Science.gov

Sample records for act site map

  1. Site and Watershed Mapping.

    ERIC Educational Resources Information Center

    Institute for Environmental Education, Cleveland, OH.

    Presented as part of a larger unit on watershed investigations are a slideshow script and a map and compass unit intended to help high school students better visualize the relationship between a water sampling site, the entire stream, community, and watershed. The script discusses features of a topographical map, shows how to read one, and…

  2. Waste Site Mapping

    NASA Technical Reports Server (NTRS)

    1994-01-01

    Old aircraft considered not restorable are melted down in on-site furnaces to reclaim the aluminum in their airframes. The process produces aluminum ingots and leaves a residue known as "dross." Because dross contains contaminants like lead silver cadmium and copper, Pima County, the dross dumping site, wanted to locate areas where dross had been dumped. Dr. Larry Lepley and Sandra L. Perry used the Landsat Thematic Mapper to screen for dross. A special two-step procedure was developed to separate the dross dumps (typically no larger than 50 meters across) from the desert background. The project has opened the door for similar applications.

  3. statement of significance, location map, site plan, landscape plan, site ...

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

    statement of significance, location map, site plan, landscape plan, site sections, evolution of cemetery landscape. - San Francisco National Cemetery, 1 Lincoln Boulevard, San Francisco, San Francisco County, CA

  4. Usability Evaluation of Public Web Mapping Sites

    NASA Astrophysics Data System (ADS)

    Wang, C.

    2014-04-01

    Web mapping sites are interactive maps that are accessed via Webpages. With the rapid development of Internet and Geographic Information System (GIS) field, public web mapping sites are not foreign to people. Nowadays, people use these web mapping sites for various reasons, in that increasing maps and related map services of web mapping sites are freely available for end users. Thus, increased users of web mapping sites led to more usability studies. Usability Engineering (UE), for instance, is an approach for analyzing and improving the usability of websites through examining and evaluating an interface. In this research, UE method was employed to explore usability problems of four public web mapping sites, analyze the problems quantitatively and provide guidelines for future design based on the test results. Firstly, the development progress for usability studies were described, and simultaneously several usability evaluation methods such as Usability Engineering (UE), User-Centered Design (UCD) and Human-Computer Interaction (HCI) were generally introduced. Then the method and procedure of experiments for the usability test were presented in detail. In this usability evaluation experiment, four public web mapping sites (Google Maps, Bing maps, Mapquest, Yahoo Maps) were chosen as the testing websites. And 42 people, who having different GIS skills (test users or experts), gender (male or female), age and nationality, participated in this test to complete the several test tasks in different teams. The test comprised three parts: a pretest background information questionnaire, several test tasks for quantitative statistics and progress analysis, and a posttest questionnaire. The pretest and posttest questionnaires focused on gaining the verbal explanation of their actions qualitatively. And the design for test tasks targeted at gathering quantitative data for the errors and problems of the websites. Then, the results mainly from the test part were analyzed. The

  5. Mapping NEHRP VS30 site classes

    USGS Publications Warehouse

    Holzer, T.L.; Padovani, A.C.; Bennett, M.J.; Noce, T.E.; Tinsley, J. C.

    2005-01-01

    Site-amplification potential in a 140-km2 area on the eastern shore of San Francisco Bay, California, was mapped with data from 210 seismic cone penetration test (SCPT) soundings. NEHRP VS30 values were computed on a 50-m grid by both taking into account the thickness and using mean values of locally measured shear-wave velocities of shallow geologic units. The resulting map of NEHRP VS30 site classes differs from other published maps that (1) do not include unit thickness and (2) are based on regional compilations of velocity. Although much of the area in the new map is now classified as NEHRP Site Class D, the velocities of the geologic deposits within this area are either near the upper or lower VS30 boundary of Class D. If maps of NEHRP site classes are to be based on geologic maps, velocity distributions of geologic units may need to be considered in the definition of VS30 boundaries of NEHRP site classes. ?? 2005, Earthquake Engineering Research Institute.

  6. Site maps and facilities listings

    SciTech Connect

    Not Available

    1993-11-01

    In September 1989, a Memorandum of Agreement among DOE offices regarding the environmental management of DOE facilities was signed by appropriate Assistant Secretaries and Directors. This Memorandum of Agreement established the criteria for EM line responsibility. It stated that EM would be responsible for all DOE facilities, operations, or sites (1) that have been assigned to DOE for environmental restoration and serve or will serve no future production need; (2) that are used for the storage, treatment, or disposal of hazardous, radioactive, and mixed hazardous waste materials that have been properly characterized, packaged, and labelled, but are not used for production; (3) that have been formally transferred to EM by another DOE office for the purpose of environmental restoration and the eventual return to service as a DOE production facility; or (4) that are used exclusively for long-term storage of DOE waste material and are not actively used for production, with the exception of facilities, operations, or sites under the direction of the DOE Office of Civilian Radioactive Waste Management. As part of the implementation of the Memorandum of Agreement, Field Offices within DOE submitted their listings of facilities, systems, operation, and sites for which EM would have line responsibility. It is intended that EM facility listings will be revised on a yearly basis so that managers at all levels will have a valid reference for the planning, programming, budgeting and execution of EM activities.

  7. 1863, 1880 & 1884 Site Maps Brookland Site Development ...

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

    1863, 1880 & 1884 Site Maps - Brookland Site Development Study, Brookland, bounded by B&O Railroad Tracks, Rhode Island & Brentwood Avenues on the south, 18th Street & South Dakota Avenue on the east, and Michigan Avenue on the North, Washington, District of Columbia, DC

  8. 1884, 1889 & 1893 Site Maps Brookland Site Development ...

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

    1884, 1889 & 1893 Site Maps - Brookland Site Development Study, Brookland, bounded by B&O Railroad Tracks, Rhode Island & Brentwood Avenues on the south, 18th Street & South Dakota Avenue on the east, and Michigan Avenue on the North, Washington, District of Columbia, DC

  9. Ground water maps of the Hanford Site

    SciTech Connect

    Kasza, G.L.; Harris, S.F.; Hartman, M.J.

    1990-12-01

    This report presents the results of the June 1990, ground water level measurement program at the 100 Areas and 200 Areas of the Hanford Site (Figure 1). The water levels beneath these areas are measured regularly on a semiannual basis and the data received are used to produce the following set of maps for public release. For clarity, the locating prefixes have been omitted from all well numbers shown on the maps. Wells in the 100 Areas have the prefix 199; wells in the 200 Areas have the prefix 299, and the wells outside these areas have the prefix 699. Ground Water Maps of the Hanford Site is prepared by the Geosciences Group, Environmental Division, Westinghouse Hanford Company, for the US Department of Energy, Richland Operations Office. 1 ref., 6 figs., 2 tabs.

  10. Mapping Recombination Initiation Sites Using Chromatin Immunoprecipitation.

    PubMed

    He, Yan; Wang, Minghui; Sun, Qi; Pawlowski, Wojciech P

    2016-01-01

    Genome-wide maps of recombination sites provide valuable information not only on the recombination pathway itself but also facilitate the understanding of genome dynamics and evolution. Here, we describe a chromatin immunoprecipitation (ChIP) protocol to map the sites of recombination initiation in plants with maize used as an example. ChIP is a method that allows identification of chromosomal sites occupied by specific proteins. Our protocol utilizes RAD51, a protein involved in repair of double-strand breaks (DSBs) that initiate meiotic recombination, to identify DSB formation hotspots. Chromatin is extracted from meiotic flowers, sheared and enriched in fragments bound to RAD51. Genomic location of the protein is then identified by next-generation sequencing. This protocol can also be used in other species of plants, animals, and fungi. PMID:27511175

  11. Identification of cis-acting elements as DNase I hypersensitive sites in lysozyme gene chromatin.

    PubMed

    Sippel, A E; Saueressig, H; Huber, M C; Hoefer, H C; Stief, A; Borgmeyer, U; Bonifer, C

    1996-01-01

    DNase I hypersensitive sites in chromatin of eukaryotic cells mark the positions of multifactorial cis-acting elements. Mapping DH sites by indirect end labeling is a convenient procedure used for identifying regulatory elements within extensive regions of chromatin and for gaining information about their functional specificity as well as their fine structure.

  12. Identification of cis-acting elements as DNase I hypersensitive sites in lysozyme gene chromatin.

    PubMed

    Sippel, A E; Saueressig, H; Huber, M C; Hoefer, H C; Stief, A; Borgmeyer, U; Bonifer, C

    1996-01-01

    DNase I hypersensitive sites in chromatin of eukaryotic cells mark the positions of multifactorial cis-acting elements. Mapping DH sites by indirect end labeling is a convenient procedure used for identifying regulatory elements within extensive regions of chromatin and for gaining information about their functional specificity as well as their fine structure. PMID:8902808

  13. 24. Site plan, 1924 Photocopied from Sanborn Map Company, Insurance ...

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

    24. Site plan, 1924 Photocopied from Sanborn Map Company, Insurance Maps of New Haven, v. 5, map no. 540, 1924 - Eli Whitney Armory, West of Whitney Avenue, Armory Street Vicinity, Hamden, New Haven County, CT

  14. 23. Site plan, 1931 Photocopied from Sanborn Map Company, Insurance ...

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

    23. Site plan, 1931 Photocopied from Sanborn Map Company, Insurance Maps of New Haven, v. 5, map no. 540, 1924 updated to 1931. - Eli Whitney Armory, West of Whitney Avenue, Armory Street Vicinity, Hamden, New Haven County, CT

  15. Site characterization and petroleum hydrocarbon plume mapping

    SciTech Connect

    Ravishankar, K.

    1996-12-31

    This paper presents a case study of site characterization and hydrocarbon contamination plume mapping/delineation in a gas processing plant in southern Mexico. The paper describes innovative and cost-effective use of passive (non-intrusive) and active (intrusive) techniques, including the use of compound-specific analytical methods for site characterization. The techniques used, on a demonstrative basis, include geophysical, geochemical, and borehole drilling. Geochemical techniques used to delineate the horizontal extent of hydrocarbon contamination at the site include soil gas surveys. The borehole drilling technique used to assess the vertical extent of contamination and confirm geophysical and geochemical data combines conventional hollow-stem auguring with direct push-probe using Geoprobe. Compound-specific analytical methods, such as hydrocarbon fingerprinting and a modified method for gasoline range organics, demonstrate the inherent merit and need for such analyses to properly characterize a site, while revealing the limitations of noncompound-specific total petroleum hydrocarbon analysis. The results indicate that the techniques used in tandem can properly delineate the nature and extent of contamination at a site; often supplement or complement data, while reducing the risk of errors and omissions during the assessment phase; and provide data constructively to focus site-specific remediation efforts. 7 figs.

  16. Mapping of sites in forest stands.

    PubMed

    Netto, Sylvio Péllico; Stefanello, Flavio R; Pelissari, Allan L; David, Hassan C

    2014-12-01

    Generally, the forest companies use the total one year planting area as a minimum stratum of the total population and, consequently, the forest inventory processing has been conducted by applying the stratified random sampling to it. This study was carried out in the National Forest of Tres Barras, Brazil, and it aimed to classify and map the sites of Pinus elliottii stands. A systematic sampling was structured into clusters and applied independently by compartments. The clusters, in maltese cross, were composed of four sampling subunits, using Prodan sampling method with a fixed number of six trees. By analysis of the methodology it was possible to confirm the hypothesis: a) the selective thinning cause expressive increase of volumetric variability within compartments; b) the variation of sites within the compartments causes volumetric expansion of variance and this grows proportionally to the quality of the sites; c) the stratification in sites results in minimum variance within them; d) the stratification in sites resulted in until to 91% reduction of variances within them. PMID:25590737

  17. GIS Surface Effects Map Archive, Nevada Test Site, Nevada

    SciTech Connect

    Grasso, Dennis N.

    2003-08-28

    The GIS Surface Effects Map Archive contains a comprehensive collection of maps showing the surface effects produced by underground nuclear testing at the Nevada Test Site. From 1951 to 1992, scientists with the U.S. Geological Survey and agencies of the U.S. Department of Energy used field and aerial-photo mapping techniques to painstakingly map such surface effects as collapse sinks, craters, cracks, fractures, faults, and pressure ridges. Shortly after each test, a complex surface effects map was produced. Of the more than 920 underground detonations conducted at the Nevada Test Site, 688 were mapped for surface effects. This archive preserves these original maps in digital format. A Geographic Information System (GIS) was used to digitally reproduce each original, hand-drawn surface effects map and to assemble these maps into the digital data sets of this archive. The archive was designed to allow easy access to the maps, while preserving the original maps for perpetuity. Users can query the detonation sites database; prepare, view, and print individual or composite maps; and perform various types of scientific analysis and management tasks. Spatial analyses and queries can be performed on detonation sites and related surface effects in conjunction with other chronological, geographical, geological, or hydrological information via links to external maps and databases. This browser interface provides information about the archive, the history of surface effects mapping at the Nevada Test Site, the methods used to produce the digital surface effects maps, and links to published reports, data tables, and maps. Location maps show testing areas, operational areas, and detonation sites. Demonstration maps illustrate the methods used to produce the digital surface effects maps and exhibit some of the characteristics and uses for these data. Use the links below to view and print individual surface effects maps, retrieve information about the detonations and types of

  18. Topographic Map of Pathfinder Landing Site

    NASA Technical Reports Server (NTRS)

    1997-01-01

    Topographic map of the landing site, to a distance of 60 meters from the lander in the LSC coordinate system. The lander is shown schematically in the center; 2.5 meter radius circle (black) centered on the camera was not mapped. Gentle relief [root mean square (rms) elevation variation 0.5 m; rms a directional slope 4O] and organization of topography into northwest and northeast-trending ridges about 20 meters apart are apparent. Roughly 30% of the illustrated area is hidden from the camera behind these ridges. Contours (0.2 m interval) and color coding of elevations were generated from a digital terrain model, which was interpolated by kriging from approximately 700 measured points. Angular and parallax point coordinates were measured manually on a large (5 m length) anaglyphic uncontrolled mosaic and used to calculate Cartesian (LSC) coordinates. Errors in azimuth on the order of 10 are therefore likely; elevation errors were minimized by referencing elevations to the local horizon. The uncertainty in range measurements increases quadratically with range. Given a measurement error of 1/2 pixel, the expected precision in range is 0.3 meter at 10 meter range, and 10 meters at 60 meter range. Repeated measurements were made, compared, and edited for consistency to improve the range precision. Systematic errors undoubtedly remain and will be corrected in future maps compiled digitally from geometrically controlled images. Cartographic processing by U.S. Geological Survey.

    NOTE: original caption as published in Science Magazine

    Mars Pathfinder is the second in NASA's Discovery program of low-cost spacecraft with highly focused science goals. The Jet Propulsion Laboratory, Pasadena, CA, developed and manages the Mars Pathfinder mission for NASA's Office of Space Science, Washington, D.C. JPL is a division of the California Institute of Technology (Caltech).

  19. Georgia Reading Excellence Act Demonstration Sites (GA READS). Executive Summary.

    ERIC Educational Resources Information Center

    Georgia State Dept. of Education, Atlanta.

    This executive summary of Georgia Reading Excellence Act Demonstration Sites (GA READS) includes the Reading Excellence overview; Georgia's plan and goals; state activities; a timeline; local activities; and a budget. The overview states that the Reading Excellence Act was authorized to carry out the following purposes: teach every child to read…

  20. 47 CFR 73.4108 - FM transmitter site map submissions.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 4 2010-10-01 2010-10-01 false FM transmitter site map submissions. 73.4108... RADIO BROADCAST SERVICES Rules Applicable to All Broadcast Stations § 73.4108 FM transmitter site map submissions. See Memorandum Opinion and Order and Public Notice, adopted October 24, 1986. 1 FCC Rcd 381...

  1. 47 CFR 73.4108 - FM transmitter site map submissions.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 4 2013-10-01 2013-10-01 false FM transmitter site map submissions. 73.4108... RADIO BROADCAST SERVICES Rules Applicable to All Broadcast Stations § 73.4108 FM transmitter site map submissions. See Memorandum Opinion and Order and Public Notice, adopted October 24, 1986. 1 FCC Rcd 381...

  2. Surface-material maps of Viking landing sites on Mars

    NASA Technical Reports Server (NTRS)

    Moore, H. J.; Keller, J. M.

    1991-01-01

    Researchers mapped the surface materials at the Viking landing sites on Mars to gain a better understanding of the materials and rock populations at the sites and to provide information for future exploration. The maps extent to about 9 m in front of each lander and are about 15 m wide - an area comparable to the area of a pixel in high resolution Viking Orbiter images. The maps are divided into the near and far fields. Data for the near fields are from 1/10 scale maps, umpublished maps, and lander images. Data for the far fields are from 1/20 scale contour maps, contoured lander camera mosaics, and lander images. Rocks are located on these maps using stereometric measurements and the contour maps. Frequency size distribution of rocks and the responses of soil-like materials to erosion by engine exhausts during landings are discussed.

  3. Surface-material maps of Viking landing sites on Mars

    NASA Astrophysics Data System (ADS)

    Moore, H. J.; Keller, J. M.

    1991-06-01

    Researchers mapped the surface materials at the Viking landing sites on Mars to gain a better understanding of the materials and rock populations at the sites and to provide information for future exploration. The maps extent to about 9 m in front of each lander and are about 15 m wide - an area comparable to the area of a pixel in high resolution Viking Orbiter images. The maps are divided into the near and far fields. Data for the near fields are from 1/10 scale maps, umpublished maps, and lander images. Data for the far fields are from 1/20 scale contour maps, contoured lander camera mosaics, and lander images. Rocks are located on these maps using stereometric measurements and the contour maps. Frequency size distribution of rocks and the responses of soil-like materials to erosion by engine exhausts during landings are discussed.

  4. Hanford Site National Environmental Policy Act (NEPA) Characterization

    SciTech Connect

    Neitzel, Duane A.; Bunn, Amoret L.; Duncan, Joanne P.; Eschbach, Tara O.; Fowler, Richard A.; Fritz, Brad G.; Goodwin, Shannon M.; Harvey, David W.; Hendrickson, Paul L.; Hoitink, Dana J.; Horton, Duane G.; Last, George V.; Poston, Ted M.; Prendergast-Kennedy, Ellen L.; Rohay, Alan C.; Scott, Michael J.; Thorne, Paul D.

    2002-09-01

    This document describes the U.S. Department of Energy's (DOE) Hanford Site environment. It is updated each year and is intended to provide a consistent description of the Hanford Site environment for the many National Environmental Policy Act (NEPA) documents being prepared by DOE contractors. No statements of significance or environmental consequences are provided. This year's report is the thirteenth revision of the original document published in 1988 and is (until replaced by the fourteenth revision) the only version that is relevant for use in the preparation of Hanford NEPA, State Environmental Policy Act (SEPA), and Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) documents. The two chapters included in this document (Chapters 4 and 6) are numbered to correspond to the chapters where such information is typically presented in environmental impact statements (Weiss) and other Hanford Site NEPA or CERCLA documentation. Chapter 4.0 (Affected Environment) describes Hanford Site climate and meteorology, geology, hydrology, ecology, cultural, archaeological, and historical resources, socioeconomics, occupational safety, and noise. Chapter 6.0 (Statutory and Regulatory Requirements) describes federal and state laws and regulations, DOE directives and permits, and presidential executive orders that are applicable to the NEPA documents prepared for Hanford Site activities.

  5. Hanford Site National Environmental Policy Act (NEPA) Characterization, Revision 15

    SciTech Connect

    Neitzel, Duane A.; Bunn, Amoret L.; Burk, Kenneth W.; Cannon, Sandra D.; Duncan, Joanne P.; Fowler, Richard A.; Fritz, Brad G.; Harvey, David W.; Hendrickson, Paul L.; Horton, Duane G.; Last, George V.; Poston, Ted M.; Prendergast-Kennedy, Ellen L.; Reidel, Steve P.; Scott, Michael J.; Thorne, Paul D.; Woody, Dave M.

    2003-09-01

    This document describes the U.S. Department of Energy's (DOE) Hanford Site environment. It is updated each year and is intended to provide a consistent description of the Hanford Site environment for the many National Environmental Policy Act (NEPA) documents being prepared by DOE contractors. No statements of significance or environmental consequences are provided. This year's report is the thirteenth revision of the original document published in 1988 and is (until replaced by the fourteenth revision) the only version that is relevant for use in the preparation of Hanford NEPA, State Environmental Policy Act (SEPA), and Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) documents. The two chapters included in this document (Chapters 4 and 6) are numbered to correspond to the chapters where such information is typically presented in environmental impact statements (Weiss) and other Hanford Site NEPA or CERCLA documentation. Chapter 4.0 (Affected Environment) describes Hanford Site climate and meteorology, geology, hydrology, ecology, cultural, archaeological, and historical resources, socioeconomics, occupational safety, and noise. Chapter 6.0 (Statutory and Regulatory Requirements) describes federal and state laws and regulations, DOE directives and permits, and presidential executive orders that are applicable to the NEPA documents prepared for Hanford Site activities.

  6. Hanford Site National Environmental Policy Act (NEPA) Characterization

    SciTech Connect

    Neitzel, Duane A.; Antonio, Ernest J.; Eschbach, Tara O.; Fowler, Richard A.; Goodwin, Shannon M.; Harvey, David W.; Hendrickson, Paul L.; Hoitink, Dana J.; Horton, Duane G.; Last, George V.; Poston, Ted M.; Prendergast, Ellen L.; Rohay, Alan C.; Thorne, Paul D.

    2001-09-01

    This document describes the U.S. Department of Energy's (DOE) Hanford Site environment. It is updated each year and is intended to provide a consistent description of the Hanford Site environment for the many National Environmental Policy Act (NEPA) documents being prepared by DOE contractors. No statements of significance or environmental consequences are provided. This year's report is the thirteenth revision of the original document published in 1988 and is (until replaced by the fourteenth revision) the only version that is relevant for use in the preparation of Hanford NEPA, State Environmental Policy Act (SEPA), and Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) documents. The two chapters included in this document (Chapters 4 and 6) are numbered to correspond to the chapters where such information is typically presented in environmental impact statements (Weiss) and other Hanford Site NEPA or CERCLA documentation. Chapter 4.0 (Affected Environment) describes Hanford Site climate and meteorology, geology, hydrology, ecology, cultural, archaeological, and historical resources, socioeconomics, occupational safety, and noise. Chapter 6.0 (Statutory and Regulatory Requirements) describes federal and state laws and regulations, DOE directives and permits, and presidential executive orders that are applicable to the NEPA documents prepared for Hanford Site activities.

  7. Hanford Site National Environmental Policy Act (NEPA) Characterization Report

    SciTech Connect

    Neitzel, Duane A.; Bunn, Amoret L.; Cannon, Sandra D.; Duncan, Joanne P.; Fowler, Richard A.; Fritz, Brad G.; Harvey, David W.; Hendrickson, Paul L.; Hoitink, Dana J.; Horton, Duane G.; Last, George V.; Poston, Ted M.; Prendergast-Kennedy, Ellen L.; Reidel, Steve P.; Rohay, Alan C.; Scott, Michael J.; Thorne, Paul D.

    2004-09-22

    This document describes the U.S. Department of Energy's (DOE) Hanford Site environment. It is updated each year and is intended to provide a consistent description of the Hanford Site environment for the many National Environmental Policy Act (NEPA) documents being prepared by DOE contractors. No statements of significance or environmental consequences are provided. This year's report is the sixteenth revision of the original document published in 1988 and is (until replaced by the seventeenth revision) the only version that is relevant for use in the preparation of Hanford NEPA, State Environmental Policy Act (SEPA), and Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) documents. The two chapters included in this document (Chapters 4 and 6) are numbered to correspond to the chapters where such information is typically presented in environmental impact statements (Weiss) and other Hanford Site NEPA or CERCLA documentation. Chapter 4.0 (Affected Environment) describes Hanford Site climate and meteorology, geology, hydrology, ecology, cultural, archaeological, and historical resources, socioeconomics, occupational safety and health, and noise. Chapter 6.0 (Statutory and Regulatory Requirements) describes federal and state laws and regulations, DOE directives and permits, and presidential executive orders that are applicable to the NEPA documents prepared for Hanford Site activities.

  8. Preliminary Correlation Map of Geomorphic Surfaces in North-Central Frenchman Flat, Nevada Test Site

    SciTech Connect

    Bechtel Nevada

    2005-08-01

    This correlation map (scale = 1:12,000) presents the results of a mapping initiative that was part of the comprehensive site characterization required to operate the Area 5 Radioactive Waste Management Site, a low-level radioactive waste disposal facility located in northern Frenchman Flat at the Nevada Test Site. Eight primary map units are recognized for Quaternary surfaces: remnants of six alluvial fan or terrace surfaces, one unit that includes colluvial aprons associated with hill slopes, and one unit for anthropogenically disturbed surfaces. This surficial geology map provides fundamental data on natural processes for reconstruction of the Quaternary history of northern Frenchman Flat, which in turn will aid in the understanding of the natural processes that act to develop the landscape, and the time-frames involved in landscape development. The mapping was conducted using color and color-infrared aerial photographs and field verification of map unit composition and boundaries. Criteria for defining the map unit composition of geomorphic surface units are based on relative geomorphic position, landform morphology, and degree of preservation of surface morphology. The bedrock units identified on this map were derived from previous published mapping efforts and are included for completeness.

  9. Groundwater maps of the Hanford Site, June 1993

    SciTech Connect

    Kasza, G.L.; Hartman, M.J.; Jordan, W.A.; Weekes, D.C.

    1994-02-01

    The Groundwater Maps of the Hanford Site, June 1993 is an update of the series of reports that document the configuration of the uppermost unconfined aquifer beneath the Hanford Site. This report series presents the semiannual water level measurements taken at site groundwater monitoring wells each June and December and the groundwater maps derived from these measurements. These reports document the changes in the groundwater level at Hanford as the site has transitioned from nuclear material production to environmental restoration and remediation. In addition, these reports provide water level data to support the various site characterization and groundwater monitoring programs currently in progress on the Hanford Site. Groundwater Maps of the Hanford Site are prepared for the US Department of Energy, Office of Environmental Restoration and Waste Management, by the Hanford Site Operations and Engineering Contractor, Westinghouse Hanford Company (WHC). This document fulfills reporting requirements specified in WHC (1993), Section 8.0 {open_quotes}Water Quality{close_quotes} and also described in the Environmental Monitoring Plan for the Hanford Site (DOE-RL 1991). Maps depicting the water table beneath the Hanford Site south of the Columbia River are presented in this report. Appendix A lists the well identification number, depth to water, casing elevating and the water level elevation for each well measured during June 1993. A summary discussion of the data is included with a well index map, the depth to water map and the contoured map of the water table surface for the Hanford Site and each of the three operational areas (the 100, 200, and 300-1100 Areas).

  10. Optimizing landfill site selection by using land classification maps.

    PubMed

    Eskandari, M; Homaee, M; Mahmoodi, S; Pazira, E; Van Genuchten, M Th

    2015-05-01

    Municipal solid waste disposal is a major environmental concern throughout the world. Proper landfill siting involves many environmental, economic, technical, and sociocultural challenges. In this study, a new quantitative method for landfill siting that reduces the number of evaluation criteria, simplifies siting procedures, and enhances the utility of available land evaluation maps was proposed. The method is demonstrated by selecting a suitable landfill site near the city of Marvdasht in Iran. The approach involves two separate stages. First, necessary criteria for preliminary landfill siting using four constraints and eight factors were obtained from a land classification map initially prepared for irrigation purposes. Thereafter, the criteria were standardized using a rating approach and then weighted to obtain a suitability map for landfill siting, with ratings in a 0-1 domain and divided into five suitability classes. Results were almost identical to those obtained with a more traditional environmental landfill siting approach. Because of far fewer evaluation criteria, the proposed weighting method was much easier to implement while producing a more convincing database for landfill siting. The classification map also considered land productivity. In the second stage, the six best alternative sites were evaluated for final landfill siting using four additional criteria. Sensitivity analyses were furthermore conducted to assess the stability of the obtained ranking. Results indicate that the method provides a precise siting procedure that should convince all pertinent stakeholders.

  11. Groundwater maps of the Hanford site, June 1995

    SciTech Connect

    Sweeney, M.D.

    1996-03-15

    The Groundwater Maps of the Hanford Site, June 1995 is a continuation of a series of reports (see Serkowski et al. 1995) that document the configuration of the water table aquifer beneath the Hanford Site (Figure 1). This series presents the results of the semiannual water level measurement program and the water table maps generated from these measurements. The reports document the changes in the groundwater level at the Hanford Site during the transition from nuclear material production to environmental restoration and remediation. In addition, these reports provide water level data to support the various site characterization and groundwater monitoring programs currently in progress on the Hanford Site. Groundwater Maps of the Hanford Site is prepared for the U.S. Department of Energy by the Hanford Site Operations and Engineering Contractor, Westinghouse Hanford Company (WHC). This document fulfills reporting requirements specified in WHC-CM-7-5, Section 8.0 ``Water Quality`` and described in the environmental monitoring plan for the Hanford Site. (DOE-RL 1993a) This document highlights the three major operations areas (the 100, 200 and 300/1100 Areas) where wastes were discharged to the soil. Each area includes a summary discussion of the data, a well index map, and a contoured map of the water table surface. Appendix A contains all of the data collected for this program.

  12. Groundwater maps of the Hanford Site Separations Area, January 1989

    SciTech Connect

    Kasza, G.L.; Schatz, A.L.

    1989-03-01

    The groundwater maps of the Hanford Site Separations Area, dated January 1989, are prepared by the Environmental Engineering and Technology Function, Environmental Division, Westinghouse Hanford Company. The groundwater maps are updated on a semiannual basis and are complementary to the Hanford Site water table map prepared by Pacific Northwest Laboratory. The Separations Area consists of the 200 East and 200 West areas and the surrounding vicinity on the Hanford Site. Chemical processing operations are carried out in the Separations Area by Westinghouse Hanford for the US Department of Energy - Richland Operations Office. This set of groundwater maps consists of: (1) Separations Area depth-to-water map, (2) Separations Area water table map, and (3) a map comparing the potentiometric surface of the Rattlesnake Ridge confined aquifer with the water table of the unconfined aquifer. The field measurements for these maps were collected during the period January 19 to February 8, 1989, and are listed in Table 1. For clarity, the locating prefixes have been omitted from all well numbers shown on the maps. Wells in the 200 Areas have the prefix 299, and the wells outside of these areas have the prefix 699.

  13. Hanford Site National Environmental Policy Act (NEPA) characterization. Revision 9

    SciTech Connect

    Neitzel, D.A.; Bjornstad, B.N.; Fosmire, C.J.

    1997-08-01

    This ninth revision of the Hanford Site National Environmental Policy Act (NEPA) Characterization presents current environmental data regarding the hanford Site and its immediate environs. This information is intended for use in preparing Chapters 4 and 6 in Hanford Site-related NEPA documents. Chapter 4.0 (Affected Environment) includes information on climate and meteorology, geology, hydrology, ecology, cultural, archaeological and historical resources, socioeconomics, and noise. Chapter 6.0 (Statutory and Regulatory Requirements) provides the preparer with the federal and state regulations, DOE directives and permits, and environmental standards directly applicable to the NEPA documents on the Hanford Site. Not all of the sections have been updated for this revision. The following lists the updated sections: climate and meteorology; ecology (threatened and endangered species section only); culture, archaeological, and historical resources; socioeconomics; all of Chapter 6.

  14. Federal Facilities Compliance Act, Conceptual Site Treatment Plan. Part 1

    SciTech Connect

    1993-10-29

    This Conceptual Site Treatment Plan was prepared by Ames Laboratory to meet the requirements of the Federal Facilities Compliance Act. Topics discussed in this document include: general discussion of the plan, including the purpose and scope; technical aspects of preparing plans, including the rationale behind the treatability groupings and a discussion of characterization issues; treatment technology needs and treatment options for specific waste streams; low-level mixed waste options; TRU waste options; and future waste generation from restoration activities.

  15. Hanford Site National Environmental Policy Act (NEPA) characterization. Revision 8

    SciTech Connect

    Neitzel, D.A.; Bjornstad, B.N.; Fosmire, C.J.; Fowler, R.A.

    1996-08-01

    This eighth revision of the Hanford Site National Environmental Policy Act (NEPA) Characterization presents current environmental data regarding the Hanford Site and its immediate environs. This information is intended for use in preparing Chapters 4 and 6 in Hanford Site-related NEPA documents. Chapter 4 (Affected Environment) includes information on climate and meteorology, geology, hydrology, ecology, historical, archaeological and cultural resources, socioeconomics, and noise. Chapter 6 (Statutory and Regulatory Requirements) provides the preparer with the federal and state regulations, DOE directives and permits, and environmental standards directly applicable to the NEPA documents on the Hanford Site. The following sections were updated in this revision: climate and meteorology; ecology (threatened and endangered species section only); historical; archaeological and cultural resources; and all of chapter 6. No conclusions or recommendations are given in this report. Rather, it is a compilation of information on the Hanford Site environment that can be used directly by Site contractors. This information can also be used by any interested individual seeking baseline data on the hanford Site and its past activities by which to evaluate projected activities and their impacts.

  16. Groundwater maps of the Hanford Site, June 1994

    SciTech Connect

    Serkowski, J.A.; Jordan, W.A.; Hartman, M.J.

    1994-12-01

    This report is a continuation of reports (Kasza et al., 1994) that document the configuration of the uppermost unconfined aquifer beneath the Hanford Site. This series presents the results of the semiannual water level measurement program and the water table maps generated from these measurements. The reports document the changes in the groundwater level at the Hanford Site during the transition from nuclear material production to environmental restoration and remediation. In addition, these reports provide water level data to support the various site characterization and ground water monitoring programs currently in progress on the Hanford Site. This report highlights the three major operations areas (the 100, 200, and 300/1100 Areas) where wastes were discharged to the soil. Each area includes a summary discussion of the data, a well index map, and a contoured map of the water table surface.

  17. Geomorphic Surface Maps of Northern Frenchman Flat, Nevada Test Site, Southern Nevada

    SciTech Connect

    Bechtel Nevada

    2005-08-01

    Large-scale (1:6000) surficial geology maps of northern Frenchman Flat were developed in 1995 as part of comprehensive site characterization required to operate a low-level radioactive waste disposal facility in that area. Seven surficial geology maps provide fundamental data on natural processes and are the platform needed to reconstruct the Quaternary history of northern Frenchman Flat. Reconstruction of the Quaternary history provides an understanding of the natural processes that act to develop the landscape, and the time-frames involved in landscape development. The mapping was conducted using color and color-infrared aerial photographs and field verification of map unit composition and boundaries. Criteria for defining the map unit composition of geomorphic surface units are based on relative geomorphic position, landform morphology, and degree of preservation of surface morphology. Seven geomorphic surfaces (Units 1 through 7) are recognized, spanning from the early Quaternary to present time.

  18. Robotic Mapping of Cultural Heritage Sites

    NASA Astrophysics Data System (ADS)

    Borrmann, D.; Heß, R.; Houshiar, H. R.; Eck, D.; Schilling, K.; Nüchter, A.

