodulin and lysyl oxidase (a major collagen cross-linking enzyme) and mapped the interaction site to 12 N-terminal amino acids on fibromodulin. This interaction also increases the activity of lysyl oxidase. Together, the data suggest a fibromodulin-modulated collagen cross-linking mechanism where fibromodulin binds to a specific part of the collagen domain and also forms a complex with lysyl oxidase, targeting the enzyme toward specific cross-linking sites. PMID:26893379

  7. Fibromodulin Interacts with Collagen Cross-linking Sites and Activates Lysyl Oxidase.

    PubMed

    Kalamajski, Sebastian; Bihan, Dominique; Bonna, Arkadiusz; Rubin, Kristofer; Farndale, Richard W

    2016-04-01

    The hallmark of fibrotic disorders is a highly cross-linked and dense collagen matrix, a property driven by the oxidative action of lysyl oxidase. Other fibrosis-associated proteins also contribute to the final collagen matrix properties, one of which is fibromodulin. Its interactions with collagen affect collagen cross-linking, packing, and fibril diameter. We investigated the possibility that a specific relationship exists between fibromodulin and lysyl oxidase, potentially imparting a specific collagen matrix phenotype. We mapped the fibromodulin-collagen interaction sites using the collagen II and III Toolkit peptide libraries. Fibromodulin interacted with the peptides containing the known collagen cross-linking sites and the MMP-1 cleavage site in collagens I and II. Interestingly, the interaction sites are closely aligned within the quarter-staggered collagen fibril, suggesting a multivalent interaction between fibromodulin and several collagen helices. Furthermore, we detected an interaction between fibromodulin and lysyl oxidase (a major collagen cross-linking enzyme) and mapped the interaction site to 12 N-terminal amino acids on fibromodulin. This interaction also increases the activity of lysyl oxidase. Together, the data suggest a fibromodulin-modulated collagen cross-linking mechanism where fibromodulin binds to a specific part of the collagen domain and also forms a complex with lysyl oxidase, targeting the enzyme toward specific cross-linking sites.

  8. 78 FR 21352 - Update on Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-10

    ... CFR Part 765 in the Federal Register on May 23, 1994, (59 FR 26714) to carry out the requirements of... amended the final rule on June 3, 2003, (68 FR 32955) to adopt several technical and ] administrative... on Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites...

  9. Current activities handbook: formerly utilized sites remedial action program

    SciTech Connect

    1981-02-27

    This volume is one of a series produced under contract with the DOE, by Politech Corporation to develop a legislative and regulatory data base to assist the FUSRAP management in addressing the institutional and socioeconomic issues involved in carrying out the Formerly Utilized Sites Remedial Action Program. This Information Handbook series contains information about all relevant government agencies at the Federal and state levels, the pertinent programs they administer, each affected state legislature, and current Federal and state legislative and regulatory initiatives. This volume is a compilation of information about the activities each of the thirteen state legislatures potentially affected by the Formerly Utilized Sites Remedial Action Program. It contains a description of the state legislative procedural rules and a schedule of each legislative session; a summary of pending relevant legislation; the name and telephone number of legislative and state agency contacts; and the full text of all bills identified.

  10. Sperry Low Temperature Geothermal Conversion System, Phase I and Phase II. Volume IV. Field activities. Final report

    SciTech Connect

    Harvey, C.

    1984-01-01

    This volume describes those activities which took place at the Sperry DOE Gravity Head plant site at the East Mesa Geothermal Reservoir near Holtville, California between February 1980, when site preparation was begun, and November 1982, when production well 87-6 was permanently abandoned. Construction activities were terminated in July 1981 following the liner collapse in well 87-6. Large amounts of program time manpower, materials, and funds had been diverted in a nine-month struggle to salvage the production well. Once these efforts proved futile, there was no rationale for continuing with the site work unless and until sufficient funding to duplicate well 87-6 was obtained. Activities reported here include: plant construction and pre-operational calibration and testing, drilling and completion of well 87-6, final repair effort on well 87-6, abandonment of well 87-6, and performance evaluation of well 87.6. (MHR)

  11. Remedial action plan and site design for stabilization of the inactive uranium mill tailings sites at Slick Rock, Colorado. Attachment 3, Ground water hydrology report: Preliminary final

    SciTech Connect

    Not Available

    1994-03-04

    The US Environmental Protection Agency (EPA) has established health and environmental protection regulations to correct and prevent ground water contamination resulting from processing activities at inactive uranium milling sites (52 FR 36000 (1987)). According to the Uranium Mill Tailings Radiation Control Act (UMTRCA) of 1978, 42 USC {section}7901 et seq., the US Department of Energy (DOE) is responsible for assessing the inactive uranium processing sites. The DOE has determined that for Slick Rock, this assessment shall include hydrogeologic site characterization for two separate uranium processing sites, the Union Carbide (UC) site and the North Continent (NC) site, and for the proposed Burro Canyon disposal site. The water resources protection strategy that describes how the proposed action will comply with the EPA ground water protection standards is presented in Attachment 4. The following site characterization activities are discussed in this attachment: Characterization of the hydrogeologic environment, including hydrostratigraphy, ground water occurrence, aquifer parameters, and areas of recharge and discharge. Characterization of existing ground water quality by comparison with background water quality and the maximum concentration limits (MCL) of the proposed EPA ground water protection standards. Definition of physical and chemical characteristics of the potential contaminant source, including concentration and leachability of the source in relation to migration in ground water and hydraulically connected surface water. Description of local water resources, including current and future use, availability, and alternative supplies.

  12. Remedial Action Plan and Site Design for Stabilization of the Inactive Uranium Mill Tailings Site, Maybell, Colorado. Remedial action selection report: Attachment 2, Geology report, Final

    SciTech Connect

    Not Available

    1994-06-01

    The Maybell uranium mill tailings site is 25 miles (mi) (40 kilometers [km]) west of the town of Craig, Colorado, in Moffat County, in the northwestern part of the state. The unincorporated town of Maybell is 5 road mi (8 km) southwest of the site. The designated site covers approximately 110 acres (ac) (45 hectares [ha]) and consists of a concave-shaped tailings pile and rubble from the demolition of the mill buildings buried in the former mill area. Contaminated materials at the Maybell processing site include the tailings pile, which has an average depth of 20 feet (ft) (6 meters [m]) and contains 2.8 million cubic yards (yd{sup 3}) (2.1 million cubic meters [m{sup 3}]) of tailings. The former mill processing area is on the north side of the site and contains 20,000 yd{sup 3} (15,000 m{sup 3}) of contaminated demolition debris. Off-pile contamination is present and includes areas adjacent to the tailings pile, as well as contamination dispersed by wind and surface water flow. The volume of off-pile contamination to be placed in the disposal cell is 550,000 yd{sup 3} (420,000 m{sup 3}). The total volume of contaminated materials to be disposed of as part of the remedial action is estimated to be 3.37 million yd{sup 3} (2.58 million m{sup 3}). Information presented in this Final Remedial Action Plan (RAP) and referenced in supporting documents represents the current disposal cell design features and ground water compliance strategy proposed by the US Department of Energy (DOE) for the Maybell, Colorado, tailings site. Both the disposal cell design and the ground water compliance strategy have changed from those proposed prior to the preliminary final RAP document as a result of prudent site-specific technical evaluations.

  13. Electrostatic fields in the active sites of lysozymes.

    PubMed

    Sun, D P; Liao, D I; Remington, S J

    1989-07-01

    Considerable experimental evidence is in support of several aspects of the mechanism that has been proposed for the catalytic activity of lysozyme. However, the enzymatically catalyzed hydrolysis of polysaccharides proceeds over 5 orders of magnitude faster than that of model compounds that mimic the configuration of the substrate in the active site of the enzyme. Although several possible explanations for this rate enhancement have been discussed elsewhere, a definitive mechanism has not emerged. Here we report striking results obtained by classical electrodynamics, which suggest that bond breakage and the consequent separation of charge in lysozyme is promoted by a large electrostatic field across the active site cleft, produced in part by a very asymmetric distribution of charged residues on the enzyme surface. Lysozymes unrelated in amino acid sequence have similar distributions of charged residues and electric fields. The results reported here suggest that the electrostatic component of the rate enhancement is greater than 9 kcal.mol-1. Thus, electrostatic interactions may play a more important role in the enzymatic mechanism than has generally been appreciated.

  14. Histidine at the active site of Neurospora tyrosinase.

    PubMed

    Pfiffner, E; Lerch, K

    1981-10-13

    The involvement of histidyl residues as potential ligands to the binuclear active-site copper of Neurospora tyrosinase was explored by dye-sensitized photooxidation. The enzymatic activity of the holoenzyme was shown to be unaffected by exposure to light in the presence of methylene blue; however, irradiation of the apoenzyme under the same conditions led to a progressive loss of its ability to be reactivated with Cu2+. This photoinactivation was paralleled by a decrease in the histidine content whereas the number of histidyl residues in the holoenzyme remained constant. Copper measurements of photooxidized, reconstituted apoenzyme demonstrated the loss of binding of one copper atom per mole of enzyme as a consequence of photosensitized oxidation of three out of nine histidine residues. Their sequence positions were determined by a comparison of the relative yields of the histidine containing peptides of photooxidized holo- and apotyrosinases. The data obtained show the preferential modification of histidyl residues 188, 193, and 289 and suggest that they constitute metal ligands to one of the two active-site copper atoms. Substitution of copper by cobalt was found to afford complete protection of the histidyl residues from being modified by dye-sensitized photooxidation. PMID:6458322

  15. TOSPAC calculations in support of the COVE 2A benchmarking activity; Yucca Mountain Site Characterization Project

    SciTech Connect

    Gauthier, J.H.; Zieman, N.B.; Miller, W.B.

    1991-10-01

    The purpose of the the Code Verification (COVE) 2A benchmarking activity is to assess the numerical accuracy of several computer programs for the Yucca Mountain Site Characterization Project of the Department of Energy. This paper presents a brief description of the computer program TOSPAC and a discussion of the calculational effort and results generated by TOSPAC for the COVE 2A problem set. The calculations were performed twice. The initial calculations provided preliminary results for comparison with the results from other COVE 2A participants. TOSPAC was modified in response to the comparison and the final calculations included a correction and several enhancements to improve efficiency. 8 refs.

  16. Trichodiene synthase. Identification of active site residues by site-directed mutagenesis.

    PubMed

    Cane, D E; Shim, J H; Xue, Q; Fitzsimons, B C; Hohn, T M

    1995-02-28

    Derivatization of 5,5'-dithiobis(2-nitrobenzoic acid)-treated trichodiene synthase with [methyl-14C]methyl methanethiosulfonate and analysis of the derived tryptic peptides suggested the presence of two cysteine residues at the active site. The corresponding C146A and C190A mutants were constructed by site-directed mutagenesis. The C190A mutant displayed partial but significantly reduced activity, with a reduction in kcat/Km of 3000 compared to the wild-type trichodiene synthase, while the C146A mutant was essentially inactive. A hybrid trichodiene synthase, constructed from amino acids 1-309 of the Fusarium sporotrichioides enzyme and amino acids 310-383 of the Gibberella pulicaris cyclase, had steady state kinetic parameters nearly identical to those of the wild-type F. sporotrichioides enzyme. From this parent hybrid, a series of mutants was constructed by site-directed mutagenesis in which the amino acids in the base-rich region, 302-306 (DRRYR), were systematically modified. Three of these mutants were overexpressed and purified to homogeneity. The importance of Arg304 for catalysis was established by the observation that the R304K mutant showed a more than 25-fold increase in Km, as well as a 200-fold reduction in kcat. In addition, analysis of the incubation products of the R304K mutant by gas chromatography-mass spectrometry (GC-MS) indicated that farnesyl diphosphate was converted not only to trichodiene but to at least two additional C15H24 hydrocarbons, mle 204. Replacement of the Tyr305 residue of trichodiene synthase with Phe had little effect on kcat, while increasing the Km by a factor of ca. 7-8.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7873527

  17. Remedial Action Plan and site design for stabilization of the inactive uranium mill tailings site at Durango, Colorado: Attachment 3, Groundwater hydrology report. Revised final report

    SciTech Connect

    Not Available

    1991-12-01

    The US Environmental Protection Agency (EPA) has established health and environmental protection regulations to correct and prevent groundwater contamination resulting from processing activities at inactive uranium milling sites. According to the Uranium Mill Tailings Radiation Control Act of 1978, (UMTRCA) the US Department of Energy (DOE) is responsible for assessing the inactive uranium processing sites. The DOE has determined this assessment shall include information on hydrogeologic site characterization. The water resources protection strategy that describes how the proposed action will comply with the EPA groundwater protection standards is presented in Attachment 4. Site characterization activities discussed in this section include: Characterization of the hydrogeologic environment; characterization of existing groundwater quality; definition of physical and chemical characteristics of the potential contaminant source; and description of local water resources.

  18. Final environmental impact statement for the Nevada Test Site and off-site locations in the state of Nevada: Mitigation action plan

    SciTech Connect

    1997-02-01

    The DOE Notice of Availability for this environmental impact statement was published in the Federal Register on Friday, October 18, 1996 (61 FR 54437). The final environmental impact statement identifies potential adverse effects resulting from the four use alternatives evaluated and discusses measures that DOE considered for the mitigation of these potential adverse effects. The Secretary of Energy signed the Record of Decision on the management and operation of the Nevada Test Site and other DOE sites in the state of Nevada on December 9, 1996. These decisions will result in the continuation of the multipurpose, multi-program use of the Nevada Test Site, under which DOE will pursue a further diversification of interagency, private industry, and public-education uses while meeting its Defense Program, Waste Management, and Environmental Restoration mission requirements at the Nevada Test Site and other Nevada sites, including the Tonopah Test Range, the Project Shoal Site, the Central Nevada Test Area, and on the Nellis Air Force Range Complex. The Record of Decision also identifies specific mitigation actions beyond the routine day-to-day physical and administrative controls needed for implementation of the decisions. These specific mitigation actions are focused on the transportation of waste and on groundwater availability. This Mitigation Action Plan elaborates on these mitigation commitments.

  19. The copper active site of CBM33 polysaccharide oxygenases.

    PubMed

    Hemsworth, Glyn R; Taylor, Edward J; Kim, Robbert Q; Gregory, Rebecca C; Lewis, Sally J; Turkenburg, Johan P; Parkin, Alison; Davies, Gideon J; Walton, Paul H

    2013-04-24

    The capacity of metal-dependent fungal and bacterial polysaccharide oxygenases, termed GH61 and CBM33, respectively, to potentiate the enzymatic degradation of cellulose opens new possibilities for the conversion of recalcitrant biomass to biofuels. GH61s have already been shown to be unique metalloenzymes containing an active site with a mononuclear copper ion coordinated by two histidines, one of which is an unusual τ-N-methylated N-terminal histidine. We now report the structural and spectroscopic characterization of the corresponding copper CBM33 enzymes. CBM33 binds copper with high affinity at a mononuclear site, significantly stabilizing the enzyme. X-band EPR spectroscopy of Cu(II)-CBM33 shows a mononuclear type 2 copper site with the copper ion in a distorted axial coordination sphere, into which azide will coordinate as evidenced by the concomitant formation of a new absorption band in the UV/vis spectrum at 390 nm. The enzyme's three-dimensional structure contains copper, which has been photoreduced to Cu(I) by the incident X-rays, confirmed by X-ray absorption/fluorescence studies of both aqueous solution and intact crystals of Cu-CBM33. The single copper(I) ion is ligated in a T-shaped configuration by three nitrogen atoms from two histidine side chains and the amino terminus, similar to the endogenous copper coordination geometry found in fungal GH61. PMID:23540833

  20. Activation of muscarinic acetylcholine receptors via their allosteric binding sites.

    PubMed Central

    Jakubík, J; Bacáková, L; Lisá, V; el-Fakahany, E E; Tucek, S

    1996-01-01

    Ligands that bind to the allosteric-binding sites on muscarinic acetylcholine receptors alter the conformation of the classical-binding sites of these receptors and either diminish or increase their affinity for muscarinic agonists and classical antagonists. It is not known whether the resulting conformational change also affects the interaction between the receptors and the G proteins. We have now found that the muscarinic receptor allosteric modulators alcuronium, gallamine, and strychnine (acting in the absence of an agonist) alter the synthesis of cAMP in Chinese hamster ovary (CHO) cells expressing the M2 or the M4 subtype of muscarinic receptors in the same direction as the agonist carbachol. In addition, most of their effects on the production of inositol phosphates in CHO cells expressing the M1 or the M3 muscarinic receptor subtypes are also similar to (although much weaker than) those of carbachol. The agonist-like effects of the allosteric modulators are not observed in CHO cells that have not been transfected with the gene for any of the subtypes of muscarinic receptors. The effects of alcuronium on the formation of cAMP and inositol phosphates are not prevented by the classical muscarinic antagonist quinuclidinyl benzilate. These observations demonstrate for the first time that the G protein-mediated functional responses of muscarinic receptors can be evoked not only from their classical, but also from their allosteric, binding sites. This represents a new mechanism of receptor activation. PMID:8710935

  1. How Force Might Activate Talin's Vinculin Binding Sites: SMD Reveals a Structural Mechanism

    PubMed Central

    Hytönen, Vesa P; Vogel, Viola

    2008-01-01

    Upon cell adhesion, talin physically couples the cytoskeleton via integrins to the extracellular matrix, and subsequent vinculin recruitment is enhanced by locally applied tensile force. Since the vinculin binding (VB) sites are buried in the talin rod under equilibrium conditions, the structural mechanism of how vinculin binding to talin is force-activated remains unknown. Taken together with experimental data, a biphasic vinculin binding model, as derived from steered molecular dynamics, provides high resolution structural insights how tensile mechanical force applied to the talin rod fragment (residues 486–889 constituting helices H1–H12) might activate the VB sites. Fragmentation of the rod into three helix subbundles is prerequisite to the sequential exposure of VB helices to water. Finally, unfolding of a VB helix into a completely stretched polypeptide might inhibit further binding of vinculin. The first events in fracturing the H1–H12 rods of talin1 and talin2 in subbundles are similar. The proposed force-activated α-helix swapping mechanism by which vinculin binding sites in talin rods are exposed works distinctly different from that of other force-activated bonds, including catch bonds. PMID:18282082

  2. Radiation inactivation study of aminopeptidase: probing the active site

    NASA Astrophysics Data System (ADS)

    Jamadar, V. K.; Jamdar, S. N.; Mohan, Hari; Dandekar, S. P.; Harikumar, P.

    2004-04-01

    Ionizing radiation inactivated purified chicken intestinal aminopeptidase in media saturated with gases in the order N 2O>N 2>air. The D 37 values in the above conditions were 281, 210 and 198 Gy, respectively. OH radical scavengers such as t-butanol and isopropanol effectively nullified the radiation-induced damage in N 2O. The radicals (SCN) 2•-, Br 2•- and I 2•- inactivated the enzyme, pointing to the involvement of aromatic amino acids and cysteine in its catalytic activity. The enzyme exhibited fluorescence emission at 340 nm which is characteristic of tryptophan. The radiation-induced loss of activity was accompanied by a decrease in the fluorescence of the enzyme suggesting a predominant influence on tryptophan residues. The enzyme inhibition was associated with a marked increase in the Km and a decrease in the Vmax and kcat values, suggesting an irreversible alteration in the catalytic site. The above observations were confirmed by pulse radiolysis studies.

  3. Mimicking enzymatic active sites on surfaces for energy conversion chemistry.

    PubMed

    Gutzler, Rico; Stepanow, Sebastian; Grumelli, Doris; Lingenfelder, Magalí; Kern, Klaus

    2015-07-21

    Metal-organic supramolecular chemistry on surfaces has matured to a point where its underlying growth mechanisms are well understood and structures of defined coordination environments of metal atoms can be synthesized in a controlled and reproducible procedure. With surface-confined molecular self-assembly, scientists have a tool box at hand which can be used to prepare structures with desired properties, as for example a defined oxidation number and spin state of the transition metal atoms within the organic matrix. From a structural point of view, these coordination sites in the supramolecular structure resemble the catalytically active sites of metallo-enzymes, both characterized by metal centers coordinated to organic ligands. Several chemical reactions take place at these embedded metal ions in enzymes and the question arises whether these reactions also take place using metal-organic networks as catalysts. Mimicking the active site of metal atoms and organic ligands of enzymes in artificial systems is the key to understanding the selectivity and efficiency of enzymatic reactions. Their catalytic activity depends on various parameters including the charge and spin configuration in the metal ion, but also on the organic environment, which can stabilize intermediate reaction products, inhibits catalytic deactivation, and serves mostly as a transport channel for the reactants and products and therefore ensures the selectivity of the enzyme. Charge and spin on the transition metal in enzymes depend on the one hand on the specific metal element, and on the other hand on its organic coordination environment. These two parameters can carefully be adjusted in surface confined metal-organic networks, which can be synthesized by virtue of combinatorial mixing of building synthons. Different organic ligands with varying functional groups can be combined with several transition metals and spontaneously assemble into ordered networks. The catalytically active metal

  4. Polarizability of the active site of cytochrome c reduces the activation barrier for electron transfer

    NASA Astrophysics Data System (ADS)

    Dinpajooh, Mohammadhasan; Martin, Daniel R.; Matyushov, Dmitry V.

    2016-06-01

    Enzymes in biology’s energy chains operate with low energy input distributed through multiple electron transfer steps between protein active sites. The general challenge of biological design is how to lower the activation barrier without sacrificing a large negative reaction free energy. We show that this goal is achieved through a large polarizability of the active site. It is polarized by allowing a large number of excited states, which are populated quantum mechanically by electrostatic fluctuations of the protein and hydration water shells. This perspective is achieved by extensive mixed quantum mechanical/molecular dynamics simulations of the half reaction of reduction of cytochrome c. The barrier for electron transfer is consistently lowered by increasing the number of excited states included in the Hamiltonian of the active site diagonalized along the classical trajectory. We suggest that molecular polarizability, in addition to much studied electrostatics of permanent charges, is a key parameter to consider in order to understand how enzymes work.

  5. Polarizability of the active site of cytochrome c reduces the activation barrier for electron transfer

    PubMed Central

    Dinpajooh, Mohammadhasan; Martin, Daniel R.; Matyushov, Dmitry V.

    2016-01-01

    Enzymes in biology’s energy chains operate with low energy input distributed through multiple electron transfer steps between protein active sites. The general challenge of biological design is how to lower the activation barrier without sacrificing a large negative reaction free energy. We show that this goal is achieved through a large polarizability of the active site. It is polarized by allowing a large number of excited states, which are populated quantum mechanically by electrostatic fluctuations of the protein and hydration water shells. This perspective is achieved by extensive mixed quantum mechanical/molecular dynamics simulations of the half reaction of reduction of cytochrome c. The barrier for electron transfer is consistently lowered by increasing the number of excited states included in the Hamiltonian of the active site diagonalized along the classical trajectory. We suggest that molecular polarizability, in addition to much studied electrostatics of permanent charges, is a key parameter to consider in order to understand how enzymes work. PMID:27306204

  6. Spectroscopic Definition of the Ferroxidase Site in M Ferritin: Comparison of Binuclear Substrate vs. Cofactor Active Sites

    PubMed Central

    Schwartz, Jennifer K.; Liu, Xiaofeng S.; Tosha, Takehiko; Theil, Elizabeth C.; Solomon, Edward I.

    2008-01-01

    Maxi ferritins, 24 subunit protein nanocages, are essential in humans, plants, bacteria, and other animals for the concentration and storage of iron as hydrated ferric oxide, while minimizing free radical generation or use by pathogens. Formation of the precursors to these ferric oxides is catalyzed at a non-heme biferrous substrate site, which has some parallels with the cofactor sites in other biferrous enzymes. A combination of circular dichroism (CD), magnetic circular dichroism (MCD), and variable-temperature, variable-field MCD (VTVH MCD) has been used to probe Fe(II) binding to the substrate active site in frog M ferritin. These data determined that the active site within each subunit consists of two inequivalent five-coordinate (5C) ferrous centers that are weakly anti-ferromagnetically coupled, consistent with a μ-1,3 carboxylate bridge. The active site ligand set is unusual and likely includes a terminal water bound to each Fe(II) center. The Fe(II) ions bind to the active sites in a concerted manner, and cooperativity among the sites in each subunit is observed, potentially providing a mechanism for the control of ferritin iron loading. Differences in geometric and electronic structure – including a weak ligand field, availability of two water ligands at the biferrous substrate site, and the single carboxylate bridge in ferritin – coincide with the divergent reaction pathways observed between this substrate site and the previously studied cofactor active sites. PMID:18576633

  7. An active-site lysine in avian liver phosphoenolpyruvate carboxykinase

    SciTech Connect

    Guidinger, P.F.; Nowak, T. )

    1991-09-10

    The participation of lysine in the catalysis by avian liver phosphoenolpyruvate carboxykinase was studied by chemical modification and by a characterization of the modified enzyme. The rate of inactivation by 2,4-pentanedione is pseudo-first-order and linearly dependent on reagent concentration with a second-order rate constant of 0.36 {plus minus} 0.025 M{sup {minus}1} min{sup {minus}1}. Inactivation by pyridoxal 5{prime}-phosphate of the reversible reaction catalyzed by phosphoenolpyruvate carboxykinase follows bimolecular kinetics with a second-order rate constant of 7,700 {plus minus} 860 m{sup {minus}1} min{sup {minus}1}. Treatment of the enzyme or one lysine residue modified concomitant with 100% loss in activity. A stoichiometry of 1:1 is observed when either the reversible or the irreversible reactions catalyzed by the enzyme are monitored. A study of k{sub obs} vs pH suggests this active-site lysine has a pK{sub a} of 8.1 and a pH-independent rate constant of inactivation of 47,700 m{sup {minus}1} min{sup {minus}1}. Proton relaxation rate measurements suggest that pyridoxal 5{prime}-phosphate modification alters binding of the phosphate-containing substrates. {sup 31}P NMR relaxation rate measurements show altered binding of the substrates in the ternary enzyme {center dot}Mn{sup 2+}{center dot}substrate complex. Circular dichroism studies show little change in secondary structure of pyridoxal 5{prime}-phosphate modified phosphoenolpyruvate carboxykinase. These results indicate that avian liver phosphoenolpyruvate carboxykinase has one reactive lysine at the active site and it is involved in the binding and activation of the phosphate-containing substrates.

  8. Perchlorate Reductase Is Distinguished by Active Site Aromatic Gate Residues.

    PubMed

    Youngblut, Matthew D; Tsai, Chi-Lin; Clark, Iain C; Carlson, Hans K; Maglaqui, Adrian P; Gau-Pan, Phonchien S; Redford, Steven A; Wong, Alan; Tainer, John A; Coates, John D

    2016-04-22

    Perchlorate is an important ion on both Earth and Mars. Perchlorate reductase (PcrAB), a specialized member of the dimethylsulfoxide reductase superfamily, catalyzes the first step of microbial perchlorate respiration, but little is known about the biochemistry, specificity, structure, and mechanism of PcrAB. Here we characterize the biophysics and phylogeny of this enzyme and report the 1.86-Å resolution PcrAB complex crystal structure. Biochemical analysis revealed a relatively high perchlorate affinity (Km = 6 μm) and a characteristic substrate inhibition compared with the highly similar respiratory nitrate reductase NarGHI, which has a relatively much lower affinity for perchlorate (Km = 1.1 mm) and no substrate inhibition. Structural analysis of oxidized and reduced PcrAB with and without the substrate analog SeO3 (2-) bound to the active site identified key residues in the positively charged and funnel-shaped substrate access tunnel that gated substrate entrance and product release while trapping transiently produced chlorate. The structures suggest gating was associated with shifts of a Phe residue between open and closed conformations plus an Asp residue carboxylate shift between monodentate and bidentate coordination to the active site molybdenum atom. Taken together, structural and mutational analyses of gate residues suggest key roles of these gate residues for substrate entrance and product release. Our combined results provide the first detailed structural insight into the mechanism of biological perchlorate reduction, a critical component of the chlorine redox cycle on Earth.

  9. Eel calcitonin binding site distribution and antinociceptive activity in rats

    SciTech Connect

    Guidobono, F.; Netti, C.; Sibilia, V.; Villa, I.; Zamboni, A.; Pecile, A.

    1986-03-01

    The distribution of binding site for (/sup 125/I)-eel-calcitonin (ECT) to rat central nervous system, studied by an autoradiographic technique, showed concentrations of binding in the diencephalon, the brain stem and the spinal cord. Large accumulations of grains were seen in the hypothalamus, the amygdala, in the fasciculus medialis prosencephali, in the fasciculus longitudinalis medialis, in the ventrolateral part of the periventricular gray matter, in the lemniscus medialis and in the raphe nuclei. The density of grains in the reticular formation and in the nucleus tractus spinalis nervi trigemini was more moderate. In the spinal cord, grains were scattered throughout the dorsal horns. Binding of the ligand was displaced equally by cold ECT and by salmon CT(sCT), indicating that both peptides bind to the same receptors. Human CT was much weaker than sCT in displacing (/sup 125/I)-ECT binding. The administration of ECT into the brain ventricles of rats dose-dependently induced a significant and long-lasting enhancement of hot-plate latencies comparable with that obtained with sCT. The antinociceptive activity induced by ECT is compatible with the topographical distribution of binding sites for the peptide and is a further indication that fish CTs are active in the mammalian brain.

  10. Perchlorate Reductase Is Distinguished by Active Site Aromatic Gate Residues.

    PubMed

    Youngblut, Matthew D; Tsai, Chi-Lin; Clark, Iain C; Carlson, Hans K; Maglaqui, Adrian P; Gau-Pan, Phonchien S; Redford, Steven A; Wong, Alan; Tainer, John A; Coates, John D

    2016-04-22

    Perchlorate is an important ion on both Earth and Mars. Perchlorate reductase (PcrAB), a specialized member of the dimethylsulfoxide reductase superfamily, catalyzes the first step of microbial perchlorate respiration, but little is known about the biochemistry, specificity, structure, and mechanism of PcrAB. Here we characterize the biophysics and phylogeny of this enzyme and report the 1.86-Å resolution PcrAB complex crystal structure. Biochemical analysis revealed a relatively high perchlorate affinity (Km = 6 μm) and a characteristic substrate inhibition compared with the highly similar respiratory nitrate reductase NarGHI, which has a relatively much lower affinity for perchlorate (Km = 1.1 mm) and no substrate inhibition. Structural analysis of oxidized and reduced PcrAB with and without the substrate analog SeO3 (2-) bound to the active site identified key residues in the positively charged and funnel-shaped substrate access tunnel that gated substrate entrance and product release while trapping transiently produced chlorate. The structures suggest gating was associated with shifts of a Phe residue between open and closed conformations plus an Asp residue carboxylate shift between monodentate and bidentate coordination to the active site molybdenum atom. Taken together, structural and mutational analyses of gate residues suggest key roles of these gate residues for substrate entrance and product release. Our combined results provide the first detailed structural insight into the mechanism of biological perchlorate reduction, a critical component of the chlorine redox cycle on Earth. PMID:26940877

  11. Operational concerns regarding chemical biological decontamination of fixed sites. Final report

    SciTech Connect

    Fleisch, D.L.

    1996-06-14

    Existing U.S. military doctrine and practice are deficient regarding CBW decontamination capabilities and procedures for fixed sites. Currently, responsibility for decontamination is left to each service component and focused on individual unit requirements. Further, joint doctrine splits the responsibility for all phases of decontamination between the theater commander and the services. Recommendations include: Doctrinal changes to emphasize realistic CBW consequences, practical solutions, and eliminate confusion regarding fixed site responsibility; OPLAN development more specific with respect to fixed sites; Additional units must be trained and equipped to provide fixed site decontamination.

  12. Site investigation of Cluster 3, Edgewood Area, Aberdeen Proving Ground, Maryland. Final report

    SciTech Connect

    Sharp, M.K.; Kean, T.B.

    1995-08-01

    The Waterways Experiment Station (WES) is currently involved in investigating several sites at the Edgewood Area (EA) of Aberdeen Proving Ground (APG), Maryland. These investigations consist of placing monitoring wells and periodically collecting samples for laboratory analysis. Additionally, several of the sites are to be investigated geophysically to determine if any anomalous areas exist. One of the sites, Cluster 3, a suspected landfill area is the focus of this report. Geophysical surveys were conducted to help delineate any anomalies indicative of buried waste, waste containers, boundaries of burial trenches, and the depth to water table. The geophysical methods utilized at the site were electromagnetic induction (EM), magnetics, and seismic refraction.

  13. Linde FUSRAP Site Remediation: Engineering Challenges and Solutions of Remedial Activities on an Active Industrial Facility - 13506

    SciTech Connect

    Beres, Christopher M.; Fort, E. Joseph; Boyle, James D.

    2013-07-01

    The Linde FUSRAP Site (Linde) is located in Tonawanda, New York at a major research and development facility for Praxair, Inc. (Praxair). Successful remediation activities at Linde combines meeting cleanup objectives of radiological contamination while minimizing impacts to Praxair business operations. The unique use of Praxair's property coupled with an array of active and abandoned utilities poses many engineering and operational challenges; each of which has been overcome during the remedial action at Linde. The U.S. Army Corps of Engineers - Buffalo District (USACE) and CABRERA SERVICES, INC. (CABRERA) have successfully faced engineering challenges such as relocation of an aboveground structure, structural protection of an active water line, and installation of active mechanical, electrical, and communication utilities to perform remediation. As remediation nears completion, continued success of engineering challenges is critical as remaining activities exist in the vicinity of infrastructure essential to business operations; an electrical substation and duct bank providing power throughout the Praxair facility. Emphasis on engineering and operations through final remediation and into site restoration will allow for the safe and successful completion of the project. (authors)

  14. An Active Site Water Network in the Plasminogen Activator Pla from Yersinia pestis

    SciTech Connect

    Eren, Elif; Murphy, Megan; Goguen, Jon; van den Berg, Bert

    2010-08-13

    The plasminogen activator Pla from Yersinia pestis is an outer membrane protease (omptin) that is important for the virulence of plague. Here, we present the high-resolution crystal structure of wild-type, enzymatically active Pla at 1.9 {angstrom}. The structure shows a water molecule located between active site residues D84 and H208, which likely corresponds to the nucleophilic water. A number of other water molecules are present in the active site, linking residues important for enzymatic activity. The R211 sidechain in loop L4 is close to the nucleophilic water and possibly involved in the stabilization of the oxyanion intermediate. Subtle conformational changes of H208 result from the binding of lipopolysaccharide to the outside of the barrel, explaining the unusual dependence of omptins on lipopolysaccharide for activity. The Pla structure suggests a model for the interaction with plasminogen substrate and provides a more detailed understanding of the catalytic mechanism of omptin proteases.

  15. Impact of single-site axonal GABAergic synaptic events on cerebellar interneuron activity.

    PubMed

    de San Martin, Javier Zorrilla; Jalil, Abdelali; Trigo, Federico F

    2015-12-01

    Axonal ionotropic receptors are present in a variety of neuronal types, and their function has largely been associated with the modulation of axonal activity and synaptic release. It is usually assumed that activation of axonal GABA(A)Rs comes from spillover, but in cerebellar molecular layer interneurons (MLIs) the GABA source is different: in these cells, GABA release activates presynaptic GABA(A) autoreceptors (autoRs) together with postsynaptic targets, producing an autoR-mediated synaptic event. The frequency of presynaptic, autoR-mediated miniature currents is twice that of their somatodendritic counterparts, suggesting that autoR-mediated responses have an important effect on interneuron activity. Here, we used local Ca(2+) photolysis in MLI axons of juvenile rats to evoke GABA release from individual varicosities to study the activation of axonal autoRs in single release sites. Our data show that single-site autoR conductances are similar to postsynaptic dendritic conductances. In conditions of high [Cl(-)](i), autoR-mediated conductances range from 1 to 5 nS; this corresponds to ∼30-150 GABA(A) channels per presynaptic varicosity, a value close to the number of channels in postsynaptic densities. Voltage responses produced by the activation of autoRs in single varicosities are amplified by a Na(v)-dependent mechanism and propagate along the axon with a length constant of 91 µm. Immunolabeling determination of synapse location shows that on average, one third of the synapses produce autoR-mediated signals that are large enough to reach the axon initial segment. Finally, we show that single-site activation of presynaptic GABA(A) autoRs leads to an increase in MLI excitability and thus conveys a strong feedback signal that contributes to spiking activity.

  16. Metal active site elasticity linked to activation of homocysteine in methionine synthases

    SciTech Connect

    Koutmos, Markos; Pejchal, Robert; Bomer, Theresa M.; Matthews, Rowena G.; Smith, Janet L.; Ludwig, Martha L.

    2008-04-02

    Enzymes possessing catalytic zinc centers perform a variety of fundamental processes in nature, including methyl transfer to thiols. Cobalamin-independent (MetE) and cobalamin-dependent (MetH) methionine synthases are two such enzyme families. Although they perform the same net reaction, transfer of a methyl group from methyltetrahydrofolate to homocysteine (Hcy) to form methionine, they display markedly different catalytic strategies, modular organization, and active site zinc centers. Here we report crystal structures of zinc-replete MetE and MetH, both in the presence and absence of Hcy. Structural investigation of the catalytic zinc sites of these two methyltransferases reveals an unexpected inversion of zinc geometry upon binding of Hcy and displacement of an endogenous ligand in both enzymes. In both cases a significant movement of the zinc relative to the protein scaffold accompanies inversion. These structures provide new information on the activation of thiols by zinc-containing enzymes and have led us to propose a paradigm for the mechanism of action of the catalytic zinc sites in these and related methyltransferases. Specifically, zinc is mobile in the active sites of MetE and MetH, and its dynamic nature helps facilitate the active site conformational changes necessary for thiol activation and methyl transfer.

  17. Active Site Detection by Spatial Conformity and Electrostatic Analysis—Unravelling a Proteolytic Function in Shrimp Alkaline Phosphatase

    PubMed Central

    Chakraborty, Sandeep; Minda, Renu; Salaye, Lipika; Bhattacharjee, Swapan K.; Rao, Basuthkar J.

    2011-01-01

    Computational methods are increasingly gaining importance as an aid in identifying active sites. Mostly these methods tend to have structural information that supplement sequence conservation based analyses. Development of tools that compute electrostatic potentials has further improved our ability to better characterize the active site residues in proteins. We have described a computational methodology for detecting active sites based on structural and electrostatic conformity - CataLytic Active Site Prediction (CLASP). In our pipelined model, physical 3D signature of any particular enzymatic function as defined by its active sites is used to obtain spatially congruent matches. While previous work has revealed that catalytic residues have large pKa deviations from standard values, we show that for a given enzymatic activity, electrostatic potential difference (PD) between analogous residue pairs in an active site taken from different proteins of the same family are similar. False positives in spatially congruent matches are further pruned by PD analysis where cognate pairs with large deviations are rejected. We first present the results of active site prediction by CLASP for two enzymatic activities - β-lactamases and serine proteases, two of the most extensively investigated enzymes. The results of CLASP analysis on motifs extracted from Catalytic Site Atlas (CSA) are also presented in order to demonstrate its ability to accurately classify any protein, putative or otherwise, with known structure. The source code and database is made available at www.sanchak.com/clasp/. Subsequently, we probed alkaline phosphatases (AP), one of the well known promiscuous enzymes, for additional activities. Such a search has led us to predict a hitherto unknown function of shrimp alkaline phosphatase (SAP), where the protein acts as a protease. Finally, we present experimental evidence of the prediction by CLASP by showing that SAP indeed has protease activity in vitro. PMID

  18. Active Sites Environmental Monitoring Program: Program plan. Revision 1

    SciTech Connect

    Ashwood, T.L.; Wickliff, D.S.; Morrissey, C.M.

    1992-02-01

    The Active Sites Environmental Monitoring Program (ASEMP), initiated in 1989, provides early detection and performance monitoring of transuranic (TRU) waste and active low-level waste (LLW) facilities at Oak Ridge National Laboratory (ORNL) in accordance with US Department of Energy (DOE) Order 5820.2A. Active LLW facilities in Solid Waste Storage Area (SWSA) 6 include Tumulus I and Tumulus II, the Interim Waste Management Facility (IWMF), LLW silos, high-range wells, asbestos silos, and fissile wells. The tumulus pads and IWMF are aboveground, high-strength concrete pads on which concrete vaults containing metal boxes of LLW are placed; the void space between the boxes and vaults is filled with grout. Eventually, these pads and vaults will be covered by an engineered multilayered cap. All other LLW facilities in SWSA 6 are below ground. In addition, this plan includes monitoring of the Hillcut Disposal Test Facility (HDTF) in SWSA 6, even though this facility was completed prior to the data of the DOE order. In SWSA 5 North, the TRU facilities include below-grade engineered caves, high-range wells, and unlined trenches. All samples from SWSA 6 are screened for alpha and beta activity, counted for gamma-emitting isotopes, and analyzed for tritium. In addition to these analytes, samples from SWSA 5 North are analyzed for specific transuranic elements.

  19. Environmental assessment of remedial action at the Lowman Uranium Mill Tailings Site near Lowman, Idaho. Final

    SciTech Connect

    Not Available

    1991-01-01

    This document assesses the environmental impacts of stabilization on site of the contaminated materials at the Lowman uranium mill tailings site. The Lowman site is 0.5 road mile northeast of the unincorporated village of Lowman, Idaho, and 73 road miles from Boise, Idaho. The Lowman site consists of piles of radioactive sands, an ore storage area, abandoned mill buildings, and windblown/waterborne contaminated areas. A total of 29.5 acres of land are contaminated and most of this land occurs within the 35-acre designated site boundary. The proposed action is to stabilize the tailings and other contaminated materials on the site. A radon barrier would be constructed over the consolidated residual radioactive materials and various erosion control measures would be implemented to ensure the long-term stability of the disposal cell. Radioactive constituents and other hazardous constituents were not detected in the groundwater beneath the Lowman site. The groundwater beneath the disposal cell would not become contaminated during or after remedial action so the maximum concentration limits or background concentrations for the contaminants listed in the draft EPA groundwater protection standards would be met at the point of compliance. No significant impacts were identified as a result of the proposed remedial action at the Lowman site.

  20. SUPERFUND TREATABILITY CLEARINGHOUSE: FINAL REPORT, PHASE I - IMMEDIATE ASSESSMENT, ACME SOLVENTS SITE

    EPA Science Inventory

    This is a site assessment and feasibility study of incineration alternatives at the ACME Solvents Site at Rockford, Illinois. The document contains laboratory results that are reported to simulate incineration conditions but no details on test methods were provided. The d...

  1. Final Outcome Evaluation Report. Demonstration and Implementation Sites. Experience-Based Career Education.

    ERIC Educational Resources Information Center

    Shively, Joe E.; Kessel, Phyllis

    Evaluation of the Appalachia Educational Laboratory's (AEL) Experience-Based Career Education (EBCE) program focused on outcome data pertaining to students, parents, and employers collected at the demonstration site at AEL, and implementation sites located in Bremen, Georgia; Crowley, Louisiana; Ames, Iowa; and Staten Island, Ithaca, and North…

  2. Active Site and Laminarin Binding in Glycoside Hydrolase Family 55*

    PubMed Central

    Bianchetti, Christopher M.; Takasuka, Taichi E.; Deutsch, Sam; Udell, Hannah S.; Yik, Eric J.; Bergeman, Lai F.; Fox, Brian G.