    2015-02-01

    In archaeological studies the use of new technologies has moved into focus in the past years creating new challenges such as the processing of the massive amounts of data. In this paper we present steps and processes for smart 3D modelling of environments by use of the mobile robot Irma3D. A robot that is equipped with multiple sensors, most importantly a photo camera and a laser scanner, enables the automation of most of the processes, including data acquisition and registration. The robot was tested in two scenarios, Ostia Antica and the Würzburg Residence. The paper describes the steps for creating 3D color reconstructions of these renown cultural heritage sites.

  19. Hanford Site National Environmental Policy Act (NEPA) characterization

    SciTech Connect

    Cushing, C.E.

    1988-09-01

    This document describes the Hanford Site environment (Chapter 4) and contains data in Chapter 5 and 6 which will guide users in the preparation of National Environmental Policy Act (NEPA)-related documents. Many NEPA compliance documents have been prepared and are being prepared by site contractors for the US Department of Energy, and examination of these documents reveals inconsistencies in the amount of detail presented and the method of presentation. Thus, it seemed necessary to prepare a consistent description of the Hanford environment to be used in preparing Chapter 4 of environmental impact statements and other site-related NEPA documentation. The material in Chapter 5 is a guide to the models used, including critical assumptions incorporated in these models, in previous Hanford NEPA documents. The users will have to select those models appropriate for the proposed action. Chapter 6 is essentially a definitive NEPA Chapter 6, which describes the applicable laws, regulations, and DOE and state orders. In this document, a complete description of the environment is presented in Chapter 4 without excessive tabular data. For these data, sources are provided. Most subjects are divided into a general description of the characteristics of the Hanford Site, followed by site-specific information where it is available on the 100, 200, 300, and other Areas. This division will allow a person requiring information to go immediately to those sections of particular interest. However, site-specific information on each of these separate areas is not always complete or available. In this case, the general Hanford Site description should be used. 131 refs., 19 figs., 32 tabs.

  20. Hanford Site National Environmental Policy Act (NEPA) Characterization

    SciTech Connect

    Duncan, Joanne P.; Burk, Kenneth W.; Chamness, Mickie A.; Fowler, Richard A.; Fritz, Brad G.; Hendrickson, Paul L.; Kennedy, Ellen P.; Last, George V.; Poston, Ted M.; Sackschewsky, Michael R.; Scott, Michael J.; Snyder, Sandra F.; Sweeney, Mark D.; Thorne, Paul D.

    2007-09-27

    This document describes the U.S. Department of Energy’s (DOE) Hanford Site environment. It is intended to provide a consistent description of the Hanford Site for the many environmental documents being prepared by DOE contractors concerning the National Environmental Policy Act (NEPA). No statements regarding significance or environmental consequences are provided. This year’s report is the eighteen revision of the original document published in 1988 and is (until replaced by the nineteenth revision) the only version that is relevant for use in the preparation of Hanford NEPA, State Environmental Policy Act (SEPA), and Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) documents. Two chapters are included in this document (Chapters 4 and 6), numbered to correspond to chapters typically presented in environmental impact statements (EISs) and other Hanford Site NEPA or CERCLA documentation. Chapter 4.0 (Affected Environment) describes Hanford Site climate and meteorology; air quality; geology; hydrology; ecology; cultural, archaeological, and historical resources; socioeconomics; noise; and occupational health and safety. Sources for extensive tabular data related to these topics are provided in the chapter. When possible, subjects are divided into a general description of the characteristics of the Hanford Site, followed by site-specific information, where available, for the 100, 200, 300 and other areas. This division allows the reader to go directly to those sections of particular interest. When specific information on each of these separate areas is not complete or available, the general Hanford Site description should be used. Chapter 6.0 (Statutory and Regulatory Requirements) describes federal and state laws and regulations, DOE directives and permits, and presidential executive orders that are applicable to NEPA documents prepared for Hanford Site activities. Information in Chapter 6 can be adapted and supplemented with

  1. Groundwater maps of the Hanford Site, December 1993

    SciTech Connect

    Kasza, G.L.; Hartman, M.J.; Jordan, W.A.; Borghese, J.V.

    1994-07-01

    This report is an update to the series of reports that document the configuration of the uppermost unconfined aquifer beneath the Hanford Site. This series presents the latest results of the semiannual water level measurement program and the water table maps generated from these measurements. The reports document the changes in the groundwater level at the Hanford Site during the transition from nuclear material production to environmental restoration and remediation. In addition, these reports provide water level data to support the various site characterization and groundwater monitoring programs currently in progress on the Hanford Site. The three major operations areas (the 100, 200 and 300/1100 Areas) where wastes were discharged to the soil are covered in this update. The water level measurements from the wells in these areas are portrayed on a set of maps to illustrate the hydrologic conditions and are also tabulated in an appendix. A summary discussion of the data is included with the well index map, the depth to water map, and the contoured map of the water table surface for each of the three areas.

  2. Groundwater maps of the Hanford Site, December 1995

    SciTech Connect

    Sweeney, M.D., Westinghouse Hanford

    1996-07-02

    This the latest in a series of reports that document the configuration of the water table aquifer beneath the Hanford Site. This series presents the results of the semiannual water level measurement program and the water table maps generated from these measurements. The reports document the changes in the groundwater level at the Hanford Site during the transition from nuclear material production to environmental restoration and remediation. In addition, these reports provide water level data to support the various site characterization and groundwater monitoring programs currently in progress on the Hanford Site.

  3. Acceptor sites for retroviral integrations map near DNase I-hypersensitive sites in chromatin.

    PubMed Central

    Vijaya, S; Steffen, D L; Robinson, H L

    1986-01-01

    Seven cellular loci with acceptor sites for retroviral integrations have been mapped for the presence of DNase I-hypersensitive sites in chromatin. Integrations in three of these loci, chicken c-erbB, rat c-myc, and a rat locus, dsi-1, had been selected for in retrovirus-induced tumors. Of the remaining four, two, designated dsi-3 and dsi-4, harbored acceptor sites for apparently unselected integrations of Moloney murine leukemia virus in a Moloney murine leukemia virus-induced thymoma, and two, designated C and F, harbored unselected acceptor sites for Moloney murine leukemia virus integrations in a rat fibroblast cell line. Each acceptor site mapped to within 500 base pairs of a DNase I-hypersensitive site. In the analyses of the unselected integrations, six hypersensitive sites were observed in 39 kilobases of DNA. The four acceptor sites in this DNA were localized between 0.05 and 0.43 kilobases of a hypersensitive site. The probability of this close association occurring by chance was calculated to be extremely low. Hypersensitive sites were mapped in cells representing the lineage in which integration had occurred as well as in an unrelated lineage. In six of the seven acceptor loci hypersensitive sites could not be detected in the unrelated lineage. Our results indicate that retroviruses preferentially integrate close to DNase I-hypersensitive sites and that many of these sites are expressed in some but not all cells. Images PMID:3490582

  4. Intonational Rises and Dialog Acts in the Australian English Map Task.

    ERIC Educational Resources Information Center

    Fletcher, Janet; Stirling, Lesley; Mushin, Ilana; Wales, Roger

    2002-01-01

    Eight map task dialogs representative of general Australian English were coded for speaker turn and for dialog acts using a version of SWBD-DAMSL, a dialog act annotation scheme. High, low, simple, and complex rising tunes, and any corresponding dialog act codes were then compared. The Australian statement high rise (usually realized as a L…

  5. 13. "CIVIL, SITE PLAN AND VICINITY MAP, AREA LOCATIONS." Test ...

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

    13. "CIVIL, SITE PLAN AND VICINITY MAP, AREA LOCATIONS." Test Area 1-125. Specifications No. ENG (NASA)-04-35363-1; Drawing No. 60-09-34; sheet 11. Ref. No. C-l. D.O. SERIES 1597/1. Approved for siting on 24 April 1962. - Edwards Air Force Base, Air Force Rocket Propulsion Laboratory, Leuhman Ridge near Highways 58 & 395, Boron, Kern County, CA

  6. PowerPoint and Concept Maps: A Great Double Act

    ERIC Educational Resources Information Center

    Simon, Jon

    2015-01-01

    This article explores how concept maps can provide a useful addition to PowerPoint slides to convey interconnections of knowledge and help students see how knowledge is often non-linear. While most accounting educators are familiar with PowerPoint, they are likely to be less familiar with concept maps and this article shows how the tool can be…

  7. S.M.A.R.T. map: Site map attribute retrieval technique

    SciTech Connect

    Brown-Rall, M.

    1995-03-29

    Plant Engineering`s Space and Site Planning (S&SP) organization at Lawrence Livermore National Laboratory (LLNL) has developed a new tool, which is a computerized mapping system that can graphically illustrate facility characteristics. The current ``base`` map being used is the LLNL Site Map prepared by Plant Engineering`s CADD Support group. Using current information in the Facility Information Tracking System (FITS) database, a Microsoft Excel spreadsheet, an electronic sort can be made, tying in the AutoCAD-generated site map to specific database fields. This link is accomplished by using a software overlay called the CadPLUS InfoEngine. The fields in the database include such things as, facility number, occupant program, population, facility age, facility quality, security level, etc. By selecting one or a combination of the fields, a map is generated, illustrating in color and hatch patterns the facilities or entities that are associated with the chosen fields. This process can be very useful for seeing the LLNL site at a glance, with highlighted characteristics for particular areas of interest. The generation of large complex graphics, using large-scale databases selectively, can be accomplished quickly. These extractions and links between data and graphics create a S.M.A.R.T. Map.

  8. Photocopy: Composite Map of Crossing Site by Daniel J. Mordell ...

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

    Photocopy: Composite Map of Crossing Site by Daniel J. Mordell from Canal Society of New York State. Bottoming Out: Useful and Interesting Notes Collected for Members of the Canal Society of New York State. Vol. 18-19. Syracuse, 1962. - Erie Canal (Enlarged), Schoharie Creek Aqueduct, Spanning Schoharie Creek, Fort Hunter, Montgomery County, NY

  9. Considerations for applying digital soil mapping to ecological sites

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recent advancements in the spatial prediction of soil properties are not currently being fully utilized for ecological studies. Linking digital soil mapping (DSM) with ecological sites (ES) has the potential to better land management decisions by improving spatial resolution and precision as well as...

  10. Antibody Recognition of Cancer-Related Gangliosides and Their Mimics Investigated Using in silico Site Mapping

    PubMed Central

    Agostino, Mark; Yuriev, Elizabeth; Ramsland, Paul A.

    2012-01-01

    Modified gangliosides may be overexpressed in certain types of cancer, thus, they are considered a valuable target in cancer immunotherapy. Structural knowledge of their interaction with antibodies is currently limited, due to the large size and high flexibility of these ligands. In this study, we apply our previously developed site mapping technique to investigate the recognition of cancer-related gangliosides by anti-ganglioside antibodies. The results reveal a potential ganglioside-binding motif in the four antibodies studied, suggesting the possibility of structural convergence in the anti-ganglioside immune response. The structural basis of the recognition of ganglioside-mimetic peptides is also investigated using site mapping and compared to ganglioside recognition. The peptides are shown to act as structural mimics of gangliosides by interacting with many of the same binding site residues as the cognate carbohydrate epitopes. These studies provide important clues as to the structural basis of immunological mimicry of carbohydrates. PMID:22536387

  11. National Environmental Policy Act source guide for the Hanford Site

    SciTech Connect

    Jansky, M.T.

    1998-09-30

    This Source Guide will assist those working with the National Environmental Policy Act (NEPA) of 1969 to become more familiar with the environmental assessments (EA) and environmental impact statements (EIS) that apply to specific activities and facilities on the Hanford Site. This document should help answer questions concerning NEPA coverage, history, processes, and the status of many of the buildings and units on and related to the Hanford Site. This document summarizes relevant EAs and EISs by briefly outlining the proposed action of each document and the decision made by the US Department of Energy (DOE) or its predecessor agencies, the US Atomic Energy Commission (AEC) and the US Energy Research and Development Administration (ERDA). The summary includes the proposed action alternatives and current status of the proposed action. If a decision officially was stated by the DOE, as in a finding of no significant impact (FONSI) or a record of decision (ROD), and the decision was located, a summary is provided. Not all federal decisions, such as FONSIs and RODS, can be found in the Federal Register (FR). For example, although significant large-action FONSIs can be found in the FR, some low-interest FONSIs might have been published elsewhere (i.e., local newspapers).

  12. Global Land Survey Impervious Mapping Project Web Site

    NASA Technical Reports Server (NTRS)

    DeColstoun, Eric Brown; Phillips, Jacqueline

    2014-01-01

    The Global Land Survey Impervious Mapping Project (GLS-IMP) aims to produce the first global maps of impervious cover at the 30m spatial resolution of Landsat. The project uses Global Land Survey (GLS) Landsat data as its base but incorporates training data generated from very high resolution commercial satellite data and using a Hierarchical segmentation program called Hseg. The web site contains general project information, a high level description of the science, examples of input and output data, as well as links to other relevant projects.

  13. Resource Conservation and Recovery Act Industrial Sites quality assurance project plan: Nevada Test Site, Nevada

    SciTech Connect

    Not Available

    1994-06-01

    This quality assurance project plan (QAPjP) describes the measures that shall be taken to ensure that the environmental data collected during characterization and closure activities of Resource Conservation and Recovery Act (RCRA) Industrial Sites at the Nevada Test Site (NTS) are meaningful, valid, defensible, and can be used to achieve project objectives. These activities are conducted by the US Department of Energy Nevada Operations Office (DOE/NV) under the Nevada Environmental Restoration (ER) Project. The Nevada ER Project consists of environmental restoration activities on the NTS, Tonopah Test Range, Nellis Air Force Range, and eight sites in five other states. The RCRA Industrial Sites subproject constitutes a component of the Nevada ER Project. Currently, this QAPjP is limited to the seven RCRA Industrial Sites identified within this document that are to be closed under an interim status and pertains to all field-investigation, analytical-laboratory, and data-review activities in support of these closures. The information presented here supplements the RCRA Industrial Sites Project Management Plan and is to be used in conjunction with the site-specific subproject sampling and analysis plans.

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

    PubMed

    Burrough, P A; Swindell, J

    1997-01-01

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

  15. Mapping Homing Endonuclease Cleavage Sites Using In Vitro Generated Protein

    PubMed Central

    Belfort, Marlene

    2015-01-01

    Mapping the precise position of endonucleolytic cleavage sites is a fundamental experimental technique used to describe the function of a homing endonuclease. However, these proteins are often recalcitrant to cloning and over-expression in biological systems because of toxicity induced by spurious DNA cleavage events. In this chapter we outline the steps to successfully express a homing endonuclease in vitro and use this product in nucleotide-resolution cleavage assays. PMID:24510259

  16. An in-depth map of polyadenylation sites in cancer.

    PubMed

    Lin, Yuefeng; Li, Zhihua; Ozsolak, Fatih; Kim, Sang Woo; Arango-Argoty, Gustavo; Liu, Teresa T; Tenenbaum, Scott A; Bailey, Timothy; Monaghan, A Paula; Milos, Patrice M; John, Bino

    2012-09-01

    We present a comprehensive map of over 1 million polyadenylation sites and quantify their usage in major cancers and tumor cell lines using direct RNA sequencing. We built the Expression and Polyadenylation Database to enable the visualization of the polyadenylation maps in various cancers and to facilitate the discovery of novel genes and gene isoforms that are potentially important to tumorigenesis. Analyses of polyadenylation sites indicate that a large fraction (∼30%) of mRNAs contain alternative polyadenylation sites in their 3' untranslated regions, independent of the cell type. The shortest 3' untranslated region isoforms are preferentially upregulated in cancer tissues, genome-wide. Candidate targets of alternative polyadenylation-mediated upregulation of short isoforms include POLR2K, and signaling cascades of cell-cell and cell-extracellular matrix contact, particularly involving regulators of Rho GTPases. Polyadenylation maps also helped to improve 3' untranslated region annotations and identify candidate regulatory marks such as sequence motifs, H3K36Me3 and Pabpc1 that are isoform dependent and occur in a position-specific manner. In summary, these results highlight the need to go beyond monitoring only the cumulative transcript levels for a gene, to separately analysing the expression of its RNA isoforms. PMID:22753024

  17. Cartographic Mapping of Mars Landing Sites: A Historical Perspective

    NASA Technical Reports Server (NTRS)

    Duxbury, Thomas C.

    2007-01-01

    Initial mapping of Mars began with the early Mariner 4, 6 and 7 flybys in the 1960's. Mariner 9 obtained the first global coverage of Mars in 1971. Viking Orbiters 1 and 2 added new and higher resolution global coverage. The US Geological Survey produced the first digital global cartographic map products in black and white and in color, the mosaicked digital image models (MDIMs). In 1989, the Phobos 88 mission added imaging as well as multispectral mapping of Mars in the equatorial region. The Mars Global Surveyor (MGS) added to the black and white and color global coverage. The most important development for Mars cartography occurred on MGS with its global coverage of Mars using the Mars Observer Laser Altimeter (MOL A) producing precision ground control in latitude, longitude and radius. The next version of the MDIM was produced at 230 m spatial resolution using MOLA precision cartographic control. The Mars Odyssey mission THEMIS instrument has completed its global infrared mapping of Mars at 100 m spatial resolution. The Mars Express mission is completing its global coverage of Mars in stereo at 100 m spatial resolution or better. MGS, Odyssey and Mars Express continue to provide limited surface coverage at the 1 to 20 m resolution. Currently the new Mars Reconnaissance Orbiter is producing images at the 10's of cm level. All of these datasets provide a rich and historic perspective of Mars covering nearly five decades and allow global cartographic map products to be produced in visual and infrared at the 100 m level with specialized cartographic maps being produced for landing sites at the meter or sub-meter spatial resolution level. This work was produced at the Jet Propulsion Laboratory, California Institute of Technology under contract to the National Aeronautics and Space Administration, NAS 7-7120.5d, within the NASA Mars Data Analysis Program and the MGS, Odyssey, Mars Express and MRO Participating Scientist Programs.

  18. Guidelines for Hanford Site implementation of the National Environmental Policy Act

    SciTech Connect

    King, S.E.

    1989-03-01

    The National Environmental Policy Act (NEPA) environmental review process is mandatory for federal agencies. Understanding and complying with NEPA is extremely important to successfully planning and implementing programs at the Hanford Site. This report is intended to help planners and decision makers understand NEPA by describing the NEPA process as it is outlined in NEPA, in regulations, and in guidance information. The requirements and guidance documents that set forth the NEPA process are discussed. Some of the major NEPA concepts and issues are also addressed. This report is intended to be used as a general road map through the maze of NEPA requirements and guidance to ensure that Hanford Site activities are conducted in compliance with NEPA. Enhanced knowledge of the NEPA process is expected to increase the ability of the Hanford Site to work with regulators, interested parties and the public to ensure that the potential environmental impacts of DOE activities are fully considered at the Hanford Site. In addition, an enhanced understanding of NEPA will help project and program managers to integrate NEPA compliance requirements with program planning. 43 refs., 6 figs., 3 tabs.

  19. Evaluation of Mapping Methodologies at a Legacy Test Site

    NASA Astrophysics Data System (ADS)

    Sussman, A. J.; Schultz-Fellenz, E. S.; Roback, R. C.; Kelley, R. E.; Drellack, S.; Reed, D.; Miller, E.; Cooper, D. I.; Sandoval, M.; Wang, R.

    2013-12-01

    On June 12th, 1985, a nuclear test with an announced yield between 20-150kt was detonated in rhyolitic lava in a vertical emplacement borehole at a depth of 608m below the surface. This test did not collapse to the surface and form a crater, but rather resulted in a subsurface collapse with more subtle surface expressions of deformation, providing an opportunity to evaluate the site using a number of surface mapping methodologies. The site was investigated over a two-year time span by several mapping teams. In order to determine the most time efficient and accurate approach for mapping post-shot surface features at a legacy test site, a number of different techniques were employed. The site was initially divided into four quarters, with teams applying various methodologies, techniques, and instrumentations to each quarter. Early methods included transect lines and site gridding with a Brunton pocket transit, flagging tape, measuring tape, and stakes; surveying using a hand-held personal GPS to locate observed features with an accuracy of × 5-10m; and extensive photo-documentation. More recent methods have incorporated the use of near survey grade GPS devices to allow careful location and mapping of surface features. Initially, gridding was employed along with the high resolution GPS surveys, but this was found to be time consuming and of little observational value. Raw visual observation (VOB) data included GPS coordinates for artifacts or features of interest, field notes, and photographs. A categorization system was used to organize the myriad of items, in order to aid in database searches and for visual presentation of findings. The collected data set was imported into a geographic information system (GIS) as points, lines, or polygons and overlain onto a digital color orthophoto map of the test site. Once these data were mapped, spectral data were collected using a high resolution field spectrometer. In addition to geo-locating the field observations with 10cm

  20. Site and Orbit Repeatabilities using Adaptive Mapping Functions

    NASA Astrophysics Data System (ADS)

    Desjardins, Camille; Gegout, Pascal; Soudarin, Laurent; Biancale, Richard; Perosanz, Felix

    2015-04-01

    The electromagnetic signals emitted by the satellite positioning systems travel at the speed of light in a straight line in a vacuum but are modified in their propagation through the neutral atmosphere by temporal and spatial changes of density, and composition and refractivity. These waves are slowed down and their trajectories are bent. This presentation summarizes the performances of the modeling of the tropospheric propagation by the ray tracing technique through the assimilations of the European Meteorological Centre (ECMWF) in the framework of realizing the geodetic reference frame. This goal is achieved by modeling the spatial variability of the propagation using the time variable three-dimensional physical parameters of the atmosphere. The tropospheric delays obtained by ray tracing in all directions throughout the meteorological model surrounding the geodetic site, are fitted by Adaptive Mapping Functions (AMF) parameterized by several tens of coefficients. The delays produced by the Horizon software are then experimented, kept unchanged or adjusted, when recovering a reference frame based on hundred sites using the GINS software. Without any adjustments of the tropospheric modeling, the subcentimetric performances of the AMF are demonstrated by the repeatability of sites positions and GPS satellites orbits. When some AMF coefficients are adjusted, the accuracy of orbits recovery in term of quadratic mean is 7 to 8 millimeters. This limit is imposed by the lack or deficiency of other models, such as non-tidal and tidal loading respectively. Hence the repeatability of the vertical position is not enhanced by changing the propagation model. At the contrary, the repeatability of the horizontal position of geodetic sites is greatly enhanced by accounting for the azimuthal variability provided by the realistic 3D shapes of the Atmosphere and the Earth and the rigorous interpolations of atmospheric parameters included in Adaptive Mapping Functions with respect

  1. A geostatistical approach to mapping site response spectral amplifications

    USGS Publications Warehouse

    Thompson, E.M.; Baise, L.G.; Kayen, R.E.; Tanaka, Y.; Tanaka, H.

    2010-01-01

    If quantitative estimates of the seismic properties do not exist at a location of interest then the site response spectral amplifications must be estimated from data collected at other locations. Currently, the most common approach employs correlations of site class with maps of surficial geology. Analogously, correlations of site class with topographic slope can be employed where the surficial geology is unknown. Our goal is to identify and validate a method to estimate site response with greater spatial resolution and accuracy for regions where additional effort is warranted. This method consists of three components: region-specific data collection, a spatial model for interpolating seismic properties, and a theoretical method for computing spectral amplifications from the interpolated seismic properties. We consider three spatial interpolation schemes: correlations with surficial geology, termed the geologic trend (GT), ordinary kriging (OK), and kriging with a trend (KT). We estimate the spectral amplifications from seismic properties using the square root of impedance method, thereby linking the frequency-dependent spectral amplifications to the depth-dependent seismic properties. Thus, the range of periods for which this method is applicable is limited by the depth of exploration. A dense survey of near-surface S-wave slowness (Ss) throughout Kobe, Japan shows that the geostatistical methods give more accurate estimates of Ss than the topographic slope and GT methods, and the OK and KT methods perform equally well. We prefer the KT model because it can be seamlessly integrated with geologic maps that cover larger regions. Empirical spectral amplifications show that the region-specific data achieve more accurate estimates of observed median short-period amplifications than the topographic slope method. ?? 2010 Elsevier B.V.

  2. Hanford Site National Environmental Policy Act (NEPA) characterization. Revision 10

    SciTech Connect

    Neitzel, D.A.; Fosmire, C.J.; Fowler, R.A.

    1998-09-01

    This document describes the US Department of Energy`s (DOE) Hanford Site environment and is numbered to correspond to the chapters where such information is presented in Hanford Site NEPA related documents. The document is intended to provide a consistent description of the Hanford Site environment for the many NEPA documents that are being prepared by contractors. The two chapters in this document (Chapters 4 and 6) are numbered this way to correspond to the chapters where such information is presented in environmental impact statements (EISs) and other Site-related NEPA or CERCLA documentation. Chapter 4.0 (Affected Environment) describes the Hanford Site environment, and includes information on climate and meteorology, geology, hydrology, ecology, cultural, archaeological and historical resources, socioeconomics, and noise. Chapter 6.0 (Statutory and Regulatory Requirements) describes applicable federal and state laws and regulations, DOE directives and permits, and environmental standards directly applicable to the NEPA documents on the Hanford Site.

  3. Hanford Site National Environmental Policy Act (NEPA) characterization. Revision 7

    SciTech Connect

    Cushing, C.E.; Baker, D.A.; Chamness, M.A.

    1995-09-01

    This seventh revision of the Hanford Site National Environmental Policy (NEPA) Characterization presents current environmental data regarding the Hanford Site and its immediate environs. This information is intended for use in preparing Site-related NEPA documentation. Chapter 4.0 summarizes up-to-date information on climate and meteorology, geology, hydrology, environmental monitoring, ecology, history and archaeology, socioeconomics, land use, and noise levels prepared by Pacific Northwest Laboratory (PNL) staff. More detailed data are available from reference sources cited or from the authors. Chapter 5.0 was not updated from the sixth revision (1994). It describes models, including their principal underlying assumptions, that are to be used in simulating realized or potential impacts from nuclear materials at the Hanford Site. Included are models of radionuclide transport in groundwater and atmospheric pathways, and of radiation dose to populations via all known pathways from known initial conditions. The updated Chapter 6.0 provides the preparer with the federal and state regulations, DOE Orders and permits, and environmental standards directly applicable to the NEPA documents on the Hanford Site, following the structure of Chapter 4.0. No conclusions or recommendations are given in this report. Rather, it is a compilation of information on the Hanford Site environment that can be used directly by Site contractors. This information can also be used by any interested individual seeking baseline data on the Hanford Site and its past activities by which to evaluate projected activities and their impacts.

  4. Hanford Site National Environmental Policy Act (NEPA) characterization. Revision 6

    SciTech Connect

    Cushing, C.E.; Baker, D.A.; Chamness, M.A.

    1994-08-01

    This sixth revision of the Hanford Site National Environmental Policy (NEPA) Characterization presents current environmental data regarding the Hanford Site and its immediate environs. This information is intended for use in preparing Site-related NEPA documentation. Chapter 4.0 summarizes up-to-date information on climate and meteorology, geology and hydrology, ecology, history and archaeology, socioeconomics, land use, and noise levels prepared by Pacific Northwest Laboratory (PNL) staff. More detailed data are available from reference sources cited or from the authors; Chapter 5.0 has been significantly updated from the fifth revision. It describes models, including their principal underlying assumptions, that are to be used in simulating realized or potential impacts from nuclear materials at the Hanford Site. Included are models of radionuclide transport in groundwater and atmospheric pathways, and of radiation dose to populations via all known pathways from known initial conditions; The updated Chapter 6.0 provides the preparer with the federal and state regulations, DOE orders and permits, and environmental standards directly applicable to the NEPA documents on the Hanford Site, following the structure of Chapter 4.0. No conclusions or recommendations are given in this report. Rather, it is a compilation of information on the Hanford Site environment that can be utilized directly by Site contractors. This information can also be used by any interested individual seeking baseline data on the Hanford Site and its past activities by which to evaluate projected activities and their impacts.

  5. Hanford Site National Environmental Policy Act (NEPA) Characterization. Revision 5

    SciTech Connect

    Cushing, C.E.

    1992-12-01

    This fifth revision of the Hanford Site National Environmental Policy (NEPA) Characterization presents current environmental data regarding the Hanford Site and its immediate environs. This information is intended for use in preparing Site-related NEPA documentation. Information is presented on climate and meteorology, geology and hydrology, ecology, history and archaeology, socioeconomics, land use, and noise levels, prepared by Pacific Northwest Laboratory (PNL) staff. Models are described that are to be used in simulating realized or potential impacts from nuclear materials at the Hanford Site. Included are models of radionuclide transport in groundwater and atmospheric pathways, and of radiation dose to populations via all known pathways from known initial conditions. Federal and state regulations, DOE orders and permits, and environmental standards directly applicable for the NEPA documents at the Hanford Site, are provided.

  6. Hanford Site National Environmental Policy Act (NEPA) Characterization

    SciTech Connect

    Cushing, C.E.

    1992-12-01

    This fifth revision of the Hanford Site National Environmental Policy (NEPA) Characterization presents current environmental data regarding the Hanford Site and its immediate environs. This information is intended for use in preparing Site-related NEPA documentation. Information is presented on climate and meteorology, geology and hydrology, ecology, history and archaeology, socioeconomics, land use, and noise levels, prepared by Pacific Northwest Laboratory (PNL) staff. Models are described that are to be used in simulating realized or potential impacts from nuclear materials at the Hanford Site. Included are models of radionuclide transport in groundwater and atmospheric pathways, and of radiation dose to populations via all known pathways from known initial conditions. Federal and state regulations, DOE orders and permits, and environmental standards directly applicable for the NEPA documents at the Hanford Site, are provided.

  7. Endonuclease recognition sites mapped on Zea mays chloroplast DNA

    PubMed Central

    Bedbrook, John R.; Bogorad, Lawrence

    1976-01-01

    The closed-circular DNA molecules of 85 × 106 daltons from Zea mays chloroplasts were isolated, digested with the restriction endonucleases Sal I, Bam I, and EcoRI, and the resulting fragments sized by agarose gel electrophoresis. A map of maize chloroplast DNA showing the relative location of all the Sal I recognition sequences and many of the Bam I and EcoRI recognition sites was determined. A DNA sequence representing approximately 15% of the Zea mays chloroplast genome is repeated. The two copies of this sequence are in an inverted orientation with respect to one another and are separated by a nonhomologous sequence representing approximately 10% of the genome length. The inverted repeats contain the genes for chloroplast ribosomal RNAs. Images PMID:16592373

  8. Hanford Site National Environmental Policy Act (NEPA) Characterization

    SciTech Connect

    Rohay, A.C.; Fosmire, C.J.; Neitzel, D.A.; Hoitink, D.J.; Harvey, D.W.; Antonio, E.J.; Wright, M.K.; Thorne, P.D.; Hendrickson, P.L.; Fowler, R.A.; Goodwin, S.M.; Poston, T.M.

    1999-09-28

    This document describes the US Department of Energy's (DOE) Hanford Site environment. It is updated each year and is intended to provide a consistent description of the Hanford Site environment for the many NEPA documents being prepared by DOE contractors. No conclusions or recommendations are provided. This year's report is the eleventh revision of the original document published in 1988 and is (until replaced by the 12th revision) the only version that is relevant for use in the preparation of Hanford NEPA; SEPA and CERCLA documents. The two chapters included in this document (Chapters 4 and 6) are numbered to correspond to the chapters where such information is presented in environmental impact statements (EISs) and other Site-related NEPA or CERCLA documentation. Chapter 4.0 (Affected Environment) describes Hanford Site climate and meteorology, geology, hydrology, ecology, cultural, archaeological and historical resources, socioeconomic; occupational safety, and noise. Sources for extensive tabular data related to these topics are provided in the chapter. Most subjects are divided into a general description of the characteristics of the Hanford Site, followed by site-specific information, where available, of the 100,200,300, and other Areas. This division allows the reader to go directly to those sections of particular interest. When specific information on each of these separate areas is not complete or available, the general Hanford Site description should be used. Chapter 6.0 (Statutory and Regulatory Requirements) is essentially a definitive NEPA Chapter 6.0, which describes applicable federal and state laws and regulations, DOE directives and permits, and environmental standards directly applicable to the NEPA documents on the Hanford Site. People preparing environmental assessments and EISs should also be cognizant of the document entitled ''Recommendations for the Preparation of Environmental Assessments and Environmental Impact Statements'' published by

  9. Hanford Site National Evnironmental Policy Act (NEPA) characterization

    SciTech Connect

    Cushing, C.E.

    1991-12-01

    This fourth revision of the Hanford Site National Environmental Policy (NEPA) Characterization presents current environmental data regarding the Hanford Site and its immediate environs. This information is intended for use in preparing Site-related NEPA documentation. In Chapter 4.0 are presented summations of up-to-date information about climate and meteorology, geology and hydrology, ecology, history and archaeology, socioeconomics, land use, and noise levels. Chapter 5.0 describes models, including their principal assumptions, that are to be used in simulating realized or potential impacts from nuclear materials at the Hanford Site. Included are models of radionuclides transport in groundwater and atmospheric pathways, and of radiation dose to populations via all known pathways from known initial conditions. Chapter 6.0 provides the preparer with the federal and state regulations, DOE orders and permits, and environmental standards directly applicable for environmental impact statements for the Hanford Site, following the structure Chapter 4.0. NO conclusions or recommendations are given in this report.

  10. Hanford Site National Evnironmental Policy Act (NEPA) characterization. Revision 4

    SciTech Connect

    Cushing, C.E.

    1991-12-01

    This fourth revision of the Hanford Site National Environmental Policy (NEPA) Characterization presents current environmental data regarding the Hanford Site and its immediate environs. This information is intended for use in preparing Site-related NEPA documentation. In Chapter 4.0 are presented summations of up-to-date information about climate and meteorology, geology and hydrology, ecology, history and archaeology, socioeconomics, land use, and noise levels. Chapter 5.0 describes models, including their principal assumptions, that are to be used in simulating realized or potential impacts from nuclear materials at the Hanford Site. Included are models of radionuclides transport in groundwater and atmospheric pathways, and of radiation dose to populations via all known pathways from known initial conditions. Chapter 6.0 provides the preparer with the federal and state regulations, DOE orders and permits, and environmental standards directly applicable for environmental impact statements for the Hanford Site, following the structure Chapter 4.0. NO conclusions or recommendations are given in this report.

  11. Federal Facility Compliance Act: Conceptual Site Treatment Plan for Lawrence Livermore National Laboratory, Livermore, California

    SciTech Connect

    Not Available

    1993-10-01

    The Department of Energy (DOE) is required by section 3021(b) of the Resource Conservation and Recovery Act (RCRA), as amended by the Federal Facility Compliance Act (the Act), to prepare plans describing the development of treatment capacities and technologies for treating mixed waste. The Act requires site treatment plans (STPs or plans) to be developed for each site at which DOE generates or stores mixed waste and submitted to the State or EPA for approval, approval with modification, or disapproval. The Lawrence Livermore National Laboratory (LLNL) Conceptual Site Treatment Plan (CSTP) is the preliminary version of the plan required by the Act and is being provided to California, the US Environmental Protection Agency (EPA), and others for review. A list of the other DOE sites preparing CSTPs is included in Appendix 1.1 of this document. Please note that Appendix 1.1 appears as Appendix A, pages A-1 and A-2 in this document.

  12. Magnetic mapping and interpretation of an archaeological site in Syria

    NASA Astrophysics Data System (ADS)

    khatib alkontar, Rozan AL; Munschy, Marc; Castel, Corinne; Quenet, Philippe

    2014-05-01

    Among the subsurface methods of exploration that have been developed to meet the new requirements of archaeological research, geophysical methods offer a very wide range of applications in the study of buried deposits. In their latest developments, the prospecting method based on the measurement of the magnetic field is particularly effective at very different types of sites, ranging from prehistoric times to the most recent. The measured magnetic field observed at a place and at a time, results from the vector sum of the main regional field, the effect of subsurface structures, local disturbances such as power lines, buildings, fences, and the diurnal variation (solar influence). The principle of the magnetic method is, from magnetic measurements on a flat plane above the prospected surface, to study the three-dimensional variations of magnetization producing the magnetic anomalies. The use of magnetic surveys for archaeological prospecting is a well-established and versatile technique, and wide ranges of data processing routines are often applied to further enhance acquired data or derive source parameters. The main purpose of this work was to acquire new magnetic data on the field and to propose quantitative interpretations of magnetic maps obtained on three archaeological sites of Bronze Age in Syria (Badiyah ANR program). More precisely, some results are presented concerning one of the three sites, the Tell Al-Rawda-site which corresponds to a circular city of Early Bronze Age with a radius of about 200 m. Several profiles are used to characterize magnetizations. A large portion of archaeological geophysical data are concerned primarily with identifying the location and spatial extent of buried remains, although the data collected are likely to contain further information relating to the depth and geometry of anomalous features. A simple magnetic model corresponding to rectangular structures uniformly magnetized associated to walls cannot explain the magnetic

  13. 78 FR 2363 - Notice of New Fee Site; Federal Lands Recreation Enhancement Act

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-11

    ... Forest Service Notice of New Fee Site; Federal Lands Recreation Enhancement Act AGENCY: Coronado National...-Arizona Recreation Resource Advisory Council (RRAC). Palisades Cabin is scheduled to become available for... Federal Recreation Lands Enhancement Act (Title VII, Pub. L. 108-447) directed the Secretary...

  14. Mapping of contamination at Savannah River Site FBWU by INEEL trolley

    SciTech Connect

    Carpenter, M.V.; Gehrke, R.J.; Helmer, R.G.; Josten, N.

    1998-01-01

    The Ford Building Waste Unit (FBWU) 643-11G is a Resource Conservation and Recovery Act/Comprehensive Environmental Response Compensation and Liability Act (RCRA/CERCLA) designated site at the Savannah River Site (SRS) in Aiken, South Carolina. Pre-Work Plan Characterization at the FBWU in May 1996 indicated that radiological contamination was present in surface and near surface soils and identified cesium-137, {sup 137}Cs, the unit specific contaminant, as being primarily in the top 15 cm of soil. The Idaho National Engineering and Environmental Laboratory (INEEL) sent the dig-face trolley system to SRS where it demonstrated its capability over a 6.1-m (20 ft.) x 9.6-m (30 ft.) area to rapidly map the contamination on-line with its large area plastic scintillation detector. Also, an extended-range (10 keV to 3 MeV) Ge detector was used at selected locations to identify and quantify the {sup 137}Cs contamination. The coordinate locations of each measurement acquired in either the scanning or fixed position mode was obtained with a survey system based on radial encoders. Topography measurements were also made during measurements to permit correction of field of view and activity concentrations for changes in the ground to detector distance.

  15. Site characterization plan: Yucca Mountain site, Nevada research and development area, Nevada: Consultation draft, Nuclear Waste Policy Act: Volume 2

    SciTech Connect

    1988-01-01

    The Yucca Mountain site in Nevada is one of three candidate sites for the first geologic repository for radioactive waste. On May 28, 1986, it was recommended for detailed study in a program of site characterization. This site characterization plan (SCP) has been prepared in accordance with the requirements of the Nuclear Waste Policy Act to summarize the information collected to date about the geologic conditions at the site; to describe the conceptual designs for the repository and the waste package and to present the plans for obtaining the geologic information necessary to demonstrate the suitability of the site for a repository, to design the repository and the waste package, to prepare an environmental impact statement, and to obtain from the US Nuclear Regulatory Commission (NRC) an authorization to construct the repository. Chapter 3 summarizes present knowledge of the regional and site hydrologic systems. The purpose of the information presented is to (1) describe the hydrology based on available literature and preliminary site-exploration activities that have been or are being performed and (2) provide information to be used to develop the hydrologic aspects of the planned site characterization program. Chapter 4 contains geochemical information about the Yucca Mountain site. The chapter references plan for continued collection of geochemical data as a part of the site characterization program. Chapter 4 describes and evaluates data on the existing climate and site meterology, and outlines the suggested procedures to be used in developing and validating methods to predict future climatic variation. 534 refs., 100 figs., 72 tabs.

  16. 77 FR 60375 - Notice of Proposed New Fee Sites; Federal Lands Recreation Enhancement Act

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-03

    ... Forest Service Notice of Proposed New Fee Sites; Federal Lands Recreation Enhancement Act AGENCY: Caribou... these recreation sites. The Al Taylor cabin recently came into Forest Service ownership. It is located... a Recreation Resource Advisory Committee. New fees would begin after April 2013. ADDRESSES:...

  17. Integrated Mapping and Imaging at a Legacy Test Site (Invited)

    NASA Astrophysics Data System (ADS)

    Sussman, A. J.; Schultz-Fellenz, E. S.; Kelley, R. E.; Sweeney, J. J.; Vigil, S.; DiBenedetto, J.; Chipman, V.

    2013-12-01

    A team of multi-disciplinary geoscientists was tasked to characterize and evaluate a legacy nuclear detonation site in order to develop research locations with the long-term goal of improving treaty monitoring, verification, and other national security applications. There was a test at the site of interest that was detonated on June 12, 1985 in a vertical emplacement borehole at a depth of 608m below the surface in rhyolites. With announced yield of 20-150 kt, the event did not collapse to the surface and form a crater, but rather experienced a subsurface collapse with more subtle surface expressions of deformation. This result provides the team with an opportunity to evaluate a number of surface and subsurface inspection technologies in a broad context. The team collected ground-based visual observation, ground penetrating radar, electromagnetic, ground-based and airborne LiDAR, ground-based and airborne hyperspectral, gravity and magnetics, dc and induction electrical methods, and active seismic data during field campaigns in the summers of 2012 and 2013. Detection of features was performed using various approaches that were assessed for accuracy, efficiency and diversity of target features. For example, whereas the primary target of the ground-based visual observation survey was to map the surface features, the target of the gravity survey was to attempt the detection of a possible subsurface collapse zone which might be located as little as 200 meters below the surface. The datasets from surveys described above are integrated into a geographical information system (GIS) database for analysis and visualization. Other presentations during this session provide further details as to some of the work conducted. Work by Los Alamos National Laboratory and Lawrence Livermore National Laboratory was sponsored by the National Nuclear Security Administration Award No. DE-AC52-06NA25946/NST10-NCNS-PD00. Work by National Security Technologies, LLC, was performed under

  18. COPPA (Children's Online Privacy Protection Act): The First Year--A Survey of Sites. A Report on Web Site Compliance.

    ERIC Educational Resources Information Center

    Center for Media Education, Washington, DC.

    The Children's Online Privacy Protection Act (COPPA) went into effect on April 21, 2000. The first Federal online privacy law, COPPA regulates the collection, use, and disclosure by commercial Web sites and online services of personally identifiable information from children under age 13. To mark the first anniversary of COPPA's implementation, a…

  19. Federal Facilities Compliance Act, Draft Site Treatment Plan: Background Volume, Part 2, Volume 1

    SciTech Connect

    1994-08-31

    This Draft Site Treatment Plan was prepared by Ames Laboratory to meet the requirements of the Federal Facilities Compliance Act. Topics discussed include: purpose and scope of the plan; site history and mission; draft plant organization; waste minimization; waste characterization; preferred option selection process; technology for treating low-level radioactive wastes and TRU wastes; future generation of mixed waste streams; funding; and process for evaluating disposal issues in support of the site treatment plan.

  20. 2013 Annual Site Inspection and Monitoring Report for Uranium Mill Tailings Radiation Control Act Title I Disposal Sites

    SciTech Connect

    None, None

    2014-03-01

    This report, in fulfillment of a license requirement, presents the results of long-term surveillance and maintenance activities conducted by the U.S. Department of Energy (DOE) Office of Legacy Management (LM) in 2013 at 19 uranium mill tailings disposal sites established under Title I of the Uranium Mill Tailings Radiation Control Act (UMTRCA) of 1978.1 These activities verified that the UMTRCA Title I disposal sites remain in compliance with license requirements. DOE operates 18 UMTRCA Title I sites under a general license granted by the U.S. Nuclear Regulatory Commission (NRC) in accordance with Title 10 Code of Federal Regulations Part 40.27 (10 CFR 40.27). As required under the general license, a long-term surveillance plan (LTSP) for each site was prepared by DOE and accepted by NRC. The Grand Junction, Colorado, Disposal Site, one of the 19 Title I sites, will not be included under the general license until the open, operating portion of the cell is closed. The open portion will be closed either when it is filled or in 2023. This site is inspected in accordance with an interim LTSP. Long-term surveillance and maintenance services for these disposal sites include inspecting and maintaining the sites; monitoring environmental media and institutional controls; conducting any necessary corrective actions; and performing administrative, records, stakeholder relations, and other regulatory stewardship functions. Annual site inspections and monitoring are conducted in accordance with site-specific LTSPs and procedures established by DOE to comply with license requirements. Each site inspection is performed to verify the integrity of visible features at the site; to identify changes or new conditions that may affect the long-term performance of the site; and to determine the need, if any, for maintenance, follow-up or contingency inspections, or corrective action in accordance with the LTSP. LTSPs and site compliance reports are available on the Internet at http://www.lm.doe.gov/.

  1. The Atacama Cosmology Telescope (ACT): Beam Profiles and First SZ Cluster Maps

    NASA Technical Reports Server (NTRS)

    Hincks, A. D.; Acquaviva, V.; Ade, P. A.; Aguirre, P.; Amiri, M.; Appel, J. W.; Barrientos, L. F.; Battistelli, E. S.; Bond, J. R.; Brown, B.; Burger, B.; Chervenak, J.; Das, S.; Devlin, M. J.; Dicker, S. R.; Doriese, W. B.; Dunkley, J.; Duenner, R.; Essinger-Hileman, T.; Fisher, R. P.; Fowler, J. W.; Hajian, A.; Halpern, M.; Hasselfield, M.; Wollack, Ed

    2010-01-01

    The Atacama Cosmology Telescope (ACT) is currently observing the cosmic microwave background with arcminute resolution at 148 GHz, 218 GHz, and 277 GHz, In this paper, we present ACT's first results. Data have been analyzed using a maximum-likelihood map-making method which uses B-splines to model and remove the atmospheric signal. It has been used to make high-precision beam maps from which we determine the experiment's window functions, This beam information directly impacts all subsequent analyses of the data. We also used the method to map a sample of galaxy clusters via the Sunyaev-Ze1'dovich (SZ) effect, and show five clusters previously detected with X-ray or SZ observations, We provide integrated Compton-y measurements for each cluster. Of particular interest is our detection of the z = 0.44 component of A3128 and our current non-detection of the low-redshift part, providing strong evidence that the further cluster is more massive as suggested by X-ray measurements. This is a compelling example of the redshift-independent mass selection of the SZ effect.

  2. THE ATACAMA COSMOLOGY TELESCOPE (ACT): BEAM PROFILES AND FIRST SZ CLUSTER MAPS

    SciTech Connect

    Hincks, A. D.; Appel, J. W.; Das, S.; Dunkley, J.; Essinger-Hileman, T.; Fisher, R. P.; Acquaviva, V.; Ade, P. A. R.; Aguirre, P.; Barrientos, L. F.; Duenner, R.; Amiri, M.; Battistelli, E. S.; Burger, B.; Bond, J. R.; Brown, B.; Chervenak, J.; Doriese, W. B.

    2010-12-15

    The Atacama Cosmology Telescope (ACT) is currently observing the cosmic microwave background with arcminute resolution at 148 GHz, 218 GHz, and 277 GHz. In this paper, we present ACT's first results. Data have been analyzed using a maximum-likelihood map-making method which uses B-splines to model and remove the atmospheric signal. It has been used to make high-precision beam maps from which we determine the experiment's window functions. This beam information directly impacts all subsequent analyses of the data. We also used the method to map a sample of galaxy clusters via the Sunyaev-Zel'dovich (SZ) effect and show five clusters previously detected with X-ray or SZ observations. We provide integrated Compton-y measurements for each cluster. Of particular interest is our detection of the z = 0.44 component of A3128 and our current non-detection of the low-redshift part, providing strong evidence that the further cluster is more massive as suggested by X-ray measurements. This is a compelling example of the redshift-independent mass selection of the SZ effect.

  3. Site characterization plan: Yucca Mountain site, Nevada research and development area, Nevada: Consultation draft, Nuclear Waste Policy Act: Volume 4

    SciTech Connect

    1988-01-01

    The Yucca Mountain site in Nevada is one of three candidate sites for the first geologic repository for radioactive waste. On May 28, 1986, it was recommended and approved by the President for detailed study in a program of site characterization. This site characterization plan (SCP) has been prepared in accordance with the requirements of the Nuclear Waste Policy Act to summarize the information collected to date about the geologic conditions at the site; to describe the conceptual designs for the repository and the waste package; and to present the plans for obtaining the geologic information necessary to demonstate the suitability of the site for a repository, to desin the repository and the waste package, to prepare an environmental impact statement, and to obtain from the US Nuclear Regulatory Commission (NRC) an authorization to construct the repository. This introduction begins with a brief section on the process for siting and developing a repository, followed by a discussion of the pertinent legislation and regulations. A description of site characterization is presented next; it describes the facilities to be constructed for the site characterization program and explains the principal activities to be conducted during the program. Finally, the purpose, content, organizing principles, and organization of this site characterization plan are outlined, and compliance with applicable regulations is discussed.

  4. Site characterization plan: Yucca Mountain site, Nevada research and development area, Nevada: Consultation draft, Nuclear Waste Policy Act: Volume 7

    SciTech Connect

    1988-01-01

    The Yucca Mountain site in Neavada is one of three candidate sites for the first geologic repository for radioactive waste. On May 28, 1986, it was recommended and approved for detailed study in a program of site characterization. This site characterization plan (SCP) has been prepared in accordance with the requirements of the Nuclear Waste Policy Act to summarize the information collected to date about the geologic conditions at the site;to describe the conceptual designs for the repository and the waste package;and to present the plans for obtaining hte geologic information necessary to demonstrate the suitability of the site for a repository, to design the repository and the waste package, to prepare and environmental impact statement, and to obtain from the US Nuclear Regulatory Commission (NRC) an authorization to construct the repository. This introduction begins with a brief section on the process for siting and developing a repository, followed by a discussion of the pertinent legislation and regulations. A description of site characterization is presented next;it describes the facilities to be constructed for the site characterization program and explains the principal activities to be conducted during the program. Finally, the purpose, content, organizing principles, and organization of this site characterization plan are outlined, and compliance with applicable regulations is discussed.

  5. Site characterization plan: Yucca Mountain site, Nevada research and development area, Nevada: Consultation draft, Nuclear Waste Policy Act

    SciTech Connect

    1988-01-01

    The Yucca Mountain site in Nevada is one of three candidate sites for the first geologic repository for radioactive waste. On May 28, 1986, it was recommended by the Secretary of Energy and approved by the President for detailed study in a program of site characterization. This site characterization plan (SCP) has been prepared by the US Department of Energy (DOE) in accordance with the requirements of the Nulcear Waste Policy Act to summarize the information collected to date about the geologic conditions at the site;to describe the conceptual designs for the repository and the waste package;and to present the plans for obtaining the geologic information necessary to demonstrate the suitability of the site for a repository, to design the repository and the waste package, to prepare an environmental impact statement, and to obtain from the US Nuclear Regulatory Commission (NRC) an authorization to construct the repository. This introduction begins with a brief section on the process for siting and developing a repository, followed by a discussion of the pertinent legislation and regulations. A description of site characterization is presented next;it describes the facilities to be constructed for the site characterization program and explains the principal activities to be conducted during the program. Finally, the purpose, content, organizing principles, and organization of the site characterization plan are oulined, and compliance with applicable regulations is discussed.

  6. Site characterization plan: Yucca Mountain site, Nevada research and development area, Nevada: Consultation draft, Nuclear Waste Policy Act: Volume 1

    SciTech Connect

    1988-01-01

    The Yucca Mountain site in Nevada is one of three candidate sites for the first geologic repository for radioactive waste. On May 28, 1986, it was recommended for detailed study in a program of site characterization. This site characterization plan (SCP) has been prepared in acordance with the requirements of the Nuclear Waste Policy Act to summarize the information collected to date about the geologic conditions at the site;to describe the conceptual designs for the repository and the waste package and to present the plans for obtaining the geologic information necessary to demonstrate the suitability of the site for a repository, to design the repository and the waste package, to prepare an environmental impact statement, and to obtain from the US Nuclear Regulatory Commission (NRC) an authorization to construct the repository. This introduction begins with a brief section on the process for siting and eveloping a repository, followed by a discussion of the pertinent legislation and regulations. A description of site characterization is presented next;it describes the facilities to be constructed for the site characterization program and explains the principal activities to be conducted during the program. Finally, the purpose, content, organizing prinicples, and organization of this site characterization plan are outlined, and compliance with applicable regulations is discussed. 880 refs., 130 figs., 25 tabs.

  7. Site characterization plan: Yucca Mountain site, Nevada research and development area, Nevada: Consultation draft, Nuclear Waste Policy Act: Volume 6

    SciTech Connect

    1988-01-01

    The Yucca Mountain site in Nevada is one of three candidate sites for the first geologic repository for radioactive waste. On May 28, 1986, it was recommended for detailed study in a program of site characterization. This site characterization plan (SCP) has been prepared in accordance with the requirements of the Nuclear Waste Policy Act to summarize the information collected to date about the geologic conditions at the site;to describe the conceptual designs for the repository and the waste package;and to present the plans for obtaining the geologic information necessary to demonstrate the suitability of the site for repository, to design the repository and the waste package, to prepare an environmental impact statement, and to obtain from the US Nuclear Regulatory Commission (NRC) an authorization to construct the repository. This introduction begins with a brief section on the process for siting and developing a repository, followed by a discussion of the pertinent legislation and regulations. A description of site characterization is presented next;it describes the facilities to be constructed for the site characterization program and explains the principal activities to be conducted during the program. Finally, the purpose, content, organizing principles, and organization of this site characterization plan are outlined, and compliance with applicable regulations is discussed.

  8. 2013 Annual Site Inspection and Monitoring Report for Uranium Mill Tailings Radiation Control Act Title II Disposal Sites

    SciTech Connect

    2013-11-01

    This report, in fulfillment of a license requirement, presents the results of long-term surveillance and maintenance activities conducted by the U.S. Department of Energy (DOE) Office of Legacy Management in 2013 at six uranium mill tailings disposal sites reclaimed under Title II of the Uranium Mill Tailings Radiation Control Act (UMTRCA) of 1978. These activities verified that the UMTRCA Title II disposal sites remain in compliance with license requirements. DOE manages six UMTRCA Title II disposal sites under a general license granted by the U.S. Nuclear Regulatory Commission (NRC) established at Title 10 Code of Federal Regulations Part 40.28. Reclamation and site transition activities continue at other sites, and DOE ultimately expects to manage approximately 27 Title II disposal sites. Long-term surveillance and maintenance activities and services for these disposal sites include inspecting and maintaining the sites; monitoring environmental media and institutional controls; conducting any necessary corrective action; and performing administrative, records, stakeholder services, and other regulatory functions. Annual site inspections and monitoring are conducted in accordance with site-specific long-term surveillance plans (LTSPs) and procedures established by DOE to comply with license requirements. Each site inspection is performed to verify the integrity of visible features at the site; to identify changes or new conditions that may affect the long-term performance of the site; and to determine the need, if any, for maintenance, follow-up inspections, or corrective action. LTSPs and site compliance reports are available online at http://www.lm.doe.gov

  9. Using Temporal Modulation Sensitivity to Select Stimulation Sites for Processor MAPs in Cochlear Implant Listeners

    PubMed Central

    Garadat, Soha N.; Zwolan, Teresa A.; Pfingst, Bryan E.

    2013-01-01

    Previous studies in our laboratory showed that temporal acuity as assessed by modulation detection thresholds (MDTs) varied across activation sites and that this site-to-site variability was subject specific. Using two 10-channel MAPs, the previous experiments showed that processor MAPs that had better across-site mean (ASM) MDTs yielded better speech recognition than MAPs with poorer ASM MDTs tested in the same subject. The current study extends our earlier work on developing more optimal fitting strategies to test the feasibility of using a site-selection approach in the clinical domain. This study examined the hypothesis that revising the clinical speech processor MAP for cochlear implant (CI) recipients by turning off selected sites that have poorer temporal acuity and reallocating frequencies to the remaining electrodes would lead to improved speech recognition. Twelve CI recipients participated in the experiments. We found that site selection procedure based on MDTs in the presence of a masker resulted in improved performance on consonant recognition and recognition of sentences in noise. In contrast, vowel recognition was poorer with the experimental MAP than with the clinical MAP, possibly due to reduced spectral resolution when sites were removed from the experimental MAP. Overall, these results suggest a promising path for improving recipient outcomes using personalized processor-fitting strategies based on a psychophysical measure of temporal acuity. PMID:23881208

  10. ChIP-seq Mapping of Distant-Acting Enhancers and Their In Vivo Activities

    SciTech Connect

    Visel, Axel; Pennacchio, Len A.

    2011-06-01

    The genomic location and function of most distant-acting transcriptional enhancers in the human genome remains unknown We performed ChIP-seq for various transcriptional coactivator proteins (such as p300) directly from different embryonic mouse tissues, identifying thousands of binding sitesTransgenic mouse experiments show that p300 and other co-activator peaks are highly predictive of genomic location AND tissue-specific activity patterns of distant-acting enhancersMost enhancers are active only in one or very few tissues Genomic location of tissue-specific p300 peaks correlates with tissue-specific expression of nearby genes Most binding sites are conserved, but the global degree of conservation varies between tissues

  11. Evolutionary computation method for pattern recognition of cis-acting sites.

    PubMed

    Howard, Daniel; Benson, Karl

    2003-11-01

    This paper develops an evolutionary method that learns inductively to recognize the makeup and the position of very short consensus sequences, cis-acting sites, which are a typical feature of promoters in genomes. The method combines a Finite State Automata (FSA) and Genetic Programming (GP) to discover candidate promoter sequences in primary sequence data. An experiment measures the success of the method for promoter prediction in the human genome. This class of method can take large base pair jumps and this may enable it to process very long genomic sequences to discover gene specific cis-acting sites, and genes which are regulated together. PMID:14642656

  12. Developing a map of geologically defined site-condition categories for California

    USGS Publications Warehouse

    Wills, C.J.; Clahan, K.B.

    2006-01-01

    Consideration of site conditions is a vital step in analyzing and predicting earthquake ground motion. The importance of amplification by soil conditions has long been recognized, but though many seismic-instrument sites have been characterized by their geologic conditions, there has been no consistent, simple classification applied to all sites. As classification of sites by shear-wave velocity has become more common, the need to go back and provide a simple uniform classification for all stations has become apparent. Within the Pacific Earthquake Engineering Research Center's Next Generation Attenuation equation project, developers of attenuation equations recognized the need to consider site conditions and asked that the California Geological Survey provide site conditions information for all stations that have recorded earthquake ground motion in California. To provide these estimates, we sorted the available shear-wave velocity data by geologic unit, generalized the geologic units, and prepared a map so that we could use the extent of the map units to transfer the velocity characteristics from the sites where they were measured to sites on the same or similar materials. This new map is different from the California Geological Survey "preliminary site-conditions map of California" in that 19 geologically defined categories are used, rather than National Earthquake Hazards Reduction Program categories. Although this map does not yet cover all of California, when completed it may provide a basis for more precise consideration of site conditions in ground-motion calculations.

  13. Resource Conservation and Recovery Act industrial site environmental restoration site characterization report - area 6 steam cleaning effluent ponds

    SciTech Connect

    1996-09-01

    The Area 6 North and South Steam Cleaning Effluent Ponds (SCEPs) are historic disposal units located at the Nevada Test Site (NTS) in Nye County, Nevada. The NTS is operated by the U.S. Department of Energy, Nevada Operations Office (DOE/NV) which has been required by the Nevada Division of Environmental Protection (NDEP) to characterize the site under the requirements of the Resource Conservation and Recovery Act (RCRA) Part B Permit for the NTS and Title 40 Code of Federal Regulations, Part 265.

  14. Finishing Strong in 2011: The Recovery Act at Work at Savannah River Site

    ScienceCinema

    None

    2016-07-12

    American Recovery and Reinvestment Act's highlights and accomplishments for 2011 projects. Covers the latest technology and robotics used for waste management. This video is an overview of the success ARRA brought to the Savannah River Site, the environment, the econonmy, and the surrounding communities.

  15. Finishing Strong in 2011: The Recovery Act at Work at Savannah River Site

    SciTech Connect

    2011-01-01

    American Recovery and Reinvestment Act's highlights and accomplishments for 2011 projects. Covers the latest technology and robotics used for waste management. This video is an overview of the success ARRA brought to the Savannah River Site, the environment, the econonmy, and the surrounding communities.

  16. Spatial Data Mining Toolbox for Mapping Suitability of Landfill Sites Using Neural Networks

    NASA Astrophysics Data System (ADS)

    Abujayyab, S. K. M.; Ahamad, M. S. S.; Yahya, A. S.; Aziz, H. A.

    2016-09-01

    Mapping the suitability of landfill sites is a complex field and is involved with multidiscipline. The purpose of this research is to create an ArcGIS spatial data mining toolbox for mapping the suitability of landfill sites at a regional scale using neural networks. The toolbox is constructed from six sub-tools to prepare, train, and process data. The employment of the toolbox is straightforward. The multilayer perceptron (MLP) neural networks structure with a backpropagation learning algorithm is used. The dataset is mined from the north states in Malaysia. A total of 14 criteria are utilized to build the training dataset. The toolbox provides a platform for decision makers to implement neural networks for mapping the suitability of landfill sites in the ArcGIS environment. The result shows the ability of the toolbox to produce suitability maps for landfill sites.

  17. Interactive NCORP Map Details Community Research Sites | Division of Cancer Prevention

    Cancer.gov

    An interactive map of the NCI Community Oncology Research Program (NCORP) with detailed information on hundreds of community sites that take part in clinical trials is available on the NCORP website. |

  18. Mapping epitopes and antigenicity by site-directed masking

    NASA Astrophysics Data System (ADS)

    Paus, Didrik; Winter, Greg

    2006-06-01

    Here we describe a method for mapping the binding of antibodies to the surface of a folded antigen. We first created a panel of mutant antigens (-lactamase) in which single surface-exposed residues were mutated to cysteine. We then chemically tethered the cysteine residues to a solid phase, thereby masking a surface patch centered on each cysteine residue and blocking the binding of antibodies to this region of the surface. By these means we mapped the epitopes of several mAbs directed to -lactamase. Furthermore, by depleting samples of polyclonal antisera to the masked antigens and measuring the binding of each depleted sample of antisera to unmasked antigen, we mapped the antigenicity of 23 different epitopes. After immunization of mice and rabbits with -lactamase in Freund's adjuvant, we found that the antisera reacted with both native and denatured antigen and that the antibody response was mainly directed to an exposed and flexible loop region of the native antigen. By contrast, after immunization in PBS, we found that the antisera reacted only weakly with denatured antigen and that the antibody response was more evenly distributed over the antigenic surface. We suggest that denatured antigen (created during emulsification in Freund's adjuvant) elicits antibodies that bind mainly to the flexible regions of the native protein and that this explains the correlation between antigenicity and backbone flexibility. Denaturation of antigen during vaccination or natural infections would therefore be expected to focus the antibody response to the flexible loops. backbone flexibility | Freund's adjuvant | conformational epitope | antisera

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

    SciTech Connect

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

    1995-12-31

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

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

    NASA Astrophysics Data System (ADS)

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

    1995-04-01

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

  1. Orbital-science investigation: Part K: geologic sketch map of the candidate Proclus Apollo landing site

    USGS Publications Warehouse

    Lucchitta, Baerbel Koesters

    1972-01-01

    A panoramic camera frame (fig. 25-69) was used as the base for a geologic sketch map (fig. 25-70) of an area near Proclus Crater. The map was prepared to investigate the usefulness of the Apollo 15 panoramic camera photography in large-scale geologic mapping and to assess the geologic value of this area as a potential Apollo landing site. The area is being considered as a landing site because of the availability of smooth plains terrain and because of the scientific value of investigating plains materials, dark halo craters, and ancient rocks that may be present in the Proclus ray material.

  2. Soils maps supplement to soil moisture ground truth, Lafayette, Indiana, site St. Charles, Missouri, site

    NASA Technical Reports Server (NTRS)

    Jones, E. B.; Olt, S. E.

    1975-01-01

    A compilation of soils information obtained as the result of a library search of data on the Lafayette, Indiana, site and St. Charles, Missouri, site is presented. Soils data for the Lafayette, Indiana, site are shown in Plates 1 and 2; and soils data for the St. Charles, Missouri, site are shown in Plates 3 and 4.

  3. Digital geologic map database of the Nevada Test Site area, Nevada

    USGS Publications Warehouse

    Wahl, R.R.; Sawyer, D.A.; Minor, S.A.; Carr, M.D.; Cole, J.C.; Swadley, W.C.; Laczniak, R.J.; Warren, R.G.; Green, K.S.; Engle, C.M.

    1997-01-01

    Forty years of geologic investigations at the Nevada Test Site (NTS) have been digitized. These data include all geologic information that: (1) has been collected, and (2) can be represented on a map within the map borders at the map scale is included in the map digital coverages. The following coverages are included with this dataset: Coverage Type Description geolpoly Polygon Geologic outcrops geolflts line Fault traces geolatts Point Bedding attitudes, etc. geolcald line Caldera boundaries geollins line Interpreted lineaments geolmeta line Metamorphic gradients The above coverages are attributed with numeric values and interpreted information. The entity files documented below show the data associated with each coverage.

  4. Digital geologic map database of the Nevada Test Site area, Nevada

    SciTech Connect

    Wahl, Ronald R.; Sawyer, David A.; Minor, Scott A.; Carr, Michael D.; Cole, James C.; Swadley, W.C.; Laczniak, Randell J.; Warren, Richard G.; Green, Katryn S.; Engle, Colin M.

    1997-09-09

    Forty years of geologic investigations at the Nevada Test Site (NTS) have been digitized. These data include all geologic information that: (1) has been collected, and (2) can be represented on a map within the map borders at the map scale is included in the map digital coverages. The following coverages are included with this dataset: Coverage Type Description geolpoly Polygon Geologic outcrops geolflts line Fault traces geolatts Point Bedding attitudes, etc. geolcald line Caldera boundaries geollins line Interpreted lineaments geolmeta line Metamorphic gradients. The above coverages are attributed with numeric values and interpreted information. The entity files documented below show the data associated with each coverage.

  5. Communication: Quantitative multi-site frequency maps for amide I vibrational spectroscopy

    SciTech Connect

    Reppert, Mike; Tokmakoff, Andrei

    2015-08-14

    An accurate method for predicting the amide I vibrational spectrum of a given protein structure has been sought for many years. Significant progress has been made recently by sampling structures from molecular dynamics simulations and mapping local electrostatic variables onto the frequencies of individual amide bonds. Agreement with experiment, however, has remained largely qualitative. Previously, we used dipeptide fragments and isotope-labeled constructs of the protein G mimic NuG2b as experimental standards for developing and testing amide I frequency maps. Here, we combine these datasets to test different frequency-map models and develop a novel method to produce an optimized four-site potential (4P) map based on the CHARMM27 force field. Together with a charge correction for glycine residues, the optimized map accurately describes both experimental datasets, with average frequency errors of 2–3 cm{sup −1}. This 4P map is shown to be convertible to a three-site field map which provides equivalent performance, highlighting the viability of both field- and potential-based maps for amide I spectral modeling. The use of multiple sampling points for local electrostatics is found to be essential for accurate map performance.

  6. Complete Bouguer gravity map of the Nevada Test Site and vicinity, Nevada

    SciTech Connect

    Healey, D.L.; Harris, R.N.; Ponce, D.A.; Oliver, H.W.

    1987-12-31

    About 15,000 gravity stations were used to create the gravity map. Gravity studies at the Nevada Test Site were undertaken to help locate geologically favorable areas for underground nuclear tests and to help characterize potential high-level nuclear waste storage sites. 48 refs. (TEM)

  7. Halogenated naphthyl methoxy piperidines for mapping serotonin transporter sites

    DOEpatents

    Goodman, Mark M.; Faraj, Bahjat

    1999-01-01

    Halogenated naphthyl methoxy piperidines having a strong affinity for the serotonin transporter are disclosed. Those compounds can be labeled with positron-emitting and/or gamma emitting halogen isotopes by a late step synthesis that maximizes the useable lifeterm of the label. The labeled compounds are useful for localizing serotonin transporter sites by positron emission tomography and/or single photon emission computed tomography.

  8. Halogenated naphthyl methoxy piperidines for mapping serotonin transporter sites

    DOEpatents

    Goodman, M.M.; Faraj, B.

    1999-07-06

    Halogenated naphthyl methoxy piperidines having a strong affinity for the serotonin transporter are disclosed. Those compounds can be labeled with positron-emitting and/or gamma emitting halogen isotopes by a late step synthesis that maximizes the useable lifeterm of the label. The labeled compounds are useful for localizing serotonin transporter sites by positron emission tomography and/or single photon emission computed tomography.

  9. Comparison of Kriging and coKriging for soil contamination mapping in abandoned mine sites

    NASA Astrophysics Data System (ADS)

    Lee, Hyeongyu; Choi, Yosoon

    2015-04-01

    Soil contamination mapping around abandoned mines is an important task for the planning and design of mine reclamation. This study compared the ordinary Kriging and the co-Kriging methods for the soil contamination mapping in abandoned mine sites. Four approaches were conducted as follows: (1) soil contamination mapping using the ordinary Kriging and Inductively Coupled Plasma (ICP) data only; (2) soil contamination mapping using the ordinary Kriging and Portable X-Ray Fluorescence (PXRF) data only; (3) soil contamination mapping using the ordinary Kriging and integrated data from ICP and PXRF; and (4) soil contamination mapping using the co-Kriging and integrated data from ICP and PXRF. Results indicate that the approach 3 provides substantial improvements over other three approaches including a more reasonable spatial pattern of soil contamination and reduction in the error of its estimates.