    2015-01-01

    The Carbohydrate Active Enzyme (CAZy) database indicates that glycoside hydrolase family 55 (GH55) contains both endo- and exo-β-1,3-glucanases. The founding structure in the GH55 is PcLam55A from the white rot fungus Phanerochaete chrysosporium (Ishida, T., Fushinobu, S., Kawai, R., Kitaoka, M., Igarashi, K., and Samejima, M. (2009) Crystal structure of glycoside hydrolase family 55 β-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium. J. Biol. Chem. 284, 10100–10109). Here, we present high resolution crystal structures of bacterial SacteLam55A from the highly cellulolytic Streptomyces sp. SirexAA-E with bound substrates and product. These structures, along with mutagenesis and kinetic studies, implicate Glu-502 as the catalytic acid (as proposed earlier for Glu-663 in PcLam55A) and a proton relay network of four residues in activating water as the nucleophile. Further, a set of conserved aromatic residues that define the active site apparently enforce an exo-glucanase reactivity as demonstrated by exhaustive hydrolysis reactions with purified laminarioligosaccharides. Two additional aromatic residues that line the substrate-binding channel show substrate-dependent conformational flexibility that may promote processive reactivity of the bound oligosaccharide in the bacterial enzymes. Gene synthesis carried out on ∼30% of the GH55 family gave 34 active enzymes (19% functional coverage of the nonredundant members of GH55). These active enzymes reacted with only laminarin from a panel of 10 different soluble and insoluble polysaccharides and displayed a broad range of specific activities and optima for pH and temperature. Application of this experimental method provides a new, systematic way to annotate glycoside hydrolase phylogenetic space for functional properties. PMID:25752603

  3. Active site loop conformation regulates promiscuous activity in a lactonase from Geobacillus kaustophilus HTA426.

    PubMed

    Zhang, Yu; An, Jiao; Yang, Guang-Yu; Bai, Aixi; Zheng, Baisong; Lou, Zhiyong; Wu, Geng; Ye, Wei; Chen, Hai-Feng; Feng, Yan; Manco, Giuseppe

    2015-01-01

    Enzyme promiscuity is a prerequisite for fast divergent evolution of biocatalysts. A phosphotriesterase-like lactonase (PLL) from Geobacillus kaustophilus HTA426 (GkaP) exhibits main lactonase and promiscuous phosphotriesterase activities. To understand its catalytic and evolutionary mechanisms, we investigated a "hot spot" in the active site by saturation mutagenesis as well as X-ray crystallographic analyses. We found that position 99 in the active site was involved in substrate discrimination. One mutant, Y99L, exhibited 11-fold improvement over wild-type in reactivity (kcat/Km) toward the phosphotriesterase substrate ethyl-paraoxon, but showed 15-fold decrease toward the lactonase substrate δ-decanolactone, resulting in a 157-fold inversion of the substrate specificity. Structural analysis of Y99L revealed that the mutation causes a ∼6.6 Å outward shift of adjacent loop 7, which may cause increased flexibility of the active site and facilitate accommodation and/or catalysis of organophosphate substrate. This study provides for the PLL family an example of how the evolutionary route from promiscuity to specificity can derive from very few mutations, which promotes alteration in the conformational adjustment of the active site loops, in turn draws the capacity of substrate binding and activity.

  4. Active Site Loop Conformation Regulates Promiscuous Activity in a Lactonase from Geobacillus kaustophilus HTA426

    PubMed Central

    Zhang, Yu; An, Jiao; Yang, Guang-Yu; Bai, Aixi; Zheng, Baisong; Lou, Zhiyong; Wu, Geng; Ye, Wei; Chen, Hai-Feng; Feng, Yan; Manco, Giuseppe

    2015-01-01

    Enzyme promiscuity is a prerequisite for fast divergent evolution of biocatalysts. A phosphotriesterase-like lactonase (PLL) from Geobacillus kaustophilus HTA426 (GkaP) exhibits main lactonase and promiscuous phosphotriesterase activities. To understand its catalytic and evolutionary mechanisms, we investigated a “hot spot” in the active site by saturation mutagenesis as well as X-ray crystallographic analyses. We found that position 99 in the active site was involved in substrate discrimination. One mutant, Y99L, exhibited 11-fold improvement over wild-type in reactivity (kcat/Km) toward the phosphotriesterase substrate ethyl-paraoxon, but showed 15-fold decrease toward the lactonase substrate δ-decanolactone, resulting in a 157-fold inversion of the substrate specificity. Structural analysis of Y99L revealed that the mutation causes a ∼6.6 Å outward shift of adjacent loop 7, which may cause increased flexibility of the active site and facilitate accommodation and/or catalysis of organophosphate substrate. This study provides for the PLL family an example of how the evolutionary route from promiscuity to specificity can derive from very few mutations, which promotes alteration in the conformational adjustment of the active site loops, in turn draws the capacity of substrate binding and activity. PMID:25706379

  5. Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site.

    PubMed

    Sunden, Fanny; Peck, Ariana; Salzman, Julia; Ressl, Susanne; Herschlag, Daniel

    2015-01-01

    Enzymes enable life by accelerating reaction rates to biological timescales. Conventional studies have focused on identifying the residues that have a direct involvement in an enzymatic reaction, but these so-called 'catalytic residues' are embedded in extensive interaction networks. Although fundamental to our understanding of enzyme function, evolution, and engineering, the properties of these networks have yet to be quantitatively and systematically explored. We dissected an interaction network of five residues in the active site of Escherichia coli alkaline phosphatase. Analysis of the complex catalytic interdependence of specific residues identified three energetically independent but structurally interconnected functional units with distinct modes of cooperativity. From an evolutionary perspective, this network is orders of magnitude more probable to arise than a fully cooperative network. From a functional perspective, new catalytic insights emerge. Further, such comprehensive energetic characterization will be necessary to benchmark the algorithms required to rationally engineer highly efficient enzymes. PMID:25902402

  6. Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site.

    PubMed

    Sunden, Fanny; Peck, Ariana; Salzman, Julia; Ressl, Susanne; Herschlag, Daniel

    2015-01-01

    Enzymes enable life by accelerating reaction rates to biological timescales. Conventional studies have focused on identifying the residues that have a direct involvement in an enzymatic reaction, but these so-called 'catalytic residues' are embedded in extensive interaction networks. Although fundamental to our understanding of enzyme function, evolution, and engineering, the properties of these networks have yet to be quantitatively and systematically explored. We dissected an interaction network of five residues in the active site of Escherichia coli alkaline phosphatase. Analysis of the complex catalytic interdependence of specific residues identified three energetically independent but structurally interconnected functional units with distinct modes of cooperativity. From an evolutionary perspective, this network is orders of magnitude more probable to arise than a fully cooperative network. From a functional perspective, new catalytic insights emerge. Further, such comprehensive energetic characterization will be necessary to benchmark the algorithms required to rationally engineer highly efficient enzymes.

  7. Remedial action plan and site design for stabilization of the inactive uranium mill tailings site at Tuba City, Arizona. Text, Appendices A, B, and C: Final report

    SciTech Connect

    Not Available

    1989-08-01

    This Remedial Action Plan (RAP) has been developed to serve a threefold purpose. It presents the series of activities which are proposed by the US Department of Energy (DOE) to accomplish long-term stabilization and control of radioactive materials at the inactive uranium processing site near Tuba City, Arizona. It provides a characterization of the present conditions of the site. It also serves to document the concurrence of the Navajo Nation, the Hopi Tribe, US Bureau of Indian Affairs (BIA), and the US Nuclear Regulatory Commission (NRC) in the remedial action. This agreement, upon execution by DOE, the Navajo Nation, and the Hopi Tribe, and concurrence by NRC, becomes Appendix B of the Cooperative Agreement. Following the introduction, contents are as follows: Section 2.0 presents the EPA standards, including a discussion of their objectives. Section 3.0 summarizes the present site characteristics and provides a definition of site-specific problems. Section 4.0 is the site design for the proposed action. Section 5.0 summarizes the plan for ensuring environmental, health, and safety protection for the surrounding community and the on-site workers. Section 6.0 presents a detailed listing of the responsibilities of the project participants. Section 7.0 describes the features of the long-term surveillance and maintenance plan. Section 8.0 presents the quality assurance aspects of the project. Section 9.0 documents the ongoing activities to keep the public informed and participating in the project.

  8. Final report of fugitive and diffuse emissions evaluations at the Hanford Site, CY 1994

    SciTech Connect

    Gleckler, B.P.; Schmidt, J.W.

    1995-02-17

    The objective of this study was to evaluate several of Hanford`s major diffuse emission sources and evaluate the effectiveness of monitoring these sources individually versus collectively. The results from this evaluation may also be utilized to demonstrate Westinghouse`s compliance status with the applicable air emissions regulations and determine if additional studies and/or evaluations are necessary. Air sampling results from four waste handling and storage facilities were collected for a one week period and analyzed. The following is a list of the selected sampling sites: Plutonium Finishing Plant; 241-BY Tank Farm; 1301-N Trench; 300 Area Trenches and North Ponds. These sites were chosen as being representative of most of the Hanford waste sites, which are known to be diffuse emission sites. The sites were evaluated on the following criteria: physical size, surface contamination levels, geology, vegetation density, surface cover, potential for occupational exposure, and potential for public exposure. The selected sites vary greatly with the selection criteria parameters, and as a result should provide representative data for most of Hanford`s waste sites.

  9. Modification No. 2 to the remedial action plan and site design for stabilization of the inactive uranium mill tailings site at Green River, Utah: Final

    SciTech Connect

    1996-11-01

    Portions of the final Remedial Action Plan (RAP) for the Green River site, Volumes 1 and 2, Appendix B of the Cooperative Agreement No. DE-FC04-81AL16257, March 1991 (DOE, 1991) have been modified. The changes to the RAP are designated as RAP Modification No. 2. These changes have been placed in a three-ring binder that will supplement the original RAP (DOE, 1991), and include the following: addendum to the Executive Summary; Section 3.5 (Ground Water part of the Site Characterization Summary); Section 4.0 (Site Design); Section5.0 (Water Resources Protection Strategy Summary); Appendix D.5 (Ground Water Hydrology); and Appendix E (Ground Water Protection Strategy). In addition to these revisions, there have been editorial changes that clarify the text, but do not change the meaning. Also, certain sections of the document, which are included in the submittal for ease of review and continuity, have been updated to reflect the final ground water protection standards and the current UMTRA Project format and content of RAPs.

  10. Final report on electric vehicle activities, September 1991--October 1994

    SciTech Connect

    Del Monaco, J.L.; Pandya, D.A.

    1995-02-01

    The data and information collected for the Public Service Electric and Gas Company`s (PSE&G) electric vehicle demonstration program were intended to support and enhance DOE`s Electric and Hybrid Vehicle Site Operator Program. The DOE Site Operator Program is focused on the life cycle and reliability of Electric Vehicles (EVs). Of particular interest are vehicles currently available with features that are likely to be put into production or demonstrate new technology. PSE&G acquired eight GMC Electric G-Vans in 1991, and three TEVans in 1993, and conducted a program plan to test and assess the overall performance of these electric vehicles. To accomplish the objectives of DOE`s Site Operator`s test program, a manual data collection system was implemented. The manual data collection system has provided energy use and mileage data. From September 1991 to October 1994 PSE&G logged 69,368 miles on eleven test vehicles. PSE&G also demonstrated the EVs to diverse groups and associations at fifty seven various events. Included in the report are lessons learned concerning maintenance, operation, public reactions, and driver`s acceptance of the electric vehicles.

  11. An economic analysis of a monitored retrievable storage site for Tennessee. Final report and appendices

    SciTech Connect

    Fox, W.F.; Mayo, J.W.; Hansen, L.T.; Quindry, K.E.

    1985-12-17

    The United States Department of Energy is charged with the task of identifying potential sites for a Monitored Retrievable Storage (MRS) Facility and reporting the results of its analysis to Congress by January 1986. DOE chose three finalist sites from 11 sites DOE analysts evaluated earlier. All three are in Tennessee, including two in Oak Ridge and one in Trousdale/Smith Counties. This paper is a summary of research undertaken on the economic effects of establishing the MRS facility in Tennessee. All three locations were considered in the analysis, but on some occasions attention is focused on the site preferred by DOE. The research was undertaken by the Center for Business and Economic Research (CBER), College of Business Administration, the University of Tennessee, Knoxville, under contract with the Tennessee Department of Economic and Community Development.

  12. PISCES field chemical emissions monitoring project: Site 102 emissions report. Final report

    SciTech Connect

    1995-12-01

    This report is one of a series sponsored by the Electric Power Research Institute in the area of trace substance emissions from fossil-fuel power plants. This report presents the results of a sampling and analytical study to characterize trace substances emissions at Site 102. Site 102 is a cyclone boiler burning a sub-bituminous coal. Site 102 employs an electrostatic precipitator for particulate control. The objective of this report is to transmit the detailed data to the US Environmental Protection Agency (EPA) to assist the Agency in evaluating utility trace chemical emissions as well as the associated health risk impacts--as mandated in Title III of the 1990 Clean Air Act Amendments. This report does not attempt to compare the results with other sites. An assessment of data from all plants that have been tested is presented in the Electric Utility Trace Substances Synthesis Report (EPRI TR-104614).

  13. Final record of decision/remedial action plan, nine sites, Sierra Army Depot, Lassen County, California

    SciTech Connect

    Arroyo, S.L.; Larson, A.M.; Parent, M.M.; Silvers, J.M.; Weaverling, P.H.

    1996-10-01

    This ROD/RAP presents the selected response actions for nine sites at SIAD. The response actions were selected by the US Department of the Army (Army) in accordance with the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA), as amended by the Superfund Amendments Reauthorization Act of 1986 (SARA)(collectively referred to as CERCLA), the National Oil and Hazardous Substances Pollution Contingency Plan (NCP), and Section 6.8 of the California Health and Safety Code. This ROD/RAP includes the factual and legal basis for selecting the response action at each of the nine sites listed above. The data used to support the selected response action are contained in the Administrative Record for each site. The State of California as represented by the Department of Toxic Substances Control (DTSC), and the Lahontan Regional Water Quality Control Board (RWQCB) concur with the selected response action at each site.

  14. Final Phase I-Phase II interim report : expedited site characterization, Morrill, Kansas.

    SciTech Connect

    LaFreniere, L. M.

    2005-10-20

    The city of Morrill, Kansas, is located in Brown County, in the northeastern corner of the state. The town lies about 7 mi east of Sabetha and about 10 mi northwest of Hiawatha (Figure 1.1). The population of Morrill as of the 2000 census was approximately 277. The Commodity Credit Corporation (CCC), an agency of the U.S. Department of Agriculture (USDA), operated a grain storage facility in the northwestern section of Morrill from 1950 until 1971. The property continued to be used for grain storage after 1971. Fourteen of the original 21 CCC/USDA circular bin structures remain today. Prior to 1986, commercial grain fumigants containing carbon tetrachloride were commonly used by the CCC/USDA and the grain storage industry to preserve grain. Contamination with carbon tetrachloride, also known as tetrachloromethane, was initially identified in groundwater at Morrill in October 1985 in public water supply well PWS5, during statewide testing of public water supply wells for volatile organic compounds (VOCs). A preliminary assessment was completed by the Kansas Department of Health and Environment (KDHE) in 1989 to obtain background information on the Morrill public water supply and to identify potential sources of the detected carbon tetrachloride contamination (KDHE 1989). Since 1991 the city of Morrill has obtained its water by pipeline from the municipal water supply of Sabetha. Water supplied through the Sabetha system comes from a surface reservoir. Former public wells in Morrill are no longer used for municipal supply. Wells PWS3, PWS4, and PWS5 were plugged in 1993. Wells PWS1 and PWS2 are no longer in active production, but they continue to be available for non-drinking purposes such as bulk hauling for agricultural uses, fire fighting, and road work (Hansen 2001). Because the KDHE found carbon tetrachloride in the groundwater at the former CCC/USDA facility at Morrill that could, in part, be linked to historical use of carbon tetrachloride-based grain

  15. Metals in the active site of native protein phosphatase-1.

    PubMed

    Heroes, Ewald; Rip, Jens; Beullens, Monique; Van Meervelt, Luc; De Gendt, Stefan; Bollen, Mathieu

    2015-08-01

    Protein phosphatase-1 (PP1) is a major protein Ser/Thr phosphatase in eukaryotic cells. Its activity depends on two metal ions in the catalytic site, which were identified as manganese in the bacterially expressed phosphatase. However, the identity of the metal ions in native PP1 is unknown. In this study, total reflection X-ray fluorescence (TXRF) was used to detect iron and zinc in PP1 that was purified from rabbit skeletal muscle. Metal exchange experiments confirmed that the distinct substrate specificity of recombinant and native PP1 is determined by the nature of their associated metals. We also found that the iron level associated with native PP1 is decreased by incubation with inhibitor-2, consistent with a function of inhibitor-2 as a PP1 chaperone. PMID:25890482

  16. Environmental assessment of remedial action at the Gunnison Uranium Mill Tailings Site near Gunnison, Colorado. Final

    SciTech Connect

    Not Available

    1992-02-01

    The presence of contaminated uranium mill tailings adjacent to the city of Gunnison has been a local concern for many years. The following issues were identified during public meetings that were held by the DOE prior to distribution of an earlier version of this EA. Many of these issues will require mitigation. Groundwater contamination; in December 1989, a herd of 105 antelope were introduced in an area that includes the Landfill disposal site. There is concern that remedial action-related traffic in the area would result in antelope mortality. The proposed Tenderfoot Mountain haul road may restrict antelope access to their water supply; a second wildlife issue concerns the potential reduction in sage grouse use of breeding grounds (leks) and nesting habitat; the proposed Tenderfoot Mountain haul road would cross areas designated as wetlands by US Army Corps of Engineers (COE); the proposed disposal site is currently used for grazing by cattle six weeks a year in the spring. Additional concerns were stated in comments on a previous version of this EA. The proposed action is to consolidate and remove all contaminated materials associated with the Gunnison processing site to the Landfill disposal site six air miles east of Gunnison. All structures on the site (e.g., water tower, office buildings) were demolished in 1991. The debris is being stored on the site until it can be incorporated into the disposal cell at the disposal site. All contaminated materials would be trucked to the Landfill disposal site on a to-be-constructed haul road that crosses BLM-administered land.

  17. Hydrogeologic site evaluation of the Department of Energy, Portsmouth Uranium Enrichment Facility. Final report. Volume I

    SciTech Connect

    Johe, D.; Taft, L.; DeNiro, D.; McCandlish, C.; St. John, K.; Craig, C.

    1986-04-01

    The purpose was to assess all available information relating to the geology and groundwater conditions beneath the DOE Reservation to determine the impact of the facility on groundwater resources at the site. Geologic cross sections were constructed, direction of groundwater flow identified, and geologic conditions described. Current groundwater monitoring programs were assessed. Areas that appear to have potential for use as waste disposal sites were identified. (ACR)

  18. Metavanadate at the active site of the phosphatase VHZ.

    PubMed

    Kuznetsov, Vyacheslav I; Alexandrova, Anastassia N; Hengge, Alvan C

    2012-09-01

    Vanadate is a potent modulator of a number of biological processes and has been shown by crystal structures and NMR spectroscopy to interact with numerous enzymes. Although these effects often occur under conditions where oligomeric forms dominate, the crystal structures and NMR data suggest that the inhibitory form is usually monomeric orthovanadate, a particularly good inhibitor of phosphatases because of its ability to form stable trigonal-bipyramidal complexes. We performed a computational analysis of a 1.14 Å structure of the phosphatase VHZ in complex with an unusual metavanadate species and compared it with two classical trigonal-bipyramidal vanadate-phosphatase complexes. The results support extensive delocalized bonding to the apical ligands in the classical structures. In contrast, in the VHZ metavanadate complex, the central, planar VO(3)(-) moiety has only one apical ligand, the nucleophilic Cys95, and a gap in electron density between V and S. A computational analysis showed that the V-S interaction is primarily ionic. A mechanism is proposed to explain the formation of metavanadate in the active site from a dimeric vanadate species that previous crystallographic evidence has shown to be able to bind to the active sites of phosphatases related to VHZ. Together, the results show that the interaction of vanadate with biological systems is not solely reliant upon the prior formation of a particular inhibitory form in solution. The catalytic properties of an enzyme may act upon the oligomeric forms primarily present in solution to generate species such as the metavanadate ion observed in the VHZ structure. PMID:22876963

  19. Guidelines for siting WECS relative to small-scale terrain features. Final report

    SciTech Connect

    Frost, W.; Shieh, C.F.

    1981-12-01

    Because real terrain is too complex and random to allow development of quantitative site selection data for specific applications, guidelines for siting wind energy conversion systems (WECS) relative to small-scale terrain features have been extracted from literature relative to analytical and experimental studies of fluid flow over geometries which represent idealized terrain features. These guidelines are presented in a format suitable for assessing the influence of small or microscale terrain features on a proposed wind turbine site. In organizing the available information, three categories of terrain were considered: (1) protrusions, topographical features that protrude well above the general level of their neighboring terrain; (2) depressions, areas such as valleys, canyons, or passes; and (3) complex terrain, so rugged or irregular that no well-defined protrusion or depression can be easily distinguished. The optimum site on a protrusion is always at the highest point. The smoother the peak of the protrusion and the more gentle the slopes on all sides the more optimum the site, providing the geometry and orientation of the depression are such that full advantage can be taken of existing strong valley winds or outflow. Where the terrain is very complex and tortuous, the highest point of the topography will be the optimum site.

  20. Zymogen Activation and Subcellular Activity of Subtilisin Kexin Isozyme 1/Site 1 Protease*

    PubMed Central

    da Palma, Joel Ramos; Burri, Dominique Julien; Oppliger, Joël; Salamina, Marco; Cendron, Laura; de Laureto, Patrizia Polverino; Seidah, Nabil Georges; Kunz, Stefan; Pasquato, Antonella

    2014-01-01

    The proprotein convertase subtilisin kexin isozyme 1 (SKI-1)/site 1 protease (S1P) plays crucial roles in cellular homeostatic functions and is hijacked by pathogenic viruses for the processing of their envelope glycoproteins. Zymogen activation of SKI-1/S1P involves sequential autocatalytic processing of its N-terminal prodomain at sites B′/B followed by the herein newly identified C′/C sites. We found that SKI-1/S1P autoprocessing results in intermediates whose catalytic domain remains associated with prodomain fragments of different lengths. In contrast to other zymogen proprotein convertases, all incompletely matured intermediates of SKI-1/S1P showed full catalytic activity toward cellular substrates, whereas optimal cleavage of viral glycoproteins depended on B′/B processing. Incompletely matured forms of SKI-1/S1P further process cellular and viral substrates in distinct subcellular compartments. Using a cell-based sensor for SKI-1/S1P activity, we found that 9 amino acid residues at the cleavage site (P1–P8) and P1′ are necessary and sufficient to define the subcellular location of processing and to determine to what extent processing of a substrate depends on SKI-1/S1P maturation. In sum, our study reveals novel and unexpected features of SKI-1/S1P zymogen activation and subcellular specificity of activity toward cellular and pathogen-derived substrates. PMID:25378398

  1. Analysis of Hydrogen Tunneling in an Enzyme Active Site using von Neumann Measurements

    PubMed Central

    Sumner, Isaiah; Iyengar, Srinivasan S.

    2010-01-01

    We build on our earlier quantum wavepacket study of hydrogen transfer in the biological enzyme, soybean lipoxygenase-1, by using von Neumann quantum measurement theory to gain qualitative insights into the transfer event. We treat the enzyme active site as a measurement device which acts on the tunneling hydrogen nucleus via the potential it exerts at each configuration. A series of changing active site geometries during the tunneling process effects a sequential projection of the initial, reactant state onto the final, product state. We study this process using several different kinds of von Neumann measurements and show how a discrete sequence of such measurements not only progressively increases the projection of the hydrogen nuclear wavepacket onto the product side but also favors proton over deuteron transfer. Several qualitative features of the hydrogen tunneling problem found in wavepacket dynamics studies are also recovered here. These include the shift in the “transition state” towards the reactant as a result of nuclear quantization, greater participation of excited states in the case of deuterium, and presence of critical points along the reaction coordinate that facilitate hydrogen and deuterium transfer and coincide with surface crossings. To further “tailor” the dynamics, we construct a perturbation to the sequence of measurements, that is a perturbation to the dynamical sequence of active site geometry evolution, which leads us to insight on the existence of sensitive regions of the reaction profile where subtle changes to the dynamics of the active site can have an effect on the hydrogen and deuterium transfer process. PMID:22933858

  2. Crystal Structure of Albaflavenone Monooxygenase Containing a Moonlighting Terpene Synthase Active Site

    SciTech Connect

    Zhao, Bin; Lei, Li; Vassylyev, Dmitry G.; Lin, Xin; Cane, David E.; Kelly, Steven L.; Yuan, Hang; Lamb, David C.; Waterman, Michael R.

    2010-01-08

    Albaflavenone synthase (CYP170A1) is a monooxygenase catalyzing the final two steps in the biosynthesis of this antibiotic in the soil bacterium, Streptomyces coelicolor A3(2). Interestingly, CYP170A1 shows no stereo selection forming equal amounts of two albaflavenol epimers, each of which is oxidized in turn to albaflavenone. To explore the structural basis of the reaction mechanism, we have studied the crystal structures of both ligand-free CYP170A1 (2.6 {angstrom}) and complex of endogenous substrate (epi-isozizaene) with CYP170A1 (3.3 {angstrom}). The structure of the complex suggests that the proximal epi-isozizaene molecules may bind to the heme iron in two orientations. In addition, much to our surprise, we have found that albaflavenone synthase also has a second, completely distinct catalytic activity corresponding to the synthesis of farnesene isomers from farnesyl diphosphate. Within the cytochrome P450 {alpha}-helical domain both the primary sequence and x-ray structure indicate the presence of a novel terpene synthase active site that is moonlighting on the P450 structure. This includes signature sequences for divalent cation binding and an {alpha}-helical barrel. This barrel is unusual because it consists of only four helices rather than six found in all other terpene synthases. Mutagenesis establishes that this barrel is essential for the terpene synthase activity of CYP170A1 but not for the monooxygenase activity. This is the first bifunctional P450 discovered to have another active site moonlighting on it and the first time a terpene synthase active site is found moonlighting on another protein.

  3. Superfund Record of Decision (EPA Region 1): Stamina Mills site, North Smithfield, RI. (First remedial action), September 1990. Final report

    SciTech Connect

    Not Available

    1990-09-28

    The five-acre Stamina Mills site is a former textile weaving and finishing facility in North Smithfield, Providence County, Rhode Island. A portion of the site is within the 100-year floodplain and wetland area of the Branch River. The manufacturing process used cleaning solvents, acids, bases and dyes for coloring, pesticides for moth proofing, and plasticizers to coat fabrics. Mill process wastes were placed in a landfill onsite. EPA initiated three removal actions from 1984 to 1990, including an extension of the municipal water supply to residents obtaining water from the affected aquifer; and treatment of two underground and one above-ground storage tanks, followed by offsite disposal. The Record of Decision (ROD) provides a final remedy and addresses both source control and management of contaminated ground water migration at the site. The primary contaminants of concern affecting the soil, debris, sediment, and ground water are VOCs including TCE and PCE; other organics including pesticides; and metals including chromium.

  4. Superfund Record of Decision (EPA Region 4): Monsanto Superfund Site, Augusta, GA. (First remedial action), December 1990. Final report

    SciTech Connect

    Not Available

    1990-12-07

    The 75-acre Monsanto site is a former industrial plant located three miles southeast of Augusta, Georgia. Land use in the area is predominantly industrial, with a wetland area located approximately 4,570 feet from the site. From 1966 to 1974, approximately 1500 pounds of arsenic were placed in two onsite landfills. The final Record of Decision (ROD) addresses ground water contamination. The primary contaminant of concern affecting the ground water is arsenic, a metal. The selected remedial action for the site includes monitoring ground water to evaluate compliance with Ground Water Protection Achievement Levels (GPALs); pumping and discharging ground water to an offsite publicly owned treatment works. The estimated present worth cost for the remedial action is $600,000.

  5. Proposed plan/Statement of basis for the Grace Road Site (631-22G) operable unit: Final action

    SciTech Connect

    Palmer, E.

    1997-08-19

    This Statement of Basis/Proposed Plan is being issued by the U. S. Department of Energy (DOE), which functions as the lead agency for the Savannah River Site (SRS) remedial activities, with concurrence by the U. S. Environmental Protection Agency (EPA), and the South Carolina Department of Health and Environmental Control (SCDHEC). The purpose of this Statement of Basis/Proposed Plan is to describe the preferred alternative for addressing the Grace Road site (GRS) located at the Savannah River Site (SRS), in Aiken, South Carolina and to provide an opportunity for public input into the remedial action selection process.

  6. 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

  7. Environmental aspects of the Brandon woods coal ash site. Final report

    SciTech Connect

    Keating, R.W.; Price, R.

    1994-05-01

    The Maryland Power Plant Research Program (PPRP) has evaluated the potential environmental effects of coal ash used as structural fill material at the Baltimore Gas and Electric Company (BG E) Brandon Woods Energy Business Park. The main purpose of the evaluation was to assess the potential for leachate constituents derived from the coal ash to affect ground and surface water quality. Ground water conditions at the site were evaluated using the water level readings collected from 21 shallow and deep monitoring wells installed by BG E prior to site development, and ground water quality data collected from the time the facility began coal ash filling operations in 1982 to December 1990. The absence of ground water quality degradation downgradient of the ash indicates that several site conditions minimize potential adverse enviromental impacts from leachate generation.

  8. Revegetation and rock cover for stabilization of inactive uranium mill tailings disposal sites. Final report

    SciTech Connect

    Beedlow, P.A.

    1984-05-01

    Guidelines for using vegetation and rock to protect inactive uranium mill tailings from erosion were developed by Pacific Northwest Laboratory as part of the Department of Energy's Uranium Mill Tailings Remedial Action Project (UMTRAP) Technology Development program. Information on soils, climate, and vegetation were collected for 20 inactive tailings sites in the western United States. Sites were grouped according to similarities in climate and vegetation. Soil loss for those sites was characterized using the Universal Soil Loss Equation. Test plots were used to evaluate (1) the interaction between vegetation and sealant barrier systems and (2) the effects of surface rock on soil water and vegetation. Lysimeter and simulation studies were used to direct and support field experiments. 49 references, 17 figures, 16 tables.

  9. Field Performance Of A Compacted Clay Landfill Final Cover At A Humid Site

    EPA Science Inventory

    A study was conducted in southern Georgia, USA, to evalaute how the hydraulic properties of the compacted clay barrier layer in a final landfill cover changed over a 4-year service life. The cover was part of a test section constructed in a large drainage lysimeter that allowed ...

  10. 78 FR 75913 - Final Tank Closure and Waste Management Environmental Impact Statement for the Hanford Site...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-13

    ... for closure (66 FR 7877, January 26, 2001). The Final EIS implements the January 6, 2006, Settlement... that the TC&WM EIS and its RODs supersede the HSW EIS and its ROD (69 FR 39449, June 30, 2004). In addition, this TC&WM EIS ROD amends the 1997 Tank Waste Remediation System ROD (TWRS ROD, 62 FR...

  11. Final guidance on numeric removal action levels for contaminated drinking water sites. Directive

    SciTech Connect

    1993-10-01

    The purpose of this memorandum is to transmit the final OERR methodology and guidance on the calculation of numeric removal action levels (RALs), to assist Superfund personnel in deciding whether to provide alternate sources of drinking water to populations adversely affected by releases of hazardous substances into the environment.

  12. Mutational Analysis of Substrate Interactions with the Active Site of Dialkylglycine Decarboxylase

    PubMed Central

    Fogle, Emily J.; Toney, Michael D.

    2010-01-01

    Pyridoxal phosphate (PLP) dependent enzymes catalyze many different types of reactions at the α-, β-, and γ-carbons of amine and amino acid substrates. Dialkylglycine decarboxylase (DGD) is an unusual PLP dependent enzyme that catalyzes two reaction types, decarboxylation and transamination, in the same active site. A structurally-based, functional model has been proposed for the DGD active site, which maintains that R406 is important in determining substrate specificity through interactions with the substrate carboxylate while W138 provides specificity for short-chain alkyl groups. The mechanistic roles of R406 and W138 were investigated using site directed mutagenesis, alternate substrates, and analysis of steady-state and half-reaction kinetics. Experiments on the R406M and R406K mutants confirm the importance of R406 in substrate binding. Surprisingly, this work also shows that the positive charge of R406 facilitates catalysis of decarboxylation. The W138F mutant demonstrates that W138 indeed acts to limit the size of the subsite C binding pocket, determining specificity for 2,2-dialkylglycines with small side chains as predicted by the model. Finally, work with the double mutant W138F/M141R shows that these mutations expand substrate specificity to include L-glutamate and lead to an increase in specificity for L-glutamate over 2-aminoisobutyrate of approximately eight orders of magnitude compared to WT DGD. PMID:20540501

  13. Complement receptor 2-mediated targeting of complement inhibitors to sites of complement activation.

    PubMed

    Song, Hongbin; He, Chun; Knaak, Christian; Guthridge, Joel M; Holers, V Michael; Tomlinson, Stephen

    2003-06-01

    In a strategy to specifically target complement inhibitors to sites of complement activation and disease, recombinant fusion proteins consisting of a complement inhibitor linked to a C3 binding region of complement receptor (CR) 2 were prepared and characterized. Natural ligands for CR2 are C3 breakdown products deposited at sites of complement activation. Fusion proteins were prepared consisting of a human CR2 fragment linked to either the N terminus or C terminus of soluble forms of the membrane complement inhibitors decay accelerating factor (DAF) or CD59. The targeted complement inhibitors bound to C3-opsonized cells, and all were significantly more effective (up to 20-fold) than corresponding untargeted inhibitors at protecting target cells from complement. CR2 fusion proteins also inhibited CR3-dependent adhesion of U937 cells to C3 opsonized erythrocytes, indicating a second potential anti-inflammatory mechanism of CR2 fusion proteins, since CR3 is involved in endothelial adhesion and diapedesis of leukocytes at inflammatory sites. Finally, the in vivo validity of the targeting strategy was confirmed by the demonstration that CR2-DAF, but not soluble DAF, targets to the kidney in mouse models of lupus nephritis that are associated with renal complement deposition.

  14. Complement receptor 2-mediated targeting of complement inhibitors to sites of complement activation.

    PubMed

    Song, Hongbin; He, Chun; Knaak, Christian; Guthridge, Joel M; Holers, V Michael; Tomlinson, Stephen

    2003-06-01

    In a strategy to specifically target complement inhibitors to sites of complement activation and disease, recombinant fusion proteins consisting of a complement inhibitor linked to a C3 binding region of complement receptor (CR) 2 were prepared and characterized. Natural ligands for CR2 are C3 breakdown products deposited at sites of complement activation. Fusion proteins were prepared consisting of a human CR2 fragment linked to either the N terminus or C terminus of soluble forms of the membrane complement inhibitors decay accelerating factor (DAF) or CD59. The targeted complement inhibitors bound to C3-opsonized cells, and all were significantly more effective (up to 20-fold) than corresponding untargeted inhibitors at protecting target cells from complement. CR2 fusion proteins also inhibited CR3-dependent adhesion of U937 cells to C3 opsonized erythrocytes, indicating a second potential anti-inflammatory mechanism of CR2 fusion proteins, since CR3 is involved in endothelial adhesion and diapedesis of leukocytes at inflammatory sites. Finally, the in vivo validity of the targeting strategy was confirmed by the demonstration that CR2-DAF, but not soluble DAF, targets to the kidney in mouse models of lupus nephritis that are associated with renal complement deposition. PMID:12813023

  15. Independent Verification Final Summary Report for the David Witherspoon, Inc. 1630 Site Knoxville, Tennessee

    SciTech Connect

    P.C. Weaver

    2009-04-29

    The primary objective of the independent verification was to determine if BJC performed the appropriate actions to meet the specified “hot spot” cleanup criteria of 500 picocuries per gram (pCi/g) uranium-238 (U-238) in surface soil. Specific tasks performed by the independent verification team (IVT) to satisfy this objective included: 1) performing radiological walkover surveys, and 2) collecting soil samples for independent analyses. The independent verification (IV) efforts were designed to evaluate radioactive contaminants (specifically U-238) in the exposed surfaces below one foot of the original site grade, given that the top one foot layer of soil on the site was removed in its entirety.

  16. Hybrid [FeFe]-hydrogenases with modified active sites show remarkable residual enzymatic activity.

    PubMed

    Siebel, Judith F; Adamska-Venkatesh, Agnieszka; Weber, Katharina; Rumpel, Sigrun; Reijerse, Edward; Lubitz, Wolfgang

    2015-02-24

    [FeFe]-hydrogenases are to date the only enzymes for which it has been demonstrated that the native inorganic binuclear cofactor of the active site Fe2(adt)(CO)3(CN)2 (adt = azadithiolate = [S-CH2-NH-CH2-S](2-)) can be synthesized on the laboratory bench and subsequently inserted into the unmaturated enzyme to yield fully functional holo-enzyme (Berggren, G. et al. (2013) Nature 499, 66-70; Esselborn, J. et al. (2013) Nat. Chem. Biol. 9, 607-610). In the current study, we exploit this procedure to introduce non-native cofactors into the enzyme. Mimics of the binuclear subcluster with a modified bridging dithiolate ligand (thiodithiolate, N-methylazadithiolate, dimethyl-azadithiolate) and three variants containing only one CN(-) ligand were inserted into the active site of the enzyme. We investigated the activity of these variants for hydrogen oxidation as well as proton reduction and their structural accommodation within the active site was analyzed using Fourier transform infrared spectroscopy. Interestingly, the monocyanide variant with the azadithiolate bridge showed ∼50% of the native enzyme activity. This would suggest that the CN(-) ligands are not essential for catalytic activity, but rather serve to anchor the binuclear subsite inside the protein pocket through hydrogen bonding. The inserted artificial cofactors with a propanedithiolate and an N-methylazadithiolate bridge as well as their monocyanide variants also showed residual activity. However, these activities were less than 1% of the native enzyme. Our findings indicate that even small changes in the dithiolate bridge of the binuclear subsite lead to a rather strong decrease of the catalytic activity. We conclude that both the Brønsted base function and the conformational flexibility of the native azadithiolate amine moiety are essential for the high catalytic activity of the native enzyme. PMID:25633077

  17. Final environmental impact assessment of the Paducah Gaseous Diffusion Plant site, Paducah, Kentucky

    SciTech Connect

    Not Available

    1982-08-01

    This document considers: the need for uranium enrichment facilities; site location; plant description; and describes the power generating facilities in light of its existing environment. The impacts from continuing operations are compared with alternatives of shutdown, relocation, and alternative power systems. (PSB)

  18. Final Report, FY 2001 200 East Vadose Test Site Hanford Washington Electrical Resistance Tomography

    SciTech Connect

    Ramirez, A.; Daily, W.; Binley, A.

    2001-06-30

    This report covers the electrical resistance tomography (ERT) work performed at the Hanford Reservation, 200 East Area Vadose test (Sisson and Lu) site during the period March 23 through May 5,2001. The purposes of the ERT work were to: (1) Compare and contrast the development of the highly concentrated sodium thiosulfate plume (FY 01 work) with the fresh river water plume observed during FY 00. (2) Use the resistance images to infer the dynamics of the plume during two or three of the sodium thio-sulfate releases and during the water ''chaser'' release. (3) Determine the influence of the site's steel casings on the ability to construct reliable ERT images. (4) Determine if the steel casings at the site can be used as long electrodes to provide useful images of at least one release. (5) Develop quantitative estimates of the noise in the data and its effect on reconstructed images. Eleven electrode arrays (nine electrodes arrays available for the FY00 work), each with 15 electrodes, were installed at the site. These were used to perform 3D surveys before, during, and after 3 different spills.

  19. Chemical, physical, and biological properties of compounds present at hazardous-waste sites. Final report

    SciTech Connect

    Not Available

    1985-09-27

    The chemical profiles are intended to serve as a concise reference with information on the physicochemical properties, transport and fate, toxicity, and regulatory standards for individual chemicals identified by the EPA Office of Waste Program Enforcement at hazardous-waste sites. The profiles can be used in conjunction with the Toxicology and Endangerment Assessment Handbooks.

  20. Technical procedures for land use, Deaf Smith County site, Texas: Environmental Field Program: Final draft

    SciTech Connect

    Not Available

    1987-09-01

    This volume contains Technical Procedures pursuant to the Land Use Site Study Plan including land use data acquisition, land use/land cover map compilation, verification of land use/land cover map accuracy, and land use/land cover data analysis. 22 refs., 5 figs.

  1. 75 FR 61174 - Warner Valley Comprehensive Site Plan, Final Environmental Impact Statement, Lassen Volcanic...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-04

    ... the Warner Valley Comprehensive Site Plan. This conservation planning effort has four main objectives... central part of the Lassen Volcanic National Park, and encompasses the 400-acre project planning area... ranching in the late 1800s by E.R. Drake, who initiated efforts to ditch and dry out the wet meadow...

  2. Active system area networks for data intensive computations. Final report

    SciTech Connect

    2002-04-01

    The goal of the Active System Area Networks (ASAN) project is to develop hardware and software technologies for the implementation of active system area networks (ASANs). The use of the term ''active'' refers to the ability of the network interfaces to perform application-specific as well as system level computations in addition to their traditional role of data transfer. This project adopts the view that the network infrastructure should be an active computational entity capable of supporting certain classes of computations that would otherwise be performed on the host CPUs. The result is a unique network-wide programming model where computations are dynamically placed within the host CPUs or the NIs depending upon the quality of service demands and network/CPU resource availability. The projects seeks to demonstrate that such an approach is a better match for data intensive network-based applications and that the advent of low-cost powerful embedded processors and configurable hardware makes such an approach economically viable and desirable.

  3. Remedial Action Plan and site design for stabilization of the inactive uranium mill tailings site at Mexican Hat, Utah: Appendix E. Final report

    SciTech Connect

    1988-07-01

    This document provides Appendix E of the Remedial Action Plan (RAP) presented in 1988 for the stabilization of the inactive uranium mill tailings at the Mexican Hat, Utah site. The RAP was developed to serve a two- fold purpose. It presents the activities proposed by the Department of Energy (DOE) to accomplish long-term stabilization and control of the residual radioactive materials (RRM) from Monument Valley, Arizona, and Mexican Hat, Utah, at the Mexican Hat disposal site. It also serves to document the concurrence of both the Navajo Nation and the Nuclear Regulatory Commission (NRC) in the remedial action. This agreement, upon execution by the DOE and the Navajo Nation and concurrence by the NRC, becomes Appendix B of the Cooperative Agreement. The RAP has been structured to provide a comprehensive understanding of the remedial action proposed for the Monument Valley and Mexican Hat sites. It includes specific design and construction requirements for the remedial action.

  4. Multi-agency radiation survey and site investigation manual (MARSIM). Final report

    SciTech Connect

    1997-12-01

    The MARSSIM provides information on planning, conducting, evaluating, and documenting building surface and surface soil final status radiological surveys for demonstrating compliance with dose or risk-based regulations or standards. The MARSSIM is a multi-agency consensus document that was developed collaboratively by four Federal agencies having authority and control over radioactive materials: Department of Defense (DOD), Department of Energy (DOE), Environmental Protection Agency (EPA), and Nuclear Regulatory Commission (NRC). The MARSSIM`s objective is to describe a consistent approach for planning, performing, and assessing building surface and surface soil final status surveys to meet established dose or risk-based release criteria, while at the same time encouraging an effective use of resources.

  5. Persistence of biologically active compounds in soil: Final report

    SciTech Connect

    Williams, S.E.

    1987-02-01

    This document describes the long-term effects of soil-applied oil shale process water on the VA fungi and Rhizobium bacteria in a native soil. Techniques include assessing the VA fungal activity at field treatment plots and using treated field soils in a bioassay to determine VA infection and Rhizobium-nodulation potentials four years after process water application. 52 refs., 32 figs., 2 tabs.

  6. Solar-collector-materials exposure to the IPH site environment. Volume 1. Final report

    SciTech Connect

    Morris, V.L.

    1982-01-01

    In-situ environmental exposure tests were conducted at nine proposed intermediate-temperature Industrial Process Heat (IPH) sites. Three types of reflector materials were evaluated for survivability at the nine sites: second-surface silvered glass, aluminized acrylic FEK-244 film on aluminumsubstrate and Alzak (electropolished aluminum) on aluminium substrate. Black chrome absorber material and low-iron float glass were evaluated for thermal, photochemical, and environmental degradation. The reflector specimens were monitored for decreases in specular and hemispherical reflectance due to soil buildup. The absorber material was evaluated for changes in solar absorptivity and emissivity, and the float glass was monitored for changes in transmissivity. Surface and subsurface defects on all materials were examined microscopically and, where deemed of note, were documented photographically.

  7. Solar-collector materials exposure to the IPH site environment. Final report

    SciTech Connect

    Morris, V.L.