  10. 75 FR 2850 - Notice of Proposed New Fee Sites; Federal Lands Recreation Enhancement Act, (Title VIII, Pub. L...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-19

    ... Forest Service Notice of Proposed New Fee Sites; Federal Lands Recreation Enhancement Act, (Title VIII... recreation sites. All sites have recently been reconstructed or amenities are being added to improve services... continued operation and maintenance of these recreation sites. Moss Springs Guard Station will be...

  11. Ultrastructural nonisotopic mapping of nucleolar transcription sites in onion protoplasts.

    PubMed

    Melcák, I; Risueño, M C; Raska, I

    1996-01-01

    The post- and preembedding ultrastructural localization of transcribing rRNA genes has been carried out in nucleoli of permeabilized onion growing root tip protoplasts by means of the nonisotopic bromouridine method. By means of both post- and preembedding approaches, major synthetic sites were identified with morphologically distinct subdomains of dense fibrillar components, with some signal also being associated with nucleolar fibrillar centers and vacuoles. Moreover, labeled medusoid fibrils within distinct domains seen in Lowicryl thin sections likely represent the morphological correlate of transcribing nucleolar genes. PMID:8812981

  12. 28 CFR Appendix C to Part 79 - Radiation Exposure Compensation Act Offset Worksheet-On Site Participants

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 28 Judicial Administration 2 2011-07-01 2011-07-01 false Radiation Exposure Compensation Act... JUSTICE (CONTINUED) CLAIMS UNDER THE RADIATION EXPOSURE COMPENSATION ACT Pt. 79, App. C Appendix C to Part 79—Radiation Exposure Compensation Act Offset Worksheet—On Site Participants Radiation...

  13. 28 CFR Appendix C to Part 79 - Radiation Exposure Compensation Act Offset Worksheet-On Site Participants

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 28 Judicial Administration 2 2014-07-01 2014-07-01 false Radiation Exposure Compensation Act... JUSTICE (CONTINUED) CLAIMS UNDER THE RADIATION EXPOSURE COMPENSATION ACT Pt. 79, App. C Appendix C to Part 79—Radiation Exposure Compensation Act Offset Worksheet—On Site Participants Radiation...

  14. 28 CFR Appendix C to Part 79 - Radiation Exposure Compensation Act Offset Worksheet-On Site Participants

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 28 Judicial Administration 2 2012-07-01 2012-07-01 false Radiation Exposure Compensation Act... JUSTICE (CONTINUED) CLAIMS UNDER THE RADIATION EXPOSURE COMPENSATION ACT Pt. 79, App. C Appendix C to Part 79—Radiation Exposure Compensation Act Offset Worksheet—On Site Participants Radiation...

  15. AthaMap: from in silico data to real transcription factor binding sites.

    PubMed

    Bülow, Lorenz; Steffens, Nils Ole; Galuschka, Claudia; Schindler, Martin; Hehl, Reinhard

    2006-01-01

    AthaMap generates a map for cis-regulatory sequences for the whole Arabidopsis thaliana genome. AthaMap was initially developed by matrix-based detection of putative transcription factor binding sites (TFBS) mostly determined from random binding site selection experiments. Now, also experimentally verified TFBS have been included for 48 different Arabidopsis thaliana transcription factors (TF). Based on these sequences, 89,416 very similar putative TFBS were determined within the genome of A. thaliana and annotated to AthaMap. Matrix- and single sequence-based binding sites can be included in colocalization analysis for the identification of combinatorial cis-regulatory elements. As an example, putative target genes of the WRKY18 transcription factor that is involved in plant-pathogen interaction were determined. New functions of AthaMap include descriptions for all annotated Arabidopsis thaliana genes and direct links to TAIR, TIGR and MIPS. Transcription factors used in the binding site determination are linked to TAIR and TRANSFAC databases. AthaMap is freely available at http://www.athamap.de. PMID:16922688

  16. Site characterization plan: Yucca Mountain site, Nevada research and development area, Nevada: Consultation draft, Nuclear Waste Policy Act

    SciTech Connect

    1988-01-01

    Chapter six describes the basis for facility design, the completed facility conceptual design, the completed analytical work relating to the resolution of design issues, and future design-related work. The basis for design and the conceptual design information presented in this chapter meet the requirements of the Nuclear Waste Policy Act of 1982, for a conceptual repository design that takes into account site-specific requirements. This information is presented to permit a critical evaluation of planned site characterization activities. Chapter seven describes waste package components, emplacement environment, design, and status of research and development that support the Nevada Nuclear Waste Storage Investigation (NNWSI) Project. The site characterization plan (SCP) discussion of waste package components is contained entirely within this chapter. The discussion of emplacement environment in this chapter is limited to considerations of the environment that influence, or which may influence, if perturbed, the waste packages and their performance (particularly hydrogeology, geochemistry, and borehole stability). The basis for conceptual waste package design as well as a description of the design is included in this chapter. The complete design will be reported in the advanced conceptual design (ACD) report and is not duplicated in the SCP. 367 refs., 173 figs., 68 tabs.

  17. Seismic hazard mapping of California incorporating spatial variability of site conditions

    USGS Publications Warehouse

    Kalkan, Erol; Wills, Chris J.; Branum, David M.

    2008-01-01

    The U.S. Geological Survey has recently released a 2008 version of the probabilistic National Seismic Hazard Maps. These maps plot the peak ground acceleration (PGA) and spectral acceleration (SA) ordinates at 0.2 and 1.0 sec with 2% and 10% probabilities of being exceeded in 50 years, corresponding to earthquake return periods of about 2,475 and 475 years, respectively. These acceleration levels were computed for uniform “firm rock” site conditions, i.e., 760 m/sec average shear-wave velocity in the upper 30 m, and therefore these maps do not show the potential spatial variability of ground motion associated with different site conditions, so we have combined the USGS National Seismic Hazard model with the California showing 17 generalized geologic units geologic units that can be defined by their shear-wave velocity (Wills and Clahan 2006), we regrouped these units into to 7 shear-wave velocities. At each shear-wave velocity value, a probabilistic seismic hazard map was generated for the entire state. By combining seismic hazard maps based on the 7 different shear-wave velocity values, a suite of seismic hazard maps was computed for California for 0.2 and 1.0 sec spectral ordinates at 2% probability of being exceeded in 50 years. The improved maps thus explicitly incorporate the site effects and their spatial variability on ground motion estimates. The SA at 1.0 sec map of seismic shaking potential for California has been now published as California Geological Survey Map Sheet 48, which is intended to be accessible and understandable to the general public.

  18. Satellite Power System (SPS) mapping of exclusion areas for rectenna sites

    NASA Technical Reports Server (NTRS)

    Blackburn, J. B., Jr.; Bavinger, B. A.

    1978-01-01

    The areas of the United States that were not available as potential sites for receiving antennas that are an integral part of the Satellite Power System concept are presented. Thirty-six variables with the potential to exclude the rectenna were mapped and coded in a computer. Some of these variables exclude a rectenna from locating within the area of its spatial influence, and other variables potentially exclude the rectenna. These maps of variables were assembled from existing data and were mapped on a grid system.

  19. Hazard maps of earthquake induced permanent displacements validated by site numerical simulation

    NASA Astrophysics Data System (ADS)

    Vessia, Giovanna; Pisano, Luca; Parise, Mario; Tromba, Giuseppe

    2016-04-01

    Hazard maps of seismically induced instability at the urban scale can be drawn by means of GIS spatial interpolation tools starting from (1) a Digital terrain model (DTM) and (2) geological and geotechnical hydro-mechanical site characterization. These maps are commonly related to a fixed return period of the natural phenomenon under study, or to a particular hazard scenario from the most significant past events. The maps could be used to guide the planning activity as well as the emergency actions, but the main limit of such maps is that typically no reliability analyses is performed. Spatial variability and uncertainties in subsoil properties, poor description of geomorphological evidence of active instability, and geometrical approximations and simplifications in DTMs, among the others, could be responsible for inaccurate maps. In this study, a possible method is proposed to control and increase the overall reliability of an hazard scenario map for earthquake-induced slope instability. The procedure can be summarized as follows: (1) GIS Statistical tools are used to improve the spatial distribution of the hydro-mechanical properties of the surface lithologies; (2) Hazard maps are drawn from the preceding information layer on both groundwater and mechanical properties of surficial deposits combined with seismic parameters propagated by means of Ground Motion Propagation Equations; (3) Point numerical stability analyses carried out by means of the Finite Element Method (e.g. Geostudio 2004) are performed to anchor hazard maps prediction to point quantitative analyses. These numerical analyses are used to generate a conversion scale from urban to point estimates in terms of permanent displacements. Although this conversion scale differs from case to case, it could be suggested as a general method to convert the results of large scale map analyses to site hazard assessment. In this study, the procedure is applied to the urban area of Castelfranci (Avellino province

  20. Multiscale site-response mapping: A case study of Parkfield, California

    USGS Publications Warehouse

    Thompson, E.M.; Baise, L.G.; Kayen, R.E.; Morgan, E.C.; Kaklamanos, J.

    2011-01-01

    The scale of previously proposed methods for mapping site-response ranges from global coverage down to individual urban regions. Typically, spatial coverage and accuracy are inversely related.We use the densely spaced strong-motion stations in Parkfield, California, to estimate the accuracy of different site-response mapping methods and demonstrate a method for integrating multiple site-response estimates from the site to the global scale. This method is simply a weighted mean of a suite of different estimates, where the weights are the inverse of the variance of the individual estimates. Thus, the dominant site-response model varies in space as a function of the accuracy of the different models. For mapping applications, site-response models should be judged in terms of both spatial coverage and the degree of correlation with observed amplifications. Performance varies with period, but in general the Parkfield data show that: (1) where a velocity profile is available, the square-rootof- impedance (SRI) method outperforms the measured VS30 (30 m divided by the S-wave travel time to 30 m depth) and (2) where velocity profiles are unavailable, the topographic slope method outperforms surficial geology for short periods, but geology outperforms slope at longer periods. We develop new equations to estimate site response from topographic slope, derived from the Next Generation Attenuation (NGA) database.

  1. 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

  2. The logical operator map identifies novel candidate markers for critical sites in patients with atrial fibrillation.

    PubMed

    Ravelli, Flavia; Masè, Michela; Cristoforetti, Alessandro; Marini, Massimiliano; Disertori, Marcello

    2014-08-01

    The identification of suitable markers for critical patterns during atrial fibrillation (AF) may be crucial to guide an effective ablation treatment. Single parameter maps, based on dominant frequency and complex fractionated electrograms, have been proposed as a tool for electrogram-guided ablation, however the specificity of these markers is debated. Experimental studies suggest that AF critical patterns may be identified on the basis of specific rate and organization features, where rapid organized and rapid fragmented activities characterize respectively localized sources and critical substrates. In this paper we introduce the logical operator map, a novel mapping tool for a point-by-point identification and localization of AF critical sites. Based on advanced signal and image processing techniques, the approach combines in a single map electrogram-derived rate and organization features with tomographic anatomical detail. The construction of the anatomically-detailed logical operator map is based on the time-domain estimation of atrial rate and organization in terms of cycle length and wave-similarity, the logical combination of these indexes to obtain suitable markers of critical sites, and the multimodal integration of electrophysiological and anatomical information by segmentation and registration techniques. Logical operator maps were constructed in 14 patients with persistent AF, showing the capability of the combined rate and organization markers to identify with high selectivity the subset of electrograms associated with localized sources and critical substrates. The precise anatomical localization of these critical sites revealed the confinement of rapid organized sources in the left atrium with organization and rate gradients towards the surrounding tissue, and the presence of rapid fragmented electrograms in proximity of the sources. By merging in a single map the most relevant electrophysiological and anatomical features of the AF process, the

  3. Impact of the resource conservation and recovery act on energy facility siting

    SciTech Connect

    Tevepaugh, C.W.

    1982-01-01

    The Resource Conservation and Recovery Act (RCRA) of 1976 is a multifaceted approach to the management of both solid and hazardous waste. The focus of this research is on the RCRA mandated proposed regulations for the siting of hazardous waste disposal facilities. This research is an analysis of the interactions among hazardous waste disposal facilities, energy supply technologies and land use issues. This study addresses the impact of RCRA hazardous waste regulations in a descriptive and exploratory manner. A literature and legislative review, interviews and letters of inquiry were synthesized to identify the relationship between RCRA hazardous waste regulations and the siting of selected energy supply technologies. The results of this synthesis were used to determine if and how RCRA influences national land use issues. It was found that the interaction between RCRA and the siting of hazardous waste disposal facilities required by energy supply technologies will impact national land use issues. All energy supply technologies reviewed generate hazardous waste. The siting of industrial functions such as energy supply facilities and hazardous waste disposal facilities will influence future development patterns. The micro-level impacts from the siting of hazardous waste disposal facilities will produce a ripple effect on land use with successive buffer zones developing around the facilities due to the interactive growth of the land use sectors.

  4. Improving a Synechocystis-based photoautotrophic chassis through systematic genome mapping and validation of neutral sites

    PubMed Central

    Pinto, Filipe; Pacheco, Catarina C.; Oliveira, Paulo; Montagud, Arnau; Landels, Andrew; Couto, Narciso; Wright, Phillip C.; Urchueguía, Javier F.; Tamagnini, Paula

    2015-01-01

    The use of microorganisms as cell factories frequently requires extensive molecular manipulation. Therefore, the identification of genomic neutral sites for the stable integration of ectopic DNA is required to ensure a successful outcome. Here we describe the genome mapping and validation of five neutral sites in the chromosome of Synechocystis sp. PCC 6803, foreseeing the use of this cyanobacterium as a photoautotrophic chassis. To evaluate the neutrality of these loci, insertion/deletion mutants were produced, and to assess their functionality, a synthetic green fluorescent reporter module was introduced. The constructed integrative vectors include a BioBrick-compatible multiple cloning site insulated by transcription terminators, constituting robust cloning interfaces for synthetic biology approaches. Moreover, Synechocystis mutants (chassis) ready to receive purpose-built synthetic modules/circuits are also available. This work presents a systematic approach to map and validate chromosomal neutral sites in cyanobacteria, and that can be extended to other organisms. PMID:26490728

  5. Improving a Synechocystis-based photoautotrophic chassis through systematic genome mapping and validation of neutral sites.

    PubMed

    Pinto, Filipe; Pacheco, Catarina C; Oliveira, Paulo; Montagud, Arnau; Landels, Andrew; Couto, Narciso; Wright, Phillip C; Urchueguía, Javier F; Tamagnini, Paula

    2015-12-01

    The use of microorganisms as cell factories frequently requires extensive molecular manipulation. Therefore, the identification of genomic neutral sites for the stable integration of ectopic DNA is required to ensure a successful outcome. Here we describe the genome mapping and validation of five neutral sites in the chromosome of Synechocystis sp. PCC 6803, foreseeing the use of this cyanobacterium as a photoautotrophic chassis. To evaluate the neutrality of these loci, insertion/deletion mutants were produced, and to assess their functionality, a synthetic green fluorescent reporter module was introduced. The constructed integrative vectors include a BioBrick-compatible multiple cloning site insulated by transcription terminators, constituting robust cloning interfaces for synthetic biology approaches. Moreover, Synechocystis mutants (chassis) ready to receive purpose-built synthetic modules/circuits are also available. This work presents a systematic approach to map and validate chromosomal neutral sites in cyanobacteria, and that can be extended to other organisms. PMID:26490728

  6. Vegetation inventory, mapping, and classification report, Fort Bowie National Historic Site

    USGS Publications Warehouse

    Studd, Sarah; Fallon, Elizabeth; Crumbacher, Laura; Drake, Sam; Villarreal, Miguel

    2013-01-01

    A vegetation mapping and characterization effort was conducted at Fort Bowie National Historic Site in 2008-10 by the Sonoran Desert Network office in collaboration with researchers from the Office of Arid lands studies, Remote Sensing Center at the University of Arizona. This vegetation mapping effort was completed under the National Park Service Vegetation Inventory program which aims to complete baseline mapping inventories at over 270 national park units. The vegetation map data was collected to provide park managers with a digital map product that met national standards of spatial and thematic accuracy, while also placing the vegetation into a regional and even national context. Work comprised of three major field phases 1) concurrent field-based classification data collection and mapping (map unit delineation), 2) development of vegetation community types at the National Vegetation Classification alliance or association level and 3) map accuracy assessment. Phase 1 was completed in late 2008 and early 2009. Community type descriptions were drafted to meet the then-current hierarchy (version 1) of the National Vegetation Classification System (NVCS) and these were applied to each of the mapped areas. This classification was developed from both plot level data and censused polygon data (map units) as this project was conducted as a concurrent mapping and classification effort. The third stage of accuracy assessment completed in the fall of 2010 consisted of a complete census of each map unit and was conducted almost entirely by park staff. Following accuracy assessment the map was amended where needed and final products were developed including this report, a digital map and full vegetation descriptions. Fort Bowie National Historic Site covers only 1000 acres yet has a relatively complex landscape, topography and geology. A total of 16 distinct communities were described and mapped at Fort Bowie NHS. These ranged from lush riparian woodlands lining the

  7. Oregon Magnetic and Gravity Maps and Data: A Web Site for Distribution of Data

    USGS Publications Warehouse

    Roberts, Carter W.; Kucks, Robert P.; Hill, Patricia L.

    2008-01-01

    This web site gives the results of a USGS project to acquire the best available, public-domain, aeromagnetic and gravity data in the United States and merge these data into uniform, composite grids for each State. The results for the State of Oregon are presented here on this site. Files of aeromagnetic and gravity grids and images are available for these States for downloading. In Oregon, 49 magnetic surveys have been knit together to form a single digital grid and map. Also, a complete Bouguer gravity anomaly grid and map was generated from 40,665 gravity station measurements in and adjacent to Oregon. In addition, a map shows the location of the aeromagnetic surveys, color-coded to the survey flight-line spacing. This project was supported by the Mineral Resource Program of the USGS.

  8. Hanford Site National Environmental Policy Act (NEPA) Characterization Report, Revision 17

    SciTech Connect

    Neitzel, Duane A.; Bunn, Amoret L.; Cannon, Sandra D.; Duncan, Joanne P.; Fowler, Richard A.; Fritz, Brad G.; Harvey, David W.; Hendrickson, Paul L.; Hoitink, Dana J.; Horton, Duane G.; Last, George V.; Poston, Ted M.; Prendergast-Kennedy, Ellen L.; Reidel, Steve P.; Rohay, Alan C.; Sackschewsky, Michael R.; Scott, Michael J.; Thorne, Paul D.

    2005-09-30

    This document describes the U.S. Department of Energy’s (DOE) Hanford Site environment. It is updated each year and is intended to provide a consistent description of the Hanford Site environment for the many environmental documents being prepared by DOE contractors concerning the National Environmental Policy Act (NEPA). No statements about significance or environmental consequences are provided. This year’s report is the seventeenth revision of the original document published in 1988 and is (until replaced by the eighteenth revision) the only version that is relevant for use in the preparation of Hanford NEPA, State Environmental Policy Act (SEPA), and Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) documents. The two chapters included in this document (Chapters 4 and 6) are numbered to correspond to the chapters where such information is typically presented in environmental impact statements (EISs) and other Hanford Site NEPA or CERCLA documentation. Chapter 4.0 (Affected Environment) describes Hanford Site climate and meteorology; air quality; geology; hydrology; ecology; cultural, archaeological, and historical resources; socioeconomics; noise; and occupational health and safety. Sources for extensive tabular data related to these topics are provided in the chapter. Most subjects are divided into a general description of the characteristics of the Hanford Site, followed by site-specific information, where available, of the 100, 200, 300, and other areas. This division allows the reader to go directly to those sections of particular interest. When specific information on each of these separate areas is not complete or available, the general Hanford Site description should be used. Chapter 6.0 (Statutory and Regulatory Requirements) describes federal and state laws and regulations, DOE directives and permits, and presidential executive orders that are applicable to the NEPA documents prepared for Hanford Site activities

  9. Developing Vs30 site-condition maps by combining observations with geologic and topographic constraints

    USGS Publications Warehouse

    Thompson, E.M.; Wald, D.J.

    2012-01-01

    Despite obvious limitations as a proxy for site amplification, the use of time-averaged shear-wave velocity over the top 30 m (VS30) remains widely practiced, most notably through its use as an explanatory variable in ground motion prediction equations (and thus hazard maps and ShakeMaps, among other applications). As such, we are developing an improved strategy for producing VS30 maps given the common observational constraints. Using the abundant VS30 measurements in Taiwan, we compare alternative mapping methods that combine topographic slope, surface geology, and spatial correlation structure. The different VS30 mapping algorithms are distinguished by the way that slope and geology are combined to define a spatial model of VS30. We consider the globally applicable slope-only model as a baseline to which we compare two methods of combining both slope and geology. For both hybrid approaches, we model spatial correlation structure of the residuals using the kriging-with-a-trend technique, which brings the map into closer agreement with the observations. Cross validation indicates that we can reduce the uncertainty of the VS30 map by up to 16% relative to the slope-only approach.

  10. Orthogonal electrode catheter array for mapping of endocardial focal site of ventricular activation

    SciTech Connect

    Desai, J.M.; Nyo, H.; Vera, Z.; Seibert, J.A.; Vogelsang, P.J. )

    1991-04-01

    Precise location of the endocardial site of origin of ventricular tachycardia may facilitate surgical and catheter ablation of this arrhythmia. The endocardial catheter mapping technique can locate the site of ventricular tachycardia within 4-8 cm2 of the earliest site recorded by the catheter. This report describes an orthogonal electrode catheter array (OECA) for mapping and radiofrequency ablation (RFA) of endocardial focal site of origin of a plunge electrode paced model of ventricular activation in dogs. The OECA is an 8 F five pole catheter with four peripheral electrodes and one central electrode (total surface area 0.8 cm{sup 2}). In eight mongrel dogs, mapping was performed by arbitrarily dividing the left ventricle (LV) into four segments. Each segment was mapped with OECA to find the earliest segment. Bipolar and unipolar electrograms were obtained. The plunge electrode (not visible on fluoroscopy) site was identified by the earliest wave front arrival times of -30 msec or earlier at two or more electrodes (unipolar electrograms) with reference to the earliest recorded surface ECG (I, AVF, and V1). Validation of the proximity of the five electrodes of the OECA to the plunge electrode was performed by digital radiography and RFA. Pathological examination was performed to document the proximity of the OECA to the plunge electrode and also for the width, depth, and microscopic changes of the ablation. To find the segment with the earliest LV activation a total of 10 {plus minus} 3 (mean {plus minus} SD) positions were mapped. Mean arrival times at the two earlier electrodes were -39 {plus minus} 4 msec and -35 {plus minus} 3 msec. Digital radiography showed the plunge electrode to be within the area covered by all five electrodes in all eight dogs. The plunge electrode was within 1 cm2 area of the region of RFA in all eight dogs.

  11. 75 FR 1333 - Notice of New Fee Site; Federal Lands Recreation Enhancement Act (Title VIII, Pub. L. 108-447)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-11

    ... (Title VIII, Pub. L. 108-447) AGENCY: Forest Service, USDA. ACTION: Notice of new fee site and.... SUPPLEMENTARY INFORMATION: The Federal Lands Recreation Enhancement Act (Title VIII, Pub. L. 108-447)...

  12. High precision landing site mapping and rover localization for Chang'e-3 mission

    NASA Astrophysics Data System (ADS)

    Liu, ZhaoQin; Di, KaiChang; Peng, Man; Wan, WenHui; Liu, Bin; Li, LiChun; Yu, TianYi; Wang, BaoFeng; Zhou, JianLiang; Chen, HongMin

    2015-01-01

    This paper presents the comprehensive results of landing site topographic mapping and rover localization in Chang'e-3 mission. High-precision topographic products of the landing site with extremely high resolutions (up to 0.05 m) were generated from descent images and registered to CE-2 DOM. Local DEM and DOM with 0.02 m resolution were produced routinely at each waypoint along the rover traverse. The lander location was determined to be (19.51256°W, 44.11884°N, -2615.451 m) using a method of DOM matching. In order to reduce error accumulation caused by wheel slippage and IMU drift in dead reckoning, cross-site visual localization and DOM matching localization methods were developed to localize the rover at waypoints; the overall traveled distance from the lander is 114.8 m from cross-site visual localization and 111.2 m from DOM matching localization. The latter is of highest accuracy and has been verified using a LRO NAC image where the rover trajeactory is directly identifiable. During CE-3 mission operations, landing site mapping and rover localization products including DEMs and DOMs, traverse maps, vertical traverse profiles were generated timely to support teleoperation tasks such as obstacle avoidance and rover path planning.

  13. 75 FR 4340 - Notice of New Recreation Fee Site; Federal Lands Recreation Enhancement Act, (Title VIII, Pub. L...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-27

    ... Forest Service Notice of New Recreation Fee Site; Federal Lands Recreation Enhancement Act, (Title VIII.... SUPPLEMENTARY INFORMATION: The Federal Recreation Lands Enhancement Act (Title VII, Pub. L. 108-447) directed... new recreation fee areas are established. The Caribou-Targhee National Forest currently has nine...

  14. 28 CFR Appendix C to Part 79 - Radiation Exposure Compensation Act Offset Worksheet-On Site Participants

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 28 Judicial Administration 2 2010-07-01 2010-07-01 false Radiation Exposure Compensation Act Offset Worksheet-On Site Participants C Appendix C to Part 79 Judicial Administration DEPARTMENT OF JUSTICE (CONTINUED) CLAIMS UNDER THE RADIATION EXPOSURE COMPENSATION ACT Pt. 79, App. C Appendix C to...

  15. 75 FR 80789 - Notice of New Fee Site; Federal Lands Recreation Enhancement Act, (Title VIII, Pub. L. 108-447)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-23

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF AGRICULTURE Forest Service Notice of New Fee Site; Federal Lands Recreation Enhancement Act, (Title VIII, Pub. L. 108... Federal Recreation Lands Enhancement Act (Title VII, Pub. L. 108-447) directed the Secretary...

  16. 77 FR 42696 - Notice of New Fee Sites; Federal Lands Recreation Enhancement Act, (Title VIII, Pub. L. 108-447)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-20

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF AGRICULTURE Forest Service Notice of New Fee Sites; Federal Lands Recreation Enhancement Act, (Title VIII, Pub. L... Enhancement Act (Title VII, Pub. L. 108-447) directed the Secretary of Agriculture to publish a six...

  17. 78 FR 52499 - Notice of New Fee Site; Federal Lands Recreation Enhancement Act, (Title VIII, Pub. L. 108-447)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-23

    ... From the Federal Register Online via the Government Publishing Office ] DEPARTMENT OF AGRICULTURE Forest Service Notice of New Fee Site; Federal Lands Recreation Enhancement Act, (Title VIII, Pub. L. 108.... SUPPLEMENTARY INFORMATION: The Federal Recreation Lands Enhancement Act (Title VII, Pub. L. 108-447)...

  18. 78 FR 66746 - Medical Device User Fee and Modernization Act; Notice to Public of Web Site Location of Fiscal...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-06

    ... Innovation Act (Pub. L. 112-144), FDA agreed, in return for additional funding from industry, to meet a... HUMAN SERVICES Food and Drug Administration Medical Device User Fee and Modernization Act; Notice to Public of Web Site Location of Fiscal Year 2014 Proposed Guidance Development AGENCY: Food and...

  19. Mapping soil attributes for site-specific management of a Montana field

    NASA Astrophysics Data System (ADS)

    Wilson, John P.; Spangrud, Damian J.; Landon, Melissa A.; Jacobsen, Jeffrey S.; Nielson, Gerald A.

    1995-01-01

    Conventional soil maps represent the distribution of soil attributes across landscapes but with less precision than is needed to obtain the full economic and environmental benefits of site- specific crop management. This study quantifies the spatial variability of three agronomically significant soil attributes: (1) thickness of mollic epipedon, (2) organic matter content (OM), and (3) pH as related to soil survey map units, spectral data, and terrain attributes for a 20 ha field in Montana. Analysis of Order 1 (1:7920-scale) Soil Survey map units indicates substantial variation in all three soil attributes. There was some evidence that similar attribute values were clustered in the field (0.40 - 0.46 Moran's Coefficients). Two spectral band ratios explained 64% of the variation in OM across the field. GPS/GIS-derived wetness index, sediment transport index, elevation, and slope gradient explained 48% of OM variation. Wetness index, slope gradient, and plan curvature combined to explain 48% of the variation in mollic epipedon thickness. Elevation and wetness index explained just 13% of pH variation. Two spectral band ratios, specific catchment area, and wetness index combined to explain 70% of the variation in OM at 66 sampling sites. Four contour map representations of OM illustrate the sensitivity of the final maps to variations in input data and interpolation method.

  20. Monitoring air quality with lichens: a comparison between mapping in forest sites and in open areas.

    PubMed

    Policnik, Helena; Simoncic, Primoz; Batic, Franc

    2008-01-01

    Four different methods of epiphytic lichen mapping were used for the assessment of air quality in the region under the influence of the Sostanj Thermal Power Plant (Salek Valley, Slovenia). Three methods were based on the presence of different lichen species (VDI, EU and ICP-Forest), the fourth on a frequency and coverage assessment of different growth forms of epiphytic lichens, e.g. crustose, foliose and fruticose (SI). A comparison of the results from the assessment of air quality between forest sites (ICP-Forest, SI) and open areas (VDI, EU and SI), obtained by the different methods of epiphytic lichen mapping, is presented in the contribution. Data showed that lichen species richness is worse in forest sites in comparison with open areas. From the data obtained it can be concluded that epiphytic lichen mapping in open areas is a better method for the assessment of air pollution in a given area than mapping in forest sites. The species-based methods in open areas are more powerful and useful for air quality assessment in polluted research areas than the SI and ICP-Forest methods.

  1. Geological mapping of the Oak Ridge K-25 Site, Oak Ridge, Tennessee

    SciTech Connect

    Lemiszki, P.J.

    1994-01-01

    The Oak Ridge K-25 Site (formerly known as the Oak Ridge Gaseous Diffusion Plant) is located in the southern Appalachian Valley and Ridge province of east Tennessee and overlies an area of folded and faulted Cambrian through Ordovician sedimentary rocks in the footwall of the Whiteoak Mountain fault. Environmental restoration plans for the area require that the geology of the site be well understood because various aspects of the groundwater system are directly influenced by stratigraphic and structural characteristics of the bedrock. This study involved mapping the bedrock geology of an 18-square mile area in and around the plant site. Field mapping focused on: (1) checking the accuracy of previously mapped stratigraphic and fault contacts, (2) dividing the bedrock into distinct stratigraphic units based on field criteria, (3) determining the geometry of map-scale folds and faults, and (4) documenting various aspects of the local fracture system. Besides accomplishing all of the above tasks, results from this study have led to a number of new hypotheses regarding various aspects of the site geology. First, faulting and folding within carbonates of the Chickamauga Supergroup in the plant area has repeated certain rock units, which requires that there be a thrust fault in the subsurface below them. This thrust fault may project to the surface with the Carters Limestone. Second, thrust slices of the Rome Formation that overlie the Chickamauga carbonates may be extremely thin and have a limited aerial extent. Third, part of the Knox Group on McKinney Ridge is folded into an anticline. Evaluating the above hypotheses will require information about the subsurface that can only be acquired through drilling and surface geophysical surveys. The geologic map produced from this study can be used to evaluate the location of coreholes that will more effectively intersect a combination of stratigraphic, structural, and hydrologic targets.

  2. Testing a small UAS for mapping artisanal diamond mining sites in Africa

    USGS Publications Warehouse

    Malpeli, Katherine C.; Chirico, Peter G.

    2015-01-01

    Remote sensing technology is advancing at an unprecedented rate. At the forefront of the new technological developments are unmanned aircraft systems (UAS). The advent of small, lightweight, low-cost, and user-friendly UAS is greatly expanding the potential applications of remote sensing technology and improving the set of tools available to researchers seeking to map and monitor terrain from above. In this article, we explore the applications of a small UAS for mapping informal diamond mining sites in Africa. We found that this technology provides aerial imagery of unparalleled resolution in a data-sparse, difficult to access, and remote terrain.

  3. Mapping Site Response Parameters on Cal Poly Pomona Campus Using the Spectral Ratio Method

    NASA Astrophysics Data System (ADS)

    HO, K. Y. K.; Polet, J.

    2014-12-01

    Site characteristics are an important factor in earthquake hazard assessment. To better understand site response differences on a small scale, as well as the seismic hazard of the area, we develop site response parameter maps of Cal Poly Pomona campus. Cal Poly Pomona is located in southern California about 40 km east of Los Angeles, within 50 km of San Andreas Fault. The campus is situated on top of the San Jose Fault. With about twenty two thousand students on campus, it is important to know the site response in this area. To this end, we apply the Horizontal-to-Vertical (H/V) spectral ratio technique, which is an empirical method that can be used in an urban environment with no environmental impact. This well-established method is based on the computation of the ratio of vertical ambient noise ground motion over horizontal ambient noise ground motion as a function of frequency. By applying the spectral ratio method and the criteria from Site Effects Assessment Using Ambient Excitations (SESAME) guidelines, we can determine fundamental frequency and a minimum site amplification factor. We installed broadband seismometers throughout the Cal Poly Pomona campus, with an initial number of about 15 sites. The sites are approximately 50 to 150 meters apart and about two hours of waveforms were recorded at each site. We used the Geopsy software to make measurements of the peak frequency and the amplitude of the main peak from the spectral ratio. These two parameters have been determined to be estimates of fundamental frequency and a minimum site amplification factor, respectively. Based on the geological map from the U.S. Geological Survey (USGS) and our data collected from Cal Poly Pomona campus, our preliminary results suggest that the area of campus that is covered by alluvial fan material tends to have a single significant spectral peak with a fundamental frequency of ~1Hz and a minimum amplification factor of ~3.7. The minimum depth of the surface layer is about 56

  4. 75 FR 26711 - Notice of New Recreation Fee Site; Federal Lands Recreation Enhancement Act, (Title VIII, Pub. L...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-12

    ... Forest Service Notice of New Recreation Fee Site; Federal Lands Recreation Enhancement Act, (Title VIII... Recreation Fee Site. SUMMARY: Bethel Motorcycle and Bethel ATV Trails are located near Saucier, MS. Currently..., Recreation Program Manager, 601-965-1617, National Forests in Mississippi, 100 West Capitol Street,...

  5. 75 FR 26714 - Notice of Proposed New Recreation Fee Site; Federal Lands Recreation Enhancement Act, (Title VIII...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-12

    ... Forest Service Notice of Proposed New Recreation Fee Site; Federal Lands Recreation Enhancement Act...: Notice of Proposed New Recreation Fee Site. SUMMARY: Rattlesnake Bay ATV Trail is located near Beaumont... Gainey, Recreation Program Manager, 601-965-1617, National Forests in Mississippi, 100 West...