    1982-01-01

    In-situ environmental exposure tests were conducted at nine proposed intermediate-temperature Industrial Process Heat (IPH) sites. Three types of reflector materials were evaluated for survivability at the nine sites: second-surface silvered glass, aluminized acrylic FEK-244 film on aluminum substrate, and Alzak (electropolished aluminum) on aluminum substrate. Black chrome absorber material and low-iron float glass were evaluated for thermal, photochemical, and environmental degradation. The reflector specimens were monitored for decreases in specular and hemispherical reflectance due to soil buildup. The absorber material was evaluated for changes in solar absorptivity and emissivity, and the float glass was monitored for changes in transmissivity. Surface and subsurface defects on all materials were examined microscopically and, where deemed of note, were documented photographically.

  8. Siting a municipal solid waste disposal facility, part II: the effects of external criteria on the final decision.

    PubMed

    Korucu, M Kemal; Karademir, Aykan

    2014-02-01

    The procedure of a multi-criteria decision analysis supported by the geographic information systems was applied to the site selection process of a planning municipal solid waste management practice based on twelve different scenarios. The scenarios included two different decision tree modes and two different weighting models for three different area requirements. The suitability rankings of the suitable sites obtained from the application of the decision procedure for the scenarios were assessed by a factorial experimental design concerning the effect of some external criteria on the final decision of the site selection process. The external criteria used in the factorial experimental design were defined as "Risk perception and approval of stakeholders" and "Visibility". The effects of the presence of these criteria in the decision trees were evaluated in detail. For a quantitative expression of the differentiations observed in the suitability rankings, the ranking data were subjected to ANOVA test after a normalization process. Then the results of these tests were evaluated by Tukey test to measure the effects of external criteria on the final decision. The results of Tukey tests indicated that the involvement of the external criteria into the decision trees produced statistically meaningful differentiations in the suitability rankings. Since the external criteria could cause considerable external costs during the operation of the disposal facilities, the presence of these criteria in the decision tree in addition to the other criteria related to environmental and legislative requisites could prevent subsequent external costs in the first place.

  9. Technical procedures for ecology: Environmental field program, Deaf Smith County Site, Texas: Final draft

    SciTech Connect

    Not Available

    1987-08-01

    This volume contains Technical Procedures pursuant to the Land Use Site Study Plan including walkover surveys for threatened, endangered, or candidate species; vegetation classification and mapping; reclamation planning; wetland and floodplain determination and characterization of playas; wildlife habitat mapping methods; mammal sampling; bird survey methods; reptile and amphibian survey methods; preexisting environmental; stress and disturbance studies methods; voucher specimens for plants; and voucher specimens to wildlife. 9 refs., 5 figs., 1 tab.

  10. Analytic study to evaluate associations between hazardous waste sites and birth defects. Final report

    SciTech Connect

    Marshall, E.G.; Gensburg, L.J.; Geary, N.S.; Deres, D.A.; Cayo, M.R.

    1995-06-01

    A study was conducted to evaluate the risk of two types of birth defects (central nervous system and musculoskeletal defects) associated with mothers` exposure to solvents, metals, and pesticides through residence near hazardous waste sites. The only environmental factor showing a statistically significant elevation in risk was living within one mile of industrial or commercial facilities emitting solvents into the air. Residence near these facilities showed elevated risk for central nervous system defects but no elevated risks for musculoskeletal defects.

  11. Barometric pressure transient testing applications at the Nevada Test Site: formation permeability analysis. Final report

    SciTech Connect

    Hanson, J.M.

    1984-12-01

    The report evaluates previous investigations of the gas permeability of the rock surrounding emplacement holes at the Nevada Test Site. The discussion sets the framework from which the present uncertainty in gas permeability can be overcome. The usefulness of the barometric pressure testing method has been established. Flow models were used to evaluate barometric pressure transients taken at NTS holes U2fe, U19ac and U20ai. 31 refs., 103 figs., 18 tabs. (ACR)

  12. Final report on decommissioning of wells, boreholes, and tiltmeter sites, Gulf Coast Interior Salt Domes of Louisiana

    SciTech Connect

    Not Available

    1989-07-01

    In the late 1970s, test holes were drilled in northern Louisiana in the vicinity of Vacherie and Rayburn`s Salt Domes as part of the Department of Energy`s (DOE) National Waste Terminal Storage (NWTS) (rename the Civilian Radioactive Waste Management (CRWM)) program. The purpose of the program was to evaluate the suitability of salt domes for long term storage or disposal of high-level nuclear waste. The Institute for Environmental Studies at Louisiana State University (IES/LSU) and Law Engineering Testing Company (LETCo) of Marietta, Georgia performed the initial field studies. In 1982, DOE awarded a contract to the Earth Technology Corporation (TETC) of Long Beach, California to continue the Gulf Coast Salt Dome studies. In 1986, DOE deferred salt domes from further consideration as repository sites. This report describes test well plugging and site abandonment activities performed by SWEC in accordance with Activity Plan (AP) 1--3, Well Plugging and Site Restoration of Work Sites in Louisiana. The objective of the work outlined in this AP was to return test sites to as near original condition as possible by plugging boreholes, removing equipment, regrading, and seeding. Appendices to this report contain forms required by State of Louisiana, used by SWEC to document decommissioning activities, and pertinent documentation related to lease/access agreements.

  13. Evaluation of the need, feasibility, and siting of the MRS in Tennessee. Draft final report

    SciTech Connect

    Colglazier, E.W. Jr.

    1985-12-16

    This summary report outlines the results of an independent assessment of the need, feasibility, and siting of the proposed Monitored Retrievable Storage (MRS) facility. The detailed reports of this assessment are included as appendices to the summary report. The Department of Energy (DOE) has concluded that the MRS is not absolutely necessary, but preferred, in order to manage and move spent fuel from reactors to a repository. The team has attemped to assess ``need`` by comparing to advantages and disadvantages of various systems, with and without the MRS. ``Feasibility has been assessed by comparing the technical and economic advantages and disadvantages. The team was not asked to recommend a preferred system. That choice will depend on the importance that are used to compare alternatives. The five key criteria selected by the team for comparing alternate systems were: economic cost, radiological risk, non-radiological transportation impacts, the likelihood of successful implementation and operation of the system, and the likelihood of meeting the schedule in the Nuclear Waste Policy Act. The team compared twelve different systems and modeled the transportation impacts and risks with three repository sites and two MRS sites.

  14. Final Clean Closure Report Site 300 Surface Impoundments Closure Lawrence Livermore National Laboratory Livermore, California

    SciTech Connect

    Haskell, K

    2006-02-14

    Lawrence Livermore National Laboratory operated two Class II surface impoundments that stored wastewater that was discharged from a number of buildings located on the Site 300 Facility (Site 300). The wastewater was the by-product of explosives processing. Reduction in the volume of water discharged from these buildings over the past several years significantly reduced the wastewater storage needs. In addition, the impoundments were constructed in 1984, and the high-density polyethylene (HDPE) geomembrane liners were nearing the end of their service life. The purpose of this project was to clean close the surface impoundments and provide new wastewater storage using above ground storage tanks at six locations. The tanks were installed and put into service prior to closure of the impoundments. This Clean Closure Report (Closure Report) complies with State Water Resources Control Board (SWRCB) Section 21400 of the California Code of Regulations Title 27 (27 CCR section 21400). As required by these regulations and guidance, this Closure Report provides the following information: (1) a brief site description; (2) the regulatory requirements relevant to clean closure of the impoundments; (3) the closure procedures; and (4) the findings and documentation of clean closure.

  15. Activity of N-coordinated multi-metal-atom active site structures for Pt-free oxygen reduction reaction catalysis: Role of *OH ligands

    NASA Astrophysics Data System (ADS)

    Holby, Edward F.; Taylor, Christopher D.

    2015-03-01

    We report calculated oxygen reduction reaction energy pathways on multi-metal-atom structures that have previously been shown to be thermodynamically favorable. We predict that such sites have the ability to spontaneously cleave the O2 bond and then will proceed to over-bind reaction intermediates. In particular, the *OH bound state has lower energy than the final 2 H2O state at positive potentials. Contrary to traditional surface catalysts, this *OH binding does not poison the multi-metal-atom site but acts as a modifying ligand that will spontaneously form in aqueous environments leading to new active sites that have higher catalytic activities. These *OH bound structures have the highest calculated activity to date.

  16. Activity of N-coordinated multi-metal-atom active site structures for Pt-free oxygen reduction reaction catalysis: Role of *OH ligands

    DOE PAGES

    Holby, Edward F.; Taylor, Christopher D.

    2015-03-19

    We report calculated oxygen reduction reaction energy pathways on multi-metal-atom structures that have previously been shown to be thermodynamically favorable. We predict that such sites have the ability to spontaneously cleave the O₂ bond and then will proceed to over-bind reaction intermediates. In particular, the *OH bound state has lower energy than the final 2 H₂O state at positive potentials. Contrary to traditional surface catalysts, this *OH binding does not poison the multi-metal-atom site but acts as a modifying ligand that will spontaneously form in aqueous environments leading to new active sites that have higher catalytic activities. These *OH boundmore » structures have the highest calculated activity to date.« less

  17. Activity of N-coordinated multi-metal-atom active site structures for Pt-free oxygen reduction reaction catalysis: Role of *OH ligands

    SciTech Connect

    Holby, Edward F.; Taylor, Christopher D.

    2015-03-19

    We report calculated oxygen reduction reaction energy pathways on multi-metal-atom structures that have previously been shown to be thermodynamically favorable. We predict that such sites have the ability to spontaneously cleave the O₂ bond and then will proceed to over-bind reaction intermediates. In particular, the *OH bound state has lower energy than the final 2 H₂O state at positive potentials. Contrary to traditional surface catalysts, this *OH binding does not poison the multi-metal-atom site but acts as a modifying ligand that will spontaneously form in aqueous environments leading to new active sites that have higher catalytic activities. These *OH bound structures have the highest calculated activity to date.

  18. Activity of N-coordinated multi-metal-atom active site structures for Pt-free oxygen reduction reaction catalysis: Role of *OH ligands

    PubMed Central

    Holby, Edward F.; Taylor, Christopher D.

    2015-01-01

    We report calculated oxygen reduction reaction energy pathways on multi-metal-atom structures that have previously been shown to be thermodynamically favorable. We predict that such sites have the ability to spontaneously cleave the O2 bond and then will proceed to over-bind reaction intermediates. In particular, the *OH bound state has lower energy than the final 2 H2O state at positive potentials. Contrary to traditional surface catalysts, this *OH binding does not poison the multi-metal-atom site but acts as a modifying ligand that will spontaneously form in aqueous environments leading to new active sites that have higher catalytic activities. These *OH bound structures have the highest calculated activity to date. PMID:25788358

  19. Characterization of the active site of chloroperoxidase using physical techniques

    SciTech Connect

    Hall, K.S.

    1986-01-01

    Chloroperoxidase (CPO) and Cytochrome P-450, two very different hemeproteins, have been shown to have similar active sites by several techniques. Recent work has demonstrated thiolate ligation from a cysteine residue to the iron in P-450. A major portion of this research has been devoted to obtaining direct evidence that CPO also has a thiolate 5th ligand from a cysteine residue. This information will provide the framework for a detailed analysis of the structure-function relationships between peroxidases, catalase and cytochrome P-450 hemeproteins. To determine whether the 5th ligand is a cysteine, methionine or a unique amino acid, specific isotope enrichment experiments were used. Preliminary /sup 1/H-NMR studies show that the carbon monoxide-CPO complex has a peak in the upfield region corresponding to alpha-protons of a thiolate amino acid. C. fumago was grown on 95% D/sub 2/O media with a small amount of /sup 1/H-cysteine added. Under these conditions C. fumago slows down the biosynthesis of cysteine by at least 50% and utilizes the exogenous cysteine in the media. GC-MS was able to show that the methylene protons next to the sulfur atom in cysteine are 80-90% protonated while these positions in methionine are approximately 73% deuterated. Comparison of the /sup 1/H-NMR spectra of CO-CPO and CO-CPO indicate the presence of a cysteine ligand in chloroperoxidase.

  20. N6-Methyldeoxyadenosine Marks Active Transcription Start Sites in Chlamydomonas

    PubMed Central

    Chen, Kai; Deng, Xin; Yu, Miao; Han, Dali; Hao, Ziyang; Liu, Jianzhao; Lu, Xingyu; Dore, Louis C; Weng, Xiaocheng; Ji, Quanjiang; Mets, Laurens; He, Chuan

    2015-01-01

    SUMMARY N6-methyldeoxyadenosine (6mA or m6A) is a DNA modification preserved in prokaryotes to eukaryotes. It is widespread in bacteria, and functions in DNA mismatch repair, chromosome segregation, and virulence regulation. In contrast, the distribution and function of 6mA in eukaryotes have been unclear. Here we present a comprehensive analysis of the 6mA landscape in the genome of Chlamydomonas using new sequencing approaches. We identified the 6mA modification in 84% of genes in Chlamydomonas. We found that 6mA mainly locates at ApT dinucleotides around transcription start sites (TSS) with a bimodal distribution, and appears to mark active genes. A periodic pattern of 6mA deposition was also observed at base resolution, which is associated with nucleosome distribution near the TSS, suggesting a possible role in nucleosome positioning. The new genome-wide mapping of 6mA and its unique distribution in the Chlamydomonas genome suggest potential regulatory roles of 6mA in gene expression in eukaryotic organisms. PMID:25936837

  1. Detection limit for activation measurements in ultralow background sites

    NASA Astrophysics Data System (ADS)

    Trache, Livius; Chesneanu, D.; Margineanu, R.; Pantelica, A.; Ghita, D. G.; Burducea, I.; Straticiuc, M.; Tang, X. D.

    2014-09-01

    We used 12C +13C fusion at the beam energies E = 6, 7 and 8 MeV to determine the sensitivity and the limits of activation method measurements in ultralow background sites. A 13C beam of 0.5 μA from the 3 MV Tandem accelerator of the Horia Hulubei National Institute of Physics and Nuclear Engineering - IFIN HH impinged on thick graphite targets. After about 24 hrs of irradiation targets were measured in two different laboratories: one with a heavy shielded Ge detector in the institute (at the surface) and one located underground in the microBequerel laboratory, in the salt mine of Slanic-Prahova, Romania. The 1369- and 2754 keV peaks from 24Na deactivation were clearly observed in the γ-ray spectra obtained for acquisitions lasting a few hours, or a few days. Determination of the detection limit in evaluating the cross sections for the target irradiated at Ec . m = 3 MeV indicates the fact that it is possible to measure gamma spectrum in underground laboratory down to Ec . m = 2 . 6 MeV. Cleaning the spectra with beta-gamma coincidences and increasing beam intensity 20 times will take as further down. The measurements are motivated by the study of the 12 C +12 C reaction at astrophysical energies.

  2. Disturbance opens recruitment sites for bacterial colonization in activated sludge.

    PubMed

    Vuono, David C; Munakata-Marr, Junko; Spear, John R; Drewes, Jörg E

    2016-01-01

    Little is known about the role of immigration in shaping bacterial communities or the factors that may dictate success or failure of colonization by bacteria from regional species pools. To address these knowledge gaps, the influence of bacterial colonization into an ecosystem (activated sludge bioreactor) was measured through a disturbance gradient (successive decreases in the parameter solids retention time) relative to stable operational conditions. Through a DNA sequencing approach, we show that the most abundant bacteria within the immigrant community have a greater probability of colonizing the receiving ecosystem, but mostly as low abundance community members. Only during the disturbance do some of these bacterial populations significantly increase in abundance beyond background levels and in few cases become dominant community members post-disturbance. Two mechanisms facilitate the enhanced enrichment of immigrant populations during disturbance: (i) the availability of resources left unconsumed by established species and (ii) the increased availability of niche space for colonizers to establish and displace resident populations. Thus, as a disturbance decreases local diversity, recruitment sites become available to promote colonization. This work advances our understanding of microbial resource management and diversity maintenance in complex ecosystems. PMID:25727891

  3. Active Site Characterization of Proteases Sequences from Different Species of Aspergillus.

    PubMed

    Morya, V K; Yadav, Virendra K; Yadav, Sangeeta; Yadav, Dinesh

    2016-09-01

    A total of 129 proteases sequences comprising 43 serine proteases, 36 aspartic proteases, 24 cysteine protease, 21 metalloproteases, and 05 neutral proteases from different Aspergillus species were analyzed for the catalytically active site residues using MEROPS database and various bioinformatics tools. Different proteases have predominance of variable active site residues. In case of 24 cysteine proteases of Aspergilli, the predominant active site residues observed were Gln193, Cys199, His364, Asn384 while for 43 serine proteases, the active site residues namely Asp164, His193, Asn284, Ser349 and Asp325, His357, Asn454, Ser519 were frequently observed. The analysis of 21 metalloproteases of Aspergilli revealed Glu298 and Glu388, Tyr476 as predominant active site residues. In general, Aspergilli species-specific active site residues were observed for different types of protease sequences analyzed. The phylogenetic analysis of these 129 proteases sequences revealed 14 different clans representing different types of proteases with diverse active site residues.

  4. A proposed definition of the 'activity' of surface sites on lactose carriers for dry powder inhalation.

    PubMed

    Grasmeijer, Floris; Frijlink, Henderik W; de Boer, Anne H

    2014-06-01

    A new definition of the activity of surface sites on lactose carriers for dry powder inhalation is proposed which relates to drug detachment during dispersion. The new definition is expected to improve the understanding of 'carrier surface site activity', which stimulates the unambiguous communication about this subject and may aid in the rational design and interpretation of future formulation studies. In contrast to the currently prevailing view on carrier surface site activity, it follows from the newly proposed definition that carrier surface site activity depends on more variables than just the physicochemical properties of the carrier surface. Because the term 'active sites' is ambiguous, it is recommended to use the term 'highly active sites' instead to denote carrier surface sites with a relatively high activity. PMID:24613490

  5. Superfund Record of Decision: (EPA Region 3): Limestone Road Site, Cumberland, Maryland, September 1986. Final report

    SciTech Connect

    Not Available

    1986-09-30

    The Limestone Road site is located 2.5 miles east southeast of Cumberland, Allegheny County, Maryland, on the western flank of Irons Mountain and includes large areas of landfilled and dumped commercial, residential, and demolition refuse. A variety of waste has reportedly been dumped into a ravine on the property such as chromium, lead, and cadmium. In addition, an alleged 11 tons of hazardous waste have been reportedly disposed of as an extension of filling and grading operations. The primary contaminants of concern include: VOCs, base-neutral compounds, TCE, PCE, and heavy metals. Remedial action is proposed and included in the report.

  6. On-site effluent toxicity studies at the Goodyear Atomic Corporation. Final report

    SciTech Connect

    Ferrante, J.G.; Bean, D.J.

    1986-04-01

    Acute on-site, flow-through bioassays were conducted with effluents from outfalls 001 and 002 at the Goodyear Atomic facility in Piketon, Ohio. Data collected during this study indicate that the effluents were not toxic to the two species of fish (creek chub and fathead minnow) and one species of invertebrates (crayfish) used as test organisms. The only evidence of an adverse effect was observed in the response of Daphnia magna to effluent 001, which produced a ''ballooning'' effect in laboratory studies while dilution and laboratory water failed to elicit the same response.

  7. Effects of whole-tree harvesting at three sites in New England. Final report

    SciTech Connect

    Hornbeck, J.W.; Pierce, R.S.; Martin, C.W.; Smith, C.T.; Tritton, L.M.; Federer, C.A.; Smith, R.B.

    1983-01-01

    Whole-tree harvesting has been operational at several locations in New England for nearly a decade. Evaluation of the environmental effects of whole-tree harvesting was begun in northern hardwoods in 1977, then expanded to central hardwoods and spruce-fir types in 1979-80. Study sites include Cockaponset State Forest in Connecticut, Weymouth Point at Chesuncook Lake in Maine, and the town of Success in New Hampshire. This progress report presents information and work completed through summer of 1983. 8 refs., 11 figs., 3 tabs.

  8. Krakow clean fossil fuels and energy efficiency program. Final report: Initial site investigation

    SciTech Connect

    1995-11-15

    Original objective of this project was to retrofit the Balice Boilerhouse with a TCS Coal Micronization system and Amerex baghouses to achieve higher combustion efficiencies and lower air emission, including SO{sub 2}, NO{sub x}, CO and particulate matter. The Balice Boilerhouse is located adjacent to the Krakow Airport and provides heating steam for the Polish Military Unit No. 1616. In May 1995 the Polish Military announced it had decided to convert its boiler house to gas; thus cancelling the TCS Project. The balance of 1995 was spent considering alternative Project sites in Krakow for the application of the TCS coal Micronization technology.

  9. On-site monitoring of construction of Terror Lake hydroelectric project, Kodiak, Alaska. Final report

    SciTech Connect

    Hosking, H.

    1984-09-01

    The report describes the effort by the Fish and Wildlife Service to monitor the construction of the first hydroelectric project built on national wildlife refuge lands under license by the Federal Energy Regulatory Commission. Recommendations are offered for use in planning other projects. Fish and wildlife species of concern included brown bears, Sitka black-tailed deer, mountain goats, raptors (including bald eagles), and several species of salmonid fish. Construction practices relating to erosion control, contaminant management, culvert placement, and siting of project structures are covered.

  10. 77 FR 56714 - Agency Information Collection (Annual-Final Report and Account) Activities Under OMB Review

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-13

    ... AFFAIRS Agency Information Collection (Annual-Final Report and Account) Activities Under OMB Review AGENCY... INFORMATION: Titles: a. Annual-Final Report and Account, VA Form 21-4706. b. Federal Fiduciary's Account, VA Form 21-4706b. c. Court Appointed Fiduciary's Account, VA Form 21-4706c. d. Account Book, VA Form...

  11. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  12. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  13. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  14. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  15. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  16. Probing the active site of cinnamoyl CoA reductase 1 (Ll-CCRH1) from Leucaena leucocephala.

    PubMed

    Sonawane, Prashant; Patel, Krunal; Vishwakarma, Rishi Kishore; Srivastava, Sameer; Singh, Somesh; Gaikwad, Sushama; Khan, Bashir M

    2013-09-01

    Lack of three dimensional crystal structure of cinnamoyl CoA reductase (CCR) limits its detailed active site characterization studies. Putative active site residues involved in the substrate/NADPH binding and catalysis for Leucaena leucocephala CCR (Ll-CCRH1; GenBank: DQ986907) were identified by amino acid sequence alignment and homology modeling. Putative active site residues and proximal H215 were subjected for site directed mutagenesis, and mutated enzymes were expressed, purified and assayed to confirm their functional roles. Mutagenesis of S136, Y170 and K174 showed complete loss of activity, indicating their pivotal roles in catalysis. Mutant S212G exhibited the catalytic efficiencies less than 10% of wild type, showing its indirect involvement in substrate binding or catalysis. R51G, D77G, F30V and I31N double mutants showed significant changes in Km values, specifying their roles in substrate binding. Finally, chemical modification and substrate protection studies corroborated the presence Ser, Tyr, Lys, Arg and carboxylate group at the active site of Ll-CCRH1. PMID:23688416

  17. Environmental assessment for device assembly facility operations, Nevada Test Site, Nye County, Nevada. Final report

    SciTech Connect

    1995-05-01

    The U.S. Department of Energy, Nevada Operations Office (DOE/NV), has prepared an environmental assessment (EA), (DOE/EA-0971), to evaluate the impacts of consolidating all nuclear explosive operations at the newly constructed Device Assembly Facility (DAF) in Area 6 of the Nevada Test Site. These operations generally include assembly, disassembly or modification, staging, transportation, testing, maintenance, repair, retrofit, and surveillance. Such operations have previously been conducted at the Nevada Test Site in older facilities located in Area 27. The DAF will provide enhanced capabilities in a state-of-the-art facility for the safe, secure, and efficient handling of high explosives in combination with special nuclear materials (plutonium and highly enriched uranium). Based on the information and analyses in the EA, DOE has determined that the proposed action would not constitute a major federal action significantly affecting the quality of the human environment within the meaning of the National Environmental Policy Act of 1969 (42 U.S.C. 4321 et seq.). Therefore, an environmental impact statement is not required, and DOE is issuing this finding of no significant impact.

  18. Avian Species Inventory at Manzanar National Historic Site, California - Final Report to the National Park Service

    USGS Publications Warehouse

    Hart, Jan; Drost, Charles

    2008-01-01

    We conducted a baseline inventory for avian species at Manzanar National Historic Site, Inyo County, Calif., from 2002 to 2005. Under the guidelines of the Mojave Network Biological Inventory Program, the primary objectives for this study were to (1) inventory and document the occurrence of avian species at Manzanar, with the goal of documenting at least 90 percent of the species present; (2) provide a geographic information system (GIS)-referenced list of sensitive species occurring at Manzanar that are rare, on Federal or State lists, or otherwise worthy of special consideration; and (3) enter all species data into the National Park Service NPSpecies database. Survey methods included general area searches, variable circular plot point-count censusing, nocturnal surveys, and nest searching. During 13 year-round survey sessions, we documented the occurrence of 132 bird species at Manzanar and confirmed breeding by 19 of these. Based on our findings, as well as review of the literature and searches for records of species occurrence, we estimate inventory completeness for regularly occurring bird species at Manzanar to be near 90 percent. No sensitive species on Federal or State lists were found. The distribution and relative abundance of common bird species at this site is now well enough known to begin development of a monitoring protocol for this group.

  19. Final Environmental Assessment for solid waste disposal, Nevada Test Site, Nye County, Nevada

    SciTech Connect

    1995-08-01

    New solid waste regulations require that the existing Nevada Test Site (NTS) municipal landfills, which receive less than 20 tons of waste per day, be permitted or closed by October 9, 1995. In order to be permitted, the existing landfills must meet specific location, groundwater monitoring, design, operation, and closure requirements. The issuance of these regulations has resulted in the need of the Department of Energy (DOE) to provide a practical, cost-effective, environmentally sound means of solid waste disposal at the NTS that is in compliance with all applicable federal, state, and local regulations. The current landfills in Areas 9 and 23 on the Nevada Test Site do not meet design requirements specified in new state and federal regulations. The DOE Nevada Operations Office prepared an environmental assessment (EA) to evaluate the potential impacts of the proposal to modify the Area 23 landfill to comply with the new regulations and to close the Area 9 landfill and reopen it as Construction and Demolition debris landfill. Based on information and analyses presented in the EA, DOE has determined that the proposed action would not constitute a major federal action significantly affecting the quality of the human environment within the meaning of the National Environmental Policy Act. Therefore, an environmental impact statement (EIS) is not required. This report contains the Environmental Assessment, as well as the Finding of No Significant Impact (FONSI).

  20. Cometabolic bioreactor demonstration at the Oak Ridge K-25 Site: Final report

    SciTech Connect

    Lucero, A.J.; Donaldson, T.L.; Jennings, H.L.; Morris, M.I.; Palumbo, A.V.; Herbes, S.E.

    1995-08-01

    The Oak Ridge National Laboratory (ORNL) conducted a demonstration of cometabolic technology for bioremediation of groundwater contaminated with trichloroethylene (TCE) and other chlorinated solvents. The technology demonstration was located at a seep from the K-1070-C/D Classified Burial Ground at the Oak Ridge K-25 Site. The technology demonstration was designed to evaluate the performance of two different types of cometabolic processes. In both cases, the TCE is cometabolized in the sense that utilization of a different primary substrate is necessary to obtain the simultaneous cometabolism of TCE. Trichloroethylene alone is unable to support growth and maintenance of the microorganisms. Methanotrophic (methane-utilizing) technology was demonstrated first; aromatic-utilizing microorganisms were demonstrated later. The demonstration was based on scaleup of laboratory and bench-scale prototype equipment that was used to establish the technical feasibility of the processes.This report documents the operation of the methanotrophic bioreactor system to treat the seep water at the demonstration site. The initial objectives were to demonstrate stable operation of the bioreactors and associated equipment, including the pretreatment and effluent polishing steps; and evaluate the biodegradation of TCE and other organics in the seep water for the three operating modes--air oxidation pretreatment, steam-stripping pretreatment, and no pretreatment.

  1. Department of Energy Site Operator Program. Final report, October 1, 1991--September 31, 1996

    SciTech Connect

    1996-12-31

    York Technical College is a two-year public institution accredited by the Commission of Colleges of the Southern Association of Colleges and Schools. York Technical College has been involved with electric vehicles since the late 1980`s. The four major objectives of the Site Operator Program were (1) field test and evaluate electric and hybrid vehicles and related components; (2) define and develop a national infrastructure system including electric charging systems, service/training education programs, utility system impacts and safety standards; (3) increase public awareness regarding environmental benefits, reduced dependency on foreign oil, technology development, and economic impacts; (4) assist local, state and federal agencies and fleet operators in developing electric and hybrid vehicle programs. The primary thrusts of the electric vehicle program at York Technical College, supporting the objectives of the Site Operator program were: (1) public awareness, (2) public education, (3) EV maintenance curriculum development and maintenance training, (4) field data collection, (5) vehicle modification and upgrade, (6) establish electric vehicle partnerships.

  2. Lower Columbia River and Estuary Ecosystem Restoration Program Reference Site Study: 2011 Restoration Analysis - FINAL REPORT

    SciTech Connect

    Borde, Amy B.; Cullinan, Valerie I.; Diefenderfer, Heida L.; Thom, Ronald M.; Kaufmann, Ronald M.; Zimmerman, Shon A.; Sagar, Jina; Buenau, Kate E.; Corbett, C.

    2012-05-31

    The Reference Site (RS) study is part of the research, monitoring, and evaluation (RME) effort developed by the Action Agencies (Bonneville Power Administration [BPA], U.S. Army Corps of Engineers, Portland District [USACE], and U.S. Bureau of Reclamation) in response to Federal Columbia River Power System (FCRPS) Biological Opinions (BiOp). While the RS study was initiated in 2007, data have been collected at relatively undisturbed reference wetland sites in the LCRE by PNNL and collaborators since 2005. These data on habitat structural metrics were previously summarized to provide baseline characterization of 51 wetlands throughout the estuarine and tidal freshwater portions of the 235-km LCRE; however, further analysis of these data has been limited. Therefore, in 2011, we conducted additional analyses of existing field data previously collected for the Columbia Estuary Ecosystem Restoration Program (CEERP) - including data collected by PNNL and others - to help inform the multi-agency restoration planning and ecosystem management work underway in the LCRE.

  3. Participation in the Creede Scientific Drilling Project as on-site Principal Investigator. Final report

    SciTech Connect

    Hulen, J.B.

    1992-06-01

    Scientific questions addressed by the Creede Scientific Drilling Project were as follows (Bethke et al., 1992): (1) Did the lacustrine sedimentary sequence filling the moat of Creede caldera serve as reservoir for the moderately-saline aqueous fluids which scavenged and then transported silver and base metals to ore-depositional sites for the rich epithermal deposits of the Creede mining district (Fig. 1)?; (2) what were the chemical and isotopic compositions of these fluids prior to their entry into the Creede fracture (later vein) system; (3) how did these chemical and isotopic compositions evolve in transit to the ore-depositional site?; (4) how did the Creede caldera form and evolve?; (5) what is the present thermal regime in Creede caldera moat? {hor_ellipsis}the, paleothermal regime?; (5) what are the hydrologic transport properties of the moat sedimentary rocks?; (6) what diagenetic or hydrothermal veins disrupt the moat sedimentary sequence, and what do their paragenetic relationships, mineralogic compositions, fluid-inclusion characteristics, and stable-isotope systematics reveal about evolution of the Creede hydrothermal system? Two Creede caldera moat drill holes were completed for this project.

  4. A pilot study for the extraction and treatment of groundwater from a manufactured gas plant site. Final report

    SciTech Connect

    1997-12-01

    This report describes a pilot study involving treatment of contaminated groundwater at a former manufactured gas plant site on the eastern seaboard of the US. The work was performed in order to provide the design basis for a full-scale groundwater extraction and treatment system at the site, as well as to develop a generic approach to selection of groundwater treatment sequences at other MGP sites. It included three main components: hydrogeologic investigations, bench-scale treatability studies, and pilot-scale treatability studies. Technologies evaluated in bench-scale work included gravity settling, filtration, and dissolved air flotation (DAF) for primary treatment of nonaqueous phase materials; biological degradation, air stripping, and carbon adsorption for secondary treatment of dissolved organics; and carbon adsorption as tertiary treatment of remaining dissolved contaminants. Pilot-scale studies focused on collecting system performance data fore three distinct levels of contamination. Two treatment trains were evaluated. One consisted of DAF, fluidized-bed biotreatment, and filtration plus carbon adsorption; the other used the same steps except to substitute air stripping for fluidized bed treatment. The final effluents produced by both treatment sequences were similar and demonstrated complete treatment of the groundwater. Besides detailing system design and performance for the treatability studies, the report includes an analysis of groundwater treatment applications to MGP sites in general, including a discussion of capital and operating costs.

  5. Barometric pressure transient testing applications at the Nevada Test Site. Nuclear chimney analysis. Final report

    SciTech Connect

    Hanson, J.M.

    1985-12-01

    Investigations of barometric pressure testing of NTS nuclear chimneys were reviewed. This review includes the models used in the interpretation, methods of analysis, and results. Analytic and semi-analytic models were presented and applied to both historical data and new data taken for this current project. An interpretation technique based on non-linear least squares methods was used to analyze this data in terms of historic and more recent chimney models. Finally, a detailed discussion of radioactive gas transport due to surface barometric pressure fluctuations was presented. This mechanism of transport, referred to as ''barometric pumping,'' is presented in terms of conditions likely to be encountered at the NTS. The report concludes with a discussion of the current understanding of gas flow properties in the alluvial and volcanic areas of the NTS, and suggestions for future efforts directed toward increasing this understanding are presented.

  6. GAS HYDRATES AT TWO SITES OF AN ACTIVE CONTINENTAL MARGIN.

    USGS Publications Warehouse

    Kvenvolden, K.A.

    1985-01-01

    Sediment containing gas hydrates from two distant Deep Sea Drilling Project sites (565 and 568), located about 670 km apart on the landward flank of the Middle America Trench, was studied to determine the geochemical conditions that characterize the occurrence of gas hydrates. Site 565 was located in the Pacific Ocean offshore the Nicoya Peninsula of Costa Rica in 3,111 m of water. The depth of the hole at this site was 328 m, and gas hydrates were recovered from 285 and 319 m. Site 568 was located about 670 km to the northwest offshore Guatemala in 2,031 m of water. At this site the hole penetrated to 418 m, and gas hydrates were encountered at 404 m.

  7. Control of active sites in selective flocculation: III -- Mechanism of site blocking

    SciTech Connect

    Behl, S.; Moudgil, B.M. . Dept. of Materials Science and Engineering)

    1993-12-01

    It has been shown in Parts I and II of this paper that heteroflocculation can be controlled by poisoning the sites for flocculant adsorption using a site blocking agent (SBA). An efficient SBA was determined to be the lower molecular weight fraction of the flocculant. In this paper, the underlying mechanism of SBA action is described. Also, the mathematical model detailed in Part I is used to determine the effect of different SBAs on apatite-dolomite separation efficiency. It has been demonstrated that the depression in flocculation is directly related to the site blocking parameter ([bar [Phi

  8. Geomorphic criteria for selecting stable uranium tailings disposal sites in New Mexico. Volume 1. Technical report. Final report

    SciTech Connect

    Wells, S.G.; Gardner, T.W.

    1985-03-01

    Essential to the disposal of uranium mill tailings in northwestern New Mexico is the geomorphic stability of the disposal site. Geomorphic stability assessment involves 3 steps: (1) evaluating the site's past geomorphic stability by determining the age of the landscape and its associated deposits; (2) quantifying short- and long-term geomorphic processes operating in the site area; and (3) evaluating the impact of mining activity and reclamation on the geomorphic stability of the site area. A heirarchy of geomorphic hazards which might impact a site area include: (1) drainage network extension/channel headcutting, (2) piping and gullying, (3) bank erosion and meander growth, (4) drainage network and channel incision, (5) channel aggradation, and (6) valley floor deposition and wind erosion. All of these processes operate on a scale of meters of change per year over historic time periods. Landscapes which have undergone significant changes in historic and Holocene time periods are valley floors. Valley floors are considered one of the most unstable landscapes for siting of uranium mill tailings.

  9. Installation-Restoration Program technical support document for Record of Decision, Cape Lisburne LRRS site. Final report

    SciTech Connect

    Not Available

    1988-02-29

    The Cape Lisburne AFS is located on a peninsula north of Kotzebue Sound on the Chukchi Sea, Alaska. The area is surrounded by steep, rocky terrain supporting an alpine tundra. This Record of Decision and supplemental support document applies to six potential hazardous waste sites identified at Cape Lisburne, AK. The recommendations for all six sites are the same; therefore, a single document for the entire installation is warranted. The findings and decisions on the Cape Lisburne AFS presented in this report are based on the following: 1987 site visit by personnel of Woodward-Clyde Consultants and the U.S. Air Force; Comprehensive literature search and review; Information gathered from governmental regulatory agencies and a review of active environmental permits issued by state and federal agencies. The following permit has been issued for one site identified during Phase I: Certificate of Consistency issued for demolition of White Alice Site (Site 6); Review of the physical, chemical and toxicological characteristics of suspected or known contaminants; Preliminary Assessment Form submitted by EPA.

  10. Dynamically achieved active site precision in enzyme catalysis.

    PubMed

    Klinman, Judith P

    2015-02-17

    CONSPECTUS: The grand challenge in enzymology is to define and understand all of the parameters that contribute to enzymes' enormous rate accelerations. The property of hydrogen tunneling in enzyme reactions has moved the focus of research away from an exclusive focus on transition state stabilization toward the importance of the motions of the heavy atoms of the protein, a role for reduced barrier width in catalysis, and the sampling of a protein conformational landscape to achieve a family of protein substates that optimize enzyme-substrate interactions and beyond. This Account focuses on a thermophilic alcohol dehydrogenase for which the chemical step of hydride transfer is rate determining across a wide range of experimental conditions. The properties of the chemical coordinate have been probed using kinetic isotope effects, indicating a transition in behavior below 30 °C that distinguishes nonoptimal from optimal C-H activation. Further, the introduction of single site mutants has the impact of either enhancing or eliminating the temperature dependent transition in catalysis. Biophysical probes, which include time dependent hydrogen/deuterium exchange and fluorescent lifetimes and Stokes shifts, have also been pursued. These studies allow the correlation of spatially resolved transitions in protein motions with catalysis. It is now possible to define a long-range network of protein motions in ht-ADH that extends from a dimer interface to the substrate binding domain across to the cofactor binding domain, over a distance of ca. 30 Å. The ongoing challenge to obtaining spatial and temporal resolution of catalysis-linked protein motions is discussed.

  11. Remedial action plan and site design for stabilization of the inactive uranium processing site at Naturita, Colorado. Remedial action selection report, Attachment 2, Geology report: Preliminary final

    SciTech Connect

    Not Available

    1993-08-01

    The uranium processing site near Naturita, Colorado, is one of 24 inactive uranium mill sites designated to be cleaned up by the US Department of Energy (DOE) under the Uranium Mill Tailings Radiation Control Act of 1978 (UMTRCA), Public Law 95-604. Part of the UMTRCA requires that the US Nuclear Regulatory Commission (NRC) concur with the DOE`s remedial action plan (RAP) and certify that the remedial action conducted at the site complies with the standards promulgated by the US Environmental Protection Agency (EPA). Included in the RAP is this Remedial Action Selection Report (RAS), which serves two purposes. First, it describes the activities that are proposed by the DOE to accomplish remediation and long-term stabilization and control of the radioactive materials at the inactive uranium processing site near Naturita, Colorado. Second, this document and the rest of the RAP, upon concurrence and execution by the DOE, the state of Colorado, and the NRC, become Appendix B of the cooperative agreement between the DOE and the State of Colorado.

  12. Remedial Action Plan and site design for stabilization of the inactive uranium mill tailings site at Durango, Colorado: Remedial action selection report. Revised final report

    SciTech Connect

    Not Available

    1991-12-01

    The uranium mill tailings site near Durango, Colorado, was one of 24 inactive uranium mill sites designated to be remediated by the US Department of Energy (DOE) under the Uranium Mill Tailings Radiation Control Act of 1978 (UMTRCA). Part of the UMTRCA requires that the US Nuclear Regulatory Commission (NRC) concur with the DOE`s Remedial Action Plan (RAP) and certify that the remedial action conducted at the site complies with the standards promulgated by the US Environmental Protection Agency (EPA). Included in the RAP is this Remedial Action Selection Report (RAS), which has been developed to serve a two-fold purpose. First, it describes the activities that have been conducted by the DOE to accomplish remediation and long-term stabilization and control of the radioactive materials at the inactive uranium mill processing site near Durango, Colorado. Secondly, this document and the rest of the RAP, upon concurrence and execution by the DOE, the State of Colorado, and the NRC, become Appendix B of the Cooperative Agreement between the DOE and the State of Colorado.

  13. Lethal Factor Active-Site Mutations Affect Catalytic Activity In Vitro

    PubMed Central

    Hammond, S. E.; Hanna, P. C.

    1998-01-01

    The lethal factor (LF) protein of Bacillus anthracis lethal toxin contains the thermolysin-like active-site and zinc-binding consensus motif HEXXH (K. R. Klimpel, N. Arora, and S. H. Leppla, Mol. Microbiol. 13:1093–1100, 1994). LF is hypothesized to act as a Zn2+ metalloprotease in the cytoplasm of macrophages, but no proteolytic activities have been previously shown on any target substrate. Here, synthetic peptides are hydrolyzed by LF in vitro. Mass spectroscopy and peptide sequencing of isolated cleavage products separated by reverse-phase high-pressure liquid chromatography indicate that LF seems to prefer proline-containing substrates. Substitution mutations within the consensus active-site residues completely abolish all in vitro catalytic functions, as does addition of 1,10-phenanthroline, EDTA, and certain amino acid hydroxamates, including the novel zinc metalloprotease inhibitor ZINCOV. In contrast, the protease inhibitors bestatin and lysine CMK, previously shown to block LF activity on macrophages, did not block LF activity in vitro. These data provide the first direct evidence that LF may act as an endopeptidase. PMID:9573135

  14. Monoclonal antibody against the active site of caeruloplasmin and the ELISA system detecting active caeruloplasmin.

    PubMed

    Hiyamuta, S; Ito, K

    1994-04-01

    Serum caeruloplasmin deficiency is a characteristic biochemical abnormality found in patients with Wilson's disease, but the mechanism of this disease is unknown. Although the phenylenediamine oxidase activity of serum caeruloplasmin is markedly low in patients with Wilson's disease, mRNA of caeruloplasmin exists to some extent. To investigate the deficiency of caeruloplasmin oxidase activity in Wilson's disease, we generated 14 monoclonal antibodies (MAbs) and selected ID1, which had the strongest reactivity, and ID2, which had neutralizing ability. We also established a system to measure active caeruloplasmin specifically using these MAbs. These MAbs and the system will be useful tools in analyzing the active site of caeruloplasmin in patients with Wilson's disease.

  15. Cloning and characterization of a novel nuclease from shrimp hepatopancreas, and prediction of its active site.

    PubMed

    Wang, W Y; Liaw, S H; Liao, T H

    2000-03-15

    Approximately 95% of the amino acid sequence of a shrimp (Penaeus japonicus) nuclease was derived from protease-digested peptides. A 1461-base cDNA for the nuclease was amplified and sequenced with degenerate primers based on the amino acid sequence and then specific primers by 3' and 5' RACE (rapid amplification of cDNA ends). It contains an open reading frame encoding a putative 21-residue signal peptide and a 381-residue mature protein. The N-terminus of the enzyme is pyroglutamate, deduced from composition and matrix-assisted laser desorption ionization-time-of-flight MS analyses, and confirmed by a glutamine residue in the cDNA sequence. The enzyme has 11 Cys residues, forming five intramolecular disulphides. The eleventh Cys residue was linked to a thiol compound with an estimated molecular mass of between 500 and 700 Da. A sequence similarity search revealed no homologous proteins but residues 205-255 shared a conserved active-site motif within a distinct group of nucleases. His(211) in this conserved motif was shown to be very important in catalysis by site-specific modification with (14)C-labelled iodoacetate. The shrimp nuclease, previously designated DNase I, does indeed possess a low level of hydrolytic activity towards RNA in the presence of Mg(2+) and Ca(2+). The conservation of functionally important residues during distant evolution might imply that the catalytic mechanisms are similar in these nucleases, which should be classified in one subfamily. Finally, an active-site structure for shrimp nuclease was proposed on the basis of published structural data and the results of mutational and biochemical analyses of Serratia nuclease.