  6. 75 FR 33763 - Notice of Proposed New Recreation Fee Sites; Federal Lands Recreation Enhancement Act (Title VIII...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-15

    ... Forest Service Notice of Proposed New Recreation Fee Sites; Federal Lands Recreation Enhancement Act...: Notice of three proposed new recreation fee sites. SUMMARY: Moss Knob Shooting Range, Nantahala National..., Recreation Program Manager, 828-524-6441, Nantahala Ranger District, Nantahala National Forest, 90 Sloan...

  7. 75 FR 5759 - Notice of New Recreation Fee Site; Federal Lands Recreation Enhancement Act, (Title VIII, Pub. L...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-04

    ... Forest Service Notice of New Recreation Fee Site; Federal Lands Recreation Enhancement Act, (Title VIII... Recreation Fee Sites. SUMMARY: The Soda Springs Ranger District of the Caribou-Targhee National Forest is... appreciate and enjoy the availability of developed recreation campground and picnicking facilities....

  8. Mapping

    ERIC Educational Resources Information Center

    Kinney, Douglas M.; McIntosh, Willard L.

    1978-01-01

    Geologic mapping in the United States increased by about one-quarter in the past year. Examinations of mapping trends were in the following categories: (1) Mapping at scales of 1:100, 000; (2) Metric-scale base maps; (3) International mapping, and (4) Planetary mapping. (MA)

  9. REVIEW: Accuracies of Global Land Cover Maps Checked against Fluxnet Sites

    NASA Astrophysics Data System (ADS)

    Gong, Peng

    2008-01-01

    Global land cover data products are key sources of information in understanding the complex interactions between human activities and global change. They play a critical role in improving performances of ecosystem, hydrological and atmospheric models. Three freely available global land cover products developed in the United States are popularly used by the scientific community. These include two global maps developed separately by the United States Geological Survey (USGS) and the University of Maryland (UMD) with NOAA Advanced Very High Resolution Radiometer (AVHRR) data, and one developed by Boston University with the EOS Moderate Resolution Imaging Spectroradiometer (MODIS) data. They are compared with known land cover types at 250 available Fluxnet sites around the world. The overall accuracies are 37%, 36% and 42%, respectively for the USGS, UMD and Boston global land cover maps. Some future global land cover mapping strategies are suggested.

  10. MapZ marks the division sites and positions FtsZ rings in Streptococcus pneumoniae.

    PubMed

    Fleurie, Aurore; Lesterlin, Christian; Manuse, Sylvie; Zhao, Chao; Cluzel, Caroline; Lavergne, Jean-Pierre; Franz-Wachtel, Mirita; Macek, Boris; Combet, Christophe; Kuru, Erkin; VanNieuwenhze, Michael S; Brun, Yves V; Sherratt, David; Grangeasse, Christophe

    2014-12-11

    In every living organism, cell division requires accurate identification of the division site and placement of the division machinery. In bacteria, this process is traditionally considered to begin with the polymerization of the highly conserved tubulin-like protein FtsZ into a ring that locates precisely at mid-cell. Over the past decades, several systems have been reported to regulate the spatiotemporal assembly and placement of the FtsZ ring. However, the human pathogen Streptococcus pneumoniae, in common with many other organisms, is devoid of these canonical systems and the mechanisms of positioning the division machinery remain unknown. Here we characterize a novel factor that locates at the division site before FtsZ and guides septum positioning in pneumococcus. Mid-cell-anchored protein Z (MapZ) forms ring structures at the cell equator and moves apart as the cell elongates, therefore behaving as a permanent beacon of division sites. MapZ then positions the FtsZ ring through direct protein-protein interactions. MapZ-mediated control differs from previously described systems mostly on the basis of negative regulation of FtsZ assembly. Furthermore, MapZ is an endogenous target of the Ser/Thr kinase StkP, which was recently shown to have a central role in cytokinesis and morphogenesis of S. pneumoniae. We show that both phosphorylated and non-phosphorylated forms of MapZ are required for proper Z-ring formation and dynamics. Altogether, this work uncovers a new mechanism for bacterial cell division that is regulated by phosphorylation and illustrates that nature has evolved a diversity of cell division mechanisms adapted to the different bacterial clades.

  11. Geometry of sets of quantum maps: A generic positive map acting on a high-dimensional system is not completely positive

    NASA Astrophysics Data System (ADS)

    Szarek, Stanisław J.; Werner, Elisabeth; Życzkowski, Karol

    2008-03-01

    We investigate the set (a) of positive, trace preserving maps acting on density matrices of size N and a sequence of its nested subsets: the sets of maps which are (b) decomposable, (c) completely positive, and (d) extended by identity impose positive partial transpose and (e) are superpositive. Working with the Hilbert-Schmidt (Euclidean) measure, we derive tight explicit two-sided bounds for the volumes of all five sets. A sample consequence is the fact that, as N increases, a generic positive map becomes not decomposable and, a fortiori, not completely positive. Due to the Jamiołkowski isomorphism, the results obtained for quantum maps are closely connected to similar relations between the volume of the set of quantum states and the volumes of its subsets (such as states with positive partial transpose or separable states) or supersets. Our approach depends on the systematic use of duality to derive quantitative estimates and on various tools of classical convexity, high-dimensional probability, and geometry of Banach spaces, some of which are not standard.

  12. Novel Electrophilic and Photoaffinity Covalent Probes for Mapping the Cannabinoid 1 Receptor Allosteric Site(s)

    PubMed Central

    2015-01-01

    Undesirable side effects associated with orthosteric agonists/antagonists of cannabinoid 1 receptor (CB1R), a tractable target for treating several pathologies affecting humans, have greatly limited their translational potential. Recent discovery of CB1R negative allosteric modulators (NAMs) has renewed interest in CB1R by offering a potentially safer therapeutic avenue. To elucidate the CB1R allosteric binding motif and thereby facilitate rational drug discovery, we report the synthesis and biochemical characterization of first covalent ligands designed to bind irreversibly to the CB1R allosteric site. Either an electrophilic or a photoactivatable group was introduced at key positions of two classical CB1R NAMs: Org27569 (1) and PSNCBAM-1 (2). Among these, 20 (GAT100) emerged as the most potent NAM in functional assays, did not exhibit inverse agonism, and behaved as a robust positive allosteric modulator of binding of orthosteric agonist CP55,940. This novel covalent probe can serve as a useful tool for characterizing CB1R allosteric ligand-binding motifs. PMID:26529344

  13. Collaborative community hazard exposure mapping: Distant Early Warning radar sites in Alaska's North Slope

    NASA Astrophysics Data System (ADS)

    Brady, M.

    2015-12-01

    A method to produce hazard exposure maps that are developed in collaboration with local coastal communities is the focus of this research. Typically efforts to map community exposure to climate threats over large areas have limited consideration of local perspectives about associated risks, constraining their utility for local management. This problem is especially acute in remote locations such as the Arctic where there are unique vulnerabilities to coastal threats that can be fully understood only through inclusion of community stakeholders. Through collaboration with community members, this study identifies important coastal assets and places and surveys local perspectives of exposure to climate threats along Alaska's vast North Slope coastline spanning multiple municipalities. To model physical exposure, the study adapts the U.S. Geological Survey's (USGS) coastal vulnerability index (CVI) to the Arctic context by incorporating the effects of open water distance determined by sea ice extent, and assigning CVI values to coastal assets and places according to direction and proximity. The study found that in addition to concerns about exposed municipal and industrial assets, North Slope communities viewed exposure of traditional activity sites as presenting a particular risk for communities. Highly exposed legacy Cold War Distant Early Warning Line sites are of particular concern with impacts ranging from financial risk to contamination of sensitive coastal marine environments. This research demonstrates a method to collaboratively map community exposure to coastal climate threats to better understand local risks and produce locally usable exposure maps.

  14. Rapid Mapping and Prioritisation of Wetland Sites in the Manawatu-Wanganui Region, New Zealand

    NASA Astrophysics Data System (ADS)

    Ausseil, Anne-Gaelle E.; Dymond, John R.; Shepherd, James D.

    2007-03-01

    The extent of wetland in New Zealand has decreased by approximately 90% since European settlement began in 1840. Remaining wetlands continue to be threatened by drainage, weeds, and pest invasion. This article presents a rapid method for broad-scale mapping and prioritising palustrine and estuarine wetlands for conservation. Classes of wetland (lacustrine, estuarine, riverine, marine, and palustrine) were mapped using Landsat ETM+ imagery and centre-points of palustrine and estuarine sites as ancillary data. The results shown are for the Manawatu-Wanganui region, which was found to have 3060 ha of palustrine and 250 ha of estuarine wetlands. To set conservation priorities, landscape indicators were computed from a land-cover map and a digital terrain model. Four global indicators were used (representativeness, area, surrounding naturalness, and connectivity), and each was assigned a value to score wetland sites in the region. The final score is an additive function that weights the relative importance of each indicator (i.e., multicriteria decision analysis). The whole process of mapping and ranking wetlands in the Manawatu-Wanganui region took only 6 weeks. The rapid methodology means that consistent wetland inventories and ranking can now actually be produced at reasonable cost, and conservation resources may therefore be better targeted. With complete inventories and priority lists of wetlands, managers will be able to plan for conservation without having to wait for the collection of detailed biologic information, which may now also be prioritised.

  15. Development and application of site mapping methods for the design of glycosaminoglycans.

    PubMed

    Agostino, Mark; Gandhi, Neha S; Mancera, Ricardo L

    2014-09-01

    Glycosaminoglycans (GAGs) are complex polysaccharides involved in a wide range of biological signaling events, as well as being important as biological structural materials. Despite the ubiquity and importance of GAG-protein interactions in biological systems and potentially as therapeutic targets, detailed structures of such interactions are sparse in availability. Computational methods can provide detailed structural knowledge of these interactions; however, they should be evaluated against suitable test systems prior to their widespread use. In this study, we have investigated the application of automated molecular docking and interaction mapping techniques to characterizing GAG-protein interactions. A series of high-resolution X-ray crystal structures of GAGs in complex with proteins was used to evaluate the approaches. Accurately scoring the pose fitting best with the crystal structure was a challenge for all docking programs evaluated. The site mapping technique offered excellent prediction of the key residues involved in ligand recognition, comparable to the best pose and improved over the top-ranked pose. A design protocol incorporating site- and ligand-based mapping techniques was developed and applied to identify GAGs capable of binding to acidic fibroblast growth factor (aFGF). The protocol was able to identify ligands known to bind to aFGF and accurately able to predict the binding modes of those ligands when using a known ligand-binding conformation of the protein. This study demonstrates the value of mapping-based techniques in identifying specific GAG epitopes recognized by proteins and for GAG-based drug design.

  16. Covariance of biophysical data with digital topograpic and land use maps over the FIFE site

    NASA Technical Reports Server (NTRS)

    Davis, F. W.; Schimel, D. S.; Friedl, M. A.; Michaelsen, J. C.; Kittel, T. G. F.; Dubayah, R.; Dozier, J.

    1992-01-01

    This paper discusses the biophysical stratification of the FIFE site, implementation of the stratification utilizing geographic information system methods, and validation of the stratification with respect to field measurements of biomass, Bowen ratio, soil moisture, and the greenness vegetation index (GVI) derived from TM satellite data. Maps of burning and topographic position were significantly associated with variation in GVI, biomass, and Bowen ratio. The stratified design did not significantly alter the estimated site-wide means for surface climate parameters but accounted for between 25 and 45 percent of the sample variance depending on the variable.

  17. Salt Repository Project site study plan for surface geological mapping: Revision 1, December 22, 1987

    SciTech Connect

    Not Available

    1988-03-01

    This site study plan describes the Surface Geological Mapping field activities to be conducted during early stages of Site Characterization for the Deaf Smith County Site, Texas. The field program has been designed to provide data useful in addressing information and design data needs resulting from Federal/State/local regulatory requirements and repository program requirements. Air and ground surveys and an extensive literature search will be conducted to map areas within and hear proposed nuclear waste repository site in the Deaf Smith County. Findings from this study may identify additional areas requiring further investigation, for which a new site study plan will be prepared. The Salt Repository Project (SRP) Networks specify the schedule under which the program will operate. The Technical and Field Services Contractor (TFSC) is responsible for conducting the field program. Data will be handled and reported in accordance with established SRP procedures. A quality assurance program will be utilized to assure that activities affecting quality are performed correctly and the appropriate documentation is maintained. 27 refs., 13 figs., 5 tabs.

  18. Validation of Innovative Exploration Technologies for Newberry Volcano: Drill Site Location Map 2010

    DOE Data Explorer

    Jaffe, Todd

    2012-01-01

    Newberry seeks to explore "blind" (no surface evidence) convective hydrothermal systems associated with a young silicic pluton on the flanks of Newberry Volcano. This project will employ a combination of innovative and conventional techniques to identify the location of subsurface geothermal fluids associated with the hot pluton. Newberry project drill site location map 2010. Once the exploration mythology is validated, it can be applied throughout the Cascade Range and elsewhere to locate and develop “blind” geothermal resources.

  19. Where to begin? Mapping transcription start sites genome-wide in Escherichia coli.

    PubMed

    Wade, Joseph T

    2015-01-01

    Recent genome-wide studies of bacterial transcription have revealed large numbers of promoters located inside genes. In this issue of the Journal of Bacteriology, Thomason and colleagues (J. Bacteriol. 197:18-28, 2015, doi:10.1128/JB.02096-14) map transcription start sites in Escherichia coli on an unprecedented scale. This work provides important insights into the regulation of transcripts that initiate inside genes and sources of variability between studies aimed at identifying these RNAs.

  20. National Environmental Policy Act (NEPA) Source Guide for the Hanford Site

    SciTech Connect

    JANSKY, M.T.

    2000-09-01

    This Source Guide will assist those working with the National Environmental Policy Act (NEPA) of 1969 to become more familiar with the environmental assessments (EA) and environmental impact statements (EIS) that apply to specific activities and facilities on the Hanford Site. This document should help answer questions concerning NEPA coverage, history, processes, and the status of many of the buildings and units on and related to the Hanford Site. This document summarizes relevant EAs and EISs by briefly outlining the proposed action of each document and the decision made by the U.S. Department of Energy (DOE) or its predecessor agencies, the U.S. Atomic Energy Commission (AEC) and the U.S. Energy Research and Development Administration (ERDA). The summary includes the proposed action alternatives and current status of the proposed action. If a decision officially was stated by the DOE, as in a finding of no significant impact (FONSI) or a record of decision (ROD), and the decision was located, a summary is provided. Not all federal decisions, such as FONSIs and RODs, can be found in the Federal Register (FR). For example, although significant large-action FONSIs can be found in the FR, some low-interest FONSIs might have been published elsewhere (i.e., local newspapers).

  1. Application of a regional approach for hazard mapping at an avalanche site in northern Italy

    NASA Astrophysics Data System (ADS)

    Bocchiola, D.; Rosso, R.

    2008-04-01

    The currently adopted approach to avalanche hazard mapping in northern Italy includes avalanche dynamic modelling, coupled with statistical analysis of snow depth at avalanche start. The 30-years and 300-years return period avalanches at a given site are modelled and their run out zone and pressure are evaluated. The snow depth in the avalanche release zone is assumed to coincide with the three days snow fall depth H72 featuring a return period of 30 years and 300 years, respectively. In the Italian alps only short series of observed snow depth are available, covering a period of 20 years or so, thus requiring a regional approach, or index value approach for the purpose of high return period quantile estimation. Based of former studies, here we apply the index value approach developed for the Lombardia region, in northern Italy, for hazard mapping in a particular avalanche site. A dynamic avalanche model is tuned using the runout data for two major observed avalanche events. Then, the 30-years and 300-years runout zone and dynamic pressure are calculated. It is then shown that the obtained hazard maps are more accurate than those obtained using the evaluation of H72 as deduced from distribution fitting in a single site.

  2. Preliminary aeromagnetic map of the Nevada Test Site and vicinity, Nevada

    SciTech Connect

    Kirchoff-Stein, K.S.; Ponce, D.A.; Chuchel, B.A.

    1989-12-31

    As part of an effort to help geologically characterize a possible high-level nuclear waste repository at Yucca Mountain, a merged aeromagnetic map of the Nevada Test Site (NTS) and vicinity was prepared from eight separate aeromagnetic surveys. Each data set was compiled and merged by Kucks and Hildenbrand (1987) as part of a statewide aeromagnetic map of Nevada (Hildenbrand and Kucks, 1988). During processing each data set was gridded at a 1-km interval, and a geomagnetic reference field was removed. Prior to merging, each grid was either upward or downward continued to 1000 ft above the ground and datum shifts were applied, where necessary, to achieve an overall constant datum. The resulting map yields an integrated picture of the total magnetic field that is useful for identifying areas of further interest and for qualitative interpretation. However, quantitative interpretation should be made using the original data, because anomaly locations and relative amplitudes may have been altered slightly during computer processing. The final merged map was compared with the individual published maps to ensure that the location of major anomalies and magnetic trends were preserved. The average difference in anomaly positions for major anomalies is about 0.4 km, which is reasonable for a 1-km grid spacing. 13 refs.

  3. 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

  4. A genome-wide map of hyper-edited RNA reveals numerous new sites.

    PubMed

    Porath, Hagit T; Carmi, Shai; Levanon, Erez Y

    2014-01-01

    Adenosine-to-inosine editing is one of the most frequent post-transcriptional modifications, manifested as A-to-G mismatches when comparing RNA sequences with their source DNA. Recently, a number of RNA-seq data sets have been screened for the presence of A-to-G editing, and hundreds of thousands of editing sites identified. Here we show that existing screens missed the majority of sites by ignoring reads with excessive ('hyper') editing that do not easily align to the genome. We show that careful alignment and examination of the unmapped reads in RNA-seq studies reveal numerous new sites, usually many more than originally discovered, and in precisely those regions that are most heavily edited. Specifically, we discover 327,096 new editing sites in the heavily studied Illumina Human BodyMap data and more than double the number of detected sites in several published screens. We also identify thousands of new sites in mouse, rat, opossum and fly. Our results establish that hyper-editing events account for the majority of editing sites. PMID:25158696

  5. A simulation of Earthquake Loss Estimation in Southeastern Korea using HAZUS and the local site classification Map

    NASA Astrophysics Data System (ADS)

    Kang, S.; Kim, K.

    2013-12-01

    Regionally varying seismic hazards can be estimated using an earthquake loss estimation system (e.g. HAZUS-MH). The estimations for actual earthquakes help federal and local authorities develop rapid, effective recovery measures. Estimates for scenario earthquakes help in designing a comprehensive earthquake hazard mitigation plan. Local site characteristics influence the ground motion. Although direct measurements are desirable to construct a site-amplification map, such data are expensive and time consuming to collect. Thus we derived a site classification map of the southern Korean Peninsula using geologic and geomorphologic data, which are readily available for the entire southern Korean Peninsula. Class B sites (mainly rock) are predominant in the area, although localized areas of softer soils are found along major rivers and seashores. The site classification map is compared with independent site classification studies to confirm our site classification map effectively represents the local behavior of site amplification during an earthquake. We then estimated the losses due to a magnitude 6.7 scenario earthquake in Gyeongju, southeastern Korea, with and without the site classification map. Significant differences in loss estimates were observed. The loss without the site classification map decreased without variation with increasing epicentral distance, while the loss with the site classification map varied from region to region, due to both the epicentral distance and local site effects. The major cause of the large loss expected in Gyeongju is the short epicentral distance. Pohang Nam-Gu is located farther from the earthquake source region. Nonetheless, the loss estimates in the remote city are as large as those in Gyeongju and are attributed to the site effect of soft soil found widely in the area.

  6. Operation and research at the Ithaca MAP3S regional precipitation chemistry site

    SciTech Connect

    Butler, T.J.; Likens, G.E.

    1991-07-01

    Annual precipitation chemistry data from network start-up through 1988 is presented for the nine MAP3S sites. Time trends show significant negative linear regressions (P < 0.10) for SO{sub 4}{sup 2-} at 2 sites, H{sup +} at 4 sites, Ca{sup ++} at 1 site, and Na{sup +} at 1 site. Significant positive regressions over time include: NH{sub 4}{sup +} at 2 sites, Ca{sup ++} at 1 site, K{sup +} at 4 sites, and Cl{sup {minus}} at 2 sites. The Ithaca site shows the highest number of significant trends, with positive trends for Cl{sup {minus}}, NH{sub 4}{sup +}, Ca{sup ++}, and K{sup +}, and a negative trend for H{sup +}. Linear regressions of annual SO{sub 4}{sup 2-} concentrations on SO2 emissions show a significant positive relationship for Whiteface, Illinois, and Ohio at p < 0.10, 0.02, and 0.05 respectively. Overall for all MAP3S sites, plus Hubbard Brook a 25% decline in SO2 emissions over the region has been accompanied by a 16.5% decline in annual precipitation concentrations of SO{sub 4}{sup 2-}. For the region as a whole, a 20% decline in combined emissions has been accompanied to a 20% decline in H{sup +} concentrations. Thus a linear relationship exists between combined emissions and precipitation H{sup +} concentrations. No strong relationship exists for NOx emissions and precipitation NO{sub 3}{sup {minus}} concentration at the annual, seasonal or monthly level. Removing the NOx transportation sector, removing high and low precipitation values, or high pH values also does little to improve the NOx -- NO{sub 3}{sup {minus}} concentration relationships. Dry deposition components such a PAN, NO2, gaseous HNO{sub 3}, or aerosol NO{sub 3}{sup {minus}} should be included in the future with precipitation NO{sub 3}{sup {minus}} to relate emissions of NOx to nitrogen deposition. 11 refs., 27 figs.,1 tab.

  7. Savannah River Site Footprint Reduction Results under the American Recovery and Reinvestment Act - 13302

    SciTech Connect

    Flora, Mary; Adams, Angelia; Pope, Robert

    2013-07-01

    The Savannah River Site (SRS) is an 802 square-kilometer United States Department of Energy (US DOE) nuclear facility located along the Savannah River near Aiken, South Carolina, managed and operated by Savannah River Nuclear Solutions. Construction of SRS began in the early 1950's to enhance the nation's nuclear weapons capability. Nuclear weapons material production began in the early 1950's, eventually utilizing five production reactors constructed to support the national defense mission. Past operations have resulted in releases of hazardous constituents and substances to soil and groundwater, resulting in 515 waste sites with contamination exceeding regulatory thresholds. More than 1,000 facilities were constructed onsite with approximately 300 of them considered radiological, nuclear or industrial in nature. In 2003, SRS entered into a Memorandum of Agreement with its regulators to accelerate the cleanup using an Area Completion strategy. The strategy was designed to focus cleanup efforts on the 14 large industrial areas of the site to realize efficiencies of scale in the characterization, assessment, and remediation activities. This strategy focuses on addressing the contaminated surface units and the vadose zone and addressing groundwater plumes subsequently. This approach streamlines characterization and remediation efforts as well as the required regulatory documentation, while enhancing the ability to make large-scale cleanup decisions. In February 2009, Congress approved the American Reinvestment and Recovery Act (ARRA) to create jobs and promote economic recovery. At SRS, ARRA funding was established in part to accelerate the completion of environmental remediation and facility deactivation and decommissioning (D and D). By late 2012, SRS achieved 85 percent footprint reduction utilizing ARRA funding by accelerating and coupling waste unit remediation with D and D of remnant facilities. Facility D and D activities were sequenced and permitted with

  8. Site-response maps for the Los Angeles region based on earthquake ground motions

    USGS Publications Warehouse

    Hartzell, Stephen H.; Harmsen, Stephen C.; Frankel, Arthur D.; Carver, David L.; Cranswick, Edward; Meremonte, Mark E.; Michael, John A.

    1996-01-01

    Ground-motion records from aftershocks of the 1994 Northridge earthquake and main-shock records from the 1971 San Fernando, 1987 Whittier Narrows, 1991 Sierra Madre, and 1994 Northridge earthquakes are used to estimate site response in the urban Los Angeles, California, area. Two frequency bands are considered, 0.5-1.5 Hz and 2.0-6.0 Hz. Instrument characteristics prevented going to lower frequencies, and frequencies above 6.0 Hz are less important to the building inventory. Site response determined at the instrumented locations is associated with the surficial geology and contoured to produce a continuous spatial estimation of site response. The maps in this report are preliminary and will evolve as more data become available and more analysis is done.

  9. Depth-to-Ice Map of an Arctic Site on Mars

    NASA Technical Reports Server (NTRS)

    2007-01-01

    Color coding in this map of a far-northern site on Mars indicates the change in nighttime ground-surface temperature between summer and fall. This site, like most of high-latitude Mars, has water ice mixed with soil near the surface. The ice is probably in a rock-hard frozen layer beneath a few centimeters or inches of looser, dry soil. The amount of temperature change at the surface likely corresponds to how close to the surface the icy material lies.

    The dense, icy layer retains heat better than the looser soil above it, so where the icy layer is closer to the surface, the surface temperature changes more slowly than where the icy layer is buried deeper. On the map, areas of the surface that cooled more slowly between summer and autumn (interpreted as having the ice closer to the surface) are coded blue and green. Areas that cooled more quickly (interpreted as having more distance to the ice) are coded red and yellow.

    The depth to the top of the icy layer estimated from these observations, as little as 5 centimeters (2 inches), matches modeling of where it would be if Mars has an active cycle of water being exchanged by diffusion between atmospheric water vapor and subsurface water ice.

    This map and its interpretation are in a May 3, 2007, report in the journal Nature by Joshua Bandfield of Arizona State University, Tempe. The Thermal Emission Imaging System camera on NASA's Mars Odyssey orbiter collected the data presented in the map. The site is centered near 67.5 degrees north latitude, 132 degrees east longitude, in the Martian arctic plains called Vastitas Borealis. It was formerly a candidate landing site for NASA's Phoenix Mars Lander mission. This site is within the portion of the planet where, in 2002, the Gamma Ray Spectrometer suite of instruments on Mars Odyssey found evidence for water ice lying just below the surface. The information from the Gamma Ray Spectrometer is averaged over patches of ground hundreds of kilometers

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

    NASA Astrophysics Data System (ADS)

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

    1996-11-01

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

  11. Applying nitrogen site-specifically using soil electrical conductivity maps and precision agriculture technology.

    PubMed

    Lund, E D; Wolcott, M C; Hanson, G P

    2001-10-16

    Soil texture varies significantly within many agricultural fields. The physical properties of soil, such as soil texture, have a direct effect on water holding capacity, cation exchange capacity, crop yield, production capability, and nitrogen (N) loss variations within a field. In short, mobile nutrients are used, lost, and stored differently as soil textures vary. A uniform application of N to varying soils results in a wide range of N availability to the crop. N applied in excess of crop usage results in a waste of the grower"s input expense, a potential negative effect on the environment, and in some crops a reduction of crop quality, yield, and harvestability. Inadequate N levels represent a lost opportunity for crop yield and profit. The global positioning system (GPS)-referenced mapping of bulk soil electrical conductivity (EC) has been shown to serve as an effective proxy for soil texture and other soil properties. Soils with a high clay content conduct more electricity than coarser textured soils, which results in higher EC values. This paper will describe the EC mapping process and provide case studies of site-specific N applications based on EC maps. Results of these case studies suggest that N can be managed site-specifically using a variety of management practices, including soil sampling, variable yield goals, and cropping history.

  12. The Potential for Mapping Nematode Distributions for Site-specific Management

    PubMed Central

    Wyse-Pester, Dawn Y.; Wiles, Lori J.; Westra, Philip

    2002-01-01

    The success of site-specific nematode management depends on a grower or advisor being able to afford to make a map of an infestation that is accurate enough for management decisions. The spatial dependence of nematode infestations and correlation of soil attributes with nematode density were assessed to investigate the scale of sampling required to obtain correlated observations of density and the use of soils data to reduce the cost of sampling. Nematodes and soil were sampled on a 76.2 × 76.2-m grid in two irrigated corn (Zea mays) fields for 2 years. Nematodes of each of three species were found in 36% to 77% of the cores from a field. Spatial dependence was detected for 10 of 16 distributions, and 22% to 67% of the variation in density within a field could be attributed to spatial correlation. Density was correlated to distances of 115 to 649 m in the directions of 0, 45, 90, and 135° from the crop row, and distances varied with direction. Correlations between nematode density and soil attributes were inconsistent between species and fields. These results indicate a potential for mapping nematode infestations for site-specific management, but provide no evidence for reducing the cost of sampling by substituting soils data for nematode counts when making a map. PMID:19265913

  13. Identifying Potential Areas for Siting Interim Nuclear Waste Facilities Using Map Algebra and Optimization Approaches

    SciTech Connect

    Omitaomu, Olufemi A; Liu, Cheng; Cetiner, Sacit M; Belles, Randy; Mays, Gary T; Tuttle, Mark A

    2013-01-01

    The renewed interest in siting new nuclear power plants in the United States has brought to the center stage, the need to site interim facilities for long-term management of spent nuclear fuel (SNF). In this paper, a two-stage approach for identifying potential areas for siting interim SNF facilities is presented. In the first stage, the land area is discretized into grids of uniform size (e.g., 100m x 100m grids). For the continental United States, this process resulted in a data matrix of about 700 million cells. Each cell of the matrix is then characterized as a binary decision variable to indicate whether an exclusion criterion is satisfied or not. A binary data matrix is created for each of the 25 siting criteria considered in this study. Using map algebra approach, cells that satisfy all criteria are clustered and regarded as potential siting areas. In the second stage, an optimization problem is formulated as a p-median problem on a rail network such that the sum of the shortest distance between nuclear power plants with SNF and the potential storage sites from the first stage is minimized. The implications of obtained results for energy policies are presented and discussed.

  14. Comprehensive mapping of O-GlcNAc modification sites using a chemically cleavable tag.

    PubMed

    Griffin, Matthew E; Jensen, Elizabeth H; Mason, Daniel E; Jenkins, Courtney L; Stone, Shannon E; Peters, Eric C; Hsieh-Wilson, Linda C

    2016-05-24

    The post-translational modification of serine or threonine residues of proteins with a single N-acetylglucosamine monosaccharide (O-GlcNAcylation) is essential for cell survival and function. However, relatively few O-GlcNAc modification sites have been mapped due to the difficulty of enriching and detecting O-GlcNAcylated peptides from complex samples. Here we describe an improved approach to quantitatively label and enrich O-GlcNAcylated proteins for site identification. Chemoenzymatic labelling followed by copper(i)-catalysed azide-alkyne cycloaddition (CuAAC) installs a new mass spectrometry (MS)-compatible linker designed for facile purification of O-GlcNAcylated proteins from cell lysates. The linker also allows subsequent quantitative release of O-GlcNAcylated proteins for downstream MS analysis. We validate the approach by unambiguously identifying several established O-GlcNAc sites on the proteins α-crystallin and O-GlcNAc transferase (OGT), as well as discovering new, previously unreported sites on OGT. Notably, these novel sites on OGT lie in key functional domains of the protein, underscoring how this site identification method may reveal important biological insights into protein activity and regulation. PMID:27063346

  15. A physical map of the X chromosome of Drosophila melanogaster: Cosmid contigs and sequence tagged sites

    SciTech Connect

    Madueno, E.; Modolell, J.; Papagiannakis, G.

    1995-04-01

    A physical map of the euchromatic X chromosome of Drosophila melanogaster has been constructed by assembling contiguous arrays of cosmids that were selected by screening a library with DNA isolated from microamplified chromosomal divisions. This map, consisting of 893 cosmids, covers {approximately}64% of the euchromatic part of the chromosome. In addition, 568 sequence tagged sites (STS), in aggregate representing 120 kb of sequenced DNA, were derived from selected cosmids. Most of these STSs, spaced at an average distance of {approximately} 35 kb along the euchromatic region of the chromosome, represent DNA tags that can be used as entry points to the fruitfly genome. Furthermore, 42 genes have been placed on the physical map, either through the hybridization of specific probes to the cosmids or through the fact that they were represented among the STSs. These provide a link between the physical and the genetic maps of D. melanogaster. Nine novel genes have been tentatively identified in Drosophila on the basis of matches between STS sequences and sequences from other species. 32 refs., 3 figs., 4 tabs.

  16. Classifications for Coastal Wetlands Planning, Protection and Restoration Act (CWPPRA) site-specific projects: 2010

    USGS Publications Warehouse

    Jones, William R.; Garber, Adrienne

    2013-01-01

    The Coastal Wetlands Planning, Protection and Restoration Act (CWPPRA) funds over 100 wetland restoration projects across Louisiana. Integral to the success of CWPPRA is its long-term monitoring program, which enables State and Federal agencies to determine the effectiveness of each restoration effort. One component of this monitoring program is the classification of high-resolution, color-infrared aerial photography at the U.S. Geological Survey’s National Wetlands Research Center in Lafayette, Louisiana. Color-infrared aerial photography (9- by 9-inch) is obtained before project construction and several times after construction. Each frame is scanned on a photogrametric scanner that produces a high-resolution image in Tagged Image File Format (TIFF). By using image-processing software, these TIFF files are then orthorectified and mosaicked to produce a seamless image of a project area and its associated reference area (a control site near the project that has common environmental features, such as marsh type, soil types, and water salinities.) The project and reference areas are then classified according to pixel value into two distinct classes, land and water. After initial land and water ratios have been established by using photography obtained before and after project construction, subsequent comparisons can be made over time to determine land-water change.

  17. The relaxase of the Rhizobium etli symbiotic plasmid shows nic site cis-acting preference.

    PubMed

    Pérez-Mendoza, Daniel; Lucas, María; Muñoz, Socorro; Herrera-Cervera, José A; Olivares, José; de la Cruz, Fernando; Sanjuán, Juan

    2006-11-01

    Genetic and biochemical characterization of TraA, the relaxase of symbiotic plasmid pRetCFN42d from Rhizobium etli, is described. After purifying the relaxase domain (N265TraA), we demonstrated nic binding and cleavage activity in vitro and thus characterized for the first time the nick site (nic) of a plasmid in the family Rhizobiaceae. We studied the range of N265TraA relaxase specificity in vitro by testing different oligonucleotides in binding and nicking assays. In addition, the ability of pRetCFN42d to mobilize different Rhizobiaceae plasmid origins of transfer (oriT) was examined. Data obtained with these approaches allowed us to establish functional and phylogenetic relationships between different plasmids of this family. Our results suggest novel characteristics of the R. etli pSym relaxase for previously described conjugative systems, with emphasis on the oriT cis-acting preference of this enzyme and its possible biological relevance.

  18. Attenuation of cadmium-induced necrotic cell death by necrostatin-1: Potential necrostatin-1 acting sites

    SciTech Connect

    Hsu, T.-S.; Yang, P.-M.; Tsai, J.-S.; Lin, L.-Y.