  16. Hydraulic Testing of Salado Formation Evaporites at the Waste Isolation Pilot Plant Site: Final Report

    SciTech Connect

    Beauheim, Richard L.; Domski, Paul S.; Roberts, Randall M.

    1999-07-01

    This report presents interpretations of hydraulic tests conducted in bedded evaporates of the Salado Formation from May 1992 through May 1995 at the Waste Isolation Pilot Plant (WIPP) site in southeastern New Mexico. The WIPP is a US Department of Energy research and development facility designed to demonstrate safe disposal of transuranic wastes from the nation's defense programs. The WIPP disposal horizon is located in the lower portion of the Permian Salado Formation. The hydraulic tests discussed in this report were performed in the WIPP underground facility by INTERA inc. (now Duke Engineering and Services, Inc.), Austin, Texas, following the Field Operations Plan and Addendum prepared by Saulnier (1988, 1991 ) under the technical direction of Sandia National Laboratories, Albuquerque, New Mexico.

  17. Geophysical investigation at Hazardous Waste Management Site 16, Radford Army Ammunition Plant Radford, Virginia. Final report

    SciTech Connect

    Llopis, J.L.; Sjostrom, K.J.

    1989-09-01

    This report describes procedural details and test results of a geophysical investigation conducted at Hazardous Waste Management Site-16 (HWMS-16), Radford Army Ammunition Plant, Va. The geophysical investigation, part of a comprehensive ground-water assessment program, was conducted to obtain subsurface information regarding HWMS-16, thus aiding in determining the most optimal locations for future monitoring wells. The two geophysical methods used in this investigation were electromagnetic (EM) induction and seismic refraction. A number of anomalous areas including a suspected sinkhole were discerned at HWMS-16. Also, the EM method proved to be effective in delineating the boundaries of covered and leveled-off landfill cells and distinguishing landfill cells used for the disposal of household waste from those used for the disposal of hazardous waste.

  18. Pilot-scale incineration of contaminated soil from the chemical insecticide corporation superfund site. Final report

    SciTech Connect

    Siag, A.; Fournier, D.J.; Waterland, L.R.

    1993-02-01

    An incineration test program was conducted at the U.S. Environmental Protection Agency's Incinerator Research Facility to evaluate the potential of incineration as an option to treat contaminated soils at the Chemical Insecticide Corporation Site. The test data show that: The organochlorine pesticides were destroyed to non-detectable quantities in the ash, the state-of-the-art scrubber removed arsenic to the 99.95% level, lime addition did not improve the arsenic removal efficiency, toxicity characteristic leaching procedure (TCLP) values for ash metals varied, lime addition reduced TCLP leachability of metals, particulate and HCl levels were within accepted limits. Incineration data that can be used for other purposes was also collected for the soil tested.

  19. Costs of remedial response actions at uncontrolled hazardous waste sites. Final report

    SciTech Connect

    Rishel, H.L.; Boston, T.M.; Schmidt, C.J.

    1982-03-01

    The primary purpose of this study was to update conceptual design cost estimates for remedial action unit operations portrayed in earlier reports. Thirty-five remedial action unit operations conceptual designs, addressing uncontrolled landfill or impoundment disposal sites, were costed for Newark, New Jersey, as well as for U.S. lower and upper cost averages within the contiguous 48 states. Such estimates were in terms of mid-1980 dollars. Total component capital costs and operating costs were estimated for each unit operation. Total and average life cycle costs were computed. One example was presented to show how to estimate the costs of complete remedial response scenarios. This report was submitted in fulfillment of Contract No. 68-01-4885 by SCS Engineers, under the sponsorship of the U.S. Environmental Protection Agency. This report covers the period from April 11, 1980, to February 18, 1981, and work completed as of April 13, 1981.

  20. Environmentally based siting assessment for synthetic-liquid-fuels facilities. Final report

    SciTech Connect

    1980-01-01

    A detailed assessment of the major environmental constraints to siting a synthetic fuels industry and the results of that assessment are used to determine on a regional basis the potential for development of such an industry with minimal environmental conflicts. Secondly, the ability to mitigate some of the constraining impacts through alternative institutional arrangements, especially in areas that are judged to have a low development potential is also assessed. Limitations of the study are delineated, but specifically, the study is limited geographically to well-defined boundaries that include the prime coal and oil shale resource areas. The critical factors used in developing the framework are air quality, water availability, socioeconomic capacity, ecological sensitivity, environmental health, and the management of Federally owned lands. (MCW)

  1. MuA Transposase: Organizing Two Reactions With One Active Site

    NASA Astrophysics Data System (ADS)

    Goldhaber-Gordon, Ilana; Baker, Tania A.

    2002-03-01

    Transposases are unusual proteins, performing at least two types of chemical reaction with a single active site. In the first reaction, the transposase cleaves the 3' end of a transposon DNA sequence. In the second reaction, the transposase transfers the cleaved 3' end into a new DNA molecule called the target. The final product is the transposon DNA attached by its 3' strands to the target DNA. The two reactions, DNA cleavage and DNA strand transfer, are chemically very similar, raising the question of how transposases avoid unintentionally cleaving the target. We have now observed that at least one transposase, the MuA protein, can cleave a target DNA --- when in the presence of a transposon DNA with a special (dideoxy nucleotide) termination. By exploring the protein's ability to cleave the target DNA under these unusual circumstances, we are learning how it prevents target cleavage when working with more standard DNA substrates.

  2. Robotics and Automation Activities at the Savannah River Site: A Site Report for SUBWOG 39F

    SciTech Connect

    Teese, G.D.

    1995-09-28

    The Savannah River Site has successfully used robots, teleoperators, and remote video to reduce exposure to ionizing radiation, improve worker safety, and improve the quality of operations. Previous reports have described the use of mobile teleoperators in coping with a high level liquid waste spill, the removal of highly contaminated equipment, and the inspection of nuclear reactor vessels. This report will cover recent applications at the Savannah River, as well as systems which SRS has delivered to other DOE site customers.

  3. Control of active sites in selective flocculation: II -- Role of site blocking agents

    SciTech Connect

    Behl, S.; Moudgil, B.M. . Dept. of Materials Science and Engineering)

    1993-12-01

    Control of heteroflocculation using a lower molecular weight fraction of the flocculant as a site blocking agent is demonstrated in the apatite-dolomite-polyethylene oxide system. The most effective SBA (site blocking agent) was determined to be the highest molecular weight fraction of the flocculant itself which was not capable of flocculating any of the components of the mixture. In the presence of the SBA, flocculant adsorption decreased significantly on apatite particles, thereby inhibiting coflocculation.

  4. Mechanism of Oxygen Reduction in Cytochrome c Oxidase and the Role of the Active Site Tyrosine.

    PubMed

    Blomberg, Margareta R A

    2016-01-26

    Cytochrome c oxidase, the terminal enzyme in the respiratory chain, reduces molecular oxygen to water and stores the released energy through electrogenic chemistry and proton pumping across the membrane. Apart from the heme-copper binuclear center, there is a conserved tyrosine residue in the active site (BNC). The tyrosine delivers both an electron and a proton during the O-O bond cleavage step, forming a tyrosyl radical. The catalytic cycle then occurs in four reduction steps, each taking up one proton for the chemistry (water formation) and one proton to be pumped. It is here suggested that in three of the reduction steps the chemical proton enters the center of the BNC, leaving the tyrosine unprotonated with radical character. The reproprotonation of the tyrosine occurs first in the final reduction step before binding the next oxygen molecule. It is also suggested that this reduction mechanism and the presence of the tyrosine are essential for the proton pumping. Density functional theory calculations on large cluster models of the active site show that only the intermediates with the proton in the center of the BNC and with an unprotonated tyrosyl radical have a high electron affinity of similar size as the electron donor, which is essential for the ability to take up two protons per electron and thus for the proton pumping. This type of reduction mechanism is also the only one that gives a free energy profile in accordance with experimental observations for the amount of proton pumping in the working enzyme.

  5. Active Site, Catalytic Cycle, and Iodination Reactions of Vanadium Iodoperoxidase: A Computational Study.

    PubMed

    Pacios, Luis F; Gálvez, Oscar

    2010-05-11

    A combined computational study using molecular surfaces and Poisson-Boltzmann electrostatic potentials for proteins and quantum calculations on complexes representing the vanadate cofactor throughout the catalytic cycle is employed to study the activity of vanadium iodoperoxidase (VIPO) from alga Laminaria digitata . A model structure of VIPO is compared with available crystal structures of chloroperoxidases (VClPOs) and bromoperoxidases (VBrPOs) focusing on properties of the active site that concern halogen specificity. It is found that VIPO displays distinctive features regarding electrostatic potentials at the site cavity and the local topography of the cavity entrance. Quantum calculations on cofactor stages throughout the catalytic cycle reveal that, while steps involving binding of hydrogen peroxide and halide oxidization agree with available data on VBrPO, final formation and subsequent release of hypohalous acid could follow a different pathway consisting of His476-assisted protonation of bonded hypoiodite and further displacement by a water molecule. Ab initio free energies of reaction computed to explore iodination of organic substrates predict strongly exoergonic reactions with HOI, whereas other possible iodination reagents give thermodynamically disfavored reactions.

  6. Surface and subsurface cleanup protocol for radionuclides, Gunnison, Colorado, UMTRA project processing site. Final [report

    SciTech Connect

    Not Available

    1993-09-01

    Surface and subsurface soil cleanup protocols for the Gunnison, Colorado, processing sits are summarized as follows: In accordance with EPA-promulgated land cleanup standards (40 CFR 192), in situ Ra-226 is to be cleaned up based on bulk concentrations not exceeding 5 and 15 pCi/g in 15-cm surface and subsurface depth increments, averaged over 100-m{sup 2} grid blocks, where the parent Ra-226 concentrations are greater than, or in secular equilibrium with, the Th-230 parent. A bulk interpretation of these EPA standards has been accepted by the Nuclear Regulatory Commission (NRC), and while the concentration of the finer-sized soil fraction less than a No. 4 mesh sieve contains the higher concentration of radioactivity, the bulk approach in effect integrates the total sample radioactivity over the entire sample mass. In locations where Th-230 has differentially migrated in subsoil relative to Ra-226, a Th-230 cleanup protocol has been developed in accordance with Supplemental Standard provisions of 40 CFR 192 for NRC/Colorado Department of Health (CDH) approval for timely implementation. Detailed elements of the protocol are contained in Appendix A, Generic Protocol from Thorium-230 Cleanup/Verification at UMTRA Project Processing Sites. The cleanup of other radionuclides or nonradiological hazards that pose a significant threat to the public and the environment will be determined and implemented in accordance with pathway analysis to assess impacts and the implications of ALARA specified in 40 CFR 192 relative to supplemental standards.

  7. High resolution seismic survey, Pen Branch Fault, Savannah River Site, South Carolina. Final report

    SciTech Connect

    Berkman, E.

    1991-04-01

    An investigation of the Pen Branch Fault at the Savannah River Site by a series of short, high resolution seismic reflection lines was conducted. The purpose was to acquire, process, and interpret 19.9 miles of data, optimized for the upper 300 ft of geologic strata, in sufficient density such that processing performed in the conventional stepwise approach, followed by detailed interpretation, would define small scale spatial variability and structural features in the vicinity of the fault leading to definition of the location of the fault, the shallowest extent of the fault, and the quantification of the sense and magnitude of motion. The depth of optimization for the last two lines was modified to the 300 ft of geologic strata immediately above basement. Three older seismic surveys, other geophysical data, and associated borehole and geologic data were reviewed. The equipment and the acquisition, processing, and interpretation procedures are discussed in the report. The report includes a detailed line by line description and discussion of the interpretation. Figures include reference maps, contour displays of the stacking and interval velocities, diagrammatic references sketches of the interpreted layering and sedimentary features, index sketches, and specific color prints made on the workstation during the course of the interpretation. A volume of manuals on seismic devices and related equipment is included.

  8. Savannah River Site Spent Nuclear Fuel Management Final Environmental Impact Statement

    SciTech Connect

    N /A

    2000-04-14

    The proposed DOE action considered in this environmental impact statement (EIS) is to implement appropriate processes for the safe and efficient management of spent nuclear fuel and targets at the Savannah River Site (SRS) in Aiken County, South Carolina, including placing these materials in forms suitable for ultimate disposition. Options to treat, package, and store this material are discussed. The material included in this EIS consists of approximately 68 metric tons heavy metal (MTHM) of spent nuclear fuel 20 MTHM of aluminum-based spent nuclear fuel at SRS, as much as 28 MTHM of aluminum-clad spent nuclear fuel from foreign and domestic research reactors to be shipped to SRS through 2035, and 20 MTHM of stainless-steel or zirconium-clad spent nuclear fuel and some Americium/Curium Targets stored at SRS. Alternatives considered in this EIS encompass a range of new packaging, new processing, and conventional processing technologies, as well as the No Action Alternative. A preferred alternative is identified in which DOE would prepare about 97% by volume (about 60% by mass) of the aluminum-based fuel for disposition using a melt and dilute treatment process. The remaining 3% by volume (about 40% by mass) would be managed using chemical separation. Impacts are assessed primarily in the areas of water resources, air resources, public and worker health, waste management, socioeconomic, and cumulative impacts.

  9. Energy conserving site design: Greenbrier case study, Chesapeake, Virginia. Final report

    SciTech Connect

    Not Available

    1980-04-01

    A specific case study of project planning for energy conservation for a major planned unit development at the 3000-acre Greenbrier development site in Chesapeake, Virginia, is summarized. The research suggests that very considerable reductions in energy conservation can be achieved within the confines of private-sector land development and residential construction with increased incremental costs of $200.00 to $3150.00 per dwelling unit. It is hypothesized that energy consumption at Greenbrier can be reduced by one-half with an average annual savings of 21,275 kWh per residential unit, using state-of-the-art technology with careful planning and control. This represents an annual savings $750.00 per unit at the current utility rate of 3.5 cents per kWh. These savings can be achieved through reduction in heating and cooling loads and application of more-efficient heating and cooling of the remaining loads. The reduction in loads are achieved by redesign of the land plan to include a higher percentage of south-facing lots, use of vegetation to modify microclimate, decreases in air infiltration, the use of 2 x 6 framing, better insulation, and the use of an insulated slab-on-grade foundation. Further energy savings can be expected by increased efficiencies in mechanical systems used for space heating and cooling and domestic hot water. When applied to the single-family portion of Greenbrier, containing 541 dwelling units, these options reduce the total end-use energy consumption 54.7%. This reduction represents an annual savings of $432,800.00 for an initial capital investment of $1.7 million.

  10. Site specific endonucleases for human genome mapping. Final report, April 1, 1992--March 31, 1994

    SciTech Connect

    Knoche, K.; Selman, S.; Hung, L.

    1994-06-01

    Current large scale genome mapping methodology suffers from a lack of tools for generating specific DNA fragments in the megabase size range. While technology such as pulsed field gel electrophoresis can resolve DNA fragments greater than 10 megabases in size, current methods for cleaving mammalian DNA using bacterial restriction enzymes are incapable of producing such fragments. Though several multidimensional approaches are underway to overcome this limitation, there currently is no single step procedure to generate specific DNA fragments in the 2-100 megabase size range. In order to overcome these limitations, we proposed to develop a family of site-specific endonucleases capable of generating DNA fragments in the 2-100 megabase size range in a single step. Additionally, we proposed to accomplish this by relaxing the specificity of a very-rare cutting intron-encoded endonucleases, I-Ppo I, and potentially using the process as a model for development of other enzymes. Our research has uncovered a great deal of information about intron-encoded endonucleases. We have found that I-Ppo I has a remarkable ability to tolerate degeneracy within its recognition sequence, and we have shown that the recognition sequence is larger than 15 base pairs. These findings suggest that a detailed study of the mechanism by which intron-encoded endonucleases recognize their target sequences should provide new sights into DNA-protein interactions; this had led to a continuation of the study of I-Ppo I in Dr. Raines` laboratory and we expect a more detailed understanding of the mechanism of I-Ppo I action to result.

  11. Detection and Characterization of Rocks and Rock Size-Frequency Distributions at the Final Four Mars Science Laboratory Landing Sites

    NASA Astrophysics Data System (ADS)

    Golombek, M.; Huertas, A.; Kipp, D.; Calef, F.

    Background: Shadows cast from rocks in High-Resolution Imaging Science Experiment (HiRISE) images were used during Phoenix landing site selection to measure the diameter and height of rocks in the northern plains using an automated rock detector algorithm that fits ellipses to the shadows and cylinders to the rocks. Results show that the size-frequency distribution of rocks >1.5 m diameter are fully resolvable in HiRISE images and follow the same exponential models developed from lander measurements of smaller rocks distributions at the landing sites. Method: Greater image complexity at prospective Mars Science landing sites required improvements in shadow segmentation, which included 4 blind deconvolution steps to sharpen the rock shadows and sectional image processing. Shadows of non-rocks were removed by fitting model size-frequency distributions to rocks 1.5-2.25 m diameter in 450 m bins, all of which significantly improved the rock detection algorithm. Conclusion: Rock distributions measured from orbit and the ground for the Phoenix landing site follow the same exponential model size-frequency distribution (within 1% rock abundance), further validating accurate extrapolations of rock abundance using HiRISE images. Size-frequency distributions determined in 450 m HiRISE bins matched model distributions and indicates average rock abundances of 5.4±2.6%, 3.9±3.0%, 0.3±1.1% and 3.3±2.7% at the Mars Science Laboratory (MSL) Eberswalde, Gale, Holden and Mawrth final four landing sites, respectively. MSL landing simulations indicate the probability of failure due to landing on a rock higher than the rover belly pan is 0.30%, 0.17%, 0.03% and 0.08% at Eberswalde, Gale, Holden, and Mawrth, respectively. Because these probabilities are less than the engineering requirement of <0.5%, all sites are safe with respect to rocks and rocks were not a factor in landing site selection.

  12. Mutation at a Strictly Conserved, Active Site Tyrosine in the Copper Amine Oxidase Leads to Uncontrolled Oxygenase Activity

    SciTech Connect

    Chen, Zhi-wei; Datta, Saumen; DuBois, Jennifer L.; Klinman, Judith P.; Mathews, F. Scott

    2010-09-07

    The copper amine oxidases carry out two copper-dependent processes: production of their own redox-active cofactor (2,4,5-trihydroxyphenylalanine quinone, TPQ) and the subsequent oxidative deamination of substrate amines. Because the same active site pocket must facilitate both reactions, individual active site residues may serve multiple roles. We have examined the roles of a strictly conserved active site tyrosine Y305 in the copper amine oxidase from Hansenula polymorpha kinetically, spetroscopically (Dubois and Klinman (2006) Biochemistry 45, 3178), and, in the present work, structurally. While the Y305A enzyme is almost identical to the wild type, a novel, highly oxygenated species replaces TPQ in the Y305F active sites. This new structure not only provides the first direct detection of peroxy intermediates in cofactor biogenesis but also indicates the critical control of oxidation chemistry that can be conferred by a single active site residue.

  13. Accommodation of GDP-Linked Sugars in the Active Site of GDP-Perosamine Synthase

    SciTech Connect

    Cook, Paul D.; Carney, Amanda E.; Holden, Hazel M.

    2009-01-12

    Perosamine (4-amino-4,6-dideoxy-d-mannose), or its N-acetylated form, is one of several dideoxy sugars found in the O-antigens of such infamous Gram-negative bacteria as Vibrio cholerae O1 and Escherichia coli O157:H7. It is added to the bacterial O-antigen via a nucleotide-linked version, namely GDP-perosamine. Three enzymes are required for the biosynthesis of GDP-perosamine starting from mannose 1-phosphate. The focus of this investigation is GDP-perosamine synthase from Caulobacter crescentus, which catalyzes the final step in GDP-perosamine synthesis, the conversion of GDP-4-keto-6-deoxymannose to GDP-perosamine. The enzyme is PLP-dependent and belongs to the aspartate aminotransferase superfamily. It contains the typically conserved active site lysine residue, which forms a Schiff base with the PLP cofactor. Two crystal structures were determined for this investigation: a site-directed mutant protein (K186A) complexed with GDP-perosamine and the wild-type enzyme complexed with an unnatural ligand, GDP-3-deoxyperosamine. These structures, determined to 1.6 and 1.7 {angstrom} resolution, respectively, revealed the manner in which products, and presumably substrates, are accommodated within the active site pocket of GDP-perosamine synthase. Additional kinetic analyses using both the natural and unnatural substrates revealed that the K{sub m} for the unnatural substrate was unperturbed relative to that of the natural substrate, but the k{sub cat} was lowered by a factor of approximately 200. Taken together, these studies shed light on why GDP-perosamine synthase functions as an aminotransferase whereas another very similar PLP-dependent enzyme, GDP-4-keto-6-deoxy-d-mannose 3-dehydratase or ColD, catalyzes a dehydration reaction using the same substrate.

  14. Identification of promiscuous ene-reductase activity by mining structural databases using active site constellations

    PubMed Central

    Steinkellner, Georg; Gruber, Christian C.; Pavkov-Keller, Tea; Binter, Alexandra; Steiner, Kerstin; Winkler, Christoph; Łyskowski, Andrzej; Schwamberger, Orsolya; Oberer, Monika; Schwab, Helmut; Faber, Kurt; Macheroux, Peter; Gruber, Karl

    2014-01-01

    The exploitation of catalytic promiscuity and the application of de novo design have recently opened the access to novel, non-natural enzymatic activities. Here we describe a structural bioinformatic method for predicting catalytic activities of enzymes based on three-dimensional constellations of functional groups in active sites (‘catalophores’). As a proof-of-concept we identify two enzymes with predicted promiscuous ene-reductase activity (reduction of activated C–C double bonds) and compare them with known ene-reductases, that is, members of the Old Yellow Enzyme family. Despite completely different amino acid sequences, overall structures and protein folds, high-resolution crystal structures reveal equivalent binding modes of typical Old Yellow Enzyme substrates and ligands. Biochemical and biocatalytic data show that the two enzymes indeed possess ene-reductase activity and reveal an inverted stereopreference compared with Old Yellow Enzymes for some substrates. This method could thus be a tool for the identification of viable starting points for the development and engineering of novel biocatalysts. PMID:24954722

  15. An ionizable active-site tryptophan imparts catalase activity to a peroxidase core.

    PubMed

    Loewen, Peter C; Carpena, Xavi; Vidossich, Pietro; Fita, Ignacio; Rovira, Carme

    2014-05-21

    Catalase peroxidases (KatG's) are bifunctional heme proteins that can disproportionate hydrogen peroxide (catalatic reaction) despite their structural dissimilarity with monofunctional catalases. Using X-ray crystallography and QM/MM calculations, we demonstrate that the catalatic reaction of KatG's involves deprotonation of the active-site Trp, which plays a role similar to that of the distal His in monofunctional catalases. The interaction of a nearby mobile arginine with the distal Met-Tyr-Trp essential adduct (in/out) acts as an electronic switch, triggering deprotonation of the adduct Trp.

  16. 317/319 Phytoremediation site monitoring report - 2009 growing season : final report.

    SciTech Connect

    Negri, C .N.; Benda, P. L.; Gopalakrishnan, G.; Energy Systems

    2010-02-10

    In 1999, Argonne National Laboratory (Argonne) designed and installed a series of engineered plantings consisting of a vegetative cover system and approximately 800 hybrid poplars and willows rooting at various predetermined depths. The plants were installed using various methods including Applied Natural Science's TreeWell{reg_sign} system. The goal of the installation was to protect downgradient surface and groundwater by intercepting the contaminated groundwater with the tree roots, removing moisture from the upgradient soil area, reducing water infiltration, preventing soil erosion, degrading and/or transpiring the residual volatile organic compounds (VOCs), and removing tritium from the subsoil and groundwater. This report presents the results of the monitoring activities conducted by Argonne's Energy Systems (ES) Division in the growing season of 2009. Monitoring of the planted trees began soon after the trees were installed in 1999 and has been conducted every summer since then. As the trees grew and consolidated their growth into the contaminated soil and groundwater, their exposure to the contaminants was progressively shown through tissue sampling. During the 2009 sampling campaign, VOC concentrations found in the French Drain area were in general consistent with or slightly lower than the 2008 results. Additionally, closely repeated, stand wide analyses showed contaminant fluctuations that may indicate short-term contaminant depletion in the area of interest of roots. This data will be useful to determine short-term removal rate by the trees. As in previous years, levels in the Hydraulic Control Area were close to background levels except for a few exceptions.

  17. Nuclear Site Security in the Event of Terrorist Activity

    SciTech Connect

    Thomson, M.L.; Sims, J.

    2008-07-01

    This paper, presented as a poster, identifies why ballistic protection should now be considered at nuclear sites to counter terrorist threats. A proven and flexible form of multi purpose protection is described in detail with identification of trial results that show its suitability for this role. (authors)

  18. Analysis of Chlamydia caviae entry sites and involvement of Cdc42 and Rac activity.

    PubMed

    Subtil, Agathe; Wyplosz, Benjamin; Balañá, María Eugenia; Dautry-Varsat, Alice

    2004-08-01

    In epithelial cells, endocytic activity is mostly dedicated to nutrient and macromolecule uptake. To invade these cells, Chlamydiaceae, like other pathogens, have evolved strategies that utilise the existing endocytic machineries and signalling pathways, but little is known about the host cell molecules involved. In this report, we show that within five minutes of infection of HeLa cells by Chlamydia caviae GPIC strain several events take place in the immediate vicinity of invasive bacteria: GM1-containing microdomains cluster, tyrosine-phosphorylated proteins accumulate, and intense actin polymerization occurs. We show that actin polymerization is controlled by the small GTPases Cdc42 and Rac, which become activated upon infection. Expression of dominant negative forms of these GTPases inhibits C. caviae entry and leads to abnormal actin polymerization. In contrast, the small GTPase Rho does not seem essential for bacterial entry. Finally, phosphatidylinositol 3-kinase activity is also required for internalization of C. caviae, probably downstream of the other molecular events reported here. We present the first scheme of the events occurring at the sites of invasion of epithelial cells by a member of the Chlamydiaceae family.

  19. Practical 4′-Phosphopantetheine Active Site Discovery from Proteomic Samples

    PubMed Central

    Meier, Jordan L.; Patel, Anand D.; Niessen, Sherry; Meehan, Michael; Kersten, Roland; Yang, Jane Y.; Rothmann, Michael; Cravatt, Benjamin F.; Dorrestein, Pieter

    2011-01-01

    Polyketide and nonribosomal peptides constitute important classes of small molecule natural products. Due to the proven biological activities of these compounds, novel methods for discovery and study of the polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) enzymes responsible for their production remains an area of intense interest, and proteomic approaches represent a relatively unexplored avenue. While these enzymes may be distinguished from the proteomic milieu by their use of the 4′-phosphopantetheine (PPant) posttranslational modification, proteomic detection of PPant peptides is hindered by their low abundance and labile nature which leaves them unassigned using traditional database searching. Here we address key experimental and computational challenges to facilitate practical discovery of this important posttranslational modification during shotgun proteomics analysis using low-resolution ion-trap mass spectrometers. Activity-based enrichment maximizes MS input of PKS/NRPS peptides, while targeted fragmentation detects putative PPant active sites. An improved data analysis pipeline allows experimental identification and validation of these PPant peptides directly from MS2 data. Finally, a machine learning approach is developed to directly detect PPant peptides from only MS2 fragmentation data. By providing new methods for analysis of an often cryptic posttranslational modification, these methods represent a first step towards the study of natural product biosynthesis in proteomic settings. PMID:21067235

  20. Active Layer and Moisture Measurements for Intensive Site 0 and 1, Barrow, Alaska

    DOE Data Explorer

    John Peterson

    2015-04-17

    These are measurements of Active Layer Thickness collected along several lines beginning in September, 2011 to the present. The data were collected at several time periods along the Site0 L2 Line, the Site1 AB Line, and an ERT Monitoring Line near Area A in Site1.

  1. Structural mechanism of RuBisCO activation by carbamylation of the active site lysine

    PubMed Central

    Stec, Boguslaw

    2012-01-01

    Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is a crucial enzyme in carbon fixation and the most abundant protein on earth. It has been studied extensively by biochemical and structural methods; however, the most essential activation step has not yet been described. Here, we describe the mechanistic details of Lys carbamylation that leads to RuBisCO activation by atmospheric CO2. We report two crystal structures of nitrosylated RuBisCO from the red algae Galdieria sulphuraria with O2 and CO2 bound at the active site. G. sulphuraria RuBisCO is inhibited by cysteine nitrosylation that results in trapping of these gaseous ligands. The structure with CO2 defines an elusive, preactivation complex that contains a metal cation Mg2+ surrounded by three H2O/OH molecules. Both structures suggest the mechanism for discriminating gaseous ligands by their quadrupole electric moments. We describe conformational changes that allow for intermittent binding of the metal ion required for activation. On the basis of these structures we propose the individual steps of the activation mechanism. Knowledge of all these elements is indispensable for engineering RuBisCO into a more efficient enzyme for crop enhancement or as a remedy to global warming. PMID:23112176

  2. FY02 Final Report on Phytoremediation of Chlorinated Ethenes in Southern Sector Sediments of the Savannah River Site

    SciTech Connect

    Brigmon, R..L.

    2004-01-30

    This final report details the operations and results of a 3-year Seepline Phytoremediation Project performed adjacent to Tims Branch, which is located in the Southern Sector of the Savannah River Site (SRS) A/M Area. Phytoremediation is a process where interactions between vegetation, associated microorganisms, and the host substrate combine to effectively degrade contaminated soils, sediments, and groundwater. Phytoremediation is a rapidly developing technology that shows promise for the effective and safe cleanup of certain hazardous wastes. It has the potential to remediate numerous volatile organic compounds (VOCs). Extensive characterization work has demonstrated that two VOCs, tetrachloroethylene (PCE) and trichloroethylene (TCE) are the major components of the VOC-contaminated groundwater that is migrating through the Southern Sector and Tims Branch seepline area (WSRC, 1999). The PCE and TCE are chlorinated ethenes (CE), and have been detected in seepline soils and ground water adjacent to the ecologically-sensitive Tims Branch seepline area.

  3. Superfund Record of Decision (EPA Region 4): Perdido Groundwater Contamination Site, Perdido, Alabama (first remedial action) September 1988. Final report

    SciTech Connect

    Not Available

    1988-09-30

    The Perdido Groundwater Contamination site is located in the Town of Perdido, Baldwin County, Alabama. Site contamination occurred as a result of a 1965 train derailment on the Louisville and Nashville Railroad (now CSX Transportation, Inc.). Chemical (particularly benzene) from derailed tank cars spilled into drainage ditches, infiltrating the underlying aquifer. The area of ground water contamination covers approximately 15 acres and is centered downgradient about 300 yards from the derailment site. The Alabama Department of Public Health, Division of Public Water Supply (ADPWS) first documented reports of taste and odor problems in resident's water wells in 1981. Further studies showed benzene contamination in 6 of 27 wells, which led to supplying bottled water to 250 affected residents. The selected remedial action for this site includes: ground water pump and treatment using air stripping or activated carbon adsorption with the reinjection of treated water back into the aquifer, and air monitoring during operations; and ground water monitoring to measure success of the cleanup. The estimated capital cost for this remedial action is $169,000 with estimated annual O C cost of $103,000.

  4. Active-Site Hydration and Water Diffusion in Cytochrome P450cam: A Highly Dynamic Process

    SciTech Connect

    Miao, Yinglong; Baudry, Jerome Y

    2011-01-01

    Long-timescale molecular dynamics simulations (300 ns) are performed on both the apo- (i.e., camphor-free) and camphor-bound cytochrome P450cam (CYP101). Water diffusion into and out of the protein active site is observed without biased sampling methods. During the course of the molecular dynamics simulation, an average of 6.4 water molecules is observed in the camphor-binding site of the apo form, compared to zero water molecules in the binding site of the substrate-bound form, in agreement with the number of water molecules observed in crystal structures of the same species. However, as many as 12 water molecules can be present at a given time in the camphor-binding region of the active site in the case of apo-P450cam, revealing a highly dynamic process for hydration of the protein active site, with water molecules exchanging rapidly with the bulk solvent. Water molecules are also found to exchange locations frequently inside the active site, preferentially clustering in regions surrounding the water molecules observed in the crystal structure. Potential-of-mean-force calculations identify thermodynamically favored trans-protein pathways for the diffusion of water molecules between the protein active site and the bulk solvent. Binding of camphor in the active site modifies the free-energy landscape of P450cam channels toward favoring the diffusion of water molecules out of the protein active site.

  5. Parameterization of an Active Thermal Erosion Site, Caribou Creek, Alaska

    NASA Astrophysics Data System (ADS)

    Busey, R.; Bolton, W. R.; Cherry, J. E.; Hinzman, L. D.

    2012-12-01

    Thermokarst features are thought to be an important mechanism for landscape change in permafrost-dominated cold regions, but few such features have been incorporated into full featured landscape models. The root of this shortcoming is that historic observations are not detailed enough to parameterize a model, and the models typically do not include the relevant processes for thermal erosion. A new, dynamic thermokarst feature has been identified at the Caribou-Poker Creek Research Watershed (CPCRW) in the boreal forest of Interior Alaska. Located adjacent to a traditional use trail, this feature terminates directly in Caribou Creek. Erosion within the feature is driven predominantly by fluvial interflow. CPCRW is a Long-Term Ecological Research site underlain by varying degrees of relatively warm, discontinuous permafrost. This poster will describe the suite of measurements that have been undertaken to parameterize the ERODE model for this site, including thorough surveys, time lapse- and aerial photography, and 3-D structure from motion algorithms.

  6. Blogs and Social Network Sites as Activity Systems: Exploring Adult Informal Learning Process through Activity Theory Framework

    ERIC Educational Resources Information Center

    Heo, Gyeong Mi; Lee, Romee

    2013-01-01

    This paper uses an Activity Theory framework to explore adult user activities and informal learning processes as reflected in their blogs and social network sites (SNS). Using the assumption that a web-based space is an activity system in which learning occurs, typical features of the components were investigated and each activity system then…

  7. Chemical-Stockpile Disposal Program. Risk analysis of the disposal of chemical munitions at regional or national sites. Final report, 3 February 1986-25 August 1987

    SciTech Connect

    Barsell, A.W.; Bellis, E.A.; Bolig, C.A.; Deremer, R.K.; Everline, C.J.

    1987-08-01

    This document was prepared for the U.S. Army to support the Final Programmatic Environmental Impact Statement for the Chemical Stockpile Disposal Program. This report describes the results of a comprehensive probabilistic assessment of the frequency and magnitude of chemical agent release for the storage, handling, on-site transportation, off-site transportation, and chemical-demilitarization plant operations associated with the disposal of the chemical stockpile at two regional disposal sites or at a single national disposal site. Rail transportation from seven sites, air transportation from two sites and water transportation from one site were the off-site transportation modes analyzed. Both internal accident initiators (e.g., human error, equipment malfunction) and external accident initiators (e.g., earthquakes, airplane crashes) were included in the analysis.

  8. Site selection, drilling, and completion of two horizontal wells in the Devonian Shales of West Virginia. Final report

    SciTech Connect

    Overbey, W.K. Jr.; Carden, R.S.; Locke, C.D.; Salamy, S.P.; Reeves, T.K.; Johnson, H.R.

    1992-03-01

    This report presents a summary of the geologic site selection studies, planning, drilling, completing, stimulating, and testing of two horizontal wells drilled in the Devonian Shales of the Appalachian Basin in West Virginia. Each horizontal well was designed and managed by BDM as the prime contractor to the Department of Energy. The first well was drilled with industry partner Cabot Oil and Gas Corporation in Putnam County, West Virginia. The second well was drilled with Consolidated Natural Gas Company in Calhoun County, West Virginia. This report summarizes four reports prepared by BDM which detail the site selection rationale and the drilling and completion operations of each well. Each horizontal well is currently producing commercial quantities of hydrocarbons. The successful application of horizontal well technology represent continued development of the technology for application to tight and unconventional natural gas resources of the United States. Continued technology development is expected to ultimately result in commercial horizontal well drilling activity by industry in the Appalachian Basin.

  9. Early Site Permit Demonstration Program: Recommendations for communication activities and public participation in the Early Site Permit Demonstration Program

    SciTech Connect

    Not Available

    1993-01-27

    On October 24, 1992, President Bush signed into law the National Energy Policy Act of 1992. The bill is a sweeping, comprehensive overhaul of the Nation`s energy laws, the first in more than a decade. Among other provisions, the National Energy Policy Act reforms the licensing process for new nuclear power plants by adopting a new approach developed by the US Nuclear Regulatory Commission (NRC) in 1989, and upheld in court in 1992. The NRC 10 CFR Part 52 rule is a three-step process that guarantees public participation at each step. The steps are: early site permit approval; standard design certifications; and, combined construction/operating licenses for nuclear power reactors. Licensing reform increases an organization`s ability to respond to future baseload electricity generation needs with less financial risk for ratepayers and the organization. Costly delays can be avoided because design, safety and siting issues will be resolved before a company starts to build a plant. Specifically, early site permit approval allows for site suitability and acceptability issues to be addressed prior to an organization`s commitment to build a plant. Responsibility for site-specific activities, including communications and public participation, rests with those organizations selected to try out early site approval. This plan has been prepared to assist those companies (referred to as sponsoring organizations) in planning their communications and public involvement programs. It provides research findings, information and recommendations to be used by organizations as a resource and starting point in developing their own plans.

  10. Active Site Structure and Peroxidase Activity of Oxidatively Modified Cytochrome c Species in Complexes with Cardiolipin.

    PubMed

    Capdevila, Daiana A; Oviedo Rouco, Santiago; Tomasina, Florencia; Tortora, Verónica; Demicheli, Verónica; Radi, Rafael; Murgida, Daniel H

    2015-12-29

    We report a resonance Raman and UV-vis characterization of the active site structure of oxidatively modified forms of cytochrome c (Cyt-c) free in solution and in complexes with cardiolipin (CL). The studied post-translational modifications of Cyt-c include methionine sulfoxidation and tyrosine nitration, which lead to altered heme axial ligation and increased peroxidase activity with respect to those of the wild-type protein. In spite of the structural and activity differences between the protein variants free in solution, binding to CL liposomes induces in all cases the formation of a spectroscopically identical bis-His axial coordination conformer that more efficiently promotes lipid peroxidation. The spectroscopic results indicate that the bis-His form is in equilibrium with small amounts of high-spin species, thus suggesting a labile distal His ligand as the basis for the CL-induced increase in enzymatic activity observed for all protein variants. For Cyt-c nitrated at Tyr74 and sulfoxidized at Met80, the measured apparent binding affinities for CL are ∼4 times larger than for wild-type Cyt-c. On the basis of these results, we propose that these post-translational modifications may amplify the pro-apoptotic signal of Cyt-c under oxidative stress conditions at CL concentrations lower than for the unmodified protein.

  11. 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

  12. 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.

  13. Active site densities, oxygen activation and adsorbed reactive oxygen in alcohol activation on npAu catalysts.

    PubMed

    Wang, Lu-Cun; Friend, C M; Fushimi, Rebecca; Madix, Robert J

    2016-07-01

    The activation of molecular O2 as well as the reactivity of adsorbed oxygen species is of central importance in aerobic selective oxidation chemistry on Au-based catalysts. Herein, we address the issue of O2 activation on unsupported nanoporous gold (npAu) catalysts by applying a transient pressure technique, a temporal analysis of products (TAP) reactor, to measure the saturation coverage of atomic oxygen, its collisional dissociation probability, the activation barrier for O2 dissociation, and the facility with which adsorbed O species activate methanol, the initial step in the catalytic cycle of esterification. The results from these experiments indicate that molecular O2 dissociation is associated with surface silver, that the density of reactive sites is quite low, that adsorbed oxygen atoms do not spill over from the sites of activation onto the surrounding surface, and that methanol reacts quite facilely with the adsorbed oxygen atoms. In addition, the O species from O2 dissociation exhibits reactivity for the selective oxidation of methanol but not for CO. The TAP experiments also revealed that the surface of the npAu catalyst is saturated with adsorbed O under steady state reaction conditions, at least for the pulse reaction. PMID:27376884

  14. Remedial Action Plan and site design for stabilization of the inactive uranium mill tailings site at Mexican Hat, Utah: Text, Appendices A--C. Final report

    SciTech Connect

    1988-07-01

    This Remedial Action Plan (RAP) has been developed to serve a two- fold purpose. It presents the activities proposed by the Department of Energy (DOE) to accomplish long-term stabilization and control of the residual radioactive materials (RRM) from Monument Valley Arizona, and Mexican Hat, Utah, at the Mexican Hat disposal site. It also serves to document the concurrence of both the Navajo Nation and the Nuclear Regulatory Commission (NRC) in the remedial action. This agreement, upon execution by DOE and the Navajo Nation and concurrence by the NRC, becomes Appendix B of the Cooperative Agreement. This document has been structured to provide a comprehensive understanding of the remedial action proposed for the Monument Valley and Mexican Hat sites. It includes specific design and construction requirements for the remedial action. Pertinent information and data are included with reference given to the supporting documents. Appendices A,B, and C are provided as part of this document. Appendix A presents regulatory compliance issues, Appendix B provides details of the engineering design, and Appendix C presents the radiological support plan.

  15. Remedial Action Plan and Site Design for stabilization of the inactive Uranium Mill Tailings sites at Slick Rock, Colorado: Appendix C to Attachment 3, Calculations. Final

    SciTech Connect

    1995-09-01

    This volume contains calculations for: Slick Rock processing sites background ground water quality; Slick Rock processing sites lysimeter water quality; Slick Rock processing sites on-site and downgradient ground water quality; Slick Rock disposal site background water quality; Burro Canyon disposal site, Slick Rock, Colorado, average hydraulic gradients and average liner ground water velocities in the upper, middle, and lower sandstone units of the Burro Canyon formation; Slick Rock--Burro Canyon disposal site, Burro Canyon pumping and slug tests--analyses; water balance and surface contours--Burro Canyon disposal cell; and analytical calculation of drawdown in a hypothetical well completed in the upper sandstone unit of the Burro Canyon formation.

  16. Reactive characterization as a probe of the nature of catalytic sites. Final report, April 15, 1988--February 14, 1993

    SciTech Connect

    Brenner, A.

    1998-05-01

    The primary goal of the last year of the research program was to create a new type of selective heterogeneous catalyst. The new catalysts were synthesized, their unusual selectivity assessed by a model reaction, and some of the parameters which are important in creating unusual selectivity in these catalysts determined. Near the end of this proposal, considerable excitement was generated by the discovery of high temperature superconductors. It was decided to briefly investigate the activity of some superconductors and related cuprates. This research was done in concert with a project funded by Ford Motor Company. Catalysts were investigated for two reactions useful in pollution control: CO oxidation and NO reduction. In addition, some stoichiometric measurements of the oxygen content of superconductors and related cuprates were made using a TPR apparatus in the lab. In addition, some experiments were done with the objective of preparing novel MO-Pd/Al{sub 2}O{sub 3} catalysts in which the Mo and Pd were in close contact. These catalysts have the potential of replacing much more expensive rhodium containing catalysts which are currently used for emissions control. Progress on the following is described: H{sub 2}-D{sub 2} exchange on transition metals; New method of determining the number of active sites; New method of determining the hydroxyl content of catalysts; H{sub 2}-D{sub 2} exchange on metal oxides; Reactive characterization and atomic isolation of active sites; Site isolated catalysts synthesized by selective poisoning; Catalysts prepared from high temperature superconductors; Mixed metal Pd-Mo catalysts; and Selective reduction of nitric oxide.

  17. Possible active site of the sweet-tasting protein thaumatin.

    PubMed

    Slootstra, J W; De Geus, P; Haas, H; Verrips, C T; Meloen, R H

    1995-10-01

    Epitopes on thaumatin and monellin were studied using the PEPSCAN-technology. The antibodies used were raised against thaumatin. Only antibodies that, in an ELISA, both recognized thaumatin and monellin were used in the PEPSCAN-analyses. On thaumatin two major overlapping epitopes were identified. On monellin no epitopes could be identified. The identified epitope region on thaumatin shares structural features with various peptide and protein sweeteners. It contains an aspartame-like site which is formed by Asp21 and Phe80, tips of the two extruding loops KGDAALDAGGR19-29 and CKRFGRPP77-84, which are spatially positioned next to each other. Furthermore, sub-sequences of the KGDAALDAGGR19-29 loop are similar to peptide-sweeteners such as L-Asp-D-Ala-L-Ala-methyl ester and L-Asp-D-Ala-Gly-methyl ester. Since the aspartame-like Asp21-Phe80 site and the peptide-sweetener-like sequences are also not present in non-sweet thaumatin-like proteins it is postulated that the KGDAALDAGGR19-29- and CKRFGRPP77-84 loop contain important sweet-taste determinants. This region has previously not been implicated as a sweet-taste determinant of thaumatin.

  18. Synthetic models of the active site of catechol oxidase: mechanistic studies.

    PubMed

    Koval, Iryna A; Gamez, Patrick; Belle, Catherine; Selmeczi, Katalin; Reedijk, Jan

    2006-09-01

    The ability of copper proteins to process dioxygen at ambient conditions has inspired numerous research groups to study their structural, spectroscopic and catalytic properties. Catechol oxidase is a type-3 copper enzyme usually encountered in plant tissues and in some insects and crustaceans. It catalyzes the conversion of a large number of catechols into the respective o-benzoquinones, which subsequently auto-polymerize, resulting in the formation of melanin, a dark pigment thought to protect a damaged tissue from pathogens. After the report of the X-ray crystal structure of catechol oxidase a few years earlier, a large number of publications devoted to the biomimetic modeling of its active site appeared in the literature. This critical review (citing 114 references) extensively discusses the synthetic models of this enzyme, with a particular emphasis on the different approaches used in the literature to study the mechanism of the catalytic oxidation of the substrate (catechol) by these compounds. These are the studies on the substrate binding to the model complexes, the structure-activity relationship, the kinetic studies of the catalytic oxidation of the substrate and finally the substrate interaction with (per)oxo-dicopper adducts. The general overview of the recognized types of copper proteins and the detailed description of the crystal structure of catechol oxidase, as well as the proposed mechanisms of the enzymatic cycle are also presented. PMID:16936929

  19. Assessment of activation products in the Savannah River Site environment

    SciTech Connect

    Carlton, W.H.; Denham, M.

    1996-07-01

    This document assesses the impact of radioactive activation products released from SRS facilities since the first reactor became operational late in 1953. The isotopes reported here are those whose release resulted in the highest dose to people living near SRS: {sup 32}P, {sup 51}Cr, {sup 60}C, and {sup 65}Zn. Release pathways, emission control features, and annual releases to the aqueous and atmospheric environments are discussed. No single incident has resulted in a major acute release of activation products to the environment. The releases were the result of normal operations of the reactors and separations facilities. Releases declined over the years as better controls were established and production was reduced. The overall radiological impact of SRS activation product atmospheric releases from 1954 through 1994 on the offsite maximally exposed individual can be characterized by a total dose of 0.76 mrem. During the same period, such an individual received a total dose of 14,400 mrem from non-SRS sources of ionizing radiation present in the environment. SRS activation product aqueous releases between 1954 and 1994 resulted in a total dose of 54 mrem to the offsite maximally exposed individual. The impact of SRS activation product releases on offsite populations also has been evaluated.

  20. Evapotranspiration Cover for the 92-Acre Area Retired Mixed Waste Pits, Area 5 Waste Management Division, Nevada National Security Site, Final CQA Report

    SciTech Connect

    NSTec Environmental Management; The Delphi Groupe, Inc.; J. A. Cesare and Associates, Inc.

    2012-01-31

    The report is the Final Construction Quality Assurance (CQA) Report for the 92-Acrew Evapotranspiration Cover, Area 5 Waste Management Division Retired Mixed Waste Pits, Nevada National Security Site, Nevada, for the period of January 20, 2011, to January 31, 2012 The Area 5 RWMS uses engineered shallow-land burial cells to dispose of packaged waste. The 92-Acre Area encompasses the southern portion of the Area 5 RWMS, which has been designated for the first final closure operations. This area contains 13 Greater Confinement Disposal (GCD) boreholes, 16 narrow trenches, and 9 broader pits. With the exception of two active pits (P03 and P06), all trenches and pits in the 92-Acre Area had operational covers approximately 2.4 meters thick, at a minimum, in most areas when this project began. The units within the 92-Acre Area are grouped into the following six informal categories based on physical location, waste types and regulatory requirements: (1) Pit 3 Mixed Waste Disposal Unit (MWDU); (2) Corrective Action Unit (CAU) 111; (3) CAU 207; (4) Low-level waste disposal units; (5) Asbestiform low-level waste disposal units; and (6) One transuranic (TRU) waste trench.

  1. Quantifying the density and utilization of active sites in non-precious metal oxygen electroreduction catalysts

    PubMed Central

    Sahraie, Nastaran Ranjbar; Kramm, Ulrike I.; Steinberg, Julian; Zhang, Yuanjian; Thomas, Arne; Reier, Tobias; Paraknowitsch, Jens-Peter; Strasser, Peter

    2015-01-01

    Carbon materials doped with transition metal and nitrogen are highly active, non-precious metal catalysts for the electrochemical conversion of molecular oxygen in fuel cells, metal air batteries, and electrolytic processes. However, accurate measurement of their intrinsic turn-over frequency and active-site density based on metal centres in bulk and surface has remained difficult to date, which has hampered a more rational catalyst design. Here we report a successful quantification of bulk and surface-based active-site density and associated turn-over frequency values of mono- and bimetallic Fe/N-doped carbons using a combination of chemisorption, desorption and 57Fe Mössbauer spectroscopy techniques. Our general approach yields an experimental descriptor for the intrinsic activity and the active-site utilization, aiding in the catalyst development process and enabling a previously unachieved level of understanding of reactivity trends owing to a deconvolution of site density and intrinsic activity. PMID:26486465

  2. Characterization of an Active Thermal Erosion Site, Caribou Creek, Alaska

    NASA Astrophysics Data System (ADS)

    Busey, R.; Bolton, W. R.; Cherry, J. E.; Hinzman, L. D.

    2013-12-01

    The goal of this project is to estimate volume loss of soil over time from this site, provide parameterizations on erodibility of ice rich permafrost and serve as a baseline for future landscape evolution simulations. Located in the zone of discontinuous permafrost, the interior region of Alaska (USA) is home to a large quantity of warm, unstable permafrost that is both high in ice content and has soil temperatures near the freezing point. Much of this permafrost maintains a frozen state despite the general warming air temperature trend in the region due to the presence of a thick insulating organic mat and a dense root network in the upper sub-surface of the soil column. At a rapidly evolving thermo-erosion site, located within the Caribou-Poker Creeks Research Watershed (part of the Bonanza Creek LTER) near Chatanika, Alaska (N65.140, W147.570), the protective organic layer and associated plants were disturbed by an adjacent traditional use trail and the shifting of a groundwater spring. These triggers have led to rapid geomorphological change on the landscape as the soil thaws and sediment is transported into the creek at the valley bottom. Since 2006 (approximately the time of initiation), the thermal erosion has grown to 170 meters length, 3 meters max depth, and 15 meters maximum width. This research combines several data sets: DGPS survey, imagery from an extremely low altitude pole-based remote sensing (3 to 5 meters above ground level), and imagery from an Unmanned Aerial System (UAS) at about 60m altitude.

  3. Molecular Basis for Enzymatic Sulfite Oxidation -- HOW THREE CONSERVED ACTIVE SITE RESIDUES SHAPE ENZYME ACTIVITY

    SciTech Connect

    Bailey, Susan; Rapson, Trevor; Johnson-Winters, Kayunta; Astashkin, Andrei; Enemark, John; Kappler, Ulrike

    2008-11-10

    Sulfite dehydrogenases (SDHs) catalyze the oxidation and detoxification of sulfite to sulfate, a reaction critical to all forms of life. Sulfite-oxidizing enzymes contain three conserved active site amino acids (Arg-55, His-57, and Tyr-236) that are crucial for catalytic competency. Here we have studied the kinetic and structural effects of two novel and one previously reported substitution (R55M, H57A, Y236F) in these residues on SDH catalysis. Both Arg-55 and His-57 were found to have key roles in substrate binding. An R55M substitution increased Km(sulfite)(app) by 2-3 orders of magnitude, whereas His-57 was required for maintaining a high substrate affinity at low pH when the imidazole ring is fully protonated. This effect may be mediated by interactions of His-57 with Arg-55 that stabilize the position of the Arg-55 side chain or, alternatively, may reflect changes in the protonation state of sulfite. Unlike what is seen for SDHWT and SDHY236F, the catalytic turnover rates of SDHR55M and SDHH57A are relatively insensitive to pH (~;;60 and 200 s-1, respectively). On the structural level, striking kinetic effects appeared to correlate with disorder (in SDHH57A and SDHY236F) or absence of Arg-55 (SDHR55M), suggesting that Arg-55 and the hydrogen bonding interactions it engages in are crucial for substrate binding and catalysis. The structure of SDHR55M has sulfate bound at the active site, a fact that coincides with a significant increase in the inhibitory effect of sulfate in SDHR55M. Thus, Arg-55 also appears to be involved in enabling discrimination between the substrate and product in SDH.

  4. Active Site Metal Occupancy and Cyclic Di-GMP Phosphodiesterase Activity of Thermotoga maritima HD-GYP.

    PubMed

    Miner, Kyle D; Kurtz, Donald M

    2016-02-16

    HD-GYPs make up a subclass of the metal-dependent HD phosphohydrolase superfamily and catalyze conversion of cyclic di(3',5')-guanosine monophosphate (c-di-GMP) to 5'-phosphoguanylyl-(3'→5')-guanosine (pGpG) and GMP. Until now, the only reported crystal structure of an HD-GYP that also exhibits c-di-GMP phosphodiesterase activity contains a His/carboxylate ligated triiron active site. However, other structural and phylogenetic correlations indicate that some HD-GYPs contain dimetal active sites. Here we provide evidence that an HD-GYP c-di-GMP phosphodiesterase, TM0186, from Thermotoga maritima can accommodate both di- and trimetal active sites. We show that an as-isolated iron-containing TM0186 has an oxo/carboxylato-bridged diferric site, and that the reduced (diferrous) form is necessary and sufficient to catalyze conversion of c-di-GMP to pGpG, but that conversion of pGpG to GMP requires more than two metals per active site. Similar c-di-GMP phosphodiesterase activities were obtained with divalent iron or manganese. On the basis of activity correlations with several putative metal ligand residue variants and molecular dynamics simulations, we propose that TM0186 can accommodate both di- and trimetal active sites. Our results also suggest that a Glu residue conserved in a subset of HD-GYPs is required for formation of the trimetal site and can also serve as a labile ligand to the dimetal site. Given the anaerobic growth requirement of T. maritima, we suggest that this HD-GYP can function in vivo with either divalent iron or manganese occupying di- and trimetal sites.

  5. A rapid and direct method for the determination of active site accessibility in proteins based on ESI-MS and active site titrations.

    PubMed

    O'Farrell, Norah; Kreiner, Michaela; Moore, Barry D; Parker, Marie-Claire

    2006-11-01

    We have developed an electrospray ionisation mass spectrometry (ESI-MS) technique that can be applied to rapidly determine the number of intact active sites in proteins. The methodology relies on inhibiting the protein with an active-site irreversible inhibitor and then using ESI-MS to determine the extent of inhibition. We have applied this methodology to a test system: a serine protease, subtilisin Carlsberg, and monitored the extent of inhibition by phenylmethylsulfonyl fluoride (PMSF), an irreversible serine hydrolase inhibitor as a function of the changes in immobilisation and hydration conditions. Two types of enzyme preparation were investigated, lyophilised enzymes and protein-coated microcrystals (PCMC).

  6. Cyanide does more to inhibit heme enzymes, than merely serving as an active-site ligand.

    PubMed

    Parashar, Abhinav; Venkatachalam, Avanthika; Gideon, Daniel Andrew; Manoj, Kelath Murali

    2014-12-12

    The toxicity of cyanide is hitherto attributed to its ability to bind to heme proteins' active site and thereby inhibit their activity. It is shown herein that the long-held interpretation is inadequate to explain several observations in heme-enzyme reaction systems. Generation of cyanide-based diffusible radicals in heme-enzyme reaction milieu could shunt electron transfers (by non-active site processes), and thus be detrimental to the efficiency of oxidative outcomes.

  7. Marine Biology Field Trip Sites. Ocean Related Curriculum Activities.

    ERIC Educational Resources Information Center

    Pauls, John

    The ocean affects all of our lives. Therefore, awareness of and information about the interconnections between humans and oceans are prerequisites to making sound decisions for the future. Project ORCA (Ocean Related Curriculum Activities) has developed interdisciplinary curriculum materials designed to meet the needs of students and teachers…

  8. Endolysosomes Are the Principal Intracellular Sites of Acid Hydrolase Activity.

    PubMed

    Bright, Nicholas A; Davis, Luther J; Luzio, J Paul

    2016-09-12

    The endocytic delivery of macromolecules from the mammalian cell surface for degradation by lysosomal acid hydrolases requires traffic through early endosomes to late endosomes followed by transient (kissing) or complete fusions between late endosomes and lysosomes. Transient or complete fusion results in the formation of endolysosomes, which are hybrid organelles from which lysosomes are re-formed. We have used synthetic membrane-permeable cathepsin substrates, which liberate fluorescent reporters upon proteolytic cleavage, as well as acid phosphatase cytochemistry to identify which endocytic compartments are acid hydrolase active. We found that endolysosomes are the principal organelles in which acid hydrolase substrates are cleaved. Endolysosomes also accumulated acidotropic probes and could be distinguished from terminal storage lysosomes, which were acid hydrolase inactive and did not accumulate acidotropic probes. Using live-cell microscopy, we have demonstrated that fusion events, which form endolysosomes, precede the onset of acid hydrolase activity. By means of sucrose and invertase uptake experiments, we have also shown that acid-hydrolase-active endolysosomes and acid-hydrolase-inactive, terminal storage lysosomes exist in dynamic equilibrium. We conclude that the terminal endocytic compartment is composed of acid-hydrolase-active, acidic endolysosomes and acid hydrolase-inactive, non-acidic, terminal storage lysosomes, which are linked and function in a lysosome regeneration cycle. PMID:27498570

  9. 75 FR 77871 - Agency Information Collection Activities: Final Collection; Comment Request

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-14

    ... for Short-Term Express Export Credit Insurance Policy to Application for Express Insurance. The form....S. Agency Information Collection Activities: Final Collection; Comment Request AGENCY: Export-Import... Agencies to comment on the proposed information collection, as required by the Paperwork Reduction Act...

  10. 76 FR 14009 - Agency Information Collection Activities: Final Collection; Comment Request

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-15

    ... export credit insurance policies. It also alerts Ex-Im Bank staff of defaults, so they can manage the... medium-term export credit insurance policies. It also alerts Ex-Im Bank staff of defaults, so they can....S. Agency Information Collection Activities: Final Collection; Comment Request AGENCY:...

  11. 75 FR 27556 - Agency Information Collection Activities: Final Collection; Comment Request

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-17

    ...-Buyer Export Credit Insurance Policy Application. SUMMARY: The Export-Import Bank of the United States... required by the Paperwork Reduction Act of 1995. The Short Term Multi-Buyer Export Credit Insurance Policy....S. Agency Information Collection Activities: Final Collection; Comment Request AGENCY:...

  12. 75 FR 8352 - Agency Information Collection Activities: Final Collection; Comment Request

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-24

    ....S. Agency Information Collection Activities: Final Collection; Comment Request AGENCY: Export-Import Bank of the U.S. ACTION: Submission for OMB review and comments request. FORM TITLE: Report of Premiums.... Affected Public: This form affects entities involved in the export of U.S. goods and services....

  13. 77 FR 41981 - Agency Information Collection Activities: Final Collection; Comment Request

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-17

    ....S. Agency Information Collection Activities: Final Collection; Comment Request AGENCY: Export-Import Bank of the U.S. ACTION: Submission for OMB review and comments request. Form Title: EIB 99-14 Export...-term (360 days and less) and medium-term (longer than 360 days), for the export of their U.S. goods...

  14. 77 FR 37041 - Agency Information Collection Activities: Final Collection; Comment Request

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-20

    ....S. Agency Information Collection Activities: Final Collection; Comment Request AGENCY: Export-Import Bank of the U.S. ACTION: Submission for OMB Review and Comments Request. Form Title: EIB 94-07... information collection, as required by the Paperwork Reduction Act of 1995. Ex-Im Bank's financial...

  15. 75 FR 66761 - Agency Information Collection Activities: Final Collection; Comment Request

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-29

    ....S. Agency Information Collection Activities: Final Collection; Comment Request AGENCY: Export-Import Bank of the U.S. ACTION: Submission for OMB Review and Comments Request. Form Title: EIB 10-01A Long... States. Its mission is to create and sustain U.S. jobs by financing U.S. exports through direct...

  16. 75 FR 57020 - Agency Information Collection Activities: Final Collection; Comment Request

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-17

    ... U.S. Agency Information Collection Activities: Final Collection; Comment Request AGENCY: Export-Import Bank of the U.S. ACTION: Submission for OMB review and comments request. Form Title: Report of... Institutions Only is used to determine the eligibility of the shipment(s) and to calculate the premium due...

  17. 76 FR 29242 - Agency Information Collection Activities: Final Collection; Comment Request

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-20

    ....S. Agency Information Collection Activities: Final Collection; Comment Request AGENCY: Export-Import Bank of the U.S. ACTION: Submission for OMB Review and Comments Request. Form Title: Report of Overdue... necessary to monitor the borrower's payments for exported goods covered under its short and...

  18. 77 FR 16549 - Agency Information Collection Activities: Final Collection; Comment Request

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-21

    ....S. Agency Information Collection Activities: Final Collection; Comment Request AGENCY: Export-Import Bank of the U.S. ACTION: Submission for OMB review and comments request. Form Title: EIB 94-07... emergency approval of Ex-Im Bank form EIB 94-07, Exporter's Certificate For Use With A Short Term...

  19. 77 FR 284 - Agency Information Collection Activities: Final Collection; Comment Request

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-04

    ....S. Agency Information Collection Activities: Final Collection; Comment Request AGENCY: Export-Import Bank of the U.S. ACTION: Submission for OMB Review and Comments Request. Form Title: Used Equipment... Export-Import Bank's determination of the appropriate term for the transaction. The form can be viewed...

  20. 75 FR 57020 - Agency Information Collection Activities: Final Collection; Comment Request

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-17

    ....S. Agency Information Collection Activities: Final Collection; Comment Request AGENCY: Export-Import Bank of the U.S. ACTION: Submission for OMB review and comments request. Form Title: Report of Premiums... eligibility of the shipment(s) and to calculate the premium due to Ex-Im Bank for its support of the...

  1. 75 FR 8353 - Agency Information Collection Activities: Final Collection; Comment Request

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-24

    ... U.S. Agency Information Collection Activities: Final Collection; Comment Request AGENCY: Export-Import Bank of the U.S. ACTION: Submission for OMB Review and Comments Request. Form Title: Application... export of U.S. goods and services. Annual Number of Respondents: 84. Estimated Time Per Respondent:...

  2. 77 FR 284 - Agency Information Collection Activities: Final Collection; Comment Request

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-04

    ....S. Agency Information Collection Activities: Final Collection; Comment Request AGENCY: Export-Import Bank of the U.S. ACTION: Submission for OMB review and comments request. Form Title: Co-Financing with... proposed co-financing transaction between a U.S. exporter, Ex-Im Bank, and a foreign export credit...

  3. 76 FR 19356 - Agency Information Collection Activities: Final Collection; Comment Request

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-07

    ....S. Agency Information Collection Activities: Final Collection; Comment Request AGENCY: Export-Import Bank of the U.S. ACTION: Submission for OMB review and comments request. Form Title: Letter of Interest... Review: Regular. Need and Use: Ex-Im Bank's Letter of Interest (LI) is a pre-export tool to help...

  4. 75 FR 54874 - Agency Information Collection Activities: Final Collection; Comment Request

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-09

    ....S. Agency Information Collection Activities: Final Collection; Comment Request AGENCY: Export-Import Bank of the U.S. ] ACTION: Submission for OMB review and comments request. Form Title: Application for... this form on paper or electronically. This is a new application form for use by small U.S....

  5. 77 FR 26277 - Agency Information Collection Activities: Final Collection; Comment Request

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-03

    ....S. Agency Information Collection Activities: Final Collection; Comment Request AGENCY: Export-Import Bank of the U.S. ACTION: Submission for OMB Review and Comments Request. Form Title: EIB 99-14 Export... credit information for their internal foreign buyer credit decision in which, in turn, commits...

  6. Installation restoration program final remedial investigation report IRP sites 8 and 10. 151st air refueling group Utah Air National Guard, Salt Lake City, Utah. Final report

    SciTech Connect

    1996-06-01

    This report presents the results from a Remedial Investigation (RI) for two sites at the Utah Air National Guard (UANG) Base located in Salt Lake City, Utah. The two sites investigated are identified as Installation Restoration Program (IRP) Site 8, a former underground storage tank (UST) location, and IRP Site 10, an existing petroleum, oil, and lubricants (POL) yard. The RI was conducted as outlined in the Remedial Investigation/Feasibility Study (RI/FS) Work Plan prepared by Stone Webster and submitted to and approved by the ANG in May 1993. The field work associated with the RI was performed in June, July, and August 1995.

  7. Outside-binding site mutations modify the active site's shapes in neuraminidase from influenza A H1N1.

    PubMed

    Tolentino-Lopez, Luis; Segura-Cabrera, Aldo; Reyes-Loyola, Paola; Zimic, Mirko; Quiliano, Miguel; Briz, Veronica; Muñoz-Fernández, Angeles; Rodríguez-Pérez, Mario; Ilizaliturri-Flores, Ian; Correa-Basurto, Jose

    2013-01-01

    The recent occurrence of 2009 influenza A (H1N1) pandemic as well as others has raised concern of a far more dangerous outcome should this virus becomes resistant to current drug therapies. The number of clinical cases that are resistant to oseltamivir (Tamiflu®) is larger than the limited number of neuraminidase (NA) mutations (H275Y, N295S, and I223R) that have been identified at the active site and that are associated to oseltamivir resistance. In this study, we have performed a comparative analysis between a set of NAs that have the most representative mutations located outside the active site. The recently crystallized NA-oseltamivir complex (PDB ID: 3NSS) was used as a wild-type structure. After selecting the target NA sequences, their three-dimensional (3D) structure was built using 3NSS as a template by homology modeling. The 3D NA models were refined by molecular dynamics (MD) simulations. The refined models were used to perform a docking study, using oseltamivir as a ligand. Furthermore, the docking results were refined by free-energy analysis using the MM-PBSA method. The analysis of the MD simulation results showed that the NA models reached convergence during the first 10 ns. Visual inspection and structural measures showed that the mutated NA active sites show structural variations. The docking and MM-PBSA results from the complexes showed different binding modes and free energy values. These results suggest that distant mutations located outside the active site of NA affect its structure and could be considered to be a new source of resistance to oseltamivir, which agrees with reports in the clinical literature.

  8. Remedial action plan and site design for stabilization of the Inactive Uranium Mill Tailings Site, Maybell, Colorado. Final report, Appendixes to attachment 3

    SciTech Connect

    Not Available

    1994-06-01

    This document contains supporting appendices to attachment 3 for the remedial action and site stabilization plan for Maybell, Colorado UMTRA site. Appendix A includes the Hydrological Services Calculations and Appendix B contains Ground Water Quality by Location data.

  9. Active site proton delivery and the lyase activity of human CYP17A1

    SciTech Connect

    Khatri, Yogan; Gregory, Michael C.; Grinkova, Yelena V.; Denisov, Ilia G.; Sligar, Stephen G.

    2014-01-03

    equivalents and protons are funneled into non-productive pathways. This is similar to previous work with other P450 catalyzed hydroxylation. However, catalysis of carbon–carbon bond scission by the T306A mutant was largely unimpeded by disruption of the CYP17A1 acid-alcohol pair. The unique response of CYP17A1 lyase activity to mutation of Thr306 is consistent with a reactive intermediate formed independently of proton delivery in the active site, and supports involvement of a nucleophilic peroxo-anion rather than the traditional Compound I in catalysis.

  10. Identification of inhibitors against the potential ligandable sites in the active cholera toxin.

    PubMed

    Gangopadhyay, Aditi; Datta, Abhijit

    2015-04-01

    The active cholera toxin responsible for the massive loss of water and ions in cholera patients via its ADP ribosylation activity is a heterodimer of the A1 subunit of the bacterial holotoxin and the human cytosolic ARF6 (ADP Ribosylation Factor 6). The active toxin is a potential target for the design of inhibitors against cholera. In this study we identified the potential ligandable sites of the active cholera toxin which can serve as binding sites for drug-like molecules. By employing an energy-based approach to identify ligand binding sites, and comparison with the results of computational solvent mapping, we identified two potential ligandable sites in the active toxin which can be targeted during structure-based drug design against cholera. Based on the probe affinities of the identified ligandable regions, docking-based virtual screening was employed to identify probable inhibitors against these sites. Several indole-based alkaloids and phosphates showed strong interactions to the important residues of the ligandable region at the A1 active site. On the other hand, 26 top scoring hits were identified against the ligandable region at the A1 ARF6 interface which showed strong hydrogen bonding interactions, including guanidines, phosphates, Leucopterin and Aristolochic acid VIa. This study has important implications in the application of hybrid structure-based and ligand-based methods against the identified ligandable sites using the identified inhibitors as reference ligands, for drug design against the active cholera toxin.

  11. Encroachment of Human Activity on Sea Turtle Nesting Sites

    NASA Astrophysics Data System (ADS)

    Ziskin, D.; Aubrecht, C.; Elvidge, C.; Tuttle, B.; Baugh, K.; Ghosh, T.

    2008-12-01

    The encroachment of anthropogenic lighting on sea turtle nesting sites poses a serious threat to the survival of these animals [Nicholas, 2001]. This danger is quantified by combining two established data sets. The first is the Nighttime Lights data produced by the NOAA National Geophysical Data Center [Elvidge et al., 1997]. The second is the Marine Turtle Database produced by the World Conservation Monitoring Centre (WCMC). The technique used to quantify the threat of encroachment is an adaptation of the method described in Aubrecht et al. [2008], which analyzes the stress on coral reef systems by proximity to nighttime lights near the shore. Nighttime lights near beaches have both a direct impact on turtle reproductive success since they disorient hatchlings when they mistake land-based lights for the sky-lit surf [Lorne and Salmon, 2007] and the lights are also a proxy for other anthropogenic threats. The identification of turtle nesting sites with high rates of encroachment will hopefully steer conservation efforts to mitigate their effects [Witherington, 1999]. Aubrecht, C, CD Elvidge, T Longcore, C Rich, J Safran, A Strong, M Eakin, KE Baugh, BT Tuttle, AT Howard, EH Erwin, 2008, A global inventory of coral reef stressors based on satellite observed nighttime lights, Geocarto International, London, England: Taylor and Francis. In press. Elvidge, CD, KE Baugh, EA Kihn, HW Kroehl, ER Davis, 1997, Mapping City Lights with Nighttime Data from the DMSP Operational Linescan System, Photogrammatic Engineering and Remote Sensing, 63:6, pp. 727-734. Lorne, JK, M Salmon, 2007, Effects of exposure to artificial lighting on orientation of hatchling sea turtles on the beach and in the ocean, Endangered Species Research, Vol. 3: 23-30. Nicholas, M, 2001, Light Pollution and Marine Turtle Hatchlings: The Straw that Breaks the Camel's Back?, George Wright Forum, 18:4, p77-82. Witherington, BE, 1999, Reducing Threats To Nesting Habitat, Research and Management Techniques for

  12. Mining Sites on the National Priorities List: NPL Site Summary Reports. Volume 4 (Oronogo-Duenweg Mining Belt to Tar Creek). Draft report (Final)

    SciTech Connect

    Houseman, V.

    1991-06-21

    Volume IV of the Mining Sites on the National Priorities List contains the following NPL Site Summary Reports: Oronogo-Deunweg Mining Belt, Palmerton Zinc, Sharon Steel/Midvale Tailings, Silver Bow Creek/Butte Area Site, Silver Mountain Mine, Smuggler Mountain, St. Louis Airport/Hazelwood Interim/Futura Coatings, Sulphur Bank Mercury Mine, and Tar Creek.

  13. Effects of Active-Site Modification and Quaternary Structure on the Regioselectivity of Catechol-O-Methyltransferase.

    PubMed

    Law, Brian J C; Bennett, Matthew R; Thompson, Mark L; Levy, Colin; Shepherd, Sarah A; Leys, David; Micklefield, Jason

    2016-02-18

    Catechol-O-methyltransferase (COMT), an important therapeutic target in the treatment of Parkinson's disease, is also being developed for biocatalytic processes, including vanillin production, although lack of regioselectivity has precluded its more widespread application. By using structural and mechanistic information, regiocomplementary COMT variants were engineered that deliver either meta- or para-methylated catechols. X-ray crystallography further revealed how the active-site residues and quaternary structure govern regioselectivity. Finally, analogues of AdoMet are accepted by the regiocomplementary COMT mutants and can be used to prepare alkylated catechols, including ethyl vanillin. PMID:26797714

  14. Reduction of Urease Activity by Interaction with the Flap Covering the Active Site

    PubMed Central

    Macomber, Lee; Minkara, Mona S.; Hausinger, Robert P.; Merz, Kenneth M.

    2015-01-01

    With the increasing appreciation for the human microbiome coupled with the global rise of antibiotic resistant organisms, it is imperative that new methods be developed to specifically target pathogens. To that end, a novel computational approach was devised to identify compounds that reduce the activity of urease, a medically important enzyme of Helicobacter pylori, Proteus mirabilis, and many other microorganisms. Urease contains a flexible loop that covers its active site; Glide was used to identify small molecules predicted to lock this loop in an open conformation. These compounds were screened against the model urease from Klebsiella aerogenes and the natural products epigallocatechin and quercetin were shown to inhibit at low and high micromolar concentrations, respectively. These molecules exhibit a strong time-dependent inactivation of urease that was not due to their oxygen sensitivity. Rather, these compounds appear to inactivate urease by reacting with a specific Cys residue located on the flexible loop. Substitution of this cysteine by alanine in the C319A variant increased the urease resistance to both epigallocatechin and quercetin, as predicted by the computational studies. Protein dynamics are integral to the function of many enzymes; thus, identification of compounds that lock an enzyme into a single conformation presents a useful approach to define potential inhibitors. PMID:25594724

  15. Mechanistic pathways of mercury removal from the organomercurial lyase active site.

    PubMed

    Silva, Pedro J; Rodrigues, Viviana

    2015-01-01

    Bacterial populations present in Hg-rich environments have evolved biological mechanisms to detoxify methylmercury and other organometallic mercury compounds. The most common resistance mechanism relies on the H(+)-assisted cleavage of the Hg-C bond of methylmercury by the organomercurial lyase MerB. Although the initial reaction steps which lead to the loss of methane from methylmercury have already been studied experimentally and computationally, the reaction steps leading to the removal of Hg(2+) from MerB and regeneration of the active site for a new round of catalysis have not yet been elucidated. In this paper, we have studied the final steps of the reaction catalyzed by MerB through quantum chemical computations at the combined MP2/CBS//B3PW91/6-31G(d) level of theory. While conceptually simple, these reaction steps occur in a complex potential energy surface where several distinct pathways are accessible and may operate concurrently. The only pathway which clearly emerges as forbidden in our analysis is the one arising from the sequential addition of two thiolates to the metal atom, due to the accumulation of negative charges in the active site. The addition of two thiols, in contrast, leads to two feasible mechanistic possibilities. The most straightforward pathway proceeds through proton transfer from the attacking thiol to Cys159 , leading to its removal from the mercury coordination sphere, followed by a slower attack of a second thiol, which removes Cys96. The other pathway involves Asp99 in an accessory role similar to the one observed earlier for the initial stages of the reaction and affords a lower activation enthalpy, around 14 kcal mol(-1), determined solely by the cysteine removal step rather than by the thiol ligation step. Addition of one thiolate to the intermediates arising from either thiol attack occurs without a barrier and produces an intermediate bound to one active site cysteine and from which Hg(SCH3)2 may be removed only after

  16. Mechanistic pathways of mercury removal from the organomercurial lyase active site

    PubMed Central

    Rodrigues, Viviana

    2015-01-01

    Bacterial populations present in Hg-rich environments have evolved biological mechanisms to detoxify methylmercury and other organometallic mercury compounds. The most common resistance mechanism relies on the H+-assisted cleavage of the Hg–C bond of methylmercury by the organomercurial lyase MerB. Although the initial reaction steps which lead to the loss of methane from methylmercury have already been studied experimentally and computationally, the reaction steps leading to the removal of Hg2+ from MerB and regeneration of the active site for a new round of catalysis have not yet been elucidated. In this paper, we have studied the final steps of the reaction catalyzed by MerB through quantum chemical computations at the combined MP2/CBS//B3PW91/6-31G(d) level of theory. While conceptually simple, these reaction steps occur in a complex potential energy surface where several distinct pathways are accessible and may operate concurrently. The only pathway which clearly emerges as forbidden in our analysis is the one arising from the sequential addition of two thiolates to the metal atom, due to the accumulation of negative charges in the active site. The addition of two thiols, in contrast, leads to two feasible mechanistic possibilities. The most straightforward pathway proceeds through proton transfer from the attacking thiol to Cys159 , leading to its removal from the mercury coordination sphere, followed by a slower attack of a second thiol, which removes Cys96. The other pathway involves Asp99 in an accessory role similar to the one observed earlier for the initial stages of the reaction and affords a lower activation enthalpy, around 14 kcal mol−1, determined solely by the cysteine removal step rather than by the thiol ligation step. Addition of one thiolate to the intermediates arising from either thiol attack occurs without a barrier and produces an intermediate bound to one active site cysteine and from which Hg(SCH3)2 may be removed only after

  17. Health assessment for Bog Creek Farm Site (BCFS) National Priorities List (NPL) site, Howell Township, Monmouth County, New Jersey, Region 2. CERCLIS No. NJD063157150. Final report

    SciTech Connect

    Not Available

    1989-04-10

    The Bog Creek Farm Site, located in a rural area of Howell Township, Monmouth County, New Jersey, is on the National Priorities List. In 1973 and 1974, various wastes were reportedly dumped at the site, including lacquer thinners, paint solvents and resins, disinfectants, animal carcasses, and residential debris. Sampling and analysis of on-site and off-site ground water, surface water, and sediments and of on-site waste and soil revealed several contaminants, primarily volatile organic compounds (VOCs), semi-volatile organic compounds, and heavy metals. Site contamination appears to be greatest immediately adjacent to an on-site waste-disposal trench. A potential public health threat exists from dermal absorption, ingestion, or inhalation of contamination from ground water, surface water, sediment, waste, and soil.

  18. Revealing the Functional States in the Active Site of BLUF Photoreceptors from Electrochromic Shift Calculations

    PubMed Central

    2014-01-01

    Photoexcitation with blue light of the flavin chromophore in BLUF photoreceptors induces a switch into a metastable signaling state that is characterized by a red-shifted absorption maximum. The red shift is due to a rearrangement in the hydrogen bond pattern around Gln63 located in the immediate proximity of the isoalloxazine ring system of the chromophore. There is a long-lasting controversy between two structural models, named Q63A and Q63J in the literature, on the local conformation of the residues Gln63 and Tyr21 in the dark state of the photoreceptor. As regards the mechanistic details of the light-activation mechanism, rotation of Gln63 is opposed by tautomerism in the Q63A and Q63J models, respectively. We provide a structure-based simulation of electrochromic shifts of the flavin chromophore in the wild type and in various site-directed mutants. The excellent overall agreement between experimental and computed data allows us to evaluate the two structural models. Compelling evidence is obtained that the Q63A model is incorrect, whereas the Q63J is fully consistent with the present computations. Finally, we confirm independently that a keto–enol tautomerization of the glutamine at position 63, which was proposed as molecular mechanism for the transition between the dark and the light-adapted state, explains the measured 10 to 15 nm red shift in flavin absorption between these two states of the protein. We believe that the accurateness of our results provides evidence that the BLUF photoreceptors absorption is fine-tuned through electrostatic interactions between the chromophore and the protein matrix, and finally that the simplicity of our theoretical model is advantageous as regards easy reproducibility and further extensions. PMID:25153778

  19. Spectroscopic definition of the copper active sites in mordenite: selective methane oxidation.

    PubMed

    Vanelderen, Pieter; Snyder, Benjamin E R; Tsai, Ming-Li; Hadt, Ryan G; Vancauwenbergh, Julie; Coussens, Olivier; Schoonheydt, Robert A; Sels, Bert F; Solomon, Edward I

    2015-05-20

    Two distinct [Cu-O-Cu](2+) sites with methane monooxygenase activity are identified in the zeolite Cu-MOR, emphasizing that this Cu-O-Cu active site geometry, having a ∠Cu-O-Cu ∼140°, is particularly formed and stabilized in zeolite topologies. Whereas in ZSM-5 a similar [Cu-O-Cu](2+) active site is located in the intersection of the two 10 membered rings, Cu-MOR provides two distinct local structures, situated in the 8 membered ring windows of the side pockets. Despite their structural similarity, as ascertained by electronic absorption and resonance Raman spectroscopy, the two Cu-O-Cu active sites in Cu-MOR clearly show different kinetic behaviors in selective methane oxidation. This difference in reactivity is too large to be ascribed to subtle differences in the ground states of the Cu-O-Cu sites, indicating the zeolite lattice tunes their reactivity through second-sphere effects. The MOR lattice is therefore functionally analogous to the active site pocket of a metalloenzyme, demonstrating that both the active site and its framework environment contribute to and direct reactivity in transition metal ion-zeolites.

  20. School Pharmacist/School Environmental Hygienic Activities at School Site.

    PubMed

    Muramatsu, Akiyoshi

    2016-01-01

    The "School Health and Safety Act" was enforced in April 2009 in Japan, and "school environmental health standards" were established by the Minister of Education, Culture, Sports, Science and Technology. In Article 24 of the Enforcement Regulations, the duties of the school pharmacist have been clarified; school pharmacists have charged with promoting health activities in schools and carrying out complete and regular checks based on the "school environmental health standards" in order to protect the health of students and staff. In supported of this, the school pharmacist group of Japan Pharmaceutical Association has created and distributed digital video discs (DVDs) on "check methods of school environmental health standards" as support material. We use the DVD to ensure the basic issues that school pharmacists deal with, such as objectives, criteria, and methods for each item to be checked, advice, and post-measures. We conduct various workshops and classes, and set up Q&A committees so that inquiries from members are answered with the help of such activities. In addition, school pharmacists try to improve the knowledge of the school staff on environmental hygiene during their in-service training. They also conduct "drug abuse prevention classes" at school and seek to improve knowledge and recognition of drugs, including "dangerous drugs". PMID:27252053

  1. An Accessory Agonist Binding Site Promotes Activation of α4β2* Nicotinic Acetylcholine Receptors.

    PubMed

    Wang, Jingyi; Kuryatov, Alexander; Sriram, Aarati; Jin, Zhuang; Kamenecka, Theodore M; Kenny, Paul J; Lindstrom, Jon

    2015-05-29

    Neuronal nicotinic acetylcholine receptors containing α4, β2, and sometimes other subunits (α4β2* nAChRs) regulate addictive and other behavioral effects of nicotine. These nAChRs exist in several stoichiometries, typically with two high affinity acetylcholine (ACh) binding sites at the interface of α4 and β2 subunits and a fifth accessory subunit. A third low affinity ACh binding site is formed when this accessory subunit is α4 but not if it is β2. Agonists selective for the accessory ACh site, such as 3-[3-(3-pyridyl)-1,2,4-oxadiazol-5-yl]benzonitrile (NS9283), cannot alone activate a nAChR but can facilitate more efficient activation in combination with agonists at the canonical α4β2 sites. We therefore suggest categorizing agonists according to their site selectivity. NS9283 binds to the accessory ACh binding site; thus it is termed an accessory site-selective agonist. We expressed (α4β2)2 concatamers in Xenopus oocytes with free accessory subunits to obtain defined nAChR stoichiometries and α4/accessory subunit interfaces. We show that α2, α3, α4, and α6 accessory subunits can form binding sites for ACh and NS9283 at interfaces with α4 subunits, but β2 and β4 accessory subunits cannot. To permit selective blockage of the accessory site, α4 threonine 126 located on the minus side of α4 that contributes to the accessory site, but not the α4β2 sites, was mutated to cysteine. Alkylation of this cysteine with a thioreactive reagent blocked activity of ACh and NS9283 at the accessory site. Accessory agonist binding sites are promising drug targets.

  2. ENVIRONMENTAL ASSESSMENT OF OKLAHOMA ABANDONED DRILLING AND PRODUCTION SITES AND ASSOCIATED PUBLIC EDUCATION/OUTREACH ACTIVITIES

    SciTech Connect

    Mike Terry

    2002-03-01

    The U.S. Department of Energy has participated with the Oklahoma Energy Resource Board (OERB) since 1995 by providing grant funding for on-going work in both environmental assessment of abandoned oilfield exploration and production sites and associated public education/outreach activities. The OERB, a state agency created in 1993 by the Oklahoma legislature, administers programs funded by an assessment of one tenth of one percent on all oil and natural gas produced and sold in the state of Oklahoma. Approximately one half of the funds are used to assess and remediate abandoned oilfield sites and the other half are being used to educate about the importance of the oil and natural gas industry and OERB's environmental efforts. Financial participation through grant funding by the U.S. D.O.E. has been $200,000 annually which represents approximately 3 percent of OERB's private funding. Most of OERB's revenues come from an assessment of 1/10th of 1% on the sale of crude and natural gas in Oklahoma. The assessment is considered voluntary in that any interest owner may ask for a refund annually of their contributions to the fund. On average, 95% of the assessment dollars have remained with OERB, which shows tremendous support by the industry. This Final Report summarizes the progress of the three year grant. The purpose of this three-year project was to continue the progress of the OERB to accomplish its environmental and educational objectives and transfer information learned to other organizations and producing states in the industry.

  3. Remediation of the site of a former active handling building at UKAEA- Winfrith

    SciTech Connect

    Armitage, Jack; Brown, Nick; Cornell, Rowland; Jessop, Gareth

    2007-07-01

    Available in abstract form only. Full text of publication follows: Since July 2000, NUKEM Limited has been carrying out the decommissioning of the former Active Handling Building, A59 at Winfrith, Dorset, United Kingdom (UK) under contract from the nuclear site licence holder, United Kingdom Atomic Energy Authority, (UKAEA). The building contained two heavily shielded suites of caves originally used to carry out remote examination of irradiated nuclear fuel elements and other supporting facilities which have all been decontaminated ready to permit building demolition. The demolition of the building structure and the removal of one cave line was completed during 2006 and the second cave line was demolished by March 2007. The remaining operations to be completed concern removal of the building slab and remediation of underlying soils to the final end point, free for unrestricted use without planning or nuclear regulatory control. Within the building base slab there are a range of contaminated items including secondary drain pipes, filter pits, storage hole liners and ventilation ducts which all have to be recovered for disposal along with around 4,000 m{sup 3} of surrounding concrete. In order to characterise the slab before its removal, supporting information has been obtained from site investigation work including a collimated low resolution, high sensitivity gamma survey using the GroundhogTM system of the foundation slab and the recovery and analysis of 27 cores obtained by drilling through the slab into the underlying soil. During removal of the slab it will be necessary to employ a variety of monitoring techniques to locate and remove the contaminated sections and then expose and monitor the underlying soil for evidence of any residual radioactivity. (authors)

  4. Isolated metal active site concentration and stability control catalytic CO2 reduction selectivity.

    PubMed

    Matsubu, John C; Yang, Vanessa N; Christopher, Phillip

    2015-03-01

    CO2 reduction by H2 on heterogeneous catalysts is an important class of reactions that has been studied for decades. However, atomic scale details of structure-function relationships are still poorly understood. Particularly, it has been suggested that metal particle size plays a unique role in controlling the stability of CO2 hydrogenation catalysts and the distribution of active sites, which dictates reactivity and selectivity. These studies often have not considered the possible role of isolated metal active sites in the observed dependences. Here, we utilize probe molecule diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) with known site-specific extinction coefficients to quantify the fraction of Rh sites residing as atomically dispersed isolated sites (Rhiso), as well as Rh sites on the surface of Rh nanoparticles (RhNP) for a series of TiO2 supported Rh catalysts. Strong correlations were observed between the catalytic reverse water gas shift turn over frequency (TOF) and the fraction of Rhiso sites and between catalytic methanation TOF and the fraction of RhNP sites. Furthermore, it was observed that reaction condition-induced disintegration of Rh nanoparticles, forming Rhiso active sites, controls the changing reactivity with time on stream. This work demonstrates that isolated atoms and nanoparticles of the same metal on the same support can exhibit uniquely different catalytic selectivity in competing parallel reaction pathways and that disintegration of nanoparticles under reaction conditions can play a significant role in controlling stability.