    2009-03-01

    Cadmium (Cd) induces necrotic death in Chinese hamster ovary (CHO) K1 cells and we have established the responsible signaling pathway. Reportedly, necrostatin-1 (Nec-1) rescues cells from necrotic death by mediating through the death domain receptor (DR) signaling pathway. We show here that Nec-1 also effectively attenuates necrotic death triggered by Cd. Two other treatments that cause necrotic cell death, one can (z-VAD-fmk/TNF-{alpha} on U937 cells) and the other cannot (etherynic acid (EA) on DLD-1 cells) be rescued by Nec-1, were also studied in parallel for comparison. Results show that Nec-1 is ineffectual in modulating intracellular calcium contents, calpain activity (a downstream protease), or reactive oxygen species production. It can counteract the reduction in mitochondrial membrane potential (MMP) caused by treating CHO K1 or U937 cells with necrosis-inducing agent. However, this effect was not found in EA-treated DLD-1 cells. Notably, Nec-1 elevates NF-{kappa}B activity in the presence or absence of necrosis-inducing agents. Our study shows that, in addition to DR-mediated necrosis, Nec-1 is effective in attenuating Cd-induced necrosis. It rescues cells with reduced MMP implying that mitochondrion is its major acting site.

  19. Consultation draft: Site characterization plan overview, Deaf Smith County Site, Texas: Nuclear Waste Policy Act (Section 113)

    SciTech Connect

    Not Available

    1988-01-01

    The Department of Energy (DOE) is preparing a site characterization plan for the candidate site in Deaf Smith County, Texas. The DOE has provided, for information and review, a consultation draft of the plan to the State of Texas and the US Nuclear Regulatory Commission. The site characterization plan is a lengthy document that describes in considerable detail the program that will be conducted to characterize the geologic, hydrologic, and other conditions relevant to the suitability of the site for a repository. The overview presented here consists of brief summaries of important topics covered in the consultation draft of the site characterization plan; it is not a substitute for the site characterization plan. The arrangement of the overview is similar to that of the plan itself, with brief descriptions of the repository system - the site, the repository, and the waste package - preceding the discussion of the characterization program to be carried out at the Deaf Smith County site. It is intended primarily for the management staff of organizations involved in the DOE's repository program or other persons who might wish to understand the general scope of the site-characterization program, the activities to be conducted, and the facilities to be constructed rather than the technical details of site characterization. 15 figs., 1 tab.

  20. Seismic Hazard Maps for Seattle, Washington, Incorporating 3D Sedimentary Basin Effects, Nonlinear Site Response, and Rupture Directivity

    USGS Publications Warehouse

    Frankel, Arthur D.; Stephenson, William J.; Carver, David L.; Williams, Robert A.; Odum, Jack K.; Rhea, Susan

    2007-01-01

    This report presents probabilistic seismic hazard maps for Seattle, Washington, based on over 500 3D simulations of ground motions from scenario earthquakes. These maps include 3D sedimentary basin effects and rupture directivity. Nonlinear site response for soft-soil sites of fill and alluvium was also applied in the maps. The report describes the methodology for incorporating source and site dependent amplification factors into a probabilistic seismic hazard calculation. 3D simulations were conducted for the various earthquake sources that can affect Seattle: Seattle fault zone, Cascadia subduction zone, South Whidbey Island fault, and background shallow and deep earthquakes. The maps presented in this document used essentially the same set of faults and distributed-earthquake sources as in the 2002 national seismic hazard maps. The 3D velocity model utilized in the simulations was validated by modeling the amplitudes and waveforms of observed seismograms from five earthquakes in the region, including the 2001 M6.8 Nisqually earthquake. The probabilistic seismic hazard maps presented here depict 1 Hz response spectral accelerations with 10%, 5%, and 2% probabilities of exceedance in 50 years. The maps are based on determinations of seismic hazard for 7236 sites with a spacing of 280 m. The maps show that the most hazardous locations for this frequency band (around 1 Hz) are soft-soil sites (fill and alluvium) within the Seattle basin and along the inferred trace of the frontal fault of the Seattle fault zone. The next highest hazard is typically found for soft-soil sites in the Duwamish Valley south of the Seattle basin. In general, stiff-soil sites in the Seattle basin exhibit higher hazard than stiff-soil sites outside the basin. Sites with shallow bedrock outside the Seattle basin have the lowest estimated hazard for this frequency band.

  1. Depth-to-Ice Map of a Southern Mars Site Near Melea Planum

    NASA Technical Reports Server (NTRS)

    2007-01-01

    Color coding in this map of a far-southern site on Mars indicates the change in nighttime ground-surface temperature between summer and fall. This site, like most of high-latitude Mars, has water ice mixed with soil near the surface. The ice is probably in a rock-hard frozen layer beneath a few centimeters or inches of looser, dry soil. The amount of temperature change at the surface likely corresponds to how close to the surface the icy material lies.

    The dense, icy layer retains heat better than the looser soil above it, so where the icy layer is closer to the surface, the surface temperature changes more slowly than where the icy layer is buried deeper. On the map, areas of the surface that cooled more slowly between summer and autumn (interpreted as having the ice closer to the surface) are coded blue and green. Areas that cooled more quickly (interpreted as having more distance to the ice) are coded red and yellow.

    The depth to the top of the icy layer estimated from these observations suggests that in some areas, but not others, water is being exchanged by diffusion between atmospheric water vapor and subsurface water ice. Differences in what type of material lies above the ice appear to affect the depth to the ice. The area in this image with the greatest seasonal change in surface temperature corresponds to an area of sand dunes.

    This map and its interpretation are in a May 3, 2007, report in the journal Nature by Joshua Bandfield of Arizona State University, Tempe. The Thermal Emission Imaging System camera on NASA's Mars Odyssey orbiter collected the data presented in the map. The site is centered near 67 degrees south latitude, 36.5 degrees east longitude, near a plain named Melea Planum. This site is within the portion of the planet where, in 2002, the Gamma Ray Spectrometer suite of instruments on Mars Odyssey found evidence for water ice lying just below the surface. The information from the Gamma Ray Spectrometer is

  2. Mapping of replication initiation sites in human ribosomal DNA by nascent-strand abundance analysis.

    PubMed Central

    Yoon, Y; Sanchez, J A; Brun, C; Huberman, J A

    1995-01-01

    New techniques for mapping mammalian DNA replication origins are needed. We have modified the existing nascent-strand size analysis technique (L. Vassilev and E.M. Johnson, Nucleic Acids Res. 17:7693-7705, 1989) to provide an independent means of studying replication initiation sites. We call the new method nascent-strand abundance analysis. We confirmed the validity of this method with replicating simian virus 40 DNA as a model. We then applied nascent-strand abundance and nascent-strand size analyses to mapping of initiation sites in human (HeLa) ribosomal DNA (rDNA), a region previously examined exclusively by two-dimensional gel electrophoresis methods (R.D. Little, T.H.K. Platt, and C.L. Schildkraut, Mol. Cell. Biol. 13:6600-6613, 1993). Our results partly confirm those obtained by two-dimensional gel electrophoresis techniques. Both studies suggest that replication initiates at relatively high frequency a few kilobase pairs upstream of the transcribed region and that many additional low-frequency initiation sites are distributed through most of the remainder of the ribosomal DNA repeat unit. PMID:7739533

  3. Detecting cell-adhesive sites in extracellular matrix using force spectroscopy mapping

    PubMed Central

    Chirasatitsin, Somyot; Engler, Adam J

    2010-01-01

    The cell microenvironment is composed of extracellular matrix (ECM), which contains specific binding sites that allow the cell to adhere to its surroundings. Cells employ focal adhesion proteins, which must be able to resist a variety of forces to bind to ECM. Current techniques for detecting the spatial arrangement of these adhesions, however, have limited resolution and those that detect adhesive forces lack sufficient spatial characterization or resolution. Using a unique application of force spectroscopy, we demonstrate here the ability to determine local changes in the adhesive property of a fibronectin substrate down to the resolution of the fibronectin antibody-functionalized tip diameter, ~20 nm. To verify the detection capabilities of force spectroscopy mapping (FSM), changes in loading rate and temperature were used to alter the bond dynamics and change the adhesion force. Microcontact printing was also used to pattern fluorescein isothiocyanate-conjugated fibronectin in order to mimic the discontinuous adhesion domains of native ECM. Fluorescent detection was used to identify the pattern while FSM was used to map cell adhesion sites in registry with the initial fluorescent image. The results show that FSM can be used to detect the adhesion domains at high resolution and may subsequently be applied to native ECM with randomly distributed cell adhesion sites. PMID:21152375

  4. Contribution of physical modelling to climate-driven landslide hazard mapping: an alpine test site

    NASA Astrophysics Data System (ADS)

    Vandromme, R.; Desramaut, N.; Baills, A.; Hohmann, A.; Grandjean, G.; Sedan, O.; Mallet, J. P.

    2012-04-01

    The aim of this work is to develop a methodology for integrating climate change scenarios into quantitative hazard assessment and especially their precipitation component. The effects of climate change will be different depending on both the location of the site and the type of landslide considered. Indeed, mass movements can be triggered by different factors. This paper describes a methodology to address this issue and shows an application on an alpine test site. Mechanical approaches represent a solution for quantitative landslide susceptibility and hazard modeling. However, as the quantity and the quality of data are generally very heterogeneous at a regional scale, it is necessary to take into account the uncertainty in the analysis. In this perspective, a new hazard modeling method is developed and integrated in a program named ALICE. This program integrates mechanical stability analysis through a GIS software taking into account data uncertainty. This method proposes a quantitative classification of landslide hazard and offers a useful tool to gain time and efficiency in hazard mapping. However, an expertise approach is still necessary to finalize the maps. Indeed it is the only way to take into account some influent factors in slope stability such as heterogeneity of the geological formations or effects of anthropic interventions. To go further, the alpine test site (Barcelonnette area, France) is being used to integrate climate change scenarios into ALICE program, and especially their precipitation component with the help of a hydrological model (GARDENIA) and the regional climate model REMO (Jacob, 2001). From a DEM, land-cover map, geology, geotechnical data and so forth the program classifies hazard zones depending on geotechnics and different hydrological contexts varying in time. This communication, realized within the framework of Safeland project, is supported by the European Commission under the 7th Framework Programme for Research and Technological

  5. Injection site radioactivity of (99m)Tc-labeled mannosylated dextran for sentinel lymph node mapping.

    PubMed

    Yamaguchi, Aiko; Hanaoka, Hirofumi; Pirmettis, Ioannis; Uehara, Tomoya; Tsushima, Yoshito; Papadopoulos, Minas; Arano, Yasushi

    2015-02-01

    The high and persistent radioactivity at the injection site hinders the accuracy and expansion of sentinel lymph node (SLN) mapping. We investigated the mechanism underlying the undesirable radioactivity after subcutaneous injection of (99m)Tc-labeled mannosylated dextran ((99m)Tc(CO)3-DCM20), a SLN mapping agent targeting mannose receptors on macrophages and dendritic cells, in a mouse model. Biodistribution studies were performed 1 h after subcutaneous injection of (99m)Tc(CO)3-DCM20 from the rear footpad of mice in the presence of varying molar amounts of DCM20 or DC15, a modified dextran without mannose. Biodistribution studies were also conducted after subcutaneous injection of [(125)I]radioiodinated mannosyl-neoglycoalbumin ((125)I-NMA) from the rear footpad. The distribution of fluorescence-labeled DCM20 and DC15 at the injection site was also compared 1 h after subcutaneous injection by immunofluorescent histochemistry. The radioactivity levels of (99m)Tc(CO)3-DCM20 at the injection site and popliteal lymph node, a SLN in this model, decreased with an increase in the molar amounts of DCM20, whereas no significant changes in biodistribution were observed after injection of (99m)Tc(CO)3-DCM20 with varying molar amounts of DC15. (125)I-NMA exhibited rapid elimination of radioactivity from both the popliteal lymph node and the injection site. The fluorescence-labeled DCM20 colocalized well with CD68-positive cells such as macrophages and dendritic cells at the injection site. While partial colocalization was observed between DC15 and CD68-positive cells, the signal intensity was very weak. These findings suggest that specific binding of (99m)Tc(CO)3-DCM20 to the mannose receptor on macrophages and dendritic cells would be responsible for the sustained radioactivity levels at the injection site. These results also imply that discriminated blockage of (99m)Tc(CO)3-DCM20 binding to mannose receptors at the injection sites would reduce the radioactivity at the

  6. 76 FR 70760 - Nexergy, Inc., Including On-Site Leased Workers From Act-I Staffing, Kelly Services and Snider...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-15

    ..., 2011 (76 FR 40401). At the request of the State agency, the Department reviewed the certification for..., Kelly Services and Snider-Blake Personnel, Including Workers Whose Unemployment Insurance (UI) Wages Are... Nexergy, Inc., including on-site leased workers from ACT-I Staffing, Snider-Black Personnel and...

  7. 76 FR 61367 - Medical Device User Fee and Modernization Act; Notice to Public of Web Site Location of Fiscal...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-04

    ... HUMAN SERVICES Food and Drug Administration Medical Device User Fee and Modernization Act; Notice to Public of Web Site Location of Fiscal Year 2012 Proposed Guidance Development AGENCY: Food and Drug Administration, HHS. ACTION: Notice. SUMMARY: The Food and Drug Administration (FDA) is announcing the Web...

  8. Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation.

    PubMed

    Ozsolak, Fatih; Kapranov, Philipp; Foissac, Sylvain; Kim, Sang Woo; Fishilevich, Elane; Monaghan, A Paula; John, Bino; Milos, Patrice M

    2010-12-10

    The emerging discoveries on the link between polyadenylation and disease states underline the need to fully characterize genome-wide polyadenylation states. Here, we report comprehensive maps of global polyadenylation events in human and yeast generated using refinements to the Direct RNA Sequencing technology. This direct approach provides a quantitative view of genome-wide polyadenylation states in a strand-specific manner and requires only attomole RNA quantities. The polyadenylation profiles revealed an abundance of unannotated polyadenylation sites, alternative polyadenylation patterns, and regulatory element-associated poly(A)(+) RNAs. We observed differences in sequence composition surrounding canonical and noncanonical human polyadenylation sites, suggesting novel noncoding RNA-specific polyadenylation mechanisms in humans. Furthermore, we observed the correlation level between sense and antisense transcripts to depend on gene expression levels, supporting the view that overlapping transcription from opposite strands may play a regulatory role. Our data provide a comprehensive view of the polyadenylation state and overlapping transcription. PMID:21145465

  9. Computer-aided mapping of stream channels beneath the Lawrence Livermore National Laboratory Super Fund Site

    SciTech Connect

    Sick, M.

    1994-12-01

    The Lawrence Livermore National Laboratory (LLNL) site rests upon 300-400 feet of highly heterogeneous braided stream sediments which have been contaminated by a plume of Volatile Organic Compounds (VOCs). The stream channels are filled with highly permeable coarse grained materials that provide quick avenues for contaminant transport. The plume of VOCs has migrated off site in the TFA area, making it the area of greatest concern. I mapped the paleo-stream channels in the TFA area using SLICE an LLNL Auto-CADD routine. SLICE constructed 2D cross sections and sub-horizontal views of chemical, geophysical, and lithologic data sets. I interpreted these 2D views as a braided stream environment, delineating the edges of stream channels. The interpretations were extracted from Auto-CADD and placed into Earth Vision`s 3D modeling and viewing routines. Several 3D correlations have been generated, but no model has yet been chosen as a best fit.

  10. Archaeological field survey automation: concurrent multisensor site mapping and automated analysis

    NASA Astrophysics Data System (ADS)

    Józefowicz, Mateusz; Sokolov, Oleksandr; Meszyński, Sebastian; Siemińska, Dominika; Kołosowski, Przemysław

    2016-04-01

    ABM SE develops mobile robots (rovers) used for analog research of Mars exploration missions. The rovers are all-terrain exploration platforms, carrying third-party payloads: scientific instrumentation. "Wisdom" ground penetrating radar for Exomars mission has been tested onboard, as well as electrical resistivity module and other devices. Robot has operated in various environments, such as Central European countryside, Dachstein ice caves or Sahara, Morocco (controlled remotely via satellite from Toruń, Poland. Currently ABM SE works on local and global positioning system for a Mars rover basing on image and IMU data. This is performed under a project from ESA. In the next Mars rover missions a Mars GIS model will be build, including an acquired GPR profile, DEM and regular image data, integrated into a concurrent 3D terrain model. It is proposed to use similar approach in surveys of archaeological sites, especially those, where solid architecture remains can be expected at shallow depths or being partially exposed. It is possible to deploy a rover that will concurrently map a selected site with GPR, 2D and 3D cameras to create a site model. The rover image processing algorithms are capable of automatic tracing of distinctive features (such as exposed structure remains on a desert ground, differences in color of the ground, etc.) and to mark regularities on a created map. It is also possible to correlate the 3D map with an aerial photo taken under any angle to achieve interpretation synergy. Currently the algorithms are an interpretation aid and their results must be confirmed by a human. The advantages of a rover over traditional approaches, such as a manual cart or a drone include: a) long hours of continuous work or work in unfavorable environment, such as high desert, frozen water pools or large areas, b) concurrent multisensory data acquisition, c) working from the ground level enables capturing of sites obstructed from the air (trees), d) it is possible to

  11. Draft environmental assessment: Deaf Smith County site, Texas. Nuclear Waste Policy Act (Section 112). [Contains Glossary

    SciTech Connect

    Not Available

    1984-12-01

    In February 1983, the US Department of Energy identified a location in Deaf Smith County, Texas, as one of nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. The potentially acceptable site was subsequently narrowed to an area of 9 square miles. To determine their suitability, the Deaf Smith site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for Nuclear Waste Repositories. These evaluations are reported in this draft environmental assessment, which is being issued for public review and comment. The DOE findings and determinations that are based on these evaluations are preliminary and subject to public review and comment. A final EA will be prepared after considering the comments received. On the basis of the evaluations reported in this draft EA, the DOE has found that the Deaf Smith site is not disqualified under the guidelines. The site is in the Permian Basin, which is one of five distinct geohydrologic settings considered for the first repository. This setting contains one other potentially acceptable site - the Swisher site. Although the Swisher site appears to be suitable for site characterization, DOE has concluded that the Deaf Smith site is the preferred site. The DOE finds that the site is suitable for site characterization because the evidence does not support a conclusion that the site will not be able to meet each of the qualifying conditions specified in the guidelines. On the basis of these findings, the DOE is proposing to nominate the Deaf Smith site as one of five sites suitable for characterization. Having compared the Deaf Smith site with the other four sites proposed for nomination, the DOE has determined that the Deaf Smith site is one of the three preferred sites for recommendation to the President as candidates for characterization.

  12. Classifications for Coastal Wetlands Planning, Protection and Restoration Act site-specific projects: 2008 and 2009

    USGS Publications Warehouse

    Jones, William R.; Garber, Adrienne

    2012-01-01

    The Coastal Wetlands Planning, Protection and Restoration Act (CWPPRA) funds over 100 wetland restoration projects across Louisiana. Integral to the success of CWPPRA is its long-term monitoring program, which enables State and Federal agencies to determine the effectiveness of each restoration effort. One component of this monitoring program is the analysis of high-resolution, color-infrared aerial photography at the U.S. Geological Survey's National Wetlands Research Center in Lafayette, Louisiana. Color-infrared aerial photography (9- by 9-inch) is obtained before project construction and several times after construction. Each frame is scanned on a photogrametric scanner that produces a high-resolution image in Tagged Image File Format (TIFF). By using image-processing software, these TIFF files are then orthorectified and mosaicked to produce a seamless image of a project area and its associated reference area (a control site near the project that has common environmental features, such as marsh type, soil types, and water salinities.) The project and reference areas are then classified according to pixel value into two distinct classes, land and water. After initial land and water ratios have been established by using photography obtained before and after project construction, subsequent comparisons can be made over time to determine land-water change. Several challenges are associated with the land-water interpretation process. Primarily, land-water classifications are often complicated by the presence of floating aquatic vegetation that occurs throughout the freshwater systems of coastal Louisiana and that is sometimes difficult to differentiate from emergent marsh. Other challenges include tidal fluctuations and water movement from strong winds, which may result in flooding and inundation of emergent marsh during certain conditions. Compensating for these events is difficult but possible by using other sources of imagery to verify marsh conditions for other

  13. Discovery and Characterization of Non-ATP Site Inhibitors of the Mitogen Activated Protein (MAP) Kinases

    SciTech Connect

    Comess, Kenneth M.; Sun, Chaohong; Abad-Zapatero, Cele; Goedken, Eric R.; Gum, Rebecca J.; Borhani, David W.; Argiriadi, Maria; Groebe, Duncan R.; Jia, Yong; Clampit, Jill E.; Haasch, Deanna L.; Smith, Harriet T.; Wang, Sanyi; Song, Danying; Coen, Michael L.; Cloutier, Timothy E.; Tang, Hua; Cheng, Xueheng; Quinn, Christopher; Liu, Bo; Xin, Zhili; Liu, Gang; Fry, Elizabeth H.; Stoll, Vincent; Ng, Teresa I.; Banach, David; Marcotte, Doug; Burns, David J.; Calderwood, David J.; Hajduk, Philip J.

    2012-03-02

    Inhibition of protein kinases has validated therapeutic utility for cancer, with at least seven kinase inhibitor drugs on the market. Protein kinase inhibition also has significant potential for a variety of other diseases, including diabetes, pain, cognition, and chronic inflammatory and immunologic diseases. However, as the vast majority of current approaches to kinase inhibition target the highly conserved ATP-binding site, the use of kinase inhibitors in treating nononcology diseases may require great selectivity for the target kinase. As protein kinases are signal transducers that are involved in binding to a variety of other proteins, targeting alternative, less conserved sites on the protein may provide an avenue for greater selectivity. Here we report an affinity-based, high-throughput screening technique that allows nonbiased interrogation of small molecule libraries for binding to all exposed sites on a protein surface. This approach was used to screen both the c-Jun N-terminal protein kinase Jnk-1 (involved in insulin signaling) and p38{alpha} (involved in the formation of TNF{alpha} and other cytokines). In addition to canonical ATP-site ligands, compounds were identified that bind to novel allosteric sites. The nature, biological relevance, and mode of binding of these ligands were extensively characterized using two-dimensional {sup 1}H/{sup 13}C NMR spectroscopy, protein X-ray crystallography, surface plasmon resonance, and direct enzymatic activity and activation cascade assays. Jnk-1 and p38{alpha} both belong to the MAP kinase family, and the allosteric ligands for both targets bind similarly on a ledge of the protein surface exposed by the MAP insertion present in the CMGC family of protein kinases and distant from the active site. Medicinal chemistry studies resulted in an improved Jnk-1 ligand able to increase adiponectin secretion in human adipocytes and increase insulin-induced protein kinase PKB phosphorylation in human hepatocytes, in

  14. Draft environmental assessment: Swisher County site, Texas. Nuclear Waste Policy Act (Section 112). [Contains Glossary

    SciTech Connect

    Not Available

    1984-12-01

    In February 1983, the US Department of Energy (DOE) identified a location in Swisher County, Texas, as one of nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. The potentially acceptable site was subsequently narrowed to an area of 9 square miles. To determine their suitability, the Swisher site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for Nuclear Waste Repositories. These evaluations are reported in this draft environmental assessment (EA), which is being issued for public review and comment. The DOE findings and determinations that are based on these evaluations are preliminary and subject to public review and comment. A final EA will be prepared after considering the comments received. On the basis of the evaluations contained in this draft EA, the DOE has found that the Swisher site is not disqualified under the guidelines. The site is contained in the Permian Basin, which is one of five distinct geohydrologic settings considered for the first repository. This setting contains one other potentially acceptable site - the Deaf Smith site. Although the Swisher site appears to be suitable for site characterization, the DOE has concluded that the Deaf Smith site is the preferred site in the Permian Basin and is proposing to nominate the Deaf Smith site rather than the Swisher site as one of the five sites suitable for characterization.

  15. Adjustment of footprint correction for airborne flux mapping over the FIFE site

    SciTech Connect

    Schuepp, P.H.; Macpherson, J.I.; Desjardins, R.L. Inst. for Aerospace Research, Ottawa Agriculture Canada, Centre for Land and Biological Resources Research, Ottawa )

    1992-11-01

    ORA meaningful interpretation of airborne flux estimates over nonuniform terrain must consider local advection from nonhomogeneous source distributions (footprint correction). An empirical procedure for footprint correction of airborne flux data obtained in the First ISLSCP Field Experiment (FIFE) 1989 is presented, based on simple analytical solutions of the diffusion equation which have been adjusted to approximate more realistic solutions. Optimized estimates of surface flux 'maps' derived from airborne observations are then constructed for maximum correlation between flux estimates and independently observed surface characteristics. This paper also includes an analysis of resolution for the given procedure, in terms of amplitude recovery of hypothetical square-wave distributions of surface flux density, and discusses its implications for the interpretation of the optimized estimates of FIFE surface flux maps. Results show that corrected spatial sink distributions are obtained by the current empirical procedure at the cost of considerable reduction in amplitude recovery of small-scale variations in surface flux density. The high spatial correlation observed between corrected flux maps and surface characteristics such as greenness or surface temperature excess is ascribed to the approximately correct positioning of the main flux gradients across the site, which can be expected to have been reproduced with amplitude recovery equal to or greater than 60 percent. 45 refs.

  16. Adjustment of footprint correction for airborne flux mapping over the FIFE site

    NASA Technical Reports Server (NTRS)

    Schuepp, P. H.; Macpherson, J. I.; Desjardins, R. L.

    1992-01-01

    A meaningful interpretation of airborne flux estimates over nonuniform terrain must consider local advection from nonhomogeneous source distributions (footprint correction). An empirical procedure for footprint correction of airborne flux data obtained in the First ISLSCP Field Experiment (FIFE) 1989 is presented, based on simple analytical solutions of the diffusion equation which have been adjusted to approximate more realistic solutions. Optimized estimates of surface flux 'maps' derived from airborne observations are then constructed for maximum correlation between flux estimates and independently observed surface characteristics. This paper also includes an analysis of resolution for the given procedure, in terms of amplitude recovery of hypothetical square-wave distributions of surface flux density, and discusses its implications for the interpretation of the optimized estimates of FIFE surface flux maps. Results show that corrected spatial sink distributions are obtained by the current empirical procedure at the cost of considerable reduction in amplitude recovery of small-scale variations in surface flux density. The high spatial correlation observed between corrected flux maps and surface characteristics such as greenness or surface temperature excess is ascribed to the approximately correct positioning of the main flux gradients across the site, which can be expected to have been reproduced with amplitude recovery equal to or greater than 60 percent.

  17. Identification and mapping of natural vegetation on a coastal site using a Worldview-2 satellite image.

    PubMed

    Rapinel, Sébastien; Clément, Bernard; Magnanon, Sylvie; Sellin, Vanessa; Hubert-Moy, Laurence

    2014-11-01

    Identification and mapping of natural vegetation are major issues for biodiversity management and conservation. Remotely sensed data with very high spatial resolution are currently used to study vegetation, but most satellite sensors are limited to four spectral bands, which is insufficient to identify some natural vegetation formations. The study objectives are to discriminate natural vegetation and identify natural vegetation formations using a Worldview-2 satellite image. The classification of the Worldview-2 image and ancillary thematic data was performed using a hybrid pixel-based and object-oriented approach. A hierarchical scheme using three levels was implemented, from land cover at a field scale to vegetation formation. This method was applied on a 48 km² site located on the French Atlantic coast which includes a classified NATURA 2000 dune and marsh system. The classification accuracy was very high, the Kappa index varying between 0.90 and 0.74 at land cover and vegetation formation levels respectively. These results show that Wordlview-2 images are suitable to identify natural vegetation. Vegetation maps derived from Worldview-2 images are more detailed than existing ones. They provide a useful medium for environmental management of vulnerable areas. The approach used to map natural vegetation is reproducible for a wider application by environmental managers.

  18. High throughput peptide mapping method for analysis of site specific monoclonal antibody oxidation.

    PubMed

    Li, Xiaojuan; Xu, Wei; Wang, Yi; Zhao, Jia; Liu, Yan-Hui; Richardson, Daisy; Li, Huijuan; Shameem, Mohammed; Yang, Xiaoyu

    2016-08-19

    Oxidation of therapeutic monoclonal antibodies (mAbs) often occurs on surface exposed methionine and tryptophan residues during their production in cell culture, purification, and storage, and can potentially impact the binding to their targets. Characterization of site specific oxidation is critical for antibody quality control. Antibody oxidation is commonly determined by peptide mapping/LC-MS methods, which normally require a long (up to 24h) digestion step. The prolonged sample preparation procedure could result in oxidation artifacts of susceptible methionine and tryptophan residues. In this paper, we developed a rapid and simple UV based peptide mapping method that incorporates an 8-min trypsin in-solution digestion protocol for analysis of oxidation. This method is able to determine oxidation levels at specific residues of a mAb based on the peptide UV traces within <1h, from either TBHP treated or UV light stressed samples. This is the simplest and fastest method reported thus far for site specific oxidation analysis, and can be applied for routine or high throughput analysis of mAb oxidation during various stability and degradation studies. By using the UV trace, the method allows more accurate measurement than mass spectrometry and can be potentially implemented as a release assay. It has been successfully used to monitor antibody oxidation in real time stability studies.

  19. High throughput peptide mapping method for analysis of site specific monoclonal antibody oxidation.

    PubMed

    Li, Xiaojuan; Xu, Wei; Wang, Yi; Zhao, Jia; Liu, Yan-Hui; Richardson, Daisy; Li, Huijuan; Shameem, Mohammed; Yang, Xiaoyu

    2016-08-19

    Oxidation of therapeutic monoclonal antibodies (mAbs) often occurs on surface exposed methionine and tryptophan residues during their production in cell culture, purification, and storage, and can potentially impact the binding to their targets. Characterization of site specific oxidation is critical for antibody quality control. Antibody oxidation is commonly determined by peptide mapping/LC-MS methods, which normally require a long (up to 24h) digestion step. The prolonged sample preparation procedure could result in oxidation artifacts of susceptible methionine and tryptophan residues. In this paper, we developed a rapid and simple UV based peptide mapping method that incorporates an 8-min trypsin in-solution digestion protocol for analysis of oxidation. This method is able to determine oxidation levels at specific residues of a mAb based on the peptide UV traces within <1h, from either TBHP treated or UV light stressed samples. This is the simplest and fastest method reported thus far for site specific oxidation analysis, and can be applied for routine or high throughput analysis of mAb oxidation during various stability and degradation studies. By using the UV trace, the method allows more accurate measurement than mass spectrometry and can be potentially implemented as a release assay. It has been successfully used to monitor antibody oxidation in real time stability studies. PMID:27432793

  20. Mapping the Sea Floor of the Historic Area Remediation Site (HARS) Offshore of New York City

    USGS Publications Warehouse

    Butman, Bradford

    2002-01-01

    The area offshore of New York City has been used for the disposal of dredged material for over a century. The area has also been used for the disposal of other materials such as acid waste, industrial waste, municipal sewage sludge, cellar dirt, and wood. Between 1976 and 1995, the New York Bight Dredged Material Disposal Site, also known as the Mud Dump Site (MDS), received on average about 6 million cubic yards of dredged material annually. In September 1997 the MDS was closed as a disposal site, and it and the surrounding area were designated as the Historic Area Remediation Site (HARS). The sea floor of the HARS, approximately 9 square nautical miles in area, currently is being remediated by placing a minimum 1-m-thick cap of clean dredged material on top of the surficial sediments that are contaminated from previous disposal of dredged and other materials. The U.S. Geological Survey (USGS) is working cooperatively with the U.S. Army Corps of Engineers (USACE) to map the sea floor geology of the HARS and changes in the characteristics of the surficial sediments over time.

  1. Mapping.

    ERIC Educational Resources Information Center

    Kinney, Douglas M.; McIntosh, Willard L.

    1979-01-01

    The area of geological mapping in the United States in 1978 increased greatly over that reported in 1977; state geological maps were added for California, Idaho, Nevada, and Alaska last year. (Author/BB)

  2. Human uroporphyrinogen III synthase: NMR-based mapping of the active site.

    PubMed

    Cunha, Luis; Kuti, Miklos; Bishop, David F; Mezei, Mihaly; Zeng, Lei; Zhou, Ming-Ming; Desnick, Robert J

    2008-05-01

    Uroporphyrinogen III synthase (URO-synthase) catalyzes the cyclization and D-ring isomerization of hydroxymethylbilane (HMB) to uroporphyrinogen (URO'gen) III, the cyclic tetrapyrrole and physiologic precursor of heme, chlorophyl, and corrin. The deficient activity of human URO-synthase results in the autosomal recessive cutaneous disorder, congenital erythropoietic porphyria. Mapping of the structural determinants that specify catalysis and, potentially, protein-protein interactions is lacking. To map the active site and assess the enzyme's possible interaction in a complex with hydroxymethylbilane-synthase (HMB-synthase) and/or uroporphyrinogen-decarboxylase (URO-decarboxylase) by NMR, an efficient expression and purification procedure was developed for these cytosolic enzymes of heme biosynthesis that enabled preparation of special isotopically-labeled protein samples for NMR characterization. Using an 800 MHz instrument, assignment of the URO-synthase backbone (13)C(alpha) (100%), (1)H(alpha) (99.6%), and nonproline (1)H(N) and (15)N resonances (94%) was achieved as well as 85% of the side-chain (13)C and (1)H resonances. NMR analyses of URO-synthase titrated with competitive inhibitors N(D)-methyl-1-formylbilane (NMF-bilane) or URO'gen III, revealed resonance perturbations of specific residues lining the cleft between the two major domains of URO synthase that mapped the enzyme's active site. In silico docking of the URO-synthase crystal structure with NMF-bilane and URO'gen III was consistent with the perturbation results and provided a 3D model of the enzyme-inhibitor complex. The absence of chemical shift changes in the (15)N spectrum of URO-synthase mixed with the homogeneous HMB-synthase holoenzyme or URO-decarboxylase precluded occurrence of a stable cytosolic enzyme complex. PMID:18004775

  3. 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

  4. Resource Conservation and Recovery Act industrial site environmental restoration, site characterization plan: Area 6 Decontamination Pond Facility. Revision 1

    SciTech Connect

    1996-08-01

    This plan presents the strategy for the characterization of the Area 6 Decontamination Pond Facility at the Nevada Test Site which will be conducted for the US Department of Energy, Nevada Operations Office, Environmental Restoration Division. The objectives of the planned activities are to: obtain sufficient, sample analytical data from which further assessment, remediation, and/or closure strategies may be developed for the site; obtain sufficient, sample analytical data for management of investigation-derived waste. The scope of the characterization may include surface radiation survey(s), surface soil sampling, subsurface soil boring (i.e., drilling), and sampling of soil in and around the pond; in situ sampling of the soil within subsurface soil borings; and sample analysis for both site characterization and waste management purposes.

  5. Acoustic mapping of the regional seafloor geology in and around Hawaiian ocean dredged-material disposal sites

    USGS Publications Warehouse

    Torresan, Michael E.; Gardner, James V.