  5. Isolated metal active site concentration and stability control catalytic CO2 reduction selectivity.

    PubMed

    Matsubu, John C; Yang, Vanessa N; Christopher, Phillip

    2015-03-01

    CO2 reduction by H2 on heterogeneous catalysts is an important class of reactions that has been studied for decades. However, atomic scale details of structure-function relationships are still poorly understood. Particularly, it has been suggested that metal particle size plays a unique role in controlling the stability of CO2 hydrogenation catalysts and the distribution of active sites, which dictates reactivity and selectivity. These studies often have not considered the possible role of isolated metal active sites in the observed dependences. Here, we utilize probe molecule diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) with known site-specific extinction coefficients to quantify the fraction of Rh sites residing as atomically dispersed isolated sites (Rhiso), as well as Rh sites on the surface of Rh nanoparticles (RhNP) for a series of TiO2 supported Rh catalysts. Strong correlations were observed between the catalytic reverse water gas shift turn over frequency (TOF) and the fraction of Rhiso sites and between catalytic methanation TOF and the fraction of RhNP sites. Furthermore, it was observed that reaction condition-induced disintegration of Rh nanoparticles, forming Rhiso active sites, controls the changing reactivity with time on stream. This work demonstrates that isolated atoms and nanoparticles of the same metal on the same support can exhibit uniquely different catalytic selectivity in competing parallel reaction pathways and that disintegration of nanoparticles under reaction conditions can play a significant role in controlling stability. PMID:25671686

  6. Site specific rationale for technical impracticability of active groundwater restoration at a former manufactured gas plant site

    SciTech Connect

    Logan, C.M.; Walden, R.H.; MacFarlane, I.D.

    1995-12-31

    The National Contingency Plan (40 CFR Part 300 ) requires that remedial strategies must, at minimum, protect human health and the environment and meet applicable and relevant or appropriate requirements (ARARs). Where groundwater is impacted, maximum contaminant levels (MCLs) and maximum contaminant level goals (MCLGs) set under the Safe Drinking Water Act are often used as ARARs, whether or not the aquifer is a reasonably anticipated future source of drinking water. The US Environmental Protection Agency now recognizes the difficulty of groundwater restoration at sites where dense nonaqueous phase liquids are present, particularly in certain complex hydrogeological settings (EPA 1993). However, demonstration of impracticability generally does not occur until active remediation (e.g., pump and treat) has been shown to be ineffective. A case study of a former manufactured gas plant (MGP) is used to demonstrate how physical and chemical properties of the aquifer and coal tar, the major waste product from MGP sites, influence the feasibility of active restoration. Field characterization investigations, laboratory studies, and groundwater modeling are integrated into a demonstration following EPA guidelines. Laboratory studies included microbiological characterization and natural biodegradation and suggest that intrinsic bioremediation is occurring at this site. This work will be useful as EPA continues to develop presumptive remedies for cleanup under Superfund.

  7. 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.

  8. 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.

  9. Extending the Diffuse Layer Model of Surface Acidity Behavior: III. Estimating Bound Site Activity Coefficients

    EPA Science Inventory

    Although detailed thermodynamic analyses of the 2-pK diffuse layer surface complexation model generally specify bound site activity coefficients for the purpose of accounting for those non-ideal excess free energies contributing to bound site electrochemical potentials, in applic...

  10. 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.

  11. 77 FR 5560 - Commercial Wind Lease Issuance and Site Assessment Activities on the Atlantic Outer Continental...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-03

    ... project proposals on those leases) in identified Wind Energy Areas (WEAs) on the OCS offshore New Jersey... Bureau of Ocean Energy Management Commercial Wind Lease Issuance and Site Assessment Activities on the... site assessment plans (SAPs) on those leases. BOEM may issue one or more commercial wind energy...

  12. The Role of OOH Binding Site and Pt Surface Structure on ORR Activities

    PubMed Central

    Jia, Qingying; Caldwell, Keegan; Ziegelbauer, Joseph M.; Kongkanand, Anusorn; Wagner, Frederick T.; Mukerjee, Sanjeev; Ramaker, David E.

    2015-01-01

    We present experimentally observed molecular adsorbate coverages (e.g., O(H), OOH and HOOH) on real operating dealloyed bimetallic PtMx (M = Ni or Co) catalysts under oxygen reduction reaction (ORR) conditions obtained using X-ray absorption near edge spectroscopy (XANES). The results reveal a complex Sabatier catalysis behavior and indicate the active ORR mechanism changes with Pt–O bond weakening from the O2 dissociative mechanism, to the peroxyl mechanism, and finally to the hydrogen peroxide mechanism. An important rearrangement of the OOH binding site, an intermediate in the ORR, enables facile H addition to OOH and faster O–O bond breaking on 111 faces at optimal Pt–O bonding strength, such as that occurring in dealloyed PtM core-shell nanoparticles. This rearrangement is identified by previous DFT calculations and confirmed from in situ measured OOH adsorption coverages during the ORR. The importance of surface structural effects and 111 ordered faces is confirmed by the higher specific ORR rates on solid core vs porous multi-core nanoparticles. PMID:26190857

  13. The balance of flexibility and rigidity in the active site residues of hen egg white lysozyme

    NASA Astrophysics Data System (ADS)

    Qi, Jian-Xun; Jiang, Fan

    2011-05-01

    The crystallographic temperature factors (B factor) of individual atoms contain important information about the thermal motion of the atoms in a macromolecule. Previously the theory of flexibility of active site has been established based on the observation that the enzyme activity is sensitive to low concentration denaturing agents. It has been found that the loss of enzyme activity occurs well before the disruption of the three-dimensional structural scaffold of the enzyme. To test the theory of conformational flexibility of enzyme active site, crystal structures were perturbed by soaking in low concentration guanidine hydrochloride solutions. It was found that many lysozyme crystals tested could still diffract until the concentration of guanidine hydrochloride reached 3 M. It was also found that the B factors averaged over individually collected data sets were more accurate. Thus it suggested that accurate measurement of crystal temperature factors could be achieved for medium-high or even medium resolution crystals by averaging over multiple data sets. Furthermore, we found that the correctly predicted active sites included not only the more flexible residues, but also some more rigid residues. Both the flexible and the rigid residues in the active site played an important role in forming the active site residue network, covering the majority of the substrate binding residues. Therefore, this experimental prediction method may be useful for characterizing the binding site and the function of a protein, such as drug targeting.

  14. Remedial action and site design for stabilization of the inactive uranium mill tailings sites at Slick Rock, Colorado. Attachment 2, Geology report: Appendix B, Preliminary final

    SciTech Connect

    Not Available

    1994-03-01

    Detailed investigations of geologic, geomorphic, and seismic conditions at the Burro Canyon site were conducted by the US Department of Energy (DOE) as a disposal site for the tailings at two processing sites near the Slick Rock, Colorado, post office. The purposes of these studies are basic site characterization and identification of potential geologic hazards that could affect long-term site stability. Subsequent engineering studies (e.g., analyses of hydrologic and liquefaction hazards) used the data developed in these studies. The geomorphic analysis was employed in the design of effective erosion protection. Studies of the regional and local seismotectonic setting, which included a detailed search for possible capable faults within a 65-km radius of the site, provided the basis for seismic design parameters.

  15. Determination of the required surface area of a final clarifier for an activated-sludge system.

    PubMed

    Yuen, Weng Ah

    2004-01-01

    A generic methodology for determining the required surface area of a final clarifier is presented. Clarification and thickening requirements are integrated to form a unified procedure for final clarifier design. The new method is based on results obtained by Yuen (2002) on the solids flux theory for a secondary clarifier; it does not require the specification of recycle rate, which is computed as an output of the method. The author shows that there is a minimum required surface area (A(m)) for a final clarifier under the thickening requirement when the designed recycle rate is set at the maximum allowable value (FR)m (at the critical state). The designed surface area and the return activated sludge pumping capacity can be determined by applying a safety factor to A(m) and (FR)m, respectively. The method is shown to conform to conventional design criteria under typical design conditions.

  16. Chemical modification studies on arginine kinase: essential cysteine and arginine residues at the active site.

    PubMed

    Zhu, Wen-Jing; Li, Miao; Wang, Xiao-Yun

    2007-12-01

    Chemical modification was used to elucidate the essential amino acids in the catalytic activity of arginine kinase (AK) from Migratoria manilensis. Among six cysteine (Cys) residues only one Cys residue was determined to be essential in the active site by Tsou's method. Furthermore, the AK modified by DTNB can be fully reactivated by dithiothreitol (DTT) in a monophasic kinetic course. At the same time, this reactivation can be slowed down in the presence of ATP, suggesting that the essential Cys is located near the ATP binding site. The ionizing groups at the AK active site were studied and the standard dissociation enthalpy (DeltaH degrees ) was 12.38kcal/mol, showing that the dissociation group may be the guanidino of arginine (Arg). Using the specific chemical modifier phenylglyoxal (PG) demonstrated that only one Arg, located near the ATP binding site, is essential for the activity of AK. PMID:17765964

  17. 1993 annual report of hazardous waste activities for the Oak Ridge K-25 site

    SciTech Connect

    Not Available

    1994-02-01

    This report is a detailed listing of all of the Hazardous Waste activities occurring at Martin Marietta`s K-25 site. Contained herein are hazardous waste notification forms, waste stream reports, generator fee forms and various TSDR reports.

  18. Technical support for geopressured-geothermal activities in Louisiana. Final geological report, 1 November 1981-31 October 1982

    SciTech Connect

    Pilger, R.H.

    1984-06-25

    This report contains the component Site-Specific Studies-Geophysics, Diagenesis, Geochemistry. Work for Site-Specific Studies is finished, and the results presented in this report are final. Individual studies have been entered separately into the data base. (ACR)

  19. Remedial action plan and site design for stabilization of the inactive uranium mill tailings site at Lowman, Idaho: Attachment 2, Geology report. Final report

    SciTech Connect

    Not Available

    1991-09-01

    Detailed investigations of geologic, geomorphic, and seismic conditions at the Lowman site in central Idaho were conducted by the Technical Assistance Contractor. The purpose of these investigations was basic site characterization and the identification of potential geologic hazards that could affect long-term site stability. Subsequent engineering studies (e.g., analyses of the hydrologic regime and liquefaction potential) use this data . The geomorphic analysis is employed in the design of effective erosion protection. Studies of the regional and local seismotectonic setting, which included a detailed search for possible capable faults within a 65-km (40-mile) radius of the site, provided the basis for estimating seismic design parameters.

  20. Anisotropic Covalency Contributions to Superexchange Pathways in Type One Copper Active Sites

    PubMed Central

    2015-01-01

    Type one (T1) Cu sites deliver electrons to catalytic Cu active sites: the mononuclear type two (T2) Cu site in nitrite reductases (NiRs) and the trinuclear Cu cluster in the multicopper oxidases (MCOs). The T1 Cu and the remote catalytic sites are connected via a Cys-His intramolecular electron-transfer (ET) bridge, which contains two potential ET pathways: P1 through the protein backbone and P2 through the H-bond between the Cys and the His. The high covalency of the T1 Cu–S(Cys) bond is shown here to activate the T1 Cu site for hole superexchange via occupied valence orbitals of the bridge. This covalency-activated electronic coupling (HDA) facilitates long-range ET through both pathways. These pathways can be selectively activated depending on the geometric and electronic structure of the T1 Cu site and thus the anisotropic covalency of the T1 Cu–S(Cys) bond. In NiRs, blue (π-type) T1 sites utilize P1 and green (σ-type) T1 sites utilize P2, with P2 being more efficient. Comparing the MCOs to NiRs, the second-sphere environment changes the conformation of the Cys-His pathway, which selectively activates HDA for superexchange by blue π sites for efficient turnover in catalysis. These studies show that a given protein bridge, here Cys-His, provides different superexchange pathways and electronic couplings depending on the anisotropic covalencies of the donor and acceptor metal sites. PMID:25310460

  1. Final Characterization Report for Corrective Action Unit 109: Area 2 U-2BU Crater, Nevada Test Site, Nevada, Revision 1

    SciTech Connect

    ITLV

    1998-12-01

    Corrective Action Unit 109, Area 2 U-2bu Crater, is an inactive Resource Conservation and Recovery Act Part A Permit disposal unit located in Area 2 at the Nevada Test Site, Nevada. The Corrective Action Unit has been characterized under the requirements of the Nevada Test Site Resource Conservation and Recovery Act, Part A Permit (NDEP, 1995) and Title 40 Code of Federal Regulations Part 265 (CFR, 1996). The site characterization was performed under the RCRA Part A Permit Characterization Plan for the U-2bu Subsidence Crater (DOE/NV, 1998c), as approved by the Nevada Division of Environmental Protection (Liebendorfer, 1998). The primary objective of the site characterization activities was to evaluate the presence, concentration, and extent of any Resource Conservation and Recovery Act contaminants in the crater. Surface soil samples were collected on April 22, 1998, and subsurface soil samples and geotechnical samples were collected from April 27-29, 1998. Soil samples were collected using a hand auger or a piston-type drive hammer to advance a 5-centimeter (2-inch) diameter steel sampling tool into the ground. The permit for the Nevada Test Site requires that Corrective Action Unit 109 be closed under 40 Code of Federal Regulations 265 Subpart G and 40 Code of Federal Regulations Part 265.310 (CFR, 1996). Analysis of the data collected during the characterization effort indicates that lead was detected in Study Area 1 at 5.7 milligrams per liter, above the regulatory level in 40 Code of Federal Regulations 261.24 of 5.0 milligrams per liter. Except for the lead detection at a single location within the crater, the original Resource Conservation Recovery Act constituents of potential concern determined between the U.S. Department of Energy, Nevada Operations Office and the Nevada Department of Environmental Protection during the Data Quality Objectives process (DOE/NV, 1998b) were not found to be present at Corrective Action Unit 109 above regulatory levels of

  2. A Hydrophobic Pocket in the Active Site of Glycolytic Aldolase Mediates Interactions with Wiskott-Aldrich Syndrome Protein

    SciTech Connect

    St-Jean,M.; Izard, T.; Sygusch, J.

    2007-01-01

    Aldolase plays essential catalytic roles in glycolysis and gluconeogenesis. However, aldolase is a highly abundant protein that is remarkably promiscuous in its interactions with other cellular proteins. In particular, aldolase binds to highly acidic amino acid sequences, including the C-terminus of the Wiskott-Aldrich syndrome protein, an actin nucleation promoting factor. Here we report the crystal structure of tetrameric rabbit muscle aldolase in complex with a C-terminal peptide of Wiskott-Aldrich syndrome protein. Aldolase recognizes a short, 4-residue DEWD motif (residues 498-501), which adopts a loose hairpin turn that folds about the central aromatic residue, enabling its tryptophan side chain to fit into a hydrophobic pocket in the active site of aldolase. The flanking acidic residues in this binding motif provide further interactions with conserved aldolase active site residues, Arg-42 and Arg-303, aligning their side chains and forming the sides of the hydrophobic pocket. The binding of Wiskott-Aldrich syndrome protein to aldolase precludes intramolecular interactions of its C-terminus with its active site, and is competitive with substrate as well as with binding by actin and cortactin. Finally, based on this structure a novel naphthol phosphate-based inhibitor of aldolase was identified and its structure in complex with aldolase demonstrated mimicry of the Wiskott-Aldrich syndrome protein-aldolase interaction. The data support a model whereby aldolase exists in distinct forms that regulate glycolysis or actin dynamics.

  3. Probing impact of active site residue mutations on stability and activity of Neisseria polysaccharea amylosucrase.

    PubMed

    Daudé, David; Topham, Christopher M; Remaud-Siméon, Magali; André, Isabelle

    2013-12-01

    The amylosucrase from Neisseria polysaccharea is a transglucosidase from the GH13 family of glycoside-hydrolases that naturally catalyzes the synthesis of α-glucans from the widely available donor sucrose. Interestingly, natural molecular evolution has modeled a dense hydrogen bond network at subsite -1 responsible for the specific recognition of sucrose and conversely, it has loosened interactions at the subsite +1 creating a highly promiscuous subsite +1. The residues forming these subsites are considered to be likely involved in the activity as well as the overall stability of the enzyme. To assess their role, a structure-based approach was followed to reshape the subsite -1. A strategy based on stability change predictions, using the FoldX algorithm, was considered to identify the best candidates for site-directed mutagenesis and guide the construction of a small targeted library. A miniaturized purification protocol was developed and both mutant stability and substrate promiscuity were explored. A range of 8 °C between extreme melting temperature values was observed and some variants were able to synthesize series of oligosaccharides with distributions differing from that of the parental enzyme. The crucial role of subsite -1 was thus highlighted and the biocatalysts generated can now be considered as starting points for further engineering purposes.

  4. Activation Analysis of the Final Optics Assemblies at the National Ignition Facility

    SciTech Connect

    Dauffy, L S; Khater, H Y; Sitaraman, S; Brereton, S J

    2008-10-14

    Commissioning shots have commenced at the National Ignition Facility (NIF) at the Lawrence Livermore National Laboratory. Within a year, the 192 laser beam facility will be operational and the experimental phase will begin. At each shot, the emitted neutrons will interact in the facility's surroundings, activating them, especially inside the target bay where the neutron flux is the highest. We are calculating the dose from those activated structures and objects in order to plan and minimize worker exposures during maintenance and normal NIF operation. This study presents the results of the activation analysis of the optics of the Final Optics Assemblies (FOA), which are a key contributor to worker exposure. Indeed, there are 48 FOAs weighting three tons each, and routine change-out and maintenance of optics and optics modules is expected. The neutron field has been characterized using the three-dimensional Monte Carlo particle transport code MCNP with subsequent activation analysis performed using the activation code, ALARA.

  5. 'Unconventional' coordination chemistry by metal chelating fragments in a metalloprotein active site.

    PubMed

    Martin, David P; Blachly, Patrick G; Marts, Amy R; Woodruff, Tessa M; de Oliveira, César A F; McCammon, J Andrew; Tierney, David L; Cohen, Seth M

    2014-04-01

    The binding of three closely related chelators: 5-hydroxy-2-methyl-4H-pyran-4-thione (allothiomaltol, ATM), 3-hydroxy-2-methyl-4H-pyran-4-thione (thiomaltol, TM), and 3-hydroxy-4H-pyran-4-thione (thiopyromeconic acid, TPMA) to the active site of human carbonic anhydrase II (hCAII) has been investigated. Two of these ligands display a monodentate mode of coordination to the active site Zn(2+) ion in hCAII that is not recapitulated in model complexes of the enzyme active site. This unprecedented binding mode in the hCAII-thiomaltol complex has been characterized by both X-ray crystallography and X-ray spectroscopy. In addition, the steric restrictions of the active site force the ligands into a 'flattened' mode of coordination compared with inorganic model complexes. This change in geometry has been shown by density functional computations to significantly decrease the strength of the metal-ligand binding. Collectively, these data demonstrate that the mode of binding by small metal-binding groups can be significantly influenced by the protein active site. Diminishing the strength of the metal-ligand bond results in unconventional modes of metal coordination not found in typical coordination compounds or even carefully engineered active site models, and understanding these effects is critical to the rational design of inhibitors that target clinically relevant metalloproteins.

  6. Site-directed mutagenesis and high-resolution NMR spectroscopy of the active site of porphobilinogen deaminase

    SciTech Connect

    Scott, A.I.; Roessner, C.A.; Stolowich, N.J.; Karuso, P.; Williams, H.J.; Grant, S.K.; Gonzalez, M.D.; Hoshino, T. )

    1988-10-18

    The active site of porphobilinogen (PBG){sup 1} deaminase from Escherichia coli has been found to contain an unusual dipyrromethane derived from four molecules of 5-aminolevulinic acid (ALA) covalently linked to Cys-242, one of the two cysteine residues conserved in E. coli and human deaminase. By use of a hemA{sup {minus}} strain of E. coli the enzyme was enriched from (5-{sup 13}C)ALA and examined by {sup 1}H-detected multiple quantum coherence spectroscopy, which revealed all of the salient features of a dipyrromethane composed of two PBG units linked heat to tail and terminating in a CH{sub 2}-S bond to a cysteine residue. Site-specific mutagenesis of Cys-99 and Cys-242, respectively, has shown that substitution of Ser for Cys-99 does not affect the enzymatic activity, whereas substitution of Ser for Cys-242 removes essentially all of the catalytic activity as measured by the conversion of the substrate PBG to uro'gen I. The NMR spectrum of the covalent complex of deaminase with the suicide inhibitor 2-bromo-(2,11-{sup 13}C{sub 2})PBG reveals that the aminomethyl terminus of the inhibitor reacts with the enzyme's cofactor at the {alpha}-free pyrrole. NMR spectroscopy of the ES{sub 2} complex confirmed a PBG-derived head-to-tail dipyrromethane attached to the {alpha}-free pyrrole position of the enzyme. A mechanistic rationale for deaminase is presented.

  7. Nuclear waste: Status of DOE`s nuclear waste site characterization activities

    SciTech Connect

    1987-12-31

    Three potential nuclear waste repository sites have been selected to carry out characterization activities-the detailed geological testing to determine the suitability of each site as a repository. The sites are Hanford in south-central Washington State, Yucca Mountain in southern Nevada, and Deaf Smith in the Texas Panhandle. Two key issues affecting the total program are the estimations of the site characterization completion data and costs and DOE`s relationship with the Nuclear Regulatory Commission which has been limited and its relations with affected states and Indian tribes which continue to be difficult.

  8. XAFS Study of the Photo-Active Site of Mo/MCM-41

    NASA Astrophysics Data System (ADS)

    Miyamoto, Daisuke; Ichikuni, Nobuyuki; Shimazu, Shogo

    2007-02-01

    An Mo/MCM-41 catalyst was prepared and used for study of propene and 1-butene photo-metathesis reactions. XAFS analysis revealed that hydrogen reduction leads to a decreased role for the Mo=O site. The Mo-O site plays an important role for the olefin photo-metathesis reaction on the H2 reduced Mo/MCM-41. From EXAFS analysis, the active site of photo-metathesis reaction is the Mo=O part for oxidized Mo/MCM-41, whereas it is the Mo-O site for reduced Mo/MCM-41.

  9. The Three Mycobacterium tuberculosis Antigen 85 Isoforms Have Unique Substrates and Activities Determined by Non-active Site Regions*

    PubMed Central

    Backus, Keriann M.; Dolan, Michael A.; Barry, Conor S.; Joe, Maju; McPhie, Peter; Boshoff, Helena I. M.; Lowary, Todd L.; Davis, Benjamin G.; Barry, Clifton E.

    2014-01-01

    The three isoforms of antigen 85 (A, B, and C) are the most abundant secreted mycobacterial proteins and catalyze transesterification reactions that synthesize mycolated arabinogalactan, trehalose monomycolate (TMM), and trehalose dimycolate (TDM), important constituents of the outermost layer of the cellular envelope of Mycobacterium tuberculosis. These three enzymes are nearly identical at the active site and have therefore been postulated to exist to evade host immunity. Distal to the active site is a second putative carbohydrate-binding site of lower homology. Mutagenesis of the three isoforms at this second site affected both substrate selectivity and overall catalytic activity in vitro. Using synthetic and natural substrates, we show that these three enzymes exhibit unique selectivity; antigen 85A more efficiently mycolates TMM to form TDM, whereas C (and to a lesser extent B) has a higher rate of activity using free trehalose to form TMM. This difference in substrate selectivity extends to the hexasaccharide fragment of cell wall arabinan. Mutation of secondary site residues from the most active isoform (C) into those present in A or B partially interconverts this substrate selectivity. These experiments in combination with molecular dynamics simulations reveal that differences in the N-terminal helix α9, the adjacent Pro216–Phe228 loop, and helix α5 are the likely cause of changes in activity and substrate selectivity. These differences explain the existence of three isoforms and will allow for future work in developing inhibitors. PMID:25028517

  10. Transcriptional activation through ETS domain binding sites in the cytochrome c oxidase subunit IV gene

    SciTech Connect

    Virbasius, J.V.; Scarpulla, R.C. )

    1991-11-01

    A mutational analysis of the rat cytochrome c oxidase subunit IV (RCO4) promoter region revealed the presence of a major control element consisting of a tandemly repeated pair of binding sites for a nuclear factor from HeLa cells. This factor was designated NRF-2 (nuclear respiratory factor 2) because a functional recognition site was also found in the human ATP synthase {beta}-subunit gene. Deletion or site-directed point mutations of the NRF-2 binding sites in the RCO4 promoter resulted in substantial loss of transcriptional activity, and synthetic oligomers of the NRF-2 binding sites from both genes stimulated a heterologous promoter when cloned in cis. NRF-2 binding a transcriptional activation required a purine-rich core sequence, GGAA. This motif is characteristic of the recognition site for a family of activators referred to as ETS domain proteins because of the similarity within their DNA-binding domains to the ets-1 proto-oncogene product. NRF-2 recognized an authentic Ets-1 site within the Moloney murine sarcoma virus long terminal repeat, and this site was able to compete for NRF-2 binding to the RCO4 promoter sequence. However, in contrast to Ets-1, which appears to be exclusive to lymphoid tissues, NRF-2 has the broad tissue distribution expected of a regulator of respiratory chain expression.

  11. Quantitative, directional measurement of electric field heterogeneity in the active site of ketosteroid isomerase.

    PubMed

    Fafarman, Aaron T; Sigala, Paul A; Schwans, Jason P; Fenn, Timothy D; Herschlag, Daniel; Boxer, Steven G

    2012-02-01

    Understanding the electrostatic forces and features within highly heterogeneous, anisotropic, and chemically complex enzyme active sites and their connection to biological catalysis remains a longstanding challenge, in part due to the paucity of incisive experimental probes of electrostatic properties within proteins. To quantitatively assess the landscape of electrostatic fields at discrete locations and orientations within an enzyme active site, we have incorporated site-specific thiocyanate vibrational probes into multiple positions within bacterial ketosteroid isomerase. A battery of X-ray crystallographic, vibrational Stark spectroscopy, and NMR studies revealed electrostatic field heterogeneity of 8 MV/cm between active site probe locations and widely differing sensitivities of discrete probes to common electrostatic perturbations from mutation, ligand binding, and pH changes. Electrostatic calculations based on active site ionization states assigned by literature precedent and computational pK(a) prediction were unable to quantitatively account for the observed vibrational band shifts. However, electrostatic models of the D40N mutant gave qualitative agreement with the observed vibrational effects when an unusual ionization of an active site tyrosine with a pK(a) near 7 was included. UV-absorbance and (13)C NMR experiments confirmed the presence of a tyrosinate in the active site, in agreement with electrostatic models. This work provides the most direct measure of the heterogeneous and anisotropic nature of the electrostatic environment within an enzyme active site, and these measurements provide incisive benchmarks for further developing accurate computational models and a foundation for future tests of electrostatics in enzymatic catalysis.

  12. Molecular dynamics explorations of active site structure in designed and evolved enzymes.

    PubMed

    Osuna, Sílvia; Jiménez-Osés, Gonzalo; Noey, Elizabeth L; Houk, K N

    2015-04-21

    This Account describes the use of molecular dynamics (MD) simulations to reveal how mutations alter the structure and organization of enzyme active sites. As proposed by Pauling about 70 years ago and elaborated by many others since then, biocatalysis is efficient when functional groups in the active site of an enzyme are in optimal positions for transition state stabilization. Changes in mechanism and covalent interactions are often critical parts of enzyme catalysis. We describe our explorations of the dynamical preorganization of active sites using MD, studying the fluctuations between active and inactive conformations normally concealed to static crystallography. MD shows how the various arrangements of active site residues influence the free energy of the transition state and relates the populations of the catalytic conformational ensemble to the enzyme activity. This Account is organized around three case studies from our laboratory. We first describe the importance of dynamics in evaluating a series of computationally designed and experimentally evolved enzymes for the Kemp elimination, a popular subject in the enzyme design field. We find that the dynamics of the active site is influenced not only by the original sequence design and subsequent mutations but also by the nature of the ligand present in the active site. In the second example, we show how microsecond MD has been used to uncover the role of remote mutations in the active site dynamics and catalysis of a transesterase, LovD. This enzyme was evolved by Tang at UCLA and Codexis, Inc., and is a useful commercial catalyst for the production of the drug simvastatin. X-ray analysis of inactive and active mutants did not reveal differences in the active sites, but relatively long time scale MD in solution showed that the active site of the wild-type enzyme preorganizes only upon binding of the acyl carrier protein (ACP) that delivers the natural acyl group to the active site. In the absence of bound ACP

  13. Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity.

    PubMed

    Schöne, Stefanie; Jurk, Marcel; Helabad, Mahdi Bagherpoor; Dror, Iris; Lebars, Isabelle; Kieffer, Bruno; Imhof, Petra; Rohs, Remo; Vingron, Martin; Thomas-Chollier, Morgane; Meijsing, Sebastiaan H

    2016-09-01

    The glucocorticoid receptor (GR) binds as a homodimer to genomic response elements, which have particular sequence and shape characteristics. Here we show that the nucleotides directly flanking the core-binding site, differ depending on the strength of GR-dependent activation of nearby genes. Our study indicates that these flanking nucleotides change the three-dimensional structure of the DNA-binding site, the DNA-binding domain of GR and the quaternary structure of the dimeric complex. Functional studies in a defined genomic context show that sequence-induced changes in GR activity cannot be explained by differences in GR occupancy. Rather, mutating the dimerization interface mitigates DNA-induced changes in both activity and structure, arguing for a role of DNA-induced structural changes in modulating GR activity. Together, our study shows that DNA sequence identity of genomic binding sites modulates GR activity downstream of binding, which may play a role in achieving regulatory specificity towards individual target genes.

  14. Correlated structural kinetics and retarded solvent dynamics at the metalloprotease active site

    SciTech Connect

    Grossman, Moran; Born, Benjamin; Heyden, Matthias; Tworowski, Dmitry; Fields, Gregg B.; Sagi, Irit; Havenith, Martina

    2011-09-18

    Solvent dynamics can play a major role in enzyme activity, but obtaining an accurate, quantitative picture of solvent activity during catalysis is quite challenging. Here, we combine terahertz spectroscopy and X-ray absorption analyses to measure changes in the coupled water-protein motions during peptide hydrolysis by a zinc-dependent human metalloprotease. These changes were tightly correlated with rearrangements at the active site during the formation of productive enzyme-substrate intermediates and were different from those in an enzyme–inhibitor complex. Molecular dynamics simulations showed a steep gradient of fast-to-slow coupled protein-water motions around the protein, active site and substrate. Our results show that water retardation occurs before formation of the functional Michaelis complex. We propose that the observed gradient of coupled protein-water motions may assist enzyme-substrate interactions through water-polarizing mechanisms that are remotely mediated by the catalytic metal ion and the enzyme active site.

  15. An overlapping kinase and phosphatase docking site regulates activity of the retinoblastoma protein.

    PubMed

    Hirschi, Alexander; Cecchini, Matthew; Steinhardt, Rachel C; Schamber, Michael R; Dick, Frederick A; Rubin, Seth M

    2010-09-01

    The phosphorylation state and corresponding activity of the retinoblastoma tumor suppressor protein (Rb) are modulated by a balance of kinase and phosphatase activities. Here we characterize the association of Rb with the catalytic subunit of protein phosphatase 1 (PP1c). A crystal structure identifies an enzyme docking site in the Rb C-terminal domain that is required for efficient PP1c activity toward Rb. The phosphatase docking site overlaps with the known docking site for cyclin-dependent kinase (Cdk), and PP1 competition with Cdk-cyclins for Rb binding is sufficient to retain Rb activity and block cell-cycle advancement. These results provide the first detailed molecular insights into Rb activation and establish a novel mechanism for Rb regulation in which kinase and phosphatase compete for substrate docking. PMID:20694007

  16. Remedial Action Plan and site design for stabilization of the inactive uranium mill tailings site at Durango, Colorado: Attachment 2, Geology report. Revised final report

    SciTech Connect

    Not Available

    1991-12-01

    Detailed investigations of geologic, geomorphic, and seismic conditions at the Bodo Canyon disposal site were conducted. The purpose of these investigations was basic site characterization and identification of potential geologic hazards that could affect long-term site stability. Subsequent engineering studies, such as analyses of hydrologic and liquefaction hazards, used the data developed in these studies. The geomorphic analysis was employed in the design of effective erosion protection. Studies of the regional and local seismotectonic setting, which included a detailed search for possible capable faults within a 65 kilometer radius of the site, provided the basis for seismic design parameters. The scope of work performed included the following: Compilation and analysis of previous published and unpublished geologic literature and maps; Review of historical and instrumental earthquake data; Review of site-specific subsurface geologic data, including lithologic and geophysical logs of exploratory boreholes advanced in the site area; Photogeologic interpretations of existing conventional aerial photographs; and, Ground reconnaissance and mapping of the site region.

  17. Remedial Action Plan and site design for stabilization of the inactive uranium mill tailings site at Gunnison, Colorado. Attachment 2, Geology report: Final report

    SciTech Connect

    Not Available

    1992-10-01

    Detailed investigations of geologic, geomorphic, and seismic conditions at the Landfill disposal site were conducted. The purpose of these studies was basic site characterization and identification of potential geologic hazards that could affect long-term site stability. Subsequent engineering studies, such as analyses of hydrologic and liquefaction hazards, used the data developed in these studies. The geomorphic analysis was employed in the design of effective erosion protection. Studies of the regional and local seismotectonic setting, which included a detailed search for possible capable faults within a 65-kilometer (km) (40-mile) radius of the site, provided the basis for seismic design parameters. The scope of work performed included the following: Compilation and analysis of previous published and unpublished geologic literature and maps. Review of historical and instrumental earthquake data. Review of site-specific subsurface geologic data, including lithologic and geophysical logs of exploratory boreholes advanced in the site area. Photogeologic interpretations of existing conventional aerial photographs. Ground reconnaissance and mapping of the site region.

  18. Final work plan : targeted groundwater sampling and monitoring well installation for potential site reclassification at Barnes, Kansas.

    SciTech Connect

    LaFreniere, L. M.

    2006-07-11

    This ''Work Plan'' outlines the scope of work for a targeted groundwater sampling investigation and monitoring well installation at Barnes, Kansas. This activity is being conducted at the request of the Kansas Department of Health and Environment (KDHE), in accordance with the intergovernmental agreement between the KDHE and the Commodity Credit Corporation (CCC), an agency of the U.S. Department of Agriculture (USDA). Data resulting from the proposed work will be used to determine the hydraulic gradient near the former CCC/USDA facility, delineate the downgradient carbon tetrachloride plume, and determine additional monitoring requirements at Barnes. The overall goal is to establish criteria for monitoring leading to potential site reclassification. The proposed work will be performed on behalf of the CCC/USDA by the Environmental Science Division of Argonne National Laboratory. Argonne is a nonprofit, multidisciplinary research center operated by the University of Chicago for the U.S. Department of Energy (DOE). The Farm Service Agency of the USDA has entered into an interagency agreement with DOE, under which Argonne provides technical assistance with environmental site characterization and remediation at former CCC/USDA grain storage facilities. Argonne issued a ''Master Work Plan'' (Argonne 2002) to provide general guidance for all investigations at former CCC/USDA facilities in Kansas. The ''Master Work Plan'', approved by the KDHE, contains the materials common to investigations at all locations in Kansas. This document must be consulted for the complete details of plans for this work associated with the former CCC/USDA facility at Barnes.

  19. Structural and Kinetic Analyses of Macrophage Migration Inhibitory Factor Active Site Interactions

    SciTech Connect

    Crichlow, G.; Lubetsky, J; Leng, L; Bucala, R; Lolis, E

    2009-01-01

    Macrophage migration inhibitory factor (MIF) is a secreted protein expressed in numerous cell types that counters the antiinflammatory effects of glucocorticoids and has been implicated in sepsis, cancer, and certain autoimmune diseases. Interestingly, the structure of MIF contains a catalytic site resembling the tautomerase/isomerase sites of microbial enzymes. While bona fide physiological substrates remain unknown, model substrates have been identified. Selected compounds that bind in the tautomerase active site also inhibit biological functions of MIF. It had previously been shown that the acetaminophen metabolite, N-acetyl-p-benzoquinone imine (NAPQI), covalently binds to the active site of MIF. In this study, kinetic data indicate that NAPQI inhibits MIF both covalently and noncovalently. The structure of MIF cocrystallized with NAPQI reveals that the NAPQI has undergone a chemical alteration forming an acetaminophen dimer (bi-APAP) and binds noncovalently to MIF at the mouth of the active site. We also find that the commonly used protease inhibitor, phenylmethylsulfonyl fluoride (PMSF), forms a covalent complex with MIF and inhibits the tautomerase activity. Crystallographic analysis reveals the formation of a stable, novel covalent bond for PMSF between the catalytic nitrogen of the N-terminal proline and the sulfur of PMSF with complete, well-defined electron density in all three active sites of the MIF homotrimer. Conclusions are drawn from the structures of these two MIF-inhibitor complexes regarding the design of novel compounds that may provide more potent reversible and irreversible inhibition of MIF.

  20. A roundup of SMOS validation activities at the HOBE site in the Skjern River Catchment, Denmark

    NASA Astrophysics Data System (ADS)

    Bircher, Simone; Richaume, Philippe; Mialon, Arnaud; Berthon, Lucie; Kerr, Yann H.; Jensen, Karsten H.

    2013-04-01

    patches of the most representative land covers (agriculture, heath and forest). This communication will give an overall insight into the validation carried out at the Danish test site by means of the collected in situ data, and present data comparisons at SMOS Levels 1C, 2 and 3. The shown results include data from different soil moisture processor versions as well as the investigation of main auxiliary parameters in the retrieval algorithm. Finally, an outlook on future planned SMOS activities in the higher northern latitudes will be given.

  1. Remedial action plan and site design for stabilization of the inactive uranium mill tailings site at Lowman, Idaho: Remedial action selection report for the Lowman UMTRA project site, Idaho. Final report

    SciTech Connect

    Matthews, M.L.; Nagel, J.

    1991-09-01

    The inactive uranium mill tailings site near Lowman, Idaho, was designated as one of 24 abandoned uranium tailings sites to be remediated by the US Department of Energy (DOE) under the Uranium Mill Tailings Radiation Control Act of 1978 (UMTRCA). The UMTRCA requires that the US Nuclear Regulatory Commission (NRC) concur with the DOE`s remedial action plan and certify that the remedial action complies with the standards promulgated by the US Environmental Protection Agency (EPA). The remedial action plan (RAP), which includes this remedial action selection report (RAS), has been developed to serve a two-fold purpose. First, it describes the activities that are proposed by the DOE to accomplish long-term stabilization and control of residual radioactive materials at the inactive uranium processing site near Lowman, Idaho. Second, this document and the remainder of the RAP, upon concurrence and execution by the DOE, the State of Idaho, and the NRC, becomes Appendix B of the Cooperative Agreement (No. DE-FC04-85AL20535) between the DOE and the State of Idaho.

  2. Monitoring Soil Erosion of a Burn Site in the Central Basin and Range Ecoregion: Final Report on Measurements at the Gleason Fire Site, Nevada

    SciTech Connect

    Miller, Julianne; Etyemezian, Vicken; Shillito, Rose; Cablk, Mary; Fenstermaker, Lynn; Shafer, David

    2013-10-01

    The increase in wildfires in arid and semi-arid parts of Nevada and elsewhere in the southwestern United States has implications for post-closure management and long-term stewardship for Soil Corrective Action Units (CAUs) on the Nevada National Security Site (NNSS) for which the Nevada Field Office of the United States Department of Energy, National Nuclear Security Administration has responsibility. For many CAUs and Corrective Action Sites, where closure-in-place alternatives are now being implemented or considered, there is a chance that these sites could burn over at some time while they still pose a risk to the environment or human health, given the long half lives of some of the radionuclide contaminants. This study was initiated to examine the effects and duration of wildfire on wind and water erodibility on sites analogous to those that exist on the NNSS. The data analyzed herein were gathered at the prescribed Gleason Fire site near Ely, Nevada, a site comparable to the northern portion of the NNSS. Quantification of wind erosion was conducted with a Portable In-Situ Wind ERosion Lab (PI-SWERL) on unburned soils, and on interspace and plant understory soils within the burned area. The PI-SWERL was used to estimate emissions of suspendible particles (particulate matter with aerodynamic diameters less than or equal to 10 micrometers) at different wind speeds. Filter samples, collected from the exhaust of the PI-SWERL during measurements, were analyzed for chemical composition. Based on nearly three years of data, the Gleason Fire site does not appear to have returned to pre burn wind erosion levels. Chemical composition data of suspendible particles are variable and show a trend toward pre-burn levels, but provide little insight into how the composition has been changing over time since the fire. Soil, runoff, and sediment data were collected from the Gleason Fire site to monitor the water erosion potential over the nearly three-year period. Soil

  3. Enhanced Enzyme Kinetic Stability by Increasing Rigidity within the Active Site*

    PubMed Central

    Xie, Yuan; An, Jiao; Yang, Guangyu; Wu, Geng; Zhang, Yong; Cui, Li; Feng, Yan

    2014-01-01

    Enzyme stability is an important issue for protein engineers. Understanding how rigidity in the active site affects protein kinetic stability will provide new insight into enzyme stabilization. In this study, we demonstrated enhanced kinetic stability of Candida antarctica lipase B (CalB) by mutating the structurally flexible residues within the active site. Six residues within 10 Å of the catalytic Ser105 residue with a high B factor were selected for iterative saturation mutagenesis. After screening 2200 colonies, we obtained the D223G/L278M mutant, which exhibited a 13-fold increase in half-life at 48 °C and a 12 °C higher T5015, the temperature at which enzyme activity is reduced to 50% after a 15-min heat treatment. Further characterization showed that global unfolding resistance against both thermal and chemical denaturation also improved. Analysis of the crystal structures of wild-type CalB and the D223G/L278M mutant revealed that the latter formed an extra main chain hydrogen bond network with seven structurally coupled residues within the flexible α10 helix that are primarily involved in forming the active site. Further investigation of the relative B factor profile and molecular dynamics simulation confirmed that the enhanced rigidity decreased fluctuation of the active site residues at high temperature. These results indicate that enhancing the rigidity of the flexible segment within the active site may provide an efficient method for improving enzyme kinetic stability. PMID:24448805

  4. Neurospora tryptophan synthase: N-terminal analysis and the sequence of the pyridoxal phosphate active site peptide

    SciTech Connect

    Pratt, M.L.; Hsu, P.Y.; DeMoss, J.A.

    1986-05-01

    Tryptophan synthase (TS), which catalyzes the final step of tryptophan biosynthesis, is a multifunctional protein requiring pyridoxal phosphate (B6P) for two of its three distinct enzyme activities. TS from Neurospora has a blocked N-terminal, is a homodimer of 150 KDa and binds one mole of B6P per mole of subunit. The authors shown the N-terminal residue to be acyl-serine. The B6P-active site of holoenzyme was labelled by reduction of the B6P-Schiff base with (/sup 3/H)-NaBH/sub 4/, and resulted in a proportionate loss of activity in the two B6P-requiring reactions. SDS-polyacrylamide gel electrophoresis of CNBr-generated peptides showed the labelled, active site peptide to be 6 KDa. The sequence of this peptide, purified to apparent homogeneity by a combination of C-18 reversed phase and TSK gel filtration HPLC is: gly-arg-pro-gly-gln-leu-his-lys-ala-glu-arg-leu-thr-glu-tyr-ala-gly-gly-ala-gln-ile-xxx-leu-lys-arg-glu-asp-leu-asn-his-xxx-gly-xxx-his-/sub ***/-ile-asn-asn-ala-leu. Although four residues (xxx, /sub ***/) are unidentified, this peptide is minimally 78% homologous with the corresponding peptide from yeast TS, in which residue (/sub ***/) is the lysine that binds B6P.

  5. Using Carbohydrate Interaction Assays to Reveal Novel Binding Sites in Carbohydrate Active Enzymes.

    PubMed

    Cockburn, Darrell; Wilkens, Casper; Dilokpimol, Adiphol; Nakai, Hiroyuki; Lewińska, Anna; Abou Hachem, Maher; Svensson, Birte

    2016-01-01

    Carbohydrate active enzymes often contain auxiliary binding sites located either on independent domains termed carbohydrate binding modules (CBMs) or as so-called surface binding sites (SBSs) on the catalytic module at a certain distance from the active site. The SBSs are usually critical for the activity of their cognate enzyme, though they are not readily detected in the sequence of a protein, but normally require a crystal structure of a complex for their identification. A variety of methods, including affinity electrophoresis (AE), insoluble polysaccharide pulldown (IPP) and surface plasmon resonance (SPR) have been used to study auxiliary binding sites. These techniques are complementary as AE allows monitoring of binding to soluble polysaccharides, IPP to insoluble polysaccharides and SPR to oligosaccharides. Here we show that these methods are useful not only for analyzing known binding sites, but also for identifying new ones, even without structural data available. We further verify the chosen assays discriminate between known SBS/CBM containing enzymes and negative controls. Altogether 35 enzymes are screened for the presence of SBSs or CBMs and several novel binding sites are identified, including the first SBS ever reported in a cellulase. This work demonstrates that combinations of these methods can be used as a part of routine enzyme characterization to identify new binding sites and advance the study of SBSs and CBMs, allowing them to be detected in the absence of structural data. PMID:27504624

  6. Using Carbohydrate Interaction Assays to Reveal Novel Binding Sites in Carbohydrate Active Enzymes

    PubMed Central

    Wilkens, Casper; Dilokpimol, Adiphol; Nakai, Hiroyuki; Lewińska, Anna; Abou Hachem, Maher; Svensson, Birte

    2016-01-01

    Carbohydrate active enzymes often contain auxiliary binding sites located either on independent domains termed carbohydrate binding modules (CBMs) or as so-called surface binding sites (SBSs) on the catalytic module at a certain distance from the active site. The SBSs are usually critical for the activity of their cognate enzyme, though they are not readily detected in the sequence of a protein, but normally require a crystal structure of a complex for their identification. A variety of methods, including affinity electrophoresis (AE), insoluble polysaccharide pulldown (IPP) and surface plasmon resonance (SPR) have been used to study auxiliary binding sites. These techniques are complementary as AE allows monitoring of binding to soluble polysaccharides, IPP to insoluble polysaccharides and SPR to oligosaccharides. Here we show that these methods are useful not only for analyzing known binding sites, but also for identifying new ones, even without structural data available. We further verify the chosen assays discriminate between known SBS/CBM containing enzymes and negative controls. Altogether 35 enzymes are screened for the presence of SBSs or CBMs and several novel binding sites are identified, including the first SBS ever reported in a cellulase. This work demonstrates that combinations of these methods can be used as a part of routine enzyme characterization to identify new binding sites and advance the study of SBSs and CBMs, allowing them to be detected in the absence of structural data. PMID:27504624

  7. 40 CFR 61.154 - Standard for active waste disposal sites.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... (20″×14″) upright format signs specified in 29 CFR 1910.145(d)(4) and this paragraph; and (iii... 40 Protection of Environment 8 2011-07-01 2011-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an...

  8. 40 CFR 61.154 - Standard for active waste disposal sites.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... (20″×14″) upright format signs specified in 29 CFR 1910.145(d)(4) and this paragraph; and (iii... 40 Protection of Environment 8 2010-07-01 2010-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an...

  9. 40 CFR 61.154 - Standard for active waste disposal sites.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... (20″×14″) upright format signs specified in 29 CFR 1910.145(d)(4) and this paragraph; and (iii... 40 Protection of Environment 9 2013-07-01 2013-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an...

  10. 77 FR 39508 - Commercial Wind Lease Issuance and Site Assessment Activities on the Atlantic Outer Continental...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-03

    ... specific project proposals on those leases) in an identified Wind Energy Area (WEA) on the OCS offshore... Bureau of Ocean Energy Management Commercial Wind Lease Issuance and Site Assessment Activities on the... Activities on the Atlantic OCS Offshore RI and MA'' to: Program Manager, Office of Renewable Energy...

  11. Effects of resource activities upon repository siting and waste containment with reference to bedded salt

    SciTech Connect

    Ashby, J.; Rowe, J.

    1980-02-01

    The primary consideration for the suitability of a nuclear waste repository site is the overall ability of the repository to safely contain radioactive waste. This report is a discussion of the past, present, and future effects of resource activities on waste containment. Past and present resource activities which provide release pathways (i.e., leaky boreholes, adjacent mines) will receive initial evaluation during the early stages of any repository site study. However, other resource activities which may have subtle effects on containment (e.g., long-term pumping causing increased groundwater gradients, invasion of saline water causing lower retardation) and all potential future resource activities must also be considered during the site evaluation process. Resource activities will affect both the siting and the designing of repositories. Ideally, sites should be located in areas of low resource activity and low potential for future activity, and repository design should seek to eliminate or minimize the adverse effects of any resource activity. Buffer zones should be created to provide areas in which resource activities that might adversely affect containment can be restricted or curtailed. This could mean removing large areas of land from resource development. The impact of these frozen assets should be assessed in terms of their economic value and of their effect upon resource reserves. This step could require a major effort in data acquisition and analysis followed by extensive numerical modeling of regional fluid flow and mass transport. Numerical models should be used to assess the effects of resource activity upon containment and should include the cumulative effects of different resource activities. Analysis by other methods is probably not possible except for relatively simple cases.

  12. Computational approaches to the determination of active site structures and reaction mechanisms in heterogeneous catalysts.

    PubMed

    Catlow, C R A; French, S A; Sokol, A A; Thomas, J M

    2005-04-15

    We apply quantum chemical methods to the study of active site structures and reaction mechanisms in mesoporous silica and metal oxide catalysts. Our approach is based on the use of both molecular cluster and embedded cluster (QM/MM) techniques, where the active site and molecular complex are described using density functional theory (DFT) and the embedding matrix simulated by shell model potentials. We consider three case studies: alkene epoxidation over the microporous TS-1 catalyst; methanol synthesis on ZnO and Cu/ZnO and C-H bond activation over Li-doped MgO.

  13. Computational approaches to the determination of active site structures and reaction mechanisms in heterogeneous catalysts.

    PubMed

    Catlow, C R A; French, S A; Sokol, A A; Thomas, J M

    2005-04-15

    We apply quantum chemical methods to the study of active site structures and reaction mechanisms in mesoporous silica and metal oxide catalysts. Our approach is based on the use of both molecular cluster and embedded cluster (QM/MM) techniques, where the active site and molecular complex are described using density functional theory (DFT) and the embedding matrix simulated by shell model potentials. We consider three case studies: alkene epoxidation over the microporous TS-1 catalyst; methanol synthesis on ZnO and Cu/ZnO and C-H bond activation over Li-doped MgO. PMID:15901543

  14. Rapid binding of a cationic active site inhibitor to wild type and mutant mouse acetylcholinesterase: Brownian dynamics simulation including diffusion in the active site gorge.

    PubMed

    Tara, S; Elcock, A H; Kirchhoff, P D; Briggs, J M; Radic, Z; Taylor, P; McCammon, J A

    1998-12-01

    It is known that anionic surface residues play a role in the long-range electrostatic attraction between acetylcholinesterase and cationic ligands. In our current investigation, we show that anionic residues also play an important role in the behavior of the ligand within the active site gorge of acetylcholinesterase. Negatively charged residues near the gorge opening not only attract positively charged ligands from solution to the enzyme, but can also restrict the motion of the ligand once it is inside of the gorge. We use Brownian dynamics techniques to calculate the rate constant kon, for wild type and mutant acetylcholinesterase with a positively charged ligand. These calculations are performed by allowing the ligand to diffuse within the active site gorge. This is an extension of previously reported work in which a ligand was allowed to diffuse only to the enzyme surface. By setting the reaction criteria for the ligand closer to the active site, better agreement with experimental data is obtained. Although a number of residues influence the movement of the ligand within the gorge, Asp74 is shown to play a particularly important role in this function. Asp74 traps the ligand within the gorge, and in this way helps to ensure a reaction.

  15. Cyanide does more to inhibit heme enzymes, than merely serving as an active-site ligand

    SciTech Connect

    Parashar, Abhinav; Venkatachalam, Avanthika; Gideon, Daniel Andrew; Manoj, Kelath Murali

    2014-12-12

    Highlights: • Cyanide (CN) is a well-studied toxic principle, known to inhibit heme-enzymes. • Inhibition is supposed to result from CN binding at the active site as a ligand. • Diverse heme enzymes’ CN inhibition profiles challenge prevailing mechanism. • Poor binding efficiency of CN at low enzyme concentrations and ligand pressures. • CN-based diffusible radicals cause ‘non-productive electron transfers’ (inhibition). - Abstract: The toxicity of cyanide is hitherto attributed to its ability to bind to heme proteins’ active site and thereby inhibit their activity. It is shown herein that the long-held interpretation is inadequate to explain several observations in heme-enzyme reaction systems. Generation of cyanide-based diffusible radicals in heme-enzyme reaction milieu could shunt electron transfers (by non-active site processes), and thus be detrimental to the efficiency of oxidative outcomes.

  16. Denaturation studies of active-site labeled papain using electron paramagnetic resonance and fluorescence spectroscopy.

    PubMed Central

    Ping, Z A; Butterfiel, D A

    1991-01-01

    A spin-labeled p-chloromercuribenzoate (SL-PMB) and a fluorescence probe, 6-acryloyl-2-dimethylaminonaphthalene (Acrylodan), both of which bind to the single SH group located in the active site of papain, were used to investigate the interaction of papain (EC 3.4.22.2) with two protein denaturants. It was found that the active site of papain was highly stable in urea solution, but underwent a large conformational change in guanidine hydrochloride solution. Electron paramagnetic resonance and fluorescence results were in agreement and both paralleled enzymatic activity of papain with respect to both the variation in pH and denaturation. These results strongly suggest that SL-PMB and Acrylodan labels can be used to characterize the physical state of the active site of the enzyme. PMID:1657229

  17. Catalysis-dependent selenium incorporation and migration in the nitrogenase active site iron-molybdenum cofactor

    PubMed Central

    Spatzal, Thomas; Perez, Kathryn A; Howard, James B; Rees, Douglas C

    2015-01-01

    Dinitrogen reduction in the biological nitrogen cycle is catalyzed by nitrogenase, a two-component metalloenzyme. Understanding of the transformation of the inert resting state of the active site FeMo-cofactor into an activated state capable of reducing dinitrogen remains elusive. Here we report the catalysis dependent, site-selective incorporation of selenium into the FeMo-cofactor from selenocyanate as a newly identified substrate and inhibitor. The 1.60 Å resolution structure reveals selenium occupying the S2B site of FeMo-cofactor in the Azotobacter vinelandii MoFe-protein, a position that was recently identified as the CO-binding site. The Se2B-labeled enzyme retains substrate reduction activity and marks the starting point for a crystallographic pulse-chase experiment of the active site during turnover. Through a series of crystal structures obtained at resolutions of 1.32–1.66 Å, including the CO-inhibited form of Av1-Se2B, the exchangeability of all three belt-sulfur sites is demonstrated, providing direct insights into unforeseen rearrangements of the metal center during catalysis. DOI: http://dx.doi.org/10.7554/eLife.11620.001 PMID:26673079

  18. Catalysis-dependent selenium incorporation and migration in the nitrogenase active site iron-molybdenum cofactor.

    PubMed

    Spatzal, Thomas; Perez, Kathryn A; Howard, James B; Rees, Douglas C

    2015-12-16

    Dinitrogen reduction in the biological nitrogen cycle is catalyzed by nitrogenase, a two-component metalloenzyme. Understanding of the transformation of the inert resting state of the active site FeMo-cofactor into an activated state capable of reducing dinitrogen remains elusive. Here we report the catalysis dependent, site-selective incorporation of selenium into the FeMo-cofactor from selenocyanate as a newly identified substrate and inhibitor. The 1.60 Å resolution structure reveals selenium occupying the S2B site of FeMo-cofactor in the Azotobacter vinelandii MoFe-protein, a position that was recently identified as the CO-binding site. The Se2B-labeled enzyme retains substrate reduction activity and marks the starting point for a crystallographic pulse-chase experiment of the active site during turnover. Through a series of crystal structures obtained at resolutions of 1.32-1.66 Å, including the CO-inhibited form of Av1-Se2B, the exchangeability of all three belt-sulfur sites is demonstrated, providing direct insights into unforeseen rearrangements of the metal center during catalysis.

  19. National Dioxin Study Tier 4 - combustion sources: final test report - Site 9, carbon-regeneration furnace CRF-A

    SciTech Connect

    Jamgochian, C.L.; Keller, L.E.; Kelly, W.

    1987-04-01

    The Environmental Protection Agency is assessing the potential for the emissions of dioxin/furans from combustion sources under Tier 4 of the National Dioxin Study. If any of the combustion sources are found to emit dioxins, the secondary purpose of the Tier 4 study is to quantify these emissions and, if possible, related the emissions to combustion parameters. Carbon-regeneration furnaces are 1 of 8 source categories that have been included in the field test program. Carbon-regeneration furnaces reactivate spent carbon from industrial or municipal water-treatment facilities. The spent carbon may contain absorbed chlorinated compounds. The report presents the results of an emission-test program conducted by Radian during May 28-31, 1985, at an industrial carbon-regeneration furnace designated as Site CRF-A. The furnace was selected after an initial information screening and a pretest survey visit. The facility is considered representative of other carbon-regeneration furnaces in the United States. Furnace CRF-A regenerates spent carbon from more than 20 plants that use activated carbon for industrial wastewater treatment. Data presented in the report include dioxin (tetra through octa homologue +2378 TCDF) and furan (tetra through octa homologue +2378 TCDF) results for both stack samples and ash samples. In addition, process data collected during sampling are also presented.

  20. Coulombic effects of remote subsites on the active site of ribonuclease A.

    PubMed

    Fisher, B M; Schultz, L W; Raines, R T

    1998-12-15

    The active-site cleft of bovine pancreatic ribonuclease A (RNase A) is lined with cationic residues that interact with a bound nucleic acid. Those residues interacting with the phosphoryl groups comprise the P0, P1, and P2 subsites, with the scissile P-O5' bond residing in the P1 subsite. Coulombic interactions between the P0 and P2 subsites and phosphoryl groups of the substrate were characterized previously [Fisher, B. M., Ha, J.-H., and Raines, R. T. (1998) Biochemistry 37, 12121-12132]. Here, the interactions between these subsites and the active-site residues His12 and His119 are described in detail. A protein variant in which the cationic residues in these subsites (Lys66 in the P0 subsite and Lys7 and Arg10 in the P2 subsite) were replaced with alanine was crystallized, both free and with bound 3'-uridine monophosphate (3'-UMP). Structures of K7A/R10A/K66A RNase A and the K7A/R10A/K66A RNase A.3'-UMP complex were determined by X-ray diffraction analysis to resolutions of 2.0 and 2.1 A, respectively. There is little observable change between these structures and that of wild-type RNase A, either free or with bound 3'-cytidine monophosphate. K7A/R10A/K66A RNase A was evaluated for its ability to cleave UpA, a dinucleotide substrate that does not span the P0 or the P2 subsites. In comparison to the wild-type enzyme, the value of kcat was decreased by 5-fold and that of kcat/Km was decreased 10-fold, suggesting that these remote subsites interact with the active site. These interactions were characterized by determining the pKa values of His12 and His119 at 0.018 and 0.142 M Na+, both in wild-type RNase A and the K7A/R10A/K66A variant. The side chains of Lys7, Arg10, and Lys66 depress the pKa values of these histidine residues, and this depression is sensitive to the salt concentration. In addition, the P0 and P2 subsites influence the interaction of His12 and His119 with each other, as demonstrated by changes in the cooperativity that gives rise to microscopic

  1. Public health assessment for Agrico Chemical Site, Pensacola, Escambia County, Florida, Region 4. Cerclis No. FLD980221857. Final report

    SciTech Connect

    1995-02-07

    The Agrico Chemical Co. Superfund site (Agrico) is a former sulfuric acid and phosphate fertilizer production facility in Pensacola, Escambia County, Florida. The authors focused their public assessment on the following chemicals: arsenic, chromium, fluoride, lead, manganese, polycyclic aromatic hydrocarbons (PAHs), sulfate and vanadium. Workers and treapassers on the site may have accidentally eaten contaminated soil or waste sludge, or gotten this material or contaminated water on their skin. Arsenic in surface soil on the site may also increase the risk of skin, bladder, liver, kidney and lung cancer. Arsenic in surface soil at the onsite baseball field, and lead and PAHs in surface soil on and off of the site would result in no apparent increase in the risk of cancer. Analysis of off-site surface soil samples has been limited to PAHs, fluoride and three analyses for lead. Based on the information the authors have, this site is a public health hazard.

  2. Superfund Record of Decision (EPA Region 6): Brio Refining Site, Harris County, Texas, March 1988. First remedial action. Final report

    SciTech Connect

    Not Available

    1988-03-31

    The 58-acre Brio Refining site is located in Harris County, Texas, approximately 20 miles southeast of Houston. The site is broken into two parcels, 49-acre Brio North and 9-acre Brio South, separated by Drive Farm Road. Between 1957 and 1982 the site refined crude oil and styrene tars to produce toluene, ethylbenzene, solvents, naphthalene, diesel fuel and kerosene. Site investigation indicate that between 500,000-700,000 sq yds of onsite soil have measurable contamination, and that high levels of VOCs exist in ground water underlying the site. The selected remedial action for the Brio Refining site includes: Excavation and incineration or biological treatment of all onsite soils, sludges, and liquids found to be above action levels defined in the Endangerment Assessment, with backfilling of all treated material passing the Toxicity Characteristics Leaching Procedure (TCLP).

  3. Substrate Shuttling Between Active Sites of Uroporphyrinogen Decarboxylase in Not Required to Generate Coproporphyrinogen

    SciTech Connect

    Phillips, J.; Warby, C; Whitby, F; Kushner, J; Hill, C

    2009-01-01

    Uroporphyrinogen decarboxylase (URO-D; EC 4.1.1.37), the fifth enzyme of the heme biosynthetic pathway, is required for the production of heme, vitamin B12, siroheme, and chlorophyll precursors. URO-D catalyzes the sequential decarboxylation of four acetate side chains in the pyrrole groups of uroporphyrinogen to produce coproporphyrinogen. URO-D is a stable homodimer, with the active-site clefts of the two subunits adjacent to each other. It has been hypothesized that the two catalytic centers interact functionally, perhaps by shuttling of reaction intermediates between subunits. We tested this hypothesis by construction of a single-chain protein (single-chain URO-D) in which the two subunits were connected by a flexible linker. The crystal structure of this protein was shown to be superimposable with wild-type activity and to have comparable catalytic activity. Mutations that impaired one or the other of the two active sites of single-chain URO-D resulted in approximately half of wild-type activity. The distributions of reaction intermediates were the same for mutant and wild-type sequences and were unaltered in a competition experiment using I and III isomer substrates. These observations indicate that communication between active sites is not required for enzyme function and suggest that the dimeric structure of URO-D is required to achieve conformational stability and to create a large active-site cleft.

  4. Crystal structure of an avian influenza polymerase PA[subscript N] reveals an endonuclease active site

    SciTech Connect

    Yuan, Puwei; Bartlam, Mark; Lou, Zhiyong; Chen, Shoudeng; Zhou, Jie; He, Xiaojing; Lv, Zongyang; Ge, Ruowen; Li, Xuemei; Deng, Tao; Fodor, Ervin; Rao, Zihe; Liu, Yingfang

    2009-11-10

    The heterotrimeric influenza virus polymerase, containing the PA, PB1 and PB2 proteins, catalyses viral RNA replication and transcription in the nucleus of infected cells. PB1 holds the polymerase active site and reportedly harbours endonuclease activity, whereas PB2 is responsible for cap binding. The PA amino terminus is understood to be the major functional part of the PA protein and has been implicated in several roles, including endonuclease and protease activities as well as viral RNA/complementary RNA promoter binding. Here we report the 2.2 angstrom (A) crystal structure of the N-terminal 197 residues of PA, termed PA(N), from an avian influenza H5N1 virus. The PA(N) structure has an alpha/beta architecture and reveals a bound magnesium ion coordinated by a motif similar to the (P)DX(N)(D/E)XK motif characteristic of many endonucleases. Structural comparisons and mutagenesis analysis of the motif identified in PA(N) provide further evidence that PA(N) holds an endonuclease active site. Furthermore, functional analysis with in vivo ribonucleoprotein reconstitution and direct in vitro endonuclease assays strongly suggest that PA(N) holds the endonuclease active site and has critical roles in endonuclease activity of the influenza virus polymerase, rather than PB1. The high conservation of this endonuclease active site among influenza strains indicates that PA(N) is an important target for the design of new anti-influenza therapeutics.

  5. Monitoring Soil Erosion on a Burned Site in the Mojave-Great Basin Transition Zone: Final Report for the Jacob Fire Site

    SciTech Connect

    Miller, Julianne; Etyemezian, Vic; Cablk, Mary E.; Shillito, Rose; Shafer, David

    2013-06-01

    A historic return interval of 100 years for large fires in the U.S. southwestern deserts is being replaced by one where fires may reoccur as frequently as every 20 to 30 years. The shortened return interval, which translates to an increase in fires, has implications for management of Soil Corrective Action Units (CAUs) and Corrective Action Sites (CASs) for which the Department of Energy, National Nuclear Security Administration Nevada Field Office has responsibility. A series of studies was initiated at uncontaminated analog sites to better understand the possible impacts of erosion and transport by wind and water should contaminated soil sites burn. The first of these studies was undertaken at the Jacob Fire site approximately 12 kilometers (7.5 miles) north of Hiko, Nevada. A lightning-caused fire burned approximately 200 hectares during August 6-8, 2008. The site is representative of a transition between Mojave and Great Basin desert ecoregions on the Nevada National Security Site (NNSS), where the largest number of Soil CAUs/CASs are located. The area that burned at the Jacob Fire site was primarily a Coleogyne ramosissima (blackbrush) and Ephedra nevadensis (Mormon tea) community, also an abundant shrub assemblage in the similar transition zone on the NNSS. This report summarizes three years of measurements after the fire. Seven measurement campaigns at the Jacob Fire site were completed. Measurements were made on burned ridge (upland) and drainage sites, and on burned and unburned sites beneath and between vegetation. A Portable In-Situ Wind Erosion Lab (PI-SWERL) was used to estimate emissions of suspended particles at different wind speeds. Context for these measurements was provided through a meteorological tower that was installed at the Jacob Fire site to obtain local, relevant environmental parameters. Filter samples, collected from the exhaust of the PI-SWERL during measurements, were analyzed for chemical composition. Runoff and water erosion were

  6. Active vibration control testing of the SPICES program: final demonstration article

    NASA Astrophysics Data System (ADS)

    Dunne, James P.; Jacobs, Jack H.

    1996-05-01

    The Synthesis and Processing of Intelligent Cost Effective Structures (SPICES) Program is a partnership program sponsored by the Advanced Research Projects Agency. The mission of the program is to develop cost effective material processing and synthesis technologies to enable new products employing active vibration suppression and control devices to be brought to market. The two year program came to fruition in 1995 through the fabrication of the final smart components and testing of an active plate combined with two trapezoidal rails, forming an active mount. Testing of the SPICES combined active mount took place at McDonnell Douglas facilities in St. Louis, MO, in October-December 1995. Approximately 15 dB reduction in overall response of a motor mounted on the active structure was achieved. Further details and results of the SPICES combined active mount demonstration testing are outlined. Results of numerous damping and control strategies that were developed and employed in the testing are presented, as well as aspects of the design and fabrication of the SPICES active mount components.

  7. Evaluation of physical activity web sites for use of behavior change theories.

    PubMed

    Doshi, Amol; Patrick, Kevin; Sallis, James F; Calfas, Karen

    2003-01-01

    Physical activity (PA) Web sites were assessed for their use of behavior change theories, including constructs of the health belief model, Transtheoretical Model, social cognitive theory, and the theory of reasoned action and planned behavior. An evaluation template for assessing PA Web sites was developed, and content validity and interrater reliability were demonstrated. Two independent raters evaluated 24 PA Web sites. Web sites varied widely in application of theory-based constructs, ranging from 5 to 48 on a 100-point scale. The most common intervention strategies were general information, social support, and realistic goal areas. Coverage of theory-based strategies was low, varying from 26% for social cognitive theory to 39% for health belief model. Overall, PA Web sites provided little assessment, feedback, or individually tailored assistance for users. They were unable to substantially tailor the on-line experience for users at different stages of change or different demographic characteristics.

  8. Final Environmental Assessment and Finding of No Significant Impact: Ground Water Compliance at the Slick Rock, Colorado, UMTRA Project Site

    SciTech Connect

    N /A

    2003-03-13

    This environmental assessment addresses the environmental effects of a proposed action and the no action alternative to comply with U.S. Environmental Protection Agency (EPA) ground water standards at the Slick Rock, Colorado, Uranium Mill Tailings Remedial Action Project sites. The sites consist of two areas designated as the North Continent (NC) site and the Union Carbide (UC) site. In 1996, the U.S. Department of Energy (DOE) completed surface cleanup at both sites and encapsulated the tailings in a disposal cell 5 miles east of the original sites. Maximum concentration limits (MCLs) referred to in this environmental assessment are the standards established in Title 40 ''Code of Federal Regulations'' Part 192 (40 CFR 192) unless noted otherwise. Ground water contaminants of potential concern at the NC site are uranium and selenium. Uranium is more prevalent, and concentrations in the majority of alluvial wells at the NC site exceed the MCL of 0.044 milligram per liter (mg/L). Selenium contamination is less prevalent; samples from only one well had concentrations exceeding the MCL of 0.01 mg/L. To achieve compliance with Subpart B of 40 CFR 192 at the NC site, DOE is proposing the strategy of natural flushing in conjunction with institutional controls and continued monitoring. Ground water flow and transport modeling has predicted that concentrations of uranium and selenium in the alluvial aquifer will decrease to levels below their respective MCLs within 50 years.

  9. Health assessment for Somersworth Municipal Landfill Site, Strafford County, Somersworth, New Hampshire, Region 1. CERCLIS No. NHD980520225. Final report

    SciTech Connect

    Not Available

    1989-04-12

    The Somersworth Municipal Landfill National Priorities List (NPL) Site is located in a predominantly residential part of central Somersworth, New Hampshire, approximately one mile southwest of downtown Somersworth. On-site soils are contaminated with low levels of volatile organic compounds (VOCs), metals and polycyclic aromatic hydrocarbons (PAHs). Groundwater beneath the site is contaminated with low levels of VOCs. The Agency for Toxic Substances and Disease Registry (ATSDR) has concluded that the Somersworth Landfill Site is of potential public health concern under current conditions because of the potential risk to human health resulting from possible exposure to hazardous substances at concentrations that may result in adverse health effects.

  10. Tetrodotoxin binding sites in human heart and human brain sodium channels. Final report, 28 June 1991-27 June 1994

    SciTech Connect

    Brown, A.M.; Hartmann, H.A.

    1994-07-28

    Tetrodotoxin (TTX) and saxitoxin (STX) are potent and lethal threats to exposed soldiers. The development of an antidote or site-specific antibodies for low affinity TTX/STX cardiac sodium channels and high affinity TTX/STX brain and peripheral nerve sodium channels requires a data base not only of the primary structure of the toxin receptor site(s) but also insight into the secondary structures of these site(s). Five goals or tasks were attempted and the first three were completed. Full-length human cardiac and brain sodium channel cDNAs have been cloned and expressed as functional proteins in Xenopus oocytes. Silent restriction sites have been introduced around the pore or P-region of the Na+ channel repeats. Site-directed mutagenesis has identified critical residues in the pore from the primary structure involved in sensitivity to TTX and STX and other pore properties. Chemical modification of cysteine mutants of these initial residues by methanethiosulfonate compounds produces an expanded data base of the secondary structure of the toxins` receptors. Specific peptides which mimic these receptors will be made to compete with the natural receptor for the toxins. We have successfully cloned the cDNAs for both human heart and brain sodium channels and expressed functional proteins. The initial chemical modification data suggests file receptor sites for TTX/STX are not interchangeable and are not the same site.

  11. Corrosion Control during Closure Activities at the Savannah River Site - 13514

    SciTech Connect

    Wiersma, Bruce J.; Subramanian, Karthik H.; Martin, Keisha B.

    2013-07-01

    Liquid radioactive wastes from the Savannah River Site (SRS) separation process are stored in large underground carbon steel tanks. Until the waste is removed from storage, transferred, and processed, the materials and structures of the tanks must maintain a confinement function by providing a barrier to the environment and by maintaining acceptable structural stability during normal service and design basis events (e.g., earthquake conditions). A corrosion control program is in place to ensure that degradation of the steel does not impact the structural and leak integrity functions of these waste tanks. The SRS is currently retrieving waste from older waste tanks and processing the waste through the vitrification for long term stabilization. The retrieval processes prepare the tanks for ultimate closure (i.e., grouting) by removing sludge by mechanical and/or sluicing methods, dissolving salt cake by adding water, and chemical cleaning of the residual sludge with oxalic acid. Each of these retrieval methods will result in waste chemistry that does not meet the requirements of the current corrosion control program. Given the short-term exposure and limited remaining service life for the tanks in which retrievals are being performed, an assessment of the need for corrosion controls in these tanks was performed. The assessment reviewed the corrosion rates in the more aggressive environments and the postulated loads on the structure during the closure activities. The assessment concluded that the current corrosion control program may be suspended for a short period of time while final retrieval of the waste is performed. (authors)

  12. Remedial actions at the former Vitro Rare Metals plant site, Canonsburg, Washington County, Pennsylvania. Final Environmental Impact Statement. Volume I

    SciTech Connect

    Not Available

    1983-07-01

    The environmental impacts associated with remedial actions in connection with residual radioactive materials remaining at the inactive uranium processing site located in Canonsburg, Washington County, Pennsylvania are evaluated. The Canonsburg site is an 18.5-acre property that was formerly owned by the Vitro Rare Metals Company. The expanded Canonsburg site would be 30-acre property that would include the Canonsburg site (the former Vitro Rare Metals plant), seven adjacent private houses, and the former Georges Pottery property. During the period 1942 through 1957 the Vitro Manufacturing Company and its successor, the Vitro Corporation of America, processed onsite residues and ores, and government-owned ores, concentrates, and scraps to extract uranium and other rare metals. The Canonsburg site is now the Canon Industrial Park. In addition to storing the residual radioactive materials of this process at the Canonsburg site, about 12,000 tons of radioactively contaminated materials were transferred to a railroad landfill in Burrell Township, Indiana County, Pennsylvania. This Canonsburg FEIS evaluates five alternatives for removing the potential public health hazard associated with the radioactively contaminated materials. In addition to no action, these alternatives involve various combinations of stabilization of the radioactively contaminated materials in place or decontamination of the Canonsburg and Burrell sites by removing the radioactively contaminated materials to another location. In addition to the two sites mentioned, a third site located in Hanover Township, Washington County, Pennsylvania has been considered as a disposal site to which the radioactively contaminated materials presently located at either of the other two sites might be moved.

  13. Conformational Change in the Active Site of Streptococcal Unsaturated Glucuronyl Hydrolase Through Site-Directed Mutagenesis at Asp-115.

    PubMed

    Nakamichi, Yusuke; Oiki, Sayoko; Mikami, Bunzo; Murata, Kousaku; Hashimoto, Wataru

    2016-08-01

    Bacterial unsaturated glucuronyl hydrolase (UGL) degrades unsaturated disaccharides generated from mammalian extracellular matrices, glycosaminoglycans, by polysaccharide lyases. Two Asp residues, Asp-115 and Asp-175 of Streptococcus agalactiae UGL (SagUGL), are completely conserved in other bacterial UGLs, one of which (Asp-175 of SagUGL) acts as a general acid and base catalyst. The other Asp (Asp-115 of SagUGL) also affects the enzyme activity, although its role in the enzyme reaction has not been well understood. Here, we show substitution of Asp-115 in SagUGL with Asn caused a conformational change in the active site. Tertiary structures of SagUGL mutants D115N and D115N/K370S with negligible enzyme activity were determined at 2.00 and 1.79 Å resolution, respectively, by X-ray crystallography. The side chain of Asn-115 is drastically shifted in both mutants owing to the interaction with several residues, including Asp-175, by formation of hydrogen bonds. This interaction between Asn-115 and Asp-175 probably prevents the mutants from triggering the enzyme reaction using Asp-175 as an acid catalyst.

  14. Final report: survey and removal of radioactive surface contamination at environmental restoration sites, Sandia National Laboratories/New Mexico. Volume 1

    SciTech Connect

    Lambert, K.A.; Mitchell, M.M.; Jean, D.; Byrd, C.S.

    1997-09-01

    This report describes the survey and removal of radioactive surface contamination at Sandia`s Environmental Restoration (ER) sites. Radiological characterization was performed as a prerequisite to beginning the Resource Conservation and Recovery Act (RCRA) corrective action process. The removal of radioactive surface contamination was performed in order to reduce potential impacts to human health and the environment. The predominant radiological contaminant of concern was depleted uranium (DU). Between October 1993 and November 1996 scanning surface radiation surveys, using gamma scintillometers, were conducted at 65 sites covering approximately 908 acres. A total of 9,518 radiation anomalies were detected at 38 sites. Cleanup activities were conducted between October 1994 and November 1996. A total of 9,122 anomalies were removed and 2,072 waste drums were generated. The majority of anomalies not removed were associated with a site that has subsurface contamination beyond the scope of this project. Verification soil samples (1,008 total samples) were collected from anomalies during cleanup activities and confirm that the soil concentration achieved in the field were far below the target cleanup level of 230 pCi/g of U-238 (the primary constituent of DU) in the soil. Cleanup was completed at 21 sites and no further radiological action is required. Seventeen sites were not completed since cleanup activities wee precluded by ongoing site activity or were beyond the original project scope.

  15. Initial field trials of the site characterization and analysis penetrometer system (SCAPS). Reconnaissance of Jacksonville Naval Air Station waste oil and solvents disposal site. Final report

    SciTech Connect

    Cooper, S.S.; Douglas, D.H.; Sharp, M.K.; Olsen, R.A.; Comes, G.D.

    1993-12-01

    At the request of the Naval Facilities Engineering Command (NAVFAC), Southern Division, Charleston, SC, the U.S. Army Engineer Waterways Experiment Station (WES) conducted the initial field trial of the Site Characterization and Analysis Penetrometer System (SCAPS) at Jacksonville Naval Air Station (NAS), Jacksonville FL. This work was carried out by a field crew consisting of personnel from WES and the Naval Ocean Systems Center during the period of 16 July 1990 to 14 August 1990. The SCAPS investigation at the Jacksonville NAS has two primary objectives: (a) to provide data that could be useful in formulating remediation plans for the facility and (b) to provide for the initial field trial of the SCAPS currently under development by WES for the U.S. Army Toxic and Hazardous Materials Agency (USATHAMA), now the U.S. Army Environmental Center. The original concepts for the SCAPS was to develop an integrated site screening characterization system whose capabilities would include (a) surface mapping, (b) geophysical surveys using magnetic, induced electromagnetic, and radar instruments, (c) measurements of soil strength, soil electrical resistivity, and laser-induced soil fluorometry Cone penetrometer, Site Characterization and Analysis Laser Induced Fluorescence(LIF), Penetrometer System(SCAPS) POL Contamination, using screening instrumentation mounted in a soil penetrometer, (d) soil and fluid samplers, and (e) computerized data acquisition, interpretation, and visualization. The goal of the SCAPS program is to provide detailed, rapid, and cost-effective surface and subsurface data for input to site assessment/remediation efforts.

  16. Remedial Action Plan and site design for stabilization of the inactive uranium mill tailings site at Gunnison, Colorado. Appendix A to Attachment 3, Tables: Final report

    SciTech Connect

    Not Available

    1992-10-01

    This volume contains the following tables: monitoring well information; static ground water levels; background ground water quality data by parameter; 1984 lysimeter tailings pore water quality by parameter; lysimeter tailings pore fluid quality data by parameter; and on site/downgradient ground water quality data by parameter.

  17. Counting Active Sites on Titanium Oxide-Silica Catalysts for Hydrogen Peroxide Activation through In Situ Poisoning with Phenylphosphonic Acid

    SciTech Connect

    Eaton, Todd R.; Boston, Andrew M.; Thompson, Anthony B.; Gray, Kimberly A.; Notestein, Justin M.

    2015-06-04

    Quantifying specific active sites in supported catalysts improves our understanding and assists in rational design. Supported oxides can undergo significant structural changes as surface densities increase from site-isolated cations to monolayers and crystallites, which changes the number of kinetically relevant sites. Herein, TiOx domains are titrated on TiOx–SiO2 selectively with phenylphosphonic acid (PPA). An ex situ method quantifies all fluid-accessible TiOx, whereas an in situ titration during cis-cyclooctene epoxidation provides previously unavailable values for the number of tetrahedral Ti sites on which H2O2 activation occurs. We use this method to determine the active site densities of 22 different catalysts with different synthesis methods, loadings, and characteristic spectra and find a single intrinsic turnover frequency for cis-cyclooctene epoxidation of (40±7) h-1. This simple method gives molecular-level insight into catalyst structure that is otherwise hidden when bulk techniques are used.

  18. Active site of tripeptidyl peptidase II from human erythrocytes is of the subtilisin type.

    PubMed Central

    Tomkinson, B; Wernstedt, C; Hellman, U; Zetterqvist, O

    1987-01-01

    The present report presents evidence that the amino acid sequence around the serine of the active site of human tripeptidyl peptidase II is of the subtilisin type. The enzyme from human erythrocytes was covalently labeled at its active site with [3H]diisopropyl fluorophosphate, and the protein was subsequently reduced, alkylated, and digested with trypsin. The labeled tryptic peptides were purified by gel filtration and repeated reversed-phase HPLC, and their amino-terminal sequences were determined. Residue 9 contained the radioactive label and was, therefore, considered to be the active serine residue. The primary structure of the part of the active site (residues 1-10) containing this residue was concluded to be Xaa-Thr-Gln-Leu-Met-Asx-Gly-Thr-Ser-Met. This amino acid sequence is homologous to the sequence surrounding the active serine of the microbial peptidases subtilisin and thermitase. These data demonstrate that human tripeptidyl peptidase II represents a potentially distinct class of human peptidases and raise the question of an evolutionary relationship between the active site of a mammalian peptidase and that of the subtilisin family of serine peptidases. PMID:3313395

  19. Evolution of anatase surface active sites probed by in situ sum-frequency phonon spectroscopy

    PubMed Central

    Cao, Yue; Chen, Shiyou; Li, Yadong; Gao, Yi; Yang, Deheng; Shen, Yuen Ron; Liu, Wei-Tao

    2016-01-01

    Surface active sites of crystals often govern their relevant surface chemistry, yet to monitor them in situ in real atmosphere remains a challenge. Using surface-specific sum-frequency spectroscopy, we identified the surface phonon mode associated with the active sites of undercoordinated titanium ions and conjoint oxygen vacancies, and used it to monitor them on anatase (TiO2) (101) under ambient conditions. In conjunction with theory, we determined related surface structure around the active sites and tracked the evolution of oxygen vacancies under ultraviolet irradiation. We further found that unlike in vacuum, the surface oxygen vacancies, which dominate the surface reactivity, are strongly regulated by ambient gas molecules, including methanol and water, as well as weakly associated species, such as nitrogen and hydrogen. The result revealed a rich interplay between prevailing ambient species and surface reactivity, which can be omnipresent in environmental and catalytic applications of titanium dioxides. PMID:27704049

  20. Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase.

    PubMed

    Fenwick, Michael K; Mehta, Angad P; Zhang, Yang; Abdelwahed, Sameh H; Begley, Tadhg P; Ealick, Steven E

    2015-03-27

    Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to generate a 5'-deoxyadenosyl radical. Canonical radical SAM enzymes are characterized by a β-barrel-like fold and SAM anchors to the differentiated iron of the cluster, which is located near the amino terminus and within the β-barrel, through its amino and carboxylate groups. Here we show that ThiC, the thiamin pyrimidine synthase in plants and bacteria, contains a tethered cluster-binding domain at its carboxy terminus that moves in and out of the active site during catalysis. In contrast to canonical radical SAM enzymes, we predict that SAM anchors to an additional active site metal through its amino and carboxylate groups. Superimposition of the catalytic domains of ThiC and glutamate mutase shows that these two enzymes share similar active site architectures, thus providing strong evidence for an evolutionary link between the radical SAM and adenosylcobalamin-dependent enzyme superfamilies.

  1. Solvent Tuning of Electrochemical Potentials in the Active Sites of HiPIP Versus Ferredoxin

    SciTech Connect

    Dey, A.; Francis, E.J.; Adams, M.W.W.; Babini, E.; Takahashi, Y.; Fukuyama, K.; Hodgson, K.O.; Hedman, B.; Solomon, E.I.; /Stanford U., Chem. Dept. /Georgia U. /Bologna U. /Osaka U. /SLAC, SSRL

    2009-04-29

    A persistent puzzle in the field of biological electron transfer is the conserved iron-sulfur cluster motif in both high potential iron-sulfur protein (HiPIP) and ferredoxin (Fd) active sites. Despite this structural similarity, HiPIPs react oxidatively at physiological potentials, whereas Fds are reduced. Sulfur K-edge x-ray absorption spectroscopy uncovers the substantial influence of hydration on this variation in reactivity. Fe-S covalency is much lower in natively hydrated Fd active sites than in HiPIPs but increases upon water removal; similarly, HiPIP covalency decreases when unfolding exposes an otherwise hydrophobically shielded active site to water. Studies on model compounds and accompanying density functional theory calculations support a correlation of Fe-S covalency with ease of oxidation and therefore suggest that hydration accounts for most of the difference between Fd and HiPIP reduction potentials.

  2. Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase

    SciTech Connect

    Fenwick, Michael K.; Mehta, Angad P.; Zhang, Yang; Abdelwahed, Sameh H.; Begley, Tadhg P.; Ealick, Steven E.

    2015-03-27

    Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to generate a 5'-deoxyadenosyl radical. Canonical radical SAM enzymes are characterized by a β-barrel-like fold and SAM anchors to the differentiated iron of the cluster, which is located near the amino terminus and within the β-barrel, through its amino and carboxylate groups. Here we show that ThiC, the thiamin pyrimidine synthase in plants and bacteria, contains a tethered cluster-binding domain at its carboxy terminus that moves in and out of the active site during catalysis. In contrast to canonical radical SAM enzymes, we predict that SAM anchors to an additional active site metal through its amino and carboxylate groups. Superimposition of the catalytic domains of ThiC and glutamate mutase shows that these two enzymes share similar active site architectures, thus providing strong evidence for an evolutionary link between the radical SAM and adenosylcobalamin-dependent enzyme superfamilies.

  3. Wasp recruitment to the T cell:APC contact site occurs independently of Cdc42 activation.

    PubMed

    Cannon, J L; Labno, C M; Bosco, G; Seth, A; McGavin, M H; Siminovitch, K A; Rosen, M K; Burkhardt, J K

    2001-08-01

    Cdc42 and WASP are critical regulators of actin polymerization whose function during T cell signaling is poorly understood. Using a novel reagent that specifically detects Cdc42-GTP in fixed cells, we found that activated Cdc42 localizes to the T cell:APC contact site in an antigen-dependent manner. TCR signaling alone was sufficient to induce localization of Cdc42-GTP, and functional Lck and Zap-70 kinases were required. WASP also localized to the T cell:APC contact site in an antigen-dependent manner. Surprisingly, WASP localization was independent of the Cdc42 binding domain but required the proline-rich domain. Our results indicate that localized WASP activation requires the integration of multiple signals: WASP is recruited via interaction with SH3 domain-containing proteins and is activated by Cdc42-GTP concentrated at the same site. PMID:11520460

  4. Proposed ground water protection strategy for the Uranium Mill Tailings Site at Green River, Utah. Final report

    SciTech Connect

    Not Available

    1994-11-01

    This document presents the US DOE water resources protection strategy for the Green River, Utah mill tailings disposal site. The modifications in the original plan are based on new information, including ground water quality data collected after remedial action was completed, and on a revised assessment of disposal cell design features, surface conditions, and site hydrogeology. All aspects are discussed in this report.