    2000-01-01

    During January and February 1998 the U.S. Geological Survey Coastal and Marine Geology Team (USGS) conducted regional high-resolution multibeam mapping surveys of the area surrounding EPA-designated ocean disposal sites located offshore of the Hawaiian Islands of Oahu, Kauai, Maui, and Hawaii. The sites are all located within 5 nautical miles of shore on insular shelves or slopes. Regional maps were required of areas much larger than the disposal sites themselves to assess both the regional seafloor geology and the immediate vicinity of the disposal sites. The purpose of the disposal site surveys was to delimit the extent of disposal material by producing detailed bathymetric and backscatter maps of the seafloor with a ± 1 m spatial accuracy and <1% depth error. The advantage of using multibeam over conventional towed, single-beam sidescan sonar is that the multibeam data are accurately georeferenced for precise location of all imaged features. The multibeam produces a coregistered acoustic-backscatter map that is often required to locate individual disposal deposits. These data were collected by the USGS as part of its regional seafloor mapping and in support of ocean disposal site monitoring studies conducted in cooperation with the US Environmental Protection Agency (EPA) and the US Army Corps of Engineers (COE).

  6. Direct optical mapping of transcription factor binding sites on field-stretched λ-DNA in nanofluidic devices

    PubMed Central

    Sriram, K. K.; Yeh, Jia-Wei; Lin, Yii-Lih; Chang, Yi-Ren; Chou, Chia-Fu

    2014-01-01

    Mapping transcription factor (TF) binding sites along a DNA backbone is crucial in understanding the regulatory circuits that control cellular processes. Here, we deployed a method adopting bioconjugation, nanofluidic confinement and fluorescence single molecule imaging for direct mapping of TF (RNA polymerase) binding sites on field-stretched single DNA molecules. Using this method, we have mapped out five of the TF binding sites of E. coli RNA polymerase to bacteriophage λ-DNA, where two promoter sites and three pseudo-promoter sites are identified with the corresponding binding frequency of 45% and 30%, respectively. Our method is quick, robust and capable of resolving protein-binding locations with high accuracy (∼ 300 bp), making our system a complementary platform to the methods currently practiced. It is advantageous in parallel analysis and less prone to false positive results over other single molecule mapping techniques such as optical tweezers, atomic force microscopy and molecular combing, and could potentially be extended to general mapping of protein–DNA interaction sites. PMID:24753422

  7. Quantitative analysis of anthropogenic relief features: automated mapping of charcoal kiln sites from high-resolution ALS data

    NASA Astrophysics Data System (ADS)

    Schneider, Anna; Takla, Melanie; Nicolay, Alexander; Raab, Alexandra; Raab, Thomas

    2014-05-01

    High-resolution digital elevation data from airborne laser scanning (ALS) allow for identification and mapping of so far unknown small-scale relief features that are hidden by forest cover. Especially as a result of historic land use, small anthropogenic landforms can occur, e.g., remains of charcoal kilns on sites that were used for charcoal production or ridge and furrow systems in former farmland areas. Mapping such relief features and analyzing their spatial distribution patterns can help to understand past land-use systems and their effects on landscapes. To efficiently detect and quantify small-scale relief features from high-resolution DEMs for larger areas, (semi-) automated mapping routines are required. In order to describe the number and spatial distribution of historic charcoal kiln sites in the area around Cottbus, Germany, we developed a GIS-based routine for the detection and mapping of kiln remnants from ALS elevation models with a resolution of 1 or 2 meters. The method is based on a template matching algorithm, using a combination of morphometric parameters, and is implemented within ArcGIS. The mapping results could be validated against a comprehensive database of kiln sites and diameters recorded from archaeological excavations in the forefield of the opencast mine Jänschwalde and from manual digitization of kiln remnants from Shaded Relief maps for the Jänschwalder Heide and the Tauersche Forst, north of Cottbus. A considerably high number of charcoal kiln sites could be detected in ALS data, and the diameters of the identified charcoal kilns are remarkable large in the area. For the Jänschwalder Heide, more than 5000 kiln sites in an area of 32 km2 were detected by manual digitization, with 1355 kiln sites that are wider than 12 m. These relatively large kiln sites could be mapped with detection rates that are close to those of manual digitization using the automated mapping routine. Detection quality was improved by the combination of

  8. Discovery and information-theoretic characterization of transcription factor binding sites that act cooperatively

    NASA Astrophysics Data System (ADS)

    Clifford, Jacob; Adami, Christoph

    2015-10-01

    Transcription factor binding to the surface of DNA regulatory regions is one of the primary causes of regulating gene expression levels. A probabilistic approach to model protein-DNA interactions at the sequence level is through position weight matrices (PWMs) that estimate the joint probability of a DNA binding site sequence by assuming positional independence within the DNA sequence. Here we construct conditional PWMs that depend on the motif signatures in the flanking DNA sequence, by conditioning known binding site loci on the presence or absence of additional binding sites in the flanking sequence of each site's locus. Pooling known sites with similar flanking sequence patterns allows for the estimation of the conditional distribution function over the binding site sequences. We apply our model to the Dorsal transcription factor binding sites active in patterning the Dorsal-Ventral axis of Drosophila development. We find that those binding sites that cooperate with nearby Twist sites on average contain about 0.5 bits of information about the presence of Twist transcription factor binding sites in the flanking sequence. We also find that Dorsal binding site detectors conditioned on flanking sequence information make better predictions about what is a Dorsal site relative to background DNA than detection without information about flanking sequence features.

  9. Discovery and information-theoretic characterization of transcription factor binding sites that act cooperatively.

    PubMed

    Clifford, Jacob; Adami, Christoph

    2015-09-02

    Transcription factor binding to the surface of DNA regulatory regions is one of the primary causes of regulating gene expression levels. A probabilistic approach to model protein-DNA interactions at the sequence level is through position weight matrices (PWMs) that estimate the joint probability of a DNA binding site sequence by assuming positional independence within the DNA sequence. Here we construct conditional PWMs that depend on the motif signatures in the flanking DNA sequence, by conditioning known binding site loci on the presence or absence of additional binding sites in the flanking sequence of each site's locus. Pooling known sites with similar flanking sequence patterns allows for the estimation of the conditional distribution function over the binding site sequences. We apply our model to the Dorsal transcription factor binding sites active in patterning the Dorsal-Ventral axis of Drosophila development. We find that those binding sites that cooperate with nearby Twist sites on average contain about 0.5 bits of information about the presence of Twist transcription factor binding sites in the flanking sequence. We also find that Dorsal binding site detectors conditioned on flanking sequence information make better predictions about what is a Dorsal site relative to background DNA than detection without information about flanking sequence features.

  10. Concept Mapping as a Support for Mars Landing-Site Selection

    NASA Technical Reports Server (NTRS)

    Cabrol, Nathalie A.; Briggs, Geoffrey A.

    1999-01-01

    The NASA Ames' Center for Mars Exploration (CMEX) serves to coordinate Mars programmatic research at ARC in the sciences, in information technology and in aero-assist and other technologies. Most recently, CMEX has been working with the Institute for Human and Machine Cognition at the University of West Florida to develop a new kind of web browser based on the application of concept maps. These Cmaps, which are demonstrably effective in science teaching, can be used to provide a new kind of information navigation tool that can make web or CD based information more meaningful and more easily navigable. CMEX expects that its 1999 CD-ROM will have this new user interface. CMEX is also engaged with the Mars Surveyor Project Office at JPL in developing an Internet-based source of materials to support the process of selecting landing sites for the next series of Mars landers. This activity -- identifying the most promising sites from which to return samples relevant to the search for evidence of life -- is one that is expected to engage the general public as well as the science community. To make the landing site data easily accessible and meaningful to the public, CMEX is planning to use the IHMC Cmap browser as its user interface.

  11. Global transcriptional start site mapping using differential RNA sequencing reveals novel antisense RNAs in Escherichia coli.

    PubMed

    Thomason, Maureen K; Bischler, Thorsten; Eisenbart, Sara K; Förstner, Konrad U; Zhang, Aixia; Herbig, Alexander; Nieselt, Kay; Sharma, Cynthia M; Storz, Gisela

    2015-01-01

    While the model organism Escherichia coli has been the subject of intense study for decades, the full complement of its RNAs is only now being examined. Here we describe a survey of the E. coli transcriptome carried out using a differential RNA sequencing (dRNA-seq) approach, which can distinguish between primary and processed transcripts, and an automated prediction algorithm for transcriptional start sites (TSS). With the criterion of expression under at least one of three growth conditions examined, we predicted 14,868 TSS candidates, including 5,574 internal to annotated genes (iTSS) and 5,495 TSS corresponding to potential antisense RNAs (asRNAs). We examined expression of 14 candidate asRNAs by Northern analysis using RNA from wild-type E. coli and from strains defective for RNases III and E, two RNases reported to be involved in asRNA processing. Interestingly, nine asRNAs detected as distinct bands by Northern analysis were differentially affected by the rnc and rne mutations. We also compared our asRNA candidates with previously published asRNA annotations from RNA-seq data and discuss the challenges associated with these cross-comparisons. Our global transcriptional start site map represents a valuable resource for identification of transcription start sites, promoters, and novel transcripts in E. coli and is easily accessible, together with the cDNA coverage plots, in an online genome browser.

  12. Digital Geologic Map of the Nevada Test Site and Vicinity, Nye, Lincoln, and Clark Counties, Nevada, and Inyo County, California

    USGS Publications Warehouse

    Slate, Janet L.; Berry, Margaret E.; Rowley, Peter D.; Fridrich, Christopher J.; Morgan, Karen S.; Workman, Jeremiah B.; Young, Owen D.; Dixon, Gary L.; Williams, Van S.; McKee, Edwin H.; Ponce, David A.; Hildenbrand, Thomas G.; Swadley, W.C.; Lundstrom, Scott C.; Ekren, E. Bartlett; Warren, Richard G.; Cole, James C.; Fleck, Robert J.; Lanphere, Marvin A.; Sawyer, David A.; Minor, Scott A.; Grunwald, Daniel J.; Laczniak, Randell J.; Menges, Christopher M.; Yount, James C.; Jayko, Angela S.

    1999-01-01

    This digital geologic map of the Nevada Test Site (NTS) and vicinity, as well as its accompanying digital geophysical maps, are compiled at 1:100,000 scale. The map compilation presents new polygon (geologic map unit contacts), line (fault, fold axis, metamorphic isograd, dike, and caldera wall) and point (structural attitude) vector data for the NTS and vicinity, Nye, Lincoln, and Clark Counties, Nevada, and Inyo County, California. The map area covers two 30 x 60-minute quadrangles-the Pahute Mesa quadrangle to the north and the Beatty quadrangle to the south-plus a strip of 7.5-minute quadrangles on the east side-72 quadrangles in all. In addition to the NTS, the map area includes the rest of the southwest Nevada volcanic field, part of the Walker Lane, most of the Amargosa Desert, part of the Funeral and Grapevine Mountains, some of Death Valley, and the northern Spring Mountains. This geologic map improves on previous geologic mapping of the same area (Wahl and others, 1997) by providing new and updated Quaternary and bedrock geology, new geophysical interpretations of faults beneath the basins, and improved GIS coverages. Concurrent publications to this one include a new isostatic gravity map (Ponce and others, 1999) and a new aeromagnetic map (Ponce, 1999).

  13. Resource Conservation and Recovery Act industrial site environmental restoration site characterization plan. Area 6 Steam Cleaning Effluent Ponds

    SciTech Connect

    1996-02-01

    This plan presents the strategy for the characterization of the Area 6 South and North Steam Cleaning Effluent Ponds (SCEPs) at the Nevada Test Site (NTS) to be conducted for the US Department of Energy, Nevada Operations Office (DOE/NV), Environmental Restoration Division (ERD). The purposes of the planned activities are to: obtain sufficient, sample analytical data from which further assessment, remediation, and/or closure strategies may be developed for the site; obtain sufficient, sample analytical data for management of investigation-derived waste (IDW). The scope of the characterization may include excavation, drilling, and sampling of soil in and around both ponds; sampling of the excavated material; in situ sampling of the soil at the bottom and on the sides of the excavations as well as within subsurface borings; and conducting sample analysis for both characterization and waste management purposes. Contaminants of concern include RCRA-regulated VOCs and metals.

  14. Resource Conservation and Recovery Act Industrial Site Environmental Restoration Site Characterization Plan, Area 6 Decontamination Pond Facility, Revision 1

    SciTech Connect

    1996-08-12

    This plan presents the strategy for the characterization of the Area 6 Decontamination Pond Facility (DPF) at the Nevada Test Site (NTS) which will be conducted for the U.S. Department of Energy, Nevada Operations OffIce (DOE/NV), Environmental Restoration Division (ERD). The objectives of the planned activities are to: o Obtain sufficient, ample analytical data from which further assessment, remediation, and/or closure strategies maybe developed for the site. o Obtain sufficient, sample analytical data for management of investigation-derived waste. All references to regulations contained in this plan are to the versions of the regulations that are current at the time of publication of this plan. The scope of the characterization may include surface radiation survey(s), surface soil sampling, subsurface soil boring (i.e., drilling), and sampling of soil in and Mound the pond; in situ sampling of the soil within subsurface soil borings; and sample analysis for both site . . characterization and waste management purposes.

  15. Airborne lidar mapping of vertical ozone distributions in support of the 1990 Clean Air Act Amendments

    NASA Technical Reports Server (NTRS)

    Uthe, Edward E.; Nielsen, Norman B.; Livingston, John M.

    1992-01-01

    The 1990 Clean Air Act Amendments mandated attainment of the ozone standard established by the U.S. Environmental Protection Agency. Improved photochemical models validated by experimental data are needed to develop strategies for reducing near surface ozone concentrations downwind of urban and industrial centers. For more than 10 years, lidar has been used on large aircraft to provide unique information on ozone distributions in the atmosphere. However, compact airborne lidar systems are needed for operation on small aircraft of the type typically used on regional air quality investigations to collect data with which to develop and validate air quality models. Data presented in this paper will consist of a comparison between airborne differential absorption lidar (DIAL) and airborne in-situ ozone measurements. Also discussed are future plans to improve the airborne ultraviolet-DIAL for ozone and other gas observations and addition of a Fourier Transform Infrared (FTIR) emission spectrometer to investigate the effects of other gas species on vertical ozone distribution.

  16. Mapping of noise impact provoked by the execution of foundation piles at high rise building sites.

    PubMed

    de Araújo, Adolpho Guido; Gusmão, Alexandre Duarte; Rabbani, Emilia Rahnemay Kohman; Fucale, Stela Paulino

    2012-01-01

    The objective of this work is to map, in a limited area inside and outside of the worksite, the environmental impact generated by sound pollution coming from the driving of foundation piles for high rise buildings, as well as to observe and check if the noise levels produced by the emitting source are tolerable in the urban environment. The methodology of the work includes a survey of technical references about the subject; measurement of noises surrounding the worksite during the foundation phase for four distinct buildings, with different types of piles: prefabricated piles, continuous helical displacement piles , traditional compaction piles and Terra Probe compaction piles. A grid of points was built due to the time of driving and after that the measurements of environmental noises were performed emitted by the execution of each type of pile using a sound level meter. The interpretation of the measurements and their impacts on the neighborhood of the building were performed using the computational tool Suffer for creating noise level contours. The X and Y axes of the grid represent the distances in meters of the area studied and the Z axis represents the noise measured in dB. The contours developed represent the mapping of the noise at the worksites and their surroundings. The mapping of the urban impact of noise, the measurement of its dimensions, and the examination of its propagation around the building are important subsides to adequate individual and collective protection procedures. Seventy one points were measured at four building sites with different types of piles, and the results showed that at only three points was the noise within the limits of the Municipal Law of Recife of 70 dB, which proves the relevance of the research. Finally, the comparative analysis between the four types of piles shows that the continuous helical displacement pile emits the lowest noise level among the four pile types studied.

  17. Mapping of noise impact provoked by the execution of foundation piles at high rise building sites.

    PubMed

    de Araújo, Adolpho Guido; Gusmão, Alexandre Duarte; Rabbani, Emilia Rahnemay Kohman; Fucale, Stela Paulino

    2012-01-01

    The objective of this work is to map, in a limited area inside and outside of the worksite, the environmental impact generated by sound pollution coming from the driving of foundation piles for high rise buildings, as well as to observe and check if the noise levels produced by the emitting source are tolerable in the urban environment. The methodology of the work includes a survey of technical references about the subject; measurement of noises surrounding the worksite during the foundation phase for four distinct buildings, with different types of piles: prefabricated piles, continuous helical displacement piles , traditional compaction piles and Terra Probe compaction piles. A grid of points was built due to the time of driving and after that the measurements of environmental noises were performed emitted by the execution of each type of pile using a sound level meter. The interpretation of the measurements and their impacts on the neighborhood of the building were performed using the computational tool Suffer for creating noise level contours. The X and Y axes of the grid represent the distances in meters of the area studied and the Z axis represents the noise measured in dB. The contours developed represent the mapping of the noise at the worksites and their surroundings. The mapping of the urban impact of noise, the measurement of its dimensions, and the examination of its propagation around the building are important subsides to adequate individual and collective protection procedures. Seventy one points were measured at four building sites with different types of piles, and the results showed that at only three points was the noise within the limits of the Municipal Law of Recife of 70 dB, which proves the relevance of the research. Finally, the comparative analysis between the four types of piles shows that the continuous helical displacement pile emits the lowest noise level among the four pile types studied. PMID:22317218

  18. Global transcriptional start site mapping in Geobacter sulfurreducens during growth with two different electron acceptors.

    PubMed

    González, Getzabeth; Labastida, Aurora; Jímenez-Jacinto, Verónica; Vega-Alvarado, Leticia; Olvera, Maricela; Morett, Enrique; Juárez, Katy

    2016-09-01

    Geobacter sulfurreducens is an anaerobic soil bacterium that is involved in biogeochemical cycles of elements such as Fe and Mn. Although significant progress has been made in the understanding of the electron transfer processes in G. sulfurreducens, little is known about the regulatory mechanisms involved in their control. To expand the study of gene regulation in G. sulfurreducens, we carried out a genome-wide identification of transcription start sites (TSS) by 5'RACE and by deep RNA sequencing of primary mRNAs in two growth conditions. TSSs were identified along G. sulfurreducens genome and over 50% of them were located in the upstream region of the associated gene, and in some cases we detected genes with more than one TSS. Our global mapping of TSSs contributes with valuable information, which is needed for the study of transcript structure and transcription regulation signals and can ultimately contribute to the understanding of transcription initiation phenomena in G. sulfurreducens. PMID:27488344

  19. Geologic map of the Mine Mountain area, Nevada Test Site, southern Nevada

    SciTech Connect

    Cashman, P.H.; Cole, J.C.

    1998-10-05

    The Mine Mountain area is a small range of hills on the west side of the central Yucca Flat basin on the Nevada Test Site, Nye County, Nevada. This map portrays the very complex relationships among the pre-Tertiary stratigraphic units of the region. Rocks and structures of the Mine Mountain area record the compounded effects of: (1) eastward-directed, foreland-vergent thrusting; (2) younger folds and thrusts formed by hinterland vergence in a general westerly direction; and (3) low-angle normal faulting formed by extension along a northeast-southwest trend. All of these structures are older than the oldest middle Miocene volcanic rocks that were deposited on the flanks of the Mine Mountain terrane. High-angle faults that post-date these volcanic rocks locally show displacements of several hundred meters, but do not strongly affect patterns in the pre-Tertiary rocks.

  20. Site-specific Probabilistic Seismic Hazard Map of Himachal Pradesh, India. Part II. Hazard Estimation

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

    This article presents site-specific probable seismic hazard of the Himachal Pradesh province, situated in a seismically active region of northwest Himalaya, using the ground motion relations presented in a companion article. Seismic recurrence parameters for all the documented probable sources are established from an updated earthquake catalogue. The contour maps of probable spectral acceleration at 0, 0.2, and 1 s (5% damping) are presented for 475 and 2475 years return periods. Also, the hazard curves and uniform hazard response spectrums are presented for all the important cities in this province. Results indicate that the present codal provision underestimates the seismic hazard at cities of Bilaspur, Shimla, Hamirpur, Chamba, Mandi, and Solan. In addition, regions near Bilaspur and Chamba exhibit higher hazard levels than what is reported in literature.

  1. Using Hadoop File System and MapReduce in a small/medium Grid site

    NASA Astrophysics Data System (ADS)

    Riahi, H.; Donvito, G.; Fanò, L.; Fasi, M.; Marzulli, G.; Spiga, D.; Valentini, A.

    2012-12-01

    Data storage and data access represent the key of CPU-intensive and data-intensive high performance Grid computing. Hadoop is an open-source data processing framework that includes fault-tolerant and scalable distributed data processing model and execution environment, named MapReduce, and distributed File System, named Hadoop distributed File System (HDFS). HDFS was deployed and tested within the Open Science Grid (OSG) middleware stack. Efforts have been taken to integrate HDFS with gLite middleware. We have tested the File System thoroughly in order to understand its scalability and fault-tolerance while dealing with small/medium site environment constraints. To benefit entirely from this File System, we made it working in conjunction with Hadoop Job scheduler to optimize the executions of the local physics analysis workflows. The performance of the analysis jobs which used such architecture seems to be promising, making it useful to follow up in the future.

  2. An integrated study of spatial multicriteria analysis and mathematical modelling for managed aquifer recharge site suitability mapping and site ranking at Northern Gaza coastal aquifer.

    PubMed

    Rahman, Mohammad Azizur; Rusteberg, Bernd; Uddin, Mohammad Salah; Lutz, Annegret; Saada, Muath Abu; Sauter, Martin

    2013-07-30

    This paper describes an integrated approach of site suitability mapping and ranking of the most suitable sites, for the implementation of Managed Aquifer Recharge (MAR) projects, using spatial multicriteria decision analysis (SMCDA) techniques and mathematical modelling. The SMCDA procedure contains constraint mapping, site suitability analysis with criteria standardization and weighting, criteria overlay by analytical hierarchy process (AHP) combined with weighted linear combination (WLC) and ordered weighted averaging (OWA), and sensitivity analysis. The hydrogeological impacts of the selected most suitable sites were quantified by using groundwater flow and transport modelling techniques. Finally, ranking of the selected sites was done with the WLC method. The integrated approach is demonstrated by a case study in the coastal aquifer of North Gaza. Constraint mapping shows that 50% of the total study area is suitable for MAR implementation. About 25% of the total area is "very good" and 25% percent is "good" for MAR, according to the site suitability analysis. Six locations were selected and ranked against six representative decision criteria. Long term (year 2003 to year 2040) groundwater flow and transport simulations were performed to quantify the selected criteria under MAR project operation conditions at the selected sites. Finally, the suitability mapping and hydrogeological investigation recommends that the location of the existing infiltration ponds, constructed near the planned North Gaza Wastewater Treatment Plant (NGWWTP) is most suitable for MAR project implementation. This paper concludes that mathematical modelling should be combined with the SMCDA technique in order to select the best location for MAR project implementation. Besides MAR project implementation, the generalised approach can be applicable for any other water resources development project that deals with site selection and implementation. PMID:23603773

  3. Mapping air pollution using Earth observation techniques for cultural heritage sites

    NASA Astrophysics Data System (ADS)

    Agapiou, Athos; Nisantzi, Argyro; Lysandrou, Vasiliki; Mamouri, Rodanthi; Alexakis, Dimitrios D.; Themistocleous, Kyriacos; Sarris, Apostolos; Hadjimitsis, Diofantos G.

    2013-08-01

    Air pollutants, together with climatic parameters, are of major importance for the deterioration of cultural heritage monuments. Atmospheric pollution is widely recognized as one of the major anthropogenic threats to architectural cultural heritage, in particular when associated with water absorption phenomena. Atmospheric particle deposition on surfaces of Monuments (of cultural heritage interest) may cause an aesthetic impact induced by a series of chemical reactions. Therefore there is a need for systematic monitoring and mapping of air pollution for areas where important archaeological sites and monuments are found. observation techniques, such as the use of satellite image for the retrieval of Aerosol Optical Thickness (AOT), are ideal for this purpose. In this paper, all important monuments of the Paphos District, listed by the Department of Antiquities of Cyprus, have been mapped using Geographical Information Systems. Several recent (2012) MODIS satellite images (both Aqua and Terra) have been used to extract the AOT values in this area. Multi-temporal analysis was performed to identify areas of high risk where AOT values are considered to be high. In situ observations have been also carried out to verify the results.

  4. Landing Site Selection and Surface Traverse Planning using the Lunar Mapping & Modeling Portal

    NASA Astrophysics Data System (ADS)

    Law, E.; Chang, G.; Bui, B.; Sadaqathullah, S.; Kim, R.; Dodge, K.; Malhotra, S.

    2013-12-01

    Introduction: The Lunar Mapping and Modeling Portal (LMMP), is a web-based Portal and a suite of interactive visualization and analysis tools for users to access mapped lunar data products (including image mosaics, digital elevation models, etc.) from past and current lunar missions (e.g., Lunar Reconnaissance Orbiter, Apollo, etc.), and to perform in-depth analyses to support lunar surface mission planning and system design for future lunar exploration and science missions. It has been widely used by many scientists mission planners, as well as educators and public outreach (e.g., Google Lunar XPRICE teams, RESOLVE project, museums etc.) This year, LMMP was used by the Lunar and Planetary Institute (LPI)'s Lunar Exploration internship program to perform lighting analysis and local hazard assessments, such as, slope, surface roughness and crater/boulder distribution to research landing sites and surface pathfinding and traversal. Our talk will include an overview of LMMP, a demonstration of the tools as well as a summary of the LPI Lunar Exploration summer interns' experience in using those tools.

  5. Genome-wide mapping of DNase I hypersensitive sites in plants.

    PubMed

    Zhang, Wenli; Jiang, Jiming

    2015-01-01

    Genomic regions associated with regulatory proteins are known to be highly sensitive to DNase I digestion and are termed DNase I hypersensitive sites (DHSs). DHSs can be identified by DNase I digestion followed by high-throughput DNA sequencing (DNase-seq). DNase-seq has become a powerful technique for genome-wide mapping of chromatin accessibility in eukaryotes with a sequenced genome. We have developed a DNase-seq procedure in plants. This procedure was adapted from the protocol originally developed for mammalian cell lines. It includes plant nuclei isolation, digestion of purified nuclei with DNase I, recovery of DNase-trimmed DNA fragments, DNase-seq library development, Illumina sequencing and data analysis. We also introduce a barcoding system for library preparation. We have conducted DNase-seq in both Arabidopsis thaliana and rice, and developed genome-wide open chromatin maps in both species. These DHS datasets have been used to detect footprints from regulatory protein binding and to reveal genome-wide nucleosome positioning patterns.

  6. Covariance of biophysical data with digital topographic and land use maps over the FIFE site

    NASA Astrophysics Data System (ADS)

    Davis, F. W.; Schimel, D. S.; Friedl, M. A.; Michaelsen, J. C.; Kittel, T. G. F.; Dubayah, R.; Dozier, J.

    1992-11-01

    Sampling design is critical in locating ground sampling stations for large-scale climatological field experiments. In the stratified sampling design adopted for the First International Satellite Land Surface Climatology Project (ISLSCP) Field Experiment (FIFE), the study region was stratified into 14 different terrain units based on land use/land cover and topographic variables that were hypothesized to have a strong influence on surface biophysical properties. Digital terrain maps were produced to facilitate ground data integration and extrapolation. This paper describes the biophysical stratification of the FIFE site, implementation of the stratification using geographic information system (GIS) techniques, and validation of the stratification with respect to field measurements of biomass, soil moisture, Bowen ratio (β), and the greenness vegetation index (GVI) derived from thematic mapper satellite data. Maps of burning and topographic position were significantly associated with variation in biomass, GVI, and β. The effects of burning and topography were stronger for the Konza Prairie Long-Term Ecological Research (KPLTER) site than for the rest of the FIFE site, where cattle grazing was a major confounding effect. The stratified design did not appreciably change the estimated site-wide means for surface climate parameters but accounted for between 25 and 45% of the sample variance depending on the variable. The design was weakened by undersampling of several strata, by high within-station variance in soil and vegetation data, and by failure to account for diverse land management practices on private lands surrounding KPLTER. We recommend that future large-scale climatological studies include the development of a digital terrain data base well in advance of field campaigns and that multitemporal imagery be used to obtain preliminary estimates of spatial and temporal variance in surface biophysical properties. We also recommend that sampling for the most

  7. Mapping of Protein–Protein Interaction Sites by the ‘Absence of Interference’ Approach

    PubMed Central

    Dhayalan, Arunkumar; Jurkowski, Tomasz P.; Laser, Heike; Reinhardt, Richard; Jia, Da; Cheng, Xiaodong; Jeltsch, Albert

    2008-01-01

    Protein–protein interactions are critical to most biological processes, and locating protein–protein interfaces on protein structures is an important task in molecular biology. We developed a new experimental strategy called the ‘absence of interference’ approach to determine surface residues involved in protein–protein interaction of established yeast two-hybrid pairs of interacting proteins. One of the proteins is subjected to high-level randomization by error-prone PCR. The resulting library is selected by yeast two-hybrid system for interacting clones that are isolated and sequenced. The interaction region can be identified by an absence or depletion of mutations. For data analysis and presentation, we developed a Web interface that analyzes the mutational spectrum and displays the mutational frequency on the surface of the structure (or a structural model) of the randomized protein†. Additionally, this interface might be of use for the display of mutational distributions determined by other types of random mutagenesis experiments. We applied the approach to map the interface of the catalytic domain of the DNA methyltransferase Dnmt3a with its regulatory factor Dnmt3L. Dnmt3a was randomized with high mutational load. A total of 76 interacting clones were isolated and sequenced, and 648 mutations were identified. The mutational pattern allowed to identify a unique interaction region on the surface of Dnmt3a, which comprises about 500−600 Å2. The results were confirmed by site-directed mutagenesis and structural analysis. The absence-of-interference approach will allow high-throughput mapping of protein interaction sites suitable for functional studies and protein docking. PMID:18191145

  8. Application of time domain induced polarization to the mapping of lithotypes in a landfill site

    NASA Astrophysics Data System (ADS)

    Gazoty, A.; Fiandaca, G.; Pedersen, J.; Auken, E.; Christiansen, A. V.; Pedersen, J. K.

    2012-01-01

    A DC resistivity (DC) and Time Domain Induced Polarization (TDIP) survey was undertaken at a decommissioned landfill site situated in Hørløkke, Denmark, for the purpose of mapping the waste deposits and to discriminate important geological units that control the hydrology of the surrounding area. It is known that both waste deposits and clay have clear signatures in TDIP data, making possible to enhance the resolution of geological structures, when compared to DC surveys alone. Four DC/TDIP profiles were carried out crossing the landfill and another seven profiles in the surroundings, giving a dense coverage over the entire area. The whole dataset was inverted using a 1-D Laterally Constrained Inversion scheme, recently implemented for IP data, in order to use the entire decay curves for reconstructing the electrical parameters of the soil in terms of the Cole-Cole polarization model. Results show that it is possible to both resolve the geometry of the buried waste body and key geological structures. In particular, it was possible to find a silt/clay lens at depth, which correlates with the flow direction of the pollution plume spreading out from the landfill, and to map a shallow sandy layer rich in clay that likely has a strong influence on the hydrology of the site. This interpretation of the geophysical findings was constrained by boreholes data, in terms of geology and gamma ray logging. The results of this study are important for the impact that the resolved geological units have in the hydrology of the area, making it possible to construct more realistic scenarios of the variation of the pollution plume as a function of the climate change.

  9. Application of time domain induced polarization to the mapping of lithotypes in a landfill site

    NASA Astrophysics Data System (ADS)

    Gazoty, A.; Fiandaca, G.; Pedersen, J.; Auken, E.; Christiansen, A. V.; Pedersen, J. K.

    2012-06-01

    A direct current (DC) resistivity and time domain induced polarization (TDIP) survey was undertaken at a decommissioned landfill site situated in Hørløkke, Denmark, for the purpose of mapping the waste deposits and to discriminate important geological units that control the hydrology of the surrounding area. It is known that both waste deposits and clay have clear signatures in TDIP data, making it possible to enhance the resolution of geological structures compared to DC surveys alone. Four DC/TDIP profiles were carried out crossing the landfill, and another seven profiles in the surroundings provide a sufficiently dense coverage of the entire area. The whole dataset was inverted using a 1-D laterally constrained inversion scheme, recently implemented for TDIP data, in order to use the entire decay curves for reconstructing the electrical parameters of the soil in terms of the Cole-Cole polarization model. Results show that it is possible to resolve both the geometry of the buried waste body and key geological structures. In particular, it was possible to find a silt/clay lens at depth that correlates with the flow direction of the pollution plume spreading out from the landfill and to map a shallow sandy layer rich in clay that likely has a strong influence on the hydrology of the site. This interpretation of the geophysical findings was constrained by borehole data, in terms of geology and gamma ray logging. The results of this study are important for the impact of the resolved geological units on the hydrology of the area, making it possible to construct more realistic scenarios of the variation of the pollution plume as a function of the climate change.

  10. Treatment of plutonium contaminated soil/sediment from the Mound site using the ACT*DE*CON{sup SM} process

    SciTech Connect

    Negri, M.C.; Swift, N.A.; North, J.P.

    1996-10-01

    The removal and/or treatment of contaminated soil is a major problem facing the US DOE. The EG&G Mound Applied Technologies site in Miamisburg, Ohio, has an estimated 1.5 million cubic feet of soils from past disposal and waste burial practices awaiting remediation from plutonium contamination. This amount includes sediment from the Miami-Erie Canal that was contaminated in 1969 following a pipe- rupture accident. Conventional soil washing techniques that use particle separation would generate too large a waste volume to be economically feasible. Therefore, innovative technologies are needed for the cleanup. The ACT*DE*CON process was developed by SELENTEC for washing soils to selectively dissolve and remove heavy metals and radionuclides. ACT*DE*CON chemically dissolves and removes heavy metals and radionuclides from soils and sediments into an aqueous medium. The ACT*DE*CON process uses oxidative carbonate/chelant chemistry to dissolve the contaminant from the sediment and hold the contaminant in solution. The objective of recent work was to document the proves conditions necessary to achieve the Mound-site and regulatory-cleanup goals using the ACT*DE*CON technology.