  5. A vegetation management plan for Fort Union Trading Post National Historic Site: Final report for interagency agreement number F154910005

    USGS Publications Warehouse

    Symstad, Amy J.

    2012-01-01

    Summary: This report provides Fort Union Trading Post National Historic Site, a small NPS unit on the border of Montana and North Dakota, a framework and reasonable tools for future vegetation management at the site in the context of probable historic, current, and desired future vegetation.

  6. Disposal of chemical agents and munitions stored at Umatilla Depot Activity, Hermiston, Oregon. Final Phase 1 environmental report

    SciTech Connect

    Zimmerman, G.P.; Hillsman, E.L.; Johnson, R.O.; Miller, R.L.; Patton, T.G.; Schoepfle, G.M.; Tolbert, V.R.; Feldman, D.L.; Hunsaker, D.B. Jr.; Kroodsma, R.L.; Morrissey, J.; Rickert, L.W.; Staub, W.P.; West, D.C.

    1993-02-01

    The Umatilla Depot Activity (UMDA) near Hermiston, Oregon, is one of eight US Army installations in the continental United States where lethal unitary chemical agents and munitions are stored, and where destruction of agents and munitions is proposed under the Chemical Stockpile Disposal Program (CSDP). The chemical agent inventory at UMDA consists of 11.6%, by weight, of the total US stockpile. The destruction of the stockpile is necessary to eliminate the risk to the public from continued storage and to dispose of obsolete and leaking munitions. In 1988 the US Army issued a Final Programmatic Environmental Impact Statement (FPEIS) for the CSDP that identified on-site disposal of agents and munitions as the environmentally preferred alternative (i.e., the alternative with the least potential to cause significant adverse impacts), using a method based on five measures of risk for potential human health and ecosystem/environmental effects; the effectiveness and adequacy of emergency preparedness capabilities also played a key role in the FPEIS selection methodology. In some instances, the FPEIS included generic data and assumptions that were developed to allow a consistent comparison of potential impacts among programmatic alternatives and did not include detailed conditions at each of the eight installations. The purpose of this Phase 1 report is to examine the proposed implementation of on-site disposal at UMDA in light of more recent and more detailed data than those included in the FPEIS. Specifically, this Phase 1 report is intended to either confirm or reject the validity of on-site disposal for the UMDA stockpile. Using the same computation methods as in the FPEIS, new population data were used to compute potential fatalities from hypothetical disposal accidents. Results indicate that onsite disposal is clearly preferable to either continued storage at UMDA or transportation of the UMDA stockpile to another depot for disposal.

  7. Mutations Closer to the Active Site Improve the Promiscuous Aldolase Activity of 4-Oxalocrotonate Tautomerase More Effectively than Distant Mutations.

    PubMed

    Rahimi, Mehran; van der Meer, Jan-Ytzen; Geertsema, Edzard M; Poddar, Harshwardhan; Baas, Bert-Jan; Poelarends, Gerrit J

    2016-07-01

    The enzyme 4-oxalocrotonate tautomerase (4-OT), which catalyzes enol-keto tautomerization as part of a degradative pathway for aromatic hydrocarbons, promiscuously catalyzes various carbon-carbon bond-forming reactions. These include the aldol condensation of acetaldehyde with benzaldehyde to yield cinnamaldehyde. Here, we demonstrate that 4-OT can be engineered into a more efficient aldolase for this condensation reaction, with a >5000-fold improvement in catalytic efficiency (kcat /Km ) and a >10(7) -fold change in reaction specificity, by exploring small libraries in which only "hotspots" are varied. The hotspots were identified by systematic mutagenesis (covering each residue), followed by a screen for single mutations that give a strong improvement in the desired aldolase activity. All beneficial mutations were near the active site of 4-OT, thus underpinning the notion that new catalytic activities of a promiscuous enzyme are more effectively enhanced by mutations close to the active site. PMID:27238293

  8. Testing the applicability of rapid on-site enzymatic activity detection for surface water monitoring

    NASA Astrophysics Data System (ADS)

    Stadler, Philipp; Vogl, Wolfgang; Juri, Koschelnik; Markus, Epp; Maximilian, Lackner; Markus, Oismüller; Monika, Kumpan; Peter, Strauss; Regina, Sommer; Gabriela, Ryzinska-Paier; Farnleitner Andreas, H.; Matthias, Zessner

    2015-04-01

    On-site detection of enzymatic activities has been suggested as a rapid surrogate for microbiological pollution monitoring of water resources (e.g. using glucuronidases, galactosidases, esterases). Due to the possible short measuring intervals enzymatic methods have high potential as near-real time water quality monitoring tools. This presentation describes results from a long termed field test. For twelve months, two ColiMinder devices (Vienna Water Monitoring, Austria) for on-site determination of enzymatic activity were tested for stream water monitoring at the experimental catchment HOAL (Hydrological Open Air Laboratory, Center for Water Resource Systems, Vienna University of Technology). The devices were overall able to follow and reflect the diverse hydrological and microbiological conditions of the monitored stream during the test period. Continuous data in high temporal resolution captured the course of enzymatic activity in stream water during diverse rainfall events. The method also proofed sensitive enough to determine diurnal fluctuations of enzymatic activity in stream water during dry periods. The method was able to capture a seasonal trend of enzymatic activity in stream water that matches the results gained from Colilert18 analysis for E. coli and coliform bacteria of monthly grab samples. Furthermore the comparison of ColiMinder data with measurements gained at the same test site with devices using the same method but having different construction design (BACTcontrol, microLAN) showed consistent measuring results. Comparative analysis showed significant differences between measured enzymatic activity (modified fishman units and pmol/min/100ml) and cultivation based analyses (most probable number, colony forming unit). Methods of enzymatic activity measures are capable to detect ideally the enzymatic activity caused by all active target bacteria members, including VBNC (viable but nonculturable) while cultivation based methods cannot detect VBNC

  9. Technical approaches to characterizing and cleaning up iron and steel mill sites under the brownfields initiative. Final report

    SciTech Connect

    1998-12-01

    EPA has developed this guide to provide decision-makers, such as city planners, private sector developers, and other involved in redeveloping brownfields, with a better understanding of the technical issues involved in assessing and cleaning up iron and steel mill sites so they can make the most informed decisions possible. This overview of the technical process involved in assessing and cleaning up brownfields sites can assist planners in making decisions at various stages of the project. An understanding of land use and industrial processes conducted in the past at a site can help the planner to conceptualize the site and identify likely areas of contamination that may require cleanup. Numerous resources are suggested to facilitate characterization of the site and consideration of cleanup technologies.

  10. Health assessment for Springfield Township Dump Site, Oakland County, Michigan, Region 5. CERCLIS No. MID980499966. Final report

    SciTech Connect

    Not Available

    1988-02-19

    The Springfield Township Dump NPL Site is located in Oakland County, approximately 35 miles northwest of Detroit, Michigan. A number of Hazardous Substance List (HSL) contaminants exist on-site including chlorinated aliphatics, benzene compounds, toluene, xylene, phthalate esters, polychlorinated biphenyl compounds (PCBs), dieldrin, lead, and chromium. Two on-site groundwater contaminants, trichloroethene and 1,1-dichloroethene were found at levels in excess of EPA's drinking-water MCLs. The highest levels of contaminants were found in on-site soils although contaminants were also detected in the site's ground water at much lower levels. The primary contaminant migration pathways include movement of contaminated groundwater, volatilization of contaminants, soil erosion and transport, and bioaccumulation. The most likely routes for human contaminant exposure are direct contact with contaminated soils and sludge, inhalation of fugitive dusts or vapors, or the ingestion of contaminated plants, animals, soil, or ground water.

  11. Threatened and endangered wildlife species of the Hanford Site related to CERCLA characterization activities

    SciTech Connect

    Fitzner, R.E.; Weiss, S.G.; Stegen, J.A.

    1994-06-01

    The US Department of Energy`s (DOE) Hanford Site has been placed on the National Priorities List, which requires that it be remediated under the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) or Superfund. Potentially contaminated areas of the Hanford Site were grouped into operable units, and detailed characterization and investigation plans were formulated. The DOE Richland Operations Office requested Westinghouse Hanford Company (WHC) to conduct a biological assessment of the potential impact of these characterization activities on the threatened, endangered, and sensitive wildlife species of the Hanford Site. Additional direction for WHC compliances with wildlife protection can be found in the Environmental Compliance Manual. This document is intended to meet these requirements, in part, for the CERCLA characterization activities, as well as for other work comparable in scope. This report documents the biological assessment and describes the pertinent components of the Hanford Site as well as the planned characterization activities. Also provided are accounts of endangered, threatened, and federal candidate wildlife species on the Hanford Site and information as to how human disturbances can affect these species. Potential effects of the characterization activities are described with recommendations for mitigation measures.

  12. The active site of low-temperature methane hydroxylation in iron-containing zeolites.

    PubMed

    Snyder, Benjamin E R; Vanelderen, Pieter; Bols, Max L; Hallaert, Simon D; Böttger, Lars H; Ungur, Liviu; Pierloot, Kristine; Schoonheydt, Robert A; Sels, Bert F; Solomon, Edward I

    2016-08-18

    An efficient catalytic process for converting methane into methanol could have far-reaching economic implications. Iron-containing zeolites (microporous aluminosilicate minerals) are noteworthy in this regard, having an outstanding ability to hydroxylate methane rapidly at room temperature to form methanol. Reactivity occurs at an extra-lattice active site called α-Fe(ii), which is activated by nitrous oxide to form the reactive intermediate α-O; however, despite nearly three decades of research, the nature of the active site and the factors determining its exceptional reactivity are unclear. The main difficulty is that the reactive species-α-Fe(ii) and α-O-are challenging to probe spectroscopically: data from bulk techniques such as X-ray absorption spectroscopy and magnetic susceptibility are complicated by contributions from inactive 'spectator' iron. Here we show that a site-selective spectroscopic method regularly used in bioinorganic chemistry can overcome this problem. Magnetic circular dichroism reveals α-Fe(ii) to be a mononuclear, high-spin, square planar Fe(ii) site, while the reactive intermediate, α-O, is a mononuclear, high-spin Fe(iv)=O species, whose exceptional reactivity derives from a constrained coordination geometry enforced by the zeolite lattice. These findings illustrate the value of our approach to exploring active sites in heterogeneous systems. The results also suggest that using matrix constraints to activate metal sites for function-producing what is known in the context of metalloenzymes as an 'entatic' state-might be a useful way to tune the activity of heterogeneous catalysts. PMID:27535535

  13. The active site of low-temperature methane hydroxylation in iron-containing zeolites

    NASA Astrophysics Data System (ADS)

    Snyder, Benjamin E. R.; Vanelderen, Pieter; Bols, Max L.; Hallaert, Simon D.; Böttger, Lars H.; Ungur, Liviu; Pierloot, Kristine; Schoonheydt, Robert A.; Sels, Bert F.; Solomon, Edward I.

    2016-08-01

    An efficient catalytic process for converting methane into methanol could have far-reaching economic implications. Iron-containing zeolites (microporous aluminosilicate minerals) are noteworthy in this regard, having an outstanding ability to hydroxylate methane rapidly at room temperature to form methanol. Reactivity occurs at an extra-lattice active site called α-Fe(II), which is activated by nitrous oxide to form the reactive intermediate α-O; however, despite nearly three decades of research, the nature of the active site and the factors determining its exceptional reactivity are unclear. The main difficulty is that the reactive species—α-Fe(II) and α-O—are challenging to probe spectroscopically: data from bulk techniques such as X-ray absorption spectroscopy and magnetic susceptibility are complicated by contributions from inactive ‘spectator’ iron. Here we show that a site-selective spectroscopic method regularly used in bioinorganic chemistry can overcome this problem. Magnetic circular dichroism reveals α-Fe(II) to be a mononuclear, high-spin, square planar Fe(II) site, while the reactive intermediate, α-O, is a mononuclear, high-spin Fe(IV)=O species, whose exceptional reactivity derives from a constrained coordination geometry enforced by the zeolite lattice. These findings illustrate the value of our approach to exploring active sites in heterogeneous systems. The results also suggest that using matrix constraints to activate metal sites for function—producing what is known in the context of metalloenzymes as an ‘entatic’ state—might be a useful way to tune the activity of heterogeneous catalysts.

  14. A Tale of Two Isomerases: Compact versus Extended Active Sites in Ketosteroid Isomerase and Phosphoglucose Isomerase

    SciTech Connect

    Somarowthu, Srinivas; Brodkin, Heather R.; D’Aquino, J. Alejandro; Ringe, Dagmar; Ondrechen, Mary Jo; Beuning, Penny J.

    2012-07-11

    Understanding the catalytic efficiency and specificity of enzymes is a fundamental question of major practical and conceptual importance in biochemistry. Although progress in biochemical and structural studies has enriched our knowledge of enzymes, the role in enzyme catalysis of residues that are not nearest neighbors of the reacting substrate molecule is largely unexplored experimentally. Here computational active site predictors, THEMATICS and POOL, were employed to identify functionally important residues that are not in direct contact with the reacting substrate molecule. These predictions then guided experiments to explore the active sites of two isomerases, Pseudomonas putida ketosteroid isomerase (KSI) and human phosphoglucose isomerase (PGI), as prototypes for very different types of predicted active sites. Both KSI and PGI are members of EC 5.3 and catalyze similar reactions, but they represent significantly different degrees of remote residue participation, as predicted by THEMATICS and POOL. For KSI, a compact active site of mostly first-shell residues is predicted, but for PGI, an extended active site in which residues in the first, second, and third layers around the reacting substrate are predicted. Predicted residues that have not been previously tested experimentally were investigated by site-directed mutagenesis and kinetic analysis. In human PGI, single-point mutations of the predicted second- and third-shell residues K362, H100, E495, D511, H396, and Q388 show significant decreases in catalytic activity relative to that of the wild type. The results of these experiments demonstrate that, as predicted, remote residues are very important in PGI catalysis but make only small contributions to catalysis in KSI.

  15. SABER: A computational method for identifying active sites for new reactions

    PubMed Central

    Nosrati, Geoffrey R; Houk, K N

    2012-01-01

    A software suite, SABER (Selection of Active/Binding sites for Enzyme Redesign), has been developed for the analysis of atomic geometries in protein structures, using a geometric hashing algorithm (Barker and Thornton, Bioinformatics 2003;19:1644–1649). SABER is used to explore the Protein Data Bank (PDB) to locate proteins with a specific 3D arrangement of catalytic groups to identify active sites that might be redesigned to catalyze new reactions. As a proof-of-principle test, SABER was used to identify enzymes that have the same catalytic group arrangement present in o-succinyl benzoate synthase (OSBS). Among the highest-scoring scaffolds identified by the SABER search for enzymes with the same catalytic group arrangement as OSBS were l-Ala d/l-Glu epimerase (AEE) and muconate lactonizing enzyme II (MLE), both of which have been redesigned to become effective OSBS catalysts, demonstrated by experiments. Next, we used SABER to search for naturally existing active sites in the PDB with catalytic groups similar to those present in the designed Kemp elimination enzyme KE07. From over 2000 geometric matches to the KE07 active site, SABER identified 23 matches that corresponded to residues from known active sites. The best of these matches, with a 0.28 Å catalytic atom RMSD to KE07, was then redesigned to be compatible with the Kemp elimination using RosettaDesign. We also used SABER to search for potential Kemp eliminases using a theozyme predicted to provide a greater rate acceleration than the active site of KE07, and used Rosetta to create a design based on the proteins identified. PMID:22492397

  16. SABER: a computational method for identifying active sites for new reactions.

    PubMed

    Nosrati, Geoffrey R; Houk, K N

    2012-05-01

    A software suite, SABER (Selection of Active/Binding sites for Enzyme Redesign), has been developed for the analysis of atomic geometries in protein structures, using a geometric hashing algorithm (Barker and Thornton, Bioinformatics 2003;19:1644-1649). SABER is used to explore the Protein Data Bank (PDB) to locate proteins with a specific 3D arrangement of catalytic groups to identify active sites that might be redesigned to catalyze new reactions. As a proof-of-principle test, SABER was used to identify enzymes that have the same catalytic group arrangement present in o-succinyl benzoate synthase (OSBS). Among the highest-scoring scaffolds identified by the SABER search for enzymes with the same catalytic group arrangement as OSBS were L-Ala D/L-Glu epimerase (AEE) and muconate lactonizing enzyme II (MLE), both of which have been redesigned to become effective OSBS catalysts, demonstrated by experiments. Next, we used SABER to search for naturally existing active sites in the PDB with catalytic groups similar to those present in the designed Kemp elimination enzyme KE07. From over 2000 geometric matches to the KE07 active site, SABER identified 23 matches that corresponded to residues from known active sites. The best of these matches, with a 0.28 Å catalytic atom RMSD to KE07, was then redesigned to be compatible with the Kemp elimination using RosettaDesign. We also used SABER to search for potential Kemp eliminases using a theozyme predicted to provide a greater rate acceleration than the active site of KE07, and used Rosetta to create a design based on the proteins identified. PMID:22492397

  17. Preliminary examination of the impacts of repository site characterization activities and facility construction and operation activities on Hanford air quality

    SciTech Connect

    Glantz, C.S.; Ramsdell, J.V.

    1986-04-01

    Air quality impacts that would result from site characterization activities and from the construction and operation of a high-level nuclear wste repository at Hanford are estimated using two simple atmospheric dispersion models, HANCHI and CHISHORT. Model results indicate that pollutant concentrations would not exceed ambient air quality standards at any point outside the Hanford fenceline or at any publicly accessible location within the Hanford Site. The increase in pollutant concentrations in nearby communities due to site activities would be minimal. HANCHI and CHISHORT are documented in the appendices of this document. Further study of the repository's impact on air quality will be conducted when more detailed project plans and work schedules are available.

  18. Conserved phosphorylation sites in the activation loop of the Arabidopsis phytosulfokine receptor PSKR1 differentially affect kinase and receptor activity.

    PubMed

    Hartmann, Jens; Linke, Dennis; Bönniger, Christine; Tholey, Andreas; Sauter, Margret

    2015-12-15

    PSK (phytosulfokine) is a plant peptide hormone perceived by a leucine-rich repeat receptor kinase. Phosphosite mapping of epitope-tagged PSKR1 (phytosulfokine receptor 1) from Arabidopsis thaliana plants identified Ser(696) and Ser(698) in the JM (juxtamembrane) region and probably Ser(886) and/or Ser(893) in the AL (activation loop) as in planta phosphorylation sites. In vitro-expressed kinase was autophosphorylated at Ser(717) in the JM, and at Ser(733), Thr(752), Ser(783), Ser(864), Ser(911), Ser(958) and Thr(998) in the kinase domain. The LC-ESI-MS/MS spectra provided support that up to three sites (Thr(890), Ser(893) and Thr(894)) in the AL were likely to be phosphorylated in vitro. These sites are evolutionarily highly conserved in PSK receptors, indicative of a conserved function. Site-directed mutagenesis of the four conserved residues in the activation segment, Thr(890), Ser(893), Thr(894) and Thr(899), differentially altered kinase activity in vitro and growth-promoting activity in planta. The T899A and the quadruple-mutated TSTT-A (T890A/S893A/T894A/T899A) mutants were both kinase-inactive, but PSKR1(T899A) retained growth-promoting activity. The T890A and S893A/T894A substitutions diminished kinase activity and growth promotion. We hypothesize that phosphorylation within the AL activates kinase activity and receptor function in a gradual and distinctive manner that may be a means to modulate the PSK response.

  19. Conserved phosphorylation sites in the activation loop of the Arabidopsis phytosulfokine receptor PSKR1 differentially affect kinase and receptor activity

    PubMed Central

    Hartmann, Jens; Linke, Dennis; Bönniger, Christine; Tholey, Andreas; Sauter, Margret

    2015-01-01

    PSK (phytosulfokine) is a plant peptide hormone perceived by a leucine-rich repeat receptor kinase. Phosphosite mapping of epitope-tagged PSKR1 (phytosulfokine receptor 1) from Arabidopsis thaliana plants identified Ser696 and Ser698 in the JM (juxtamembrane) region and probably Ser886 and/or Ser893 in the AL (activation loop) as in planta phosphorylation sites. In vitro-expressed kinase was autophosphorylated at Ser717 in the JM, and at Ser733, Thr752, Ser783, Ser864, Ser911, Ser958 and Thr998 in the kinase domain. The LC–ESI–MS/MS spectra provided support that up to three sites (Thr890, Ser893 and Thr894) in the AL were likely to be phosphorylated in vitro. These sites are evolutionarily highly conserved in PSK receptors, indicative of a conserved function. Site-directed mutagenesis of the four conserved residues in the activation segment, Thr890, Ser893, Thr894 and Thr899, differentially altered kinase activity in vitro and growth-promoting activity in planta. The T899A and the quadruple-mutated TSTT-A (T890A/S893A/T894A/T899A) mutants were both kinase-inactive, but PSKR1(T899A) retained growth-promoting activity. The T890A and S893A/T894A substitutions diminished kinase activity and growth promotion. We hypothesize that phosphorylation within the AL activates kinase activity and receptor function in a gradual and distinctive manner that may be a means to modulate the PSK response. PMID:26472115

  20. Remedial actions at the former Vitro Rare Metals plant site, Canonsburg, Washington County, Pennsylvania. Final Environmental Impact Statement. Volume II. Appendices

    SciTech Connect

    Not Available

    1983-07-01

    This report provides a summary of the conceptual design and other information necessary to understand the proposed remedial action at the expanded Canonsburg, Pennsylvania site. This design constitutes the current approach to stabilizing the radioactively contaminated materials in place in a manner that would fully protect the public health and environment. This summary is intended to provide sufficient detail for the reader to understand the proposed remedial action and the anticipated environmental impacts. The site conceptual design has been developed using available data. In some cases, elements of the design have not been developed fully and will be made final during the detailed design process.

  1. Remedial action plan and site design for stabilization of the inactive uranium mill tailings sites at Slick Rock, Colorado: Remedial Action Selection Report. Preliminary final

    SciTech Connect

    Not Available

    1994-03-01

    This proposed remedial action plan incorporates the results of detailed investigation of geologic, geomorphic, and seismic conditions at the proposed disposal site. The proposed remedial action will consist of relocating the uranium mill tailings, contaminated vicinity property materials, demolition debris, and windblown/waterborne materials to a permanent repository at the proposed Burro Canyon disposal cell. The proposed disposal site will be geomorphically stable. Seismic design parameters were developed for the geotechnical analyses of the proposed cell. Cell stability was analyzed to ensure long-term performance of the disposal cell in meeting design standards, including slope stability, settlement, and liquefaction potential. The proposed cell cover and erosion protection features were also analyzed and designed to protect the RRM (residual radioactive materials) against surface water and wind erosion. The location of the proposed cell precludes the need for permanent drainage or interceptor ditches. Rock to be used on the cell top-, side-, and toeslopes was sized to withstand probable maximum precipitation events.

  2. Remedial action plan and site design for stabilization of the inactive uranium mill tailings sites at Slick Rock, Colorado. Final report

    SciTech Connect

    1996-08-01

    This document contains the page changes for Attachment 3, Ground Water Hydrology Report dated August, 1996 for the Remedial Action Plan and Site Design for Stabilization of the Inactive Uranium Mill Tailings at Slick Rock, Colorado. This portion of Attachment 3 contains the Table of Contents pages i and ii, and pages numbered 3-3 through 3-56 of the Ground Water Hydrology Report. Also included are the cover sheets for Appendix A, B, and C to Attachment 3.

  3. Salton Sea Scientific Drilling Project: A summary of drilling and engineering activities and scientific results. Final report

    SciTech Connect

    Ross, H.P.; Forsgren, C.K.

    1992-04-01

    The Salton Sea Scientific g Project (SSSDP) completed the first major well in the United States Continental Scientific Drilling Program. The well (State 2-14) was drilled to 10,W ft (3,220 m) in the Salton Sea Geothermal Field in California`s Imperial Valley, to permit scientific study of a deep, high-temperature portion of an active geothermal system. The program was designed to investigate, through drilling and testing, the subsurface thermal, chemical, and mineralogical environments of this geothermal area. Extensive samples and data, including cores, cuttings, geothermal fluids and gases, and geophysical logs, were collected for future scientific analysis, interpretation, and publication. Short duration flow tests were conducted on reservoirs at a depth of approximately 6,120 ft (1,865 m) and at 10,136 ft (3,089 m). This report summarizes all major activities of the SSSDP, from project inception in the fall of 1984 through brine-pond cleanup and site restoration, ending in February 1989. This report presents a balanced summary of drilling, coring, logging, and flow-test operations, and a brief summary of technical and scientific results. Frequent reference is made to original records, data, and publication of results. The report also reviews the proposed versus the final well design, and operational summaries, such as the bit record, the casing and cementing program, and the coring program. Summaries are and the results of three flow tests. Several teamed during the project.

  4. Remedial action plan and site design for stabilization of the inactive Uranium Mill Tailings Site at Lowman, Idaho. Attachment 4, Water resources protection strategy: Final report

    SciTech Connect

    Not Available

    1991-09-01

    The DOE proposes to achieve compliance with the proposed EPA groundwater protection standards (Subparts A and B of 40 CFR 192) by meeting the EPA maximum concentration limits (MCLs) or background concentrations for designated hazardous constituents in groundwater in the uppermost aquifer (alluvium/weathered granodiorite) at the point of compliance (POC) at the Lowman disposal site near Lowman, Idaho. The proposed remedial action in conjunction with existing hydrogeological conditions at the Lowman site will ensure sufficient protection of human health and the environment. The DOE has concluded that the EPA groundwater protection standards will be met at the POC because, with the exception of antimony, none of the hazardous constituents that exceed laboratory method detection limits within the radioactive sand pore fluids were above the proposed concentration limits. The DOE has demonstrated that antimony will meet the proposed concentration limits at the POC through attenuation in subsoils beneath the disposal cell and by dilution in groundwater underflow. The Lowman processing site is in compliance with Subpart B of 40 CFR 192 because statistical analyses of groundwater samples indicate no groundwater contamination.

  5. Public health assessment for Limestone Road Site, Cumberland, Allegany County, Maryland, Region 3. Cerclis No. MDD980691588. Final report

    SciTech Connect

    Not Available

    1994-01-06

    The Limestone Road Site, located in Cumberland, Maryland, has been evaluated for potential health risks to the neighboring residential community. The site is classified as an indeterminate public health hazard because of possible past and present exposure to surface soil contamination. Surface soil contamination has not been adequately characterized to determine levels of exposure. Also, drinking water samples from two residential wells contained lead at levels above health comparison values. Surface water and sediment sampling indicated that some off-site migration of heavy metals including chromium, cadmium, barium, lead and nickel has occurred. Levels of some of these contaminants exceed USEPA Ambient Water Quality Criteria for the protection of human health.

  6. Health assessment for South Andover National Priorities List (NPL) Site, Andover, Minnesota, Region 5. CERCLIS No. MND980609614. Final report

    SciTech Connect

    Not Available

    1989-04-06

    The South Andover National Priorities List Site is located in Andover, Minnesota. The site is located in a semi-industrial area characterized by used-car dealerships, and auto part and salvage operations. The surficial aquifer is contaminated with volatile organic compounds (VOCs), bis(2-ethylhexyl) phthalate (DEHP), and metals. The contamination present in the soil, deeper aquifer, air, and biota has not been fully characterized. A supplemental Remedial Investigation and Feasibility Study (RI/FS) will be conducted in 1989. Removal of tires, which cover much of the site, is ongoing; it will be completed in the spring of 1989.

  7. Wobble Pairs of the HDV Ribozyme Play Specific Roles in Stabilization of Active Site Dynamics

    PubMed Central

    Sripathi, Kamali N.; Banáš, Pavel; Reblova, Kamila; Šponer, Jiři; Otyepka, Michal

    2015-01-01

    The hepatitis delta virus (HDV) is the only known human pathogen whose genome contains a catalytic RNA motif (ribozyme). The overall architecture of the HDV ribozyme is that of a double-nested pseudoknot, with two GU pairs flanking the active site. Although extensive studies have shown that mutation of either wobble results in decreased catalytic activity, little work has focused on linking these mutations to specific structural effects on catalytic fitness. Here we use molecular dynamics simulations based on an activated structure to probe the active site dynamics as a result of wobble pair mutations. In both wild-type and mutant ribozymes, the in-line fitness of the active site (as a measure of catalytic proficiency) strongly depends on the presence of a C75(N3H3+)N1(O5′) hydrogen bond, which positions C75 as the general acid for the reaction. Our mutational analyses show that each GU wobble supports catalytically fit conformations in distinct ways; the reverse G25U20 wobble promotes high in-line fitness, high occupancy of the C75(N3H3+)G1(O5′) general-acid hydrogen bond and stabilization of the G1U37 wobble, while the G1U37 wobble acts more locally by stabilizing high in-line fitness and the C75(N3H3+)G1(O5′) hydrogen bond. We also find that stable type I A-minor and P1.1 hydrogen bonding above and below the active site, respectively, prevent local structural disorder from spreading and disrupting global conformation. Taken together, our results define specific, often redundant architectural roles for several structural motifs of the HDV ribozyme active site, expanding the known roles of these motifs within all HDV-like ribozymes and other structured RNAs. PMID:25631765

  8. Tuned by metals: the TET peptidase activity is controlled by 3 metal binding sites

    PubMed Central

    Colombo, Matteo; Girard, Eric; Franzetti, Bruno

    2016-01-01

    TET aminopeptidases are dodecameric particles shared in the three life domains involved in various biological processes, from carbon source provider in archaea to eye-pressure regulation in humans. Each subunit contains a dinuclear metal site (M1 and M2) responsible for the enzyme catalytic activity. However, the role of each metal ion is still uncharacterized. Noteworthy, while mesophilic TETs are activated by Mn2+, hyperthermophilic TETs prefers Co2+. Here, by means of anomalous x-ray crystallography and enzyme kinetics measurements of the TET3 aminopeptidase from the hyperthermophilic organism Pyrococcus furiosus (PfTET3), we show that M2 hosts the catalytic activity of the enzyme, while M1 stabilizes the TET3 quaternary structure and controls the active site flexibility in a temperature dependent manner. A new third metal site (M3) was found in the substrate binding pocket, modulating the PfTET3 substrate preferences. These data show that TET activity is tuned by the molecular interplay among three metal sites. PMID:26853450

  9. Human Activities in Natura 2000 Sites: A Highly Diversified Conservation Network

    NASA Astrophysics Data System (ADS)

    Tsiafouli, Maria A.; Apostolopoulou, Evangelia; Mazaris, Antonios D.; Kallimanis, Athanasios S.; Drakou, Evangelia G.; Pantis, John D.

    2013-05-01

    The Natura 2000 network was established across the European Union's (EU) Member States with the aim to conserve biodiversity, while ensuring the sustainability of human activities. However, to what kind and to what extent Natura 2000 sites are subject to human activities and how this varies across Member States remains unspecified. Here, we analyzed 111,269 human activity records from 14,727 protected sites in 20 Member States. The frequency of occurrence of activities differs among countries, with more than 86 % of all sites being subjected to agriculture or forestry. Activities like hunting, fishing, urbanization, transportation, and tourism are more frequently recorded in south European sites than in northern or eastern ones. The observed variations indicate that Natura 2000 networks are highly heterogeneous among EU Member States. Our analysis highlights the importance of agriculture in European landscapes and indicates possible targets for policy interventions at national, European, or "sub-European" level. The strong human presence in the Natura 2000 network throughout Member States, shows that conservation initiatives could succeed only by combining social and ecological sustainability and by ensuring the integration of policies affecting biodiversity.

  10. Active-Site Monovalent Cations Revealed in a 1.55 Å Resolution Hammerhead Ribozyme Structure

    PubMed Central

    Anderson, Michael; Schultz, Eric P.; Martick, Monika; Scott, William G.

    2013-01-01

    We have obtained a 1.55 Å crystal structure of a hammerhead ribozyme derived from Schistosoma mansoni in conditions that permit detailed observations of Na+ ion binding in the ribozyme's active site. At least two such Na+ ions are observed. The first Na+ ion binds to the N7 of G10.1 and the adjacent A9 phosphate in a manner identical to that previously observed for divalent cations. A second Na+ ion binds to the Hoogsteen face of G12, the general base in the hammerhead cleavage reaction, thereby potentially dissipating the negative charge of the catalytically active enolate form of the nucleotide base. A potential but more ambiguous third site bridges the A9 and scissile phosphates in a manner consistent with previous predictions. Hammerhead ribozymes have been observed to be active in the presence of high concentrations of monovalent cations, including Na+, but the mechanism by which monovalent cations substitute for divalent cations in hammerhead catalysis remains unclear. Our results enable us to suggest that Na+ directly and specifically substitutes for divalent cations in the hammerhead active site. The detailed geometry of the pre-catalytic active site complex is also revealed with a new level of precision, thanks to the quality of the electron density maps obtained from what is currently the highest resolution ribozyme structure in the protein data bank. PMID:23711504

  11. Structure of inorganic pyrophosphatase from Staphylococcus aureus reveals conformational flexibility of the active site.

    PubMed

    Gajadeera, Chathurada S; Zhang, Xinyi; Wei, Yinan; Tsodikov, Oleg V

    2015-02-01

    Cytoplasmic inorganic pyrophosphatase (PPiase) is an enzyme essential for survival of organisms, from bacteria to human. PPiases are divided into two structurally distinct families: family I PPiases are Mg(2+)-dependent and present in most archaea, eukaryotes and prokaryotes, whereas the relatively less understood family II PPiases are Mn(2+)-dependent and present only in some archaea, bacteria and primitive eukaryotes. Staphylococcus aureus (SA), a dangerous pathogen and a frequent cause of hospital infections, contains a family II PPiase (PpaC), which is an attractive potential target for development of novel antibacterial agents. We determined a crystal structure of SA PpaC in complex with catalytic Mn(2+) at 2.1Å resolution. The active site contains two catalytic Mn(2+) binding sites, each half-occupied, reconciling the previously observed 1:1 Mn(2+):enzyme stoichiometry with the presence of two divalent metal ion sites in the apo-enzyme. Unexpectedly, despite the absence of the substrate or products in the active site, the two domains of SA PpaC form a closed active site, a conformation observed in structures of other family II PPiases only in complex with substrate or product mimics. A region spanning residues 295-298, which contains a conserved substrate binding RKK motif, is flipped out of the active site, an unprecedented conformation for a PPiase. Because the mutant of Arg295 to an alanine is devoid of activity, this loop likely undergoes an induced-fit conformational change upon substrate binding and product dissociation. This closed conformation of SA PPiase may serve as an attractive target for rational design of inhibitors of this enzyme. PMID:25576794

  12. Probe molecule studies: Active species in alcohol synthesis. Final report, July 1993--July 1994

    SciTech Connect

    Blackmond, D.G.; Wender, I.; Oukaci, R.; Wang, Jian

    1994-07-01

    The objectives of this project are to investigate the role(s) of cobalt and copper in constructing the active sites for the formation of higher alcohols from CO/H{sub 2} over the Co-Cu based catalysts by using different reduction treatments and applying selected characterization tools such as TPR, TPD, XRD and XPS as well as to generate mechanistic information on the reaction pathway(s) and key intermediate(s) of higher alcohol synthesis from CO/H{sub 2} over Co-Cu/ZnO catalysts by the approach of in-situ addition of a probe molecule (nitromethane).

  13. Analysis of active site residues of the antiviral protein from summer leaves from Phytolacca americana by site-directed mutagenesis.

    PubMed

    Poyet, J L; Hoeveler, A; Jongeneel, C V

    1998-12-30

    The summer leaf isoform of the pokeweed (Phytolacca americana) antiviral protein, PAP II, was produced in high yields from inclusion bodies in recombinant E. coli. On the basis of its sequence similarity with the spring leaf isoform (PAP I) and with the A chain of ricin, a three-dimensional model of the protein was constructed as an aid in the design of active site mutants. PAP II variants mutated in residues Asp 88 (D88N), Tyr 117 (Y117S), Glu 172 (E172Q), Arg 175 (R175H) and a combination of Asp 88 and Arg 175 (D88N/R175H) were produced in E. coli and assayed for their ability to inhibit protein synthesis in a rabbit reticulocyte lysate. All of these mutations had effects deleterious to the enzymatic activity of PAP II. The results were interpreted in the light of three reaction mechanisms proposed for ribosome-inactivating proteins (RIPs). We conclude that none of the proposed mechanisms is entirely consistent with the data presented here.

  14. NMR structure of the active conformation of the Varkud satellite ribozyme cleavage site

    PubMed Central

    Hoffmann, Bernd; Mitchell, G. Thomas; Gendron, Patrick; Major, François; Andersen, Angela A.; Collins, Richard A.; Legault, Pascale

    2003-01-01

    Substrate cleavage by the Neurospora Varkud satellite (VS) ribozyme involves a structural change in the stem-loop I substrate from an inactive to an active conformation. We have determined the NMR solution structure of a mutant stem-loop I that mimics the active conformation of the cleavage site internal loop. This structure shares many similarities, but also significant differences, with the previously determined structures of the inactive internal loop. The active internal loop displays different base-pairing interactions and forms a novel RNA fold composed exclusively of sheared G-A base pairs. From chemical-shift mapping we identified two Mg2+ binding sites in the active internal loop. One of the Mg2+ binding sites forms in the active but not the inactive conformation of the internal loop and is likely important for catalysis. Using the structure comparison program mc-search, we identified the active internal loop fold in other RNA structures. In Thermus thermophilus 16S rRNA, this RNA fold is directly involved in a long-range tertiary interaction. An analogous tertiary interaction may form between the active internal loop of the substrate and the catalytic domain of the VS ribozyme. The combination of NMR and bioinformatic approaches presented here has identified a novel RNA fold and provides insights into the structural basis of catalytic function in the Neurospora VS ribozyme. PMID:12782785

  15. Immobilized low-activity waste site borehole 299-E17-21

    SciTech Connect

    Reidel, S.P.; Reynolds, K.D.; Horton, D.G.

    1998-08-01

    The Tank Waste Remediation System (TWRS) is the group at the Hanford Site responsible for the safe underground storage of liquid waste from previous Hanford Site operations, the storage and disposal of immobilized tank waste, and closure of underground tanks. The current plan is to dispose of immobilized low-activity tank waste (ILAW) in new facilities in the southcentral part of 200-East Area and in four existing vaults along the east side of 200-East Area. Boreholes 299-E17-21, B8501, and B8502 were drilled at the southwest corner of the ILAW site in support of the Performance Assessment activities for the disposal options. This report summarizes the initial geologic findings, field tests conducted on those boreholes, and ongoing studies. One deep (480 feet) borehole and two shallow (50 feet) boreholes were drilled at the southwest corner of the ILAW site. The primary factor dictating the location of the boreholes was their characterization function with respect to developing the geohydrologic model for the site and satisfying associated Data Quality Objectives. The deep borehole was drilled to characterize subsurface conditions beneath the ILAW site, and two shallow boreholes were drilled to support an ongoing environmental tracer study. The tracer study will supply information to the Performance Assessment. All the boreholes provide data on the vadose zone and saturated zone in a previously uncharacterized area.

  16. Maintenance of plastid RNA editing activities independently of their target sites

    PubMed Central

    Tillich, Michael; Poltnigg, Peter; Kushnir, Sergei; Schmitz-Linneweber, Christian

    2006-01-01

    RNA editing in plant organelles is mediated by site-specific, nuclear-encoded factors. Previous data suggested that the maintenance of these factors depends on the presence of their rapidly evolving cognate sites. The surprising ability of allotetraploid Nicotiana tabacum (tobacco) to edit a foreign site in the chloroplast ndhA messenger RNA was thought to be inherited from its diploid male ancestor, Nicotiana tomentosiformis. Here, we show that the same ndhA editing activity is also present in Nicotiana sylvestris, which is the female diploid progenitor of tobacco and which lacks the ndhA site. Hence, heterologous editing is not simply a result of tobacco's allopolyploid genome organization. Analyses of other editing sites after sexual or somatic transfer between land plants showed that heterologous editing occurs at a surprisingly high frequency. This suggests that the corresponding editing activities are conserved despite the absence of their target sites, potentially because they serve other functions in the plant cell. PMID:16415790

  17. Health assessment for Brown Wood Preserving Site, Suwannee County, Live Oak, Florida, Region 4. CERCLIS No. FLD980728935. Final report

    SciTech Connect

    Not Available

    1989-04-24

    The Brown Wood Preserving site is a National Priorities List (NPL) site located at the intersection of Saw Mill Road and Gold Kist Road, west of the city of Live Oak, Suwannee County, Florida. Surface soil and surface water at the disposal lagoon area were contaminated with polynuclear aromatic hydrocarbons (PAHs). Groundwater was also tested for PAHs with none found; however, analytical detection limits were greater than appropriate health-based guideline values. The site is located in an area of intermediate karst (sinkhole) development. This area of direct aquifer recharge is surrounded by residences using private potable wells. The exposures of concern for humans include dermal absorption and inhalation of dust from contaminated surface soil. Residents reside 100 feet northwest of the site and may constitute a susceptible population because of their proximity to contaminated soils.

  18. Health assessment for Beacon Heights Landfill site, Beacon Falls, Connecticut, Region 1. CERCLIS No. CTD072122062. Addendum. Final report

    SciTech Connect

    Not Available

    1991-06-20

    The Beacon Heights Landfill National Priorities List (NPL) Site is located in Beacon Falls, Connecticut. From the 1920's to 1979, municipal and industrial wastes were disposed of at the landfill. Leachate from the landfill has migrated into the local groundwater aquifers. Two residential wells to the northwest of the site have been contaminated with site-related contaminants. This site is of potential public health concern because of the risk to human health resulting from possible exposure to hazardous substances at concentrations that may result in adverse health effects. As noted in Human Exposure Pathways Section below, human exposure to benzene, chlorobenzene, chloroethane, and methylene chloride may have occurred via ingestion, inhalation, and direct dermal contact with contaminated groundwater. No health study follow-up is indicated at this time.

  19. A facile reflux procedure to increase active surface sites form highly active and durable supported palladium@platinum bimetallic nanodendrites

    NASA Astrophysics Data System (ADS)

    Wang, Qin; Li, Yingjun; Liu, Baocang; Xu, Guangran; Zhang, Geng; Zhao, Qi; Zhang, Jun

    2015-11-01

    A series of well-dispersed bimetallic Pd@Pt nanodendrites uniformly supported on XC-72 carbon black are fabricated by using different capping agents. These capping agents are essential for the branched morphology control. However, the surfactant adsorbed on the nanodendrites surface blocks the access of reactant molecules to the active surface sites, and the catalytic activities of these bimetallic nanodendrites are significantly restricted. Herein, a facile reflux procedure to effectively remove the capping agent molecules without significantly affecting their sizes is reported for activating supported nanocatalysts. More significantly, the structure and morphology of the nanodendrites can also be retained, enhancing the numbers of active surface sites, catalytic activity and stability toward methanol and ethanol electro-oxidation reactions. The as-obtained hot water reflux-treated Pd@Pt/C catalyst manifests superior catalytic activity and stability both in terms of surface and mass specific activities, as compared to the untreated catalysts and the commercial Pt/C and Pd/C catalysts. We anticipate that this effective and facile removal method has more general applicability to highly active nanocatalysts prepared with various surfactants, and should lead to improvements in environmental protection and energy production.

  20. Record of decision remedial alternative selection for the Grace Road site (631-22G) operable unit: Final action

    SciTech Connect

    Palmer, E.

    1997-01-01

    This decision document presents the selected remedial action for the Grace Road Site located at the Savannah River Site near Aiken, South Carolina. The selected action was developed in accordance with CERCLA, as amended, and to the extent practicable, the National Oil and Hazardous Substances Pollution Contingency Plan (NCP). The selected remedy satisfies both CERCLA and RCRA 3004 requirements. This decision is based on the Administrative Record File for this specific RCRA/CERCLA unit.