  11. Improving the Apollo 12 landing site mapping with Chandrayaan M3 data

    NASA Astrophysics Data System (ADS)

    Chemin, Yann; Crawford, Ian; Bugiolacchi, Roberto; Irfan, Huma; Alexander, Louise

    2014-05-01

    The geology of the Apollo 12 landing site has been the subject of many studies, including recently by Korotev et al. (2011) and Snape et al. (2013). This research attempts to bring additional understanding from a remote sensing perspective using the Moon Mineralogy Mapper (M3) sensor data, onboard the Chandrayaan lunar orbiter. This has a higher spatial-spectral resolution sensor than the Clementine UV-Vis sensor and provides the opportunity to study the lunar surface with detailed spectral signatures. Mapping of FeO (wt%) and TiO2 (wt%) is done using the methods of Lucey et al. (2000) and Wilcox et al. (2005). A FeO & TiO2 processing module (i.feotio2) is made specifically for this research within the Free & Open Source Software GRASS GIS. Attempts will be made to estimate the lava flow thickness using the method of Bugiolacchi et al. (2006) and individual lava layers thicknesses (Weider et al., 2010). Integration of this new information will be put in perspective and integrated with previous work. Analysis from the combined higher spatial and spectral resolutions will improve the accuracy of the geological mapping at the Apollo 12 landing site. References Bugiolacchi, R., Spudis, P.D., Guest, J.E., 2006. Stratigraphy and composition of lava flows in Mare Nubium and Mare Cognitum. Meteoritics & Planetary Science. 41(2):285-304. Korotev, R.L., Jolliff, B.L., Zeigler, R.A., Seddio, S.M., Haskin, L.A., 2011. Apollo 12 revisited. Geochimica et Cosmochimica Acta. 75(6):1540-1573. Lucey, P.G., Blewett, D.T., Jolliff, B.L., 2000. Lunar iron and titanium abundance algorithms based on final processing of Clementine ultraviolet-visible images. J. Geophys. Res. 105(E8): 20297-20305. Snape, J.F., Alexander, L., Crawford, I.A., Joy, K.H., 2013. Basaltic Regolith Sample 12003,314: A New Member of the Apollo 12 Feldspathic Basalt Suite? Lunar and Planetary Institute Science Conference Abstracts 44:1044. Weider, S.Z., Crawford, I.A. and Joy, K.H., "Individual lava flow

  12. Multiple docking sites on substrate proteins form a modular system that mediates recognition by ERK MAP kinase

    PubMed Central

    Jacobs, Dave; Glossip, Danielle; Xing, Heming; Muslin, Anthony J.; Kornfeld, Kerry

    1999-01-01

    MAP kinases phosphorylate specific groups of substrate proteins. Here we show that the amino acid sequence FXFP is an evolutionarily conserved docking site that mediates ERK MAP kinase binding to substrates in multiple protein families. FXFP and the D box, a different docking site, form a modular recognition system, as they can function independently or in combination. FXFP is specific for ERK, whereas the D box mediates binding to ERK and JNK MAP kinase, suggesting that the partially overlapping substrate specificities of ERK and JNK result from recognition of shared and unique docking sites. These findings enabled us to predict new ERK substrates and design peptide inhibitors of ERK that functioned in vitro and in vivo. PMID:9925641

  13. Geologic map of Paleozoic rocks in the Calico Hills, Nevada Test Site, southern Nevada

    SciTech Connect

    Cole, J.C.; Cashman, P.H.

    1998-11-01

    The Calico Hills area in the southwestern part of the Nevada Test Site, Nye County, Nevada, exposes a core of pre-Tertiary rocks surrounded by middle Miocene volcanic strata. This map portrays the very complex relationships among the pre-Tertiary stratigraphic units of the region. The Devonian and Mississippian rocks of the Calico Hills are distinct from age-equivalent carbonate-shelf or submarine-fan strata in other parts of the Nevada Test Site. The Calico Hills strata are interpreted to have been deposited beyond the continental shelf edge from alternating silicic and carbonate clastic sources. Structures of the Calico Hills area record the compounded effects of: (1) eastward-directed, foreland-vergent thrusting; (2) younger folds, kink zones, and thrusts formed by hinterland-vergent deformation toward northwesterly and northerly directions; and (3) low-angle normal faults that displaced blocks of Middle Paleozoic carbonate strata across the contractionally deformed terrane. All of these structures are older than any of the middle Miocene volcanic rocks that were erupted across the Calico Hills.

  14. Geophysical Applications in Mapping the Subsurface Structure of Archaeological Site at Lembah Bujang, Kedah, Malaysia

    NASA Astrophysics Data System (ADS)

    Sapiai, Sarmiza M.; Saad, Rosli; Nawawi, M. N. M.; Shyeh, S. K.; Saidin, Mohd Mokhtar

    2010-07-01

    Lembah Bujang is one of Peninsular Malaysia's most important areas for archaeology as excavations in this area have revealed many traces of Malaysia's prehistory. The site is one of the oldest known place human activities the Peninsula. The aim of this study is to map and understand the subsurface structure of the survey area which is one of the archaeologically interesting areas. Geophysical methods are used because it is nondestructive and do not disturb the site. The methods are relatively quick and the results are used as a guide for subsequent excavation work. So it can greatly help in setting the digging priorities as geophysical surveying can reveal, for instance, important subsurface features like monuments, tunnels, voids, or buried walls. The geophysical methods used in this study were the magnetic gradiometer, 2-D electrical resistivity and ground penetrating radar (GPR) method. The integration of these three methods can be beneficial as each method has its strength and limitation. The specific area of study is in Sungai Batu and the results show that the sedimentation consists of sandy clay, alluvium and boulders with a depth of between 0 m to 15 m.

  15. Near-surface gas mapping studies of salt geologic features at Weeks Island and other sites

    SciTech Connect

    Molecke, M.A.; Carney, K.R.; Autin, W.J.; Overton, E.B.

    1996-10-01

    Field sampling and rapid gas analysis techniques were used to survey near-surface soil gases for geotechnical diagnostic purposes at the Weeks Island Strategic Petroleum Reserve (SPR) site and other salt dome locations in southern Louisiana. This report presents the complete data, results and interpretations obtained during 1995. Weeks Island 1994 gas survey results are also briefly summarized; this earlier study did not find a definitive correlation between sinkhole No. 1 and soil gases. During 1995, several hundred soil gas samples were obtained and analyzed in the field by gas chromatography, for profiling low concentrations and gas anomalies at ppm to percent levels. The target gases included hydrogen, methane, ethane and ethylene. To supplement the field data, additional gas samples were collected at various site locations for laboratory analysis of target gases at ppb levels. Gases in the near-surface soil originate predominantly from the oil, from petrogenic sources within the salt, or from surface microbial activity. Surveys were conducted across two Weeks Island sinkholes, several mapped anomalous zones in the salt, and over the SPR repository site and its perimeter. Samples were also taken at other south Louisiana salt dome locations for comparative purposes. Notable results from these studies are that elevated levels of hydrogen and methane (1) were positively associated with anomalous gassy or shear zones in the salt dome(s) and (2) are also associated with suspected salt fracture (dilatant) zones over the edges of the SPR repository. Significantly elevated areas of hydrogen, methane, plus some ethane, were found over anomalous shear zones in the salt, particularly in a location over high pressure gas pockets in the salt, identified in the mine prior to SPR operations. Limited stable isotope ratio analyses, SIRA, were also conducted and determined that methane samples were of petrogenic origin, not biogenic.

  16. Fault-rupture hazards, the Alquist-Priolo Fault Hazard Act, and siting decisions in California

    SciTech Connect

    Slosson, J.E. ); Keaton, J.R. ); Johnson, J.A.

    1994-06-01

    The Alquist-Priolo Act was enacted in 1971 and became operational in 1972 as an aftermath of the 1971 San Fernando Earthquake. State Senator Alfred E. Alquist and Assemblyman Paul V. Priolo are to be commended for moving rapidly toward improved earthquake loss reduction. Unfortunately, those who were worried about the concept that too much knowledge will adversely impact the economy of California were more influential and politically astute than those who support the concept that proper use of science and technology can reduce the loss of life as well as the astronomically high dollar losses associated with earthquakes. The estimated dollar loss of over $5.9 billion for the 1989 Loma Prieta earthquake (McNutt and Sydnor, 1990) clearly indicates that the Alquist-Priolo Act may be of little value, even along a strike-slip plate boundary, as none of the damage or losses resulted from surface fault rupture. Similar notable absence of fault rupture damage is reported for the 1987 Whittier earthquake (over $100 million loss; Shakal, 1987) and the 1983 Coalinga earthquake ($31 million loss; Tierney, 1985). The damage, property loss and loss of life from these earthquakes resulted from factors which are not addressed by the Alquist-Priolo Act. Even though considerable fault-rupture damage occurred during the 1992 Landers earthquake, most of the problems were associated with rupture of lifelines, such as water mains, and not collapse of structures for human occupancy.

  17. Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing

    PubMed Central

    2012-01-01

    Background Genetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. Construction of a high-density and high-quality genetic map would be of great benefit in the production of superior grapes to meet human demand. High throughput and low cost of the recently developed next generation sequencing (NGS) technology have resulted in its wide application in genome research. Sequencing restriction-site associated DNA (RAD) might be an efficient strategy to simplify genotyping. Combining NGS with RAD has proven to be powerful for single nucleotide polymorphism (SNP) marker development. Results An F1 population of 100 individual plants was developed. In-silico digestion-site prediction was used to select an appropriate restriction enzyme for construction of a RAD sequencing library. Next generation RAD sequencing was applied to genotype the F1 population and its parents. Applying a cluster strategy for SNP modulation, a total of 1,814 high-quality SNP markers were developed: 1,121 of these were mapped to the female genetic map, 759 to the male map, and 1,646 to the integrated map. A comparison of the genetic maps to the published Vitis vinifera genome revealed both conservation and variations. Conclusions The applicability of next generation RAD sequencing for genotyping a grape F1 population was demonstrated, leading to the successful development of a genetic map with high density and quality using our designed SNP markers. Detailed analysis revealed that this newly developed genetic map can be used for a variety of genome investigations, such as QTL detection, sequence assembly and genome comparison. PMID:22908993

  18. Maps of Indian Territory, the Dawes Act, and Will Rogers' Enrollment Case File. The Constitution Community: The Development of the Industrial United States (1870-1900).

    ERIC Educational Resources Information Center

    Kelly, Kerry C.

    This lesson offers historical background on federal Indian policy from 1870 to 1900, focusing on the Dawes Act of 1887 (with two resources). It provides four primary source documents, including maps of Indian Territory (Oklahoma) and Will Roger's application for enrollment in the Five Civilized Tribes. The lesson relates to the powers granted to…

  19. Vegetation maps at the passage of the Taylor Grazing Act (1934): A baseline to evaluate rangeland change after a regime shift

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Data from New Mexico range survey maps created shortly after the passage of the Taylor Grazing Act in 1934 have been preserved and are being used to document changes in vegetation. The range survey data were collected at the time of a critical shift in rangeland policy and practice in federal lands...

  20. Geologic map of the MTM 25047 and 20047 quadrangles, central Chryse Planitia/Viking 1 Lander site, Mars

    USGS Publications Warehouse

    Crumpler, L.S.; Craddock, R.A.; Aubele, J.C.

    2001-01-01

    This map uses Viking Orbiter image data and Viking 1 Lander image data to evaluate the geologic history of a part of Chryse Planitia, Mars. The map area lies at the termini of the Maja and Kasei Valles outwash channels and includes the site of the Viking 1 Lander. The photomosaic base for these quadrangles was assembled from 98 Viking Orbiter frames comprising 1204 pixels per line and 1056 lines and ranging in resolution from 20 to 200 m/pixel. These orbital image data were supplemented with images of the surface as seen from the Viking 1 Lander, one of only three sites on the martian surface where planetary geologic mapping is assisted by ground truth.

  1. Mapping of the Lunokhod-1 Landing Site: A Case Study for Future Lunar Exploration

    NASA Astrophysics Data System (ADS)

    Karachevtseva, I.; Oberst, J.; Konopikhin, A.; Shingareva, K.; Gusakova, E.; Kokhanov, A.; Baskakova, M.; Peters, O.; Scholten, F.; Wählisch, M.; Robinson, M.

    2012-04-01

    Introduction. Luna-17 landed on November 17, 1970 and deployed Lunokhod-1, the first remotely operated roving vehicle ever to explore a planetary surface. Within 332 days, the vehicle conquered a traverse of approx. 10 km. The rover was equipped with a navigation camera system as well as a scanner camera with which panoramic images were obtained. From separated stations, stereoscopic views were obtained. The history of the Lunokhods came back into focus recently, when the Lunar Reconnaissance Orbiter [1] obtained images from orbit at highest resolutions of 0.5-0.25 m/pixel. The Luna-17 landing platform as well as the roving vehicles at their final resting positions can clearly be identified. In addition, the rover tracks are clearly visible in most areas. From LRO stereo images, digital elevation model (DEM) of the Lunokhod-1 landing site areas have been derived [2]. These are useful to study the topographic profile and slopes of the traverse. The data are also useful to study the 3-D morphology of craters in the surroundings. Methodology. Lunokhod-1 area mapping have been done using GIS techniques. With CraterTools [3] we digitized craters in the Lunokhod-1 traverse area and created a geodatabase, which consists at this moment of about 45,000 craters including their diameters and depths, obtained from the DEM [4]. The LRO DEM also was used to measure traverse. We used automatic GIS functions for calculating various surface parameters of the Lunokhod-1 area surface including slopes, roughness, crater cumulative and spatial densities, and prepared respective thematic maps. We also measured relative depth (ratio D/H) and inner slopes of craters and classified craters by their morphological type using automatic and visual methods. Vertical profiles through several craters using the high resolution DEM have been done, and the results show good agreement with the topographic models with contours in 10cm that have been obtained from the Lunokhod-1 stereo images [5]. The

  2. A terrain-based site characterization map of California with implications for the contiguous United States

    USGS Publications Warehouse

    Yong, Alan K.; Hough, Susan E.; Iwahashi, Junko; Braverman, Amy

    2012-01-01

    We present an approach based on geomorphometry to predict material properties and characterize site conditions using the VS30 parameter (time‐averaged shear‐wave velocity to a depth of 30 m). Our framework consists of an automated terrain classification scheme based on taxonomic criteria (slope gradient, local convexity, and surface texture) that systematically identifies 16 terrain types from 1‐km spatial resolution (30 arcsec) Shuttle Radar Topography Mission digital elevation models (SRTM DEMs). Using 853 VS30 values from California, we apply a simulation‐based statistical method to determine the mean VS30 for each terrain type in California. We then compare the VS30 values with models based on individual proxies, such as mapped surface geology and topographic slope, and show that our systematic terrain‐based approach consistently performs better than semiempirical estimates based on individual proxies. To further evaluate our model, we apply our California‐based estimates to terrains of the contiguous United States. Comparisons of our estimates with 325 VS30 measurements outside of California, as well as estimates based on the topographic slope model, indicate our method to be statistically robust and more accurate. Our approach thus provides an objective and robust method for extending estimates of VS30 for regions where in situ measurements are sparse or not readily available.

  3. A remote characterization system for subsurface mapping of buried waste sites

    SciTech Connect

    Sandness, G.A.; Bennett, D.W.

    1992-10-01

    Mapping of buried objects and regions of chemical and radiological contamination is required at US Department of Energy (DOE) buried waste sites. The DOE Office of Technology Development Robotics Integrated Program has initiated a project to develop and demonstrate a remotely controlled subsurface sensing system, called the Remote Characterization System (RCS). This project, a collaborative effort by five of the National Laboratories, involves the development of a unique low-signature survey vehicle, a base station, radio telemetry data links, satellite-based vehicle tracking, stereo vision, and sensors for non-invasive inspection of the surface and subsurface. To minimize interference with on-board sensors, the survey vehicle has been constructed predominatantly of non-metallic materials. The vehicle is self-propelled and will be guided by an operator located at a remote base station. The RCS sensors will be environmentally sealed and internally cooled to preclude contamination during use. Ground-penetrating radar, magnetometers, and conductivity devices are planned for geophysical surveys. Chemical and radiological sensors will be provided to locate hot spots and to provide isotopic concentration data.

  4. SELMAP - SELEX affinity landscape MAPping of transcription factor binding sites using integrated microfluidics

    PubMed Central

    Chen, Dana; Orenstein, Yaron; Golodnitsky, Rada; Pellach, Michal; Avrahami, Dorit; Wachtel, Chaim; Ovadia-Shochat, Avital; Shir-Shapira, Hila; Kedmi, Adi; Juven-Gershon, Tamar; Shamir, Ron; Gerber, Doron

    2016-01-01

    Transcription factors (TFs) alter gene expression in response to changes in the environment through sequence-specific interactions with the DNA. These interactions are best portrayed as a landscape of TF binding affinities. Current methods to study sequence-specific binding preferences suffer from limited dynamic range, sequence bias, lack of specificity and limited throughput. We have developed a microfluidic-based device for SELEX Affinity Landscape MAPping (SELMAP) of TF binding, which allows high-throughput measurement of 16 proteins in parallel. We used it to measure the relative affinities of Pho4, AtERF2 and Btd full-length proteins to millions of different DNA binding sites, and detected both high and low-affinity interactions in equilibrium conditions, generating a comprehensive landscape of the relative TF affinities to all possible DNA 6-mers, and even DNA10-mers with increased sequencing depth. Low quantities of both the TFs and DNA oligomers were sufficient for obtaining high-quality results, significantly reducing experimental costs. SELMAP allows in-depth screening of hundreds of TFs, and provides a means for better understanding of the regulatory processes that govern gene expression. PMID:27628341

  5. Expression patterns of FLAGELLIN SENSING 2 map to bacterial entry sites in plant shoots and roots

    PubMed Central

    Beck, Martina; Wyrsch, Ines; Strutt, James; Wimalasekera, Rinukshi; Webb, Alex; Boller, Thomas; Robatzek, Silke

    2014-01-01

    Pathogens can colonize all plant organs and tissues. To prevent this, each cell must be capable of autonomously triggering defence. Therefore, it is generally assumed that primary sensors of the immune system are constitutively present. One major primary sensor against bacterial infection is the FLAGELLIN SENSING 2 (FLS2) pattern recognition receptor (PRR). To gain insights into its expression pattern, the FLS2 promoter activity in β-glucuronidase (GUS) reporter lines was monitored. The data show that pFLS2::GUS activity is highest in cells and tissues vulnerable to bacterial entry and colonization, such as stomata, hydathodes, and lateral roots. GUS activity is also high in the vasculature and, by monitoring Ca2+ responses in the vasculature, it was found that this tissue contributes to flg22-induced Ca2+ burst. The FLS2 promoter is also regulated in a tissue- and cell type-specific manner and is responsive to hormones, damage, and biotic stresses. This results in stimulus-dependent expansion of the FLS2 expression domain. In summary, a tissue- and cell type-specific map of FLS2 expression has been created correlating with prominent entry sites and target tissues of plant bacterial pathogens. PMID:25205577

  6. SELMAP - SELEX affinity landscape MAPping of transcription factor binding sites using integrated microfluidics.

    PubMed

    Chen, Dana; Orenstein, Yaron; Golodnitsky, Rada; Pellach, Michal; Avrahami, Dorit; Wachtel, Chaim; Ovadia-Shochat, Avital; Shir-Shapira, Hila; Kedmi, Adi; Juven-Gershon, Tamar; Shamir, Ron; Gerber, Doron

    2016-01-01

    Transcription factors (TFs) alter gene expression in response to changes in the environment through sequence-specific interactions with the DNA. These interactions are best portrayed as a landscape of TF binding affinities. Current methods to study sequence-specific binding preferences suffer from limited dynamic range, sequence bias, lack of specificity and limited throughput. We have developed a microfluidic-based device for SELEX Affinity Landscape MAPping (SELMAP) of TF binding, which allows high-throughput measurement of 16 proteins in parallel. We used it to measure the relative affinities of Pho4, AtERF2 and Btd full-length proteins to millions of different DNA binding sites, and detected both high and low-affinity interactions in equilibrium conditions, generating a comprehensive landscape of the relative TF affinities to all possible DNA 6-mers, and even DNA10-mers with increased sequencing depth. Low quantities of both the TFs and DNA oligomers were sufficient for obtaining high-quality results, significantly reducing experimental costs. SELMAP allows in-depth screening of hundreds of TFs, and provides a means for better understanding of the regulatory processes that govern gene expression. PMID:27628341

  7. Spirit rover localization and topographic mapping at the landing site of Gusev crater, Mars

    USGS Publications Warehouse

    Li, R.; Archinal, B.A.; Arvidson, R. E.; Bell, J.; Christensen, P.; Crumpler, L.; Des Marais, D.J.; Di, K.; Duxbury, T.; Golombek, M.P.; Grant, J. A.; Greeley, R.; Guinn, J.; Johnson, Aaron H.; Kirk, R.L.; Maimone, M.; Matthies, L.H.; Malin, M.; Parker, T.; Sims, M.; Thompson, S.; Squyres, S. W.; Soderblom, L.A.

    2006-01-01

    By sol 440, the Spirit rover has traversed a distance of 3.76 km (actual distance traveled instead of odometry). Localization of the lander and the rover along the traverse has been successfully performed at the Gusev crater landing site. We localized the lander in the Gusev crater using two-way Doppler radio positioning and cartographic triangulations through landmarks visible in both orbital and ground images. Additional high-resolution orbital images were used to verify the determined lander position. Visual odometry and bundle adjustment technologies were applied to compensate for wheel slippage, azimuthal angle drift, and other navigation errors (which were as large as 10.5% in the Husband Hill area). We generated topographic products, including 72 ortho maps and three-dimensional (3-D) digital terrain models, 11 horizontal and vertical traverse profiles, and one 3-D crater model (up to sol 440). Also discussed in this paper are uses of the data for science operations planning, geological traverse surveys, surveys of wind-related features, and other science applications. Copyright 2006 by the American Geophysical Union.

  8. Predicting and mapping potential Whooping Crane stopover habitat to guide site selection for wind energy projects.

    PubMed

    Belaire, J Amy; Kreakie, Betty J; Keitt, Timothy; Minor, Emily

    2014-04-01

    Migratory stopover habitats are often not part of planning for conservation or new development projects. We identified potential stopover habitats within an avian migratory flyway and demonstrated how this information can guide the site-selection process for new development. We used the random forests modeling approach to map the distribution of predicted stopover habitat for the Whooping Crane (Grus americana), an endangered species whose migratory flyway overlaps with an area where wind energy development is expected to become increasingly important. We then used this information to identify areas for potential wind power development in a U.S. state within the flyway (Nebraska) that minimize conflicts between Whooping Crane stopover habitat and the development of clean, renewable energy sources. Up to 54% of our study area was predicted to be unsuitable as Whooping Crane stopover habitat and could be considered relatively low risk for conflicts between Whooping Cranes and wind energy development. We suggest that this type of analysis be incorporated into the habitat conservation planning process in areas where incidental take permits are being considered for Whooping Cranes or other species of concern. Field surveys should always be conducted prior to construction to verify model predictions and understand baseline conditions. PMID:24372936

  9. Predicting and mapping potential Whooping Crane stopover habitat to guide site selection for wind energy projects.

    PubMed

    Belaire, J Amy; Kreakie, Betty J; Keitt, Timothy; Minor, Emily

    2014-04-01

    Migratory stopover habitats are often not part of planning for conservation or new development projects. We identified potential stopover habitats within an avian migratory flyway and demonstrated how this information can guide the site-selection process for new development. We used the random forests modeling approach to map the distribution of predicted stopover habitat for the Whooping Crane (Grus americana), an endangered species whose migratory flyway overlaps with an area where wind energy development is expected to become increasingly important. We then used this information to identify areas for potential wind power development in a U.S. state within the flyway (Nebraska) that minimize conflicts between Whooping Crane stopover habitat and the development of clean, renewable energy sources. Up to 54% of our study area was predicted to be unsuitable as Whooping Crane stopover habitat and could be considered relatively low risk for conflicts between Whooping Cranes and wind energy development. We suggest that this type of analysis be incorporated into the habitat conservation planning process in areas where incidental take permits are being considered for Whooping Cranes or other species of concern. Field surveys should always be conducted prior to construction to verify model predictions and understand baseline conditions.

  10. Combined geophysical methods for mapping infiltration pathways at the Aurora Water Aquifer recharge and recovery site

    NASA Astrophysics Data System (ADS)

    Jasper, Cameron A.

    Although aquifer recharge and recovery systems are a sustainable, decentralized, low cost, and low energy approach for the reclamation, treatment, and storage of post- treatment wastewater, they can suffer from poor infiltration rates and the development of a near-surface clogging layer within infiltration ponds. One such aquifer recharge and recovery system, the Aurora Water site in Colorado, U.S.A, functions at about 25% of its predicted capacity to recharge floodplain deposits by flooding infiltration ponds with post-treatment wastewater extracted from river bank aquifers along the South Platte River. The underwater self-potential method was developed to survey self-potential signals at the ground surface in a flooded infiltration pond for mapping infiltration pathways. A method for using heat as a groundwater tracer within the infiltration pond used an array of in situ high-resolution temperature sensing probes. Both relatively positive and negative underwater self-potential anomalies are consistent with observed recovery well pumping rates and specific discharge estimates from temperature data. Results from electrical resistivity tomography and electromagnetics surveys provide consistent electrical conductivity distributions associated with sediment textures. A lab method was developed for resistivity tests of near-surface sediment samples. Forward numerical modeling synthesizes the geophysical information to best match observed self- potential anomalies and provide permeability distributions, which is important for effective aquifer recharge and recovery system design, and optimization strategy development.

  11. Audit Report on "Waste Processing and Recovery Act Acceleration Efforts for Contact-Handled Transuranic Waste at the Hanford Site"

    SciTech Connect

    2010-05-01

    The Department of Energy's Office of Environmental Management's (EM), Richland Operations Office (Richland), is responsible for disposing of the Hanford Site's (Hanford) transuranic (TRU) waste, including nearly 12,000 cubic meters of radioactive contact-handled TRU wastes. Prior to disposing of this waste at the Department's Waste Isolation Pilot Plant (WIPP), Richland must certify that it meets WIPP's waste acceptance criteria. To be certified, the waste must be characterized, screened for prohibited items, treated (if necessary) and placed into a satisfactory disposal container. In a February 2008 amendment to an existing Record of Decision (Decision), the Department announced its plan to ship up to 8,764 cubic meters of contact-handled TRU waste from Hanford and other waste generator sites to the Advanced Mixed Waste Treatment Project (AMWTP) at Idaho's National Laboratory (INL) for processing and certification prior to disposal at WIPP. The Department decided to maximize the use of the AMWTP's automated waste processing capabilities to compact and, thereby, reduce the volume of contact-handled TRU waste. Compaction reduces the number of shipments and permits WIPP to more efficiently use its limited TRU waste disposal capacity. The Decision noted that the use of AMWTP would avoid the time and expense of establishing a processing capability at other sites. In May 2009, EM allocated $229 million of American Recovery and Reinvestment Act of 2009 (Recovery Act) funds to support Hanford's Solid Waste Program, including Hanford's contact-handled TRU waste. Besides providing jobs, these funds were intended to accelerate cleanup in the short term. We initiated this audit to determine whether the Department was effectively using Recovery Act funds to accelerate processing of Hanford's contact-handled TRU waste. Relying on the availability of Recovery Act funds, the Department changed course and approved an alternative plan that could increase costs by about $25 million

  12. MAP-21 Reauthorization Act

    THOMAS, 113th Congress

    Sen. Boxer, Barbara [D-CA

    2014-05-12

    05/15/2014 Committee on Environment and Public Works. Ordered to be reported with amendments favorably. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  13. Eliminate the MAP Act

    THOMAS, 113th Congress

    Rep. Chabot, Steve [R-OH-1

    2013-06-14

    06/25/2013 Referred to the Subcommittee on Horticulture, Research, Biotechnology, and Foreign Agriculture. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  14. Using integrated geospatial mapping and conceptual site models to guide risk-based environmental clean-up decisions.

    PubMed

    Mayer, Henry J; Greenberg, Michael R; Burger, Joanna; Gochfield, Michael; Powers, Charles; Kosson, David; Keren, Roger; Danis, Christine; Vyas, Vikram

    2005-04-01

    Government and private sector organizations are increasingly turning to the use of maps and other visual models to provide a depiction of environmental hazards and the potential risks they represent to humans and ecosystems. Frequently, the graphic presentation is tailored to address a specific contaminant, its location and possible exposure pathways, and potential receptors. Its format is usually driven by the data available, choice of graphics technology, and the audience being served. A format that is effective for displaying one contaminant at one scale at one site, however, may be ineffective in accurately portraying the circumstances surrounding a different contaminant at the same site, or the same contaminant at a different site, because of limitations in available data or the graphics technology being used. This is the daunting challenge facing the U.S. Department of Energy (DOE), which is responsible for the nation's legacy wastes from nuclear weapons research, testing, and production at over 100 sites in the United States. In this article, we discuss the development and use of integrated geospatial mapping and conceptual site models to identify hazards and evaluate alternative long-term environmental clean-up strategies at DOE sites located across the United States. While the DOE probably has the greatest need for such information, the Department of Defense and other public and private responsible parties for many large and controversial National Priority List or Superfund sites would benefit from a similar approach.

  15. First-generation site-response maps for the Los Angeles region based on earthquake ground motions

    USGS Publications Warehouse

    Hartzell, S.; Harmsen, S.; Frankel, A.; Carver, D.; Cranswick, E.; Meremonte, M.; Michael, J.

    1998-01-01

    Ground-motion records from aftershocks of the 1994 Northridge earthquake and mainshock records from the 1971 San Fernando, 1987 Whittier Narrows, 1991 Sierra Madre, and 1994 Northridge earthquakes are used to estimate site response relative to a rock site for the urban Los Angeles area. Site response is estimated at 232 mainshock and 201 aftershock sites relative to a low-amplitude site in the Santa Monica Mountains. Average amplification values are calculated for the frequency bands: 1 to 3, 3 to 5, and 5 to 7 Hz. These bands are chosen based on limitations in aftershock recording equipment at lower frequencies and reduced significance to the building inventory at higher frequencies. Site amplification factors determined at the instrumented locations are grouped by the surficial geology and contoured to produce a continuous spatial estimation of amplification. The maps in this article represent the first attempt to produce estimates of site amplification based on observations of ground motion for such a large areal extent of the Los Angeles region. These maps are expected to evolve as more data become available and more analysis is done.

  16. Mapping Microbial Populations Relative to Sites of Ongoing Serpentinization: Results from the Tablelands Ophiolite Complex, Canada

    NASA Astrophysics Data System (ADS)

    Schrenk, M. O.; Brazelton, W. J.; Woodruff, Q.; Szponar, N.; Morrill, P. L.

    2010-12-01

    The aqueous alteration of ultramafic rocks (serpentinization) has been suggested to be a favorable process for the habitability of astrobodies in our solar system including subsurface environments of Mars and Europa. Serpentinization produces copious quantities of hydrogen and small organic molecules, and leads to highly reducing, highly alkaline conditions (up to pH 12) and a lack of dissolved inorganic carbon, which both stimulates and challenges microbial activities. Several environments on Earth provide insight into the relationships between serpentinization and microbial life including slow-spreading mid-ocean ridges, subduction zones, and ophiolite materials emplaced along continental margins. The Tablelands, an ophiolite in western Newfoundland, Canada provides an opportunity to carefully document and map the relationships between geochemical energy, microbial growth, and physiology. Alkaline fluids at the Tablelands originate from 500-million year old oceanic crust and accumulate in shallow pools or seep from beneath serpentinized talus. Fluids, rocks, and gases were collected from the Tablelands during a series of field excursions in 2009 and 2010, and geochemical, microscopic, molecular, and cultivation-based approaches were used to study the serpentinite microbial ecosystem. These samples provide an opportunity to generate a comprehensive map of microbial communities and their activities in space and time. Data indicate that a low but detectable stock of microorganisms inhabit high pH pools associated with end-member serpentinite fluids. Enrichment cultures yielded brightly pigmented colonies related to Alphaproteobacteria, presumably carrying out anoxygenic photosynthesis, and Firmicutes, presumably catalyzing the fermentation of organic matter. Culture-independent analyses of SSU rRNA using T-RFLP indicated low diversity communities of Firmicutes and Archaea in standing alkaline pools, communities of Beta- and Gammaproteobacteria at high pH seeps, and

  17. Digital geologic map of the Nevada Test Site and vicinity, Nye, Lincoln, and Clark Counties, Nevada, and Inyo County, California

    SciTech Connect

    Slate, J.L.; Berry, M.E.; Rowley, P.D.; Fridrich, C.J.; Morgan, K.S.; Workman, J.B.; Young, O.D.; Dixon, G.L.; Williams, V.S.; McKee, E.H.; Ponce, D.A.; Hildenbrand, T.G.; Swadley, W.C.; Lundstrom, S.C.; Ekren, E.B.; Warren, R.G.; Cole, J.C.; Fleck, R.J.; Lanphere, M.A.; Sawyer, D.A.; Minor, S.A.; Grunwald, D.J.; Laczniak, R.J.; Menges, C.M.; Yount, J.C.; Jayko, A.S.

    2000-03-08

    This digital geologic map of the Nevada Test Site (NTS) and vicinity, as well as its accompanying digital geophysical maps, are compiled at 1:100,000 scale. The map area covers two 30 {times} 60-minute quadrangles-the Pahute Mesa quadrangle to the north and the Beatty quadrangle to the south-plus a strip of 7 1/2-minute quadrangles on the east side. In addition to the NTS, the map area includes the rest of the southwest Nevada volcanic field, part of the Walker Lane, most of the Amargosa Desert, part of the Funeral and Grapevine Mountains, some of Death Valley, and the northern Spring Mountains. This geologic map improves on previous geologic mapping of the same area by providing new and updated Quaternary and bedrock geology, new geophysical interpretations of faults beneath the basins, and improved GIS coverages. This publication also includes a new isostatic gravity map and a new aeromagnetic map. The primary purpose of the three maps is to provide an updated geologic framework to aid interpretation of ground-water flow through and off the NTS. The NTS is centrally located within the area of the Death Valley regional ground-water flow system of southwestern Nevada and adjacent California. During the last 40 years, DOE and its predecessor agencies have conducted about 900 nuclear tests on the NTS, of which 100 were atmospheric tests and the rest were underground tests. More than 200 of the tests were detonated at or beneath the water table, which commonly is about 500 to 600 m below the surface. Because contaminants introduced by these test may move into water supplies off the NTS, rates and directions of ground-water flow must be determined. Knowledge about the ground water also is needed to properly appraise potential future effects of the possible nuclear waste repository at Yucca Mountain, adjacent to the NTS.

  18. Structure-function analysis of the extracellular domain of the pneumococcal cell division site positioning protein MapZ

    NASA Astrophysics Data System (ADS)

    Manuse, Sylvie; Jean, Nicolas L.; Guinot, Mégane; Lavergne, Jean-Pierre; Laguri, Cédric; Bougault, Catherine M.; Vannieuwenhze, Michael S.; Grangeasse, Christophe; Simorre, Jean-Pierre

    2016-06-01

    Accurate placement of the bacterial division site is a prerequisite for the generation of two viable and identical daughter cells. In Streptococcus pneumoniae, the positive regulatory mechanism involving the membrane protein MapZ positions precisely the conserved cell division protein FtsZ at the cell centre. Here we characterize the structure of the extracellular domain of MapZ and show that it displays a bi-modular structure composed of two subdomains separated by a flexible serine-rich linker. We further demonstrate in vivo that the N-terminal subdomain serves as a pedestal for the C-terminal subdomain, which determines the ability of MapZ to mark the division site. The C-terminal subdomain displays a patch of conserved amino acids and we show that this patch defines a structural motif crucial for MapZ function. Altogether, this structure-function analysis of MapZ provides the first molecular characterization of a positive regulatory process of bacterial cell division.

  19. Structure–function analysis of the extracellular domain of the pneumococcal cell division site positioning protein MapZ

    PubMed Central

    Manuse, Sylvie; Jean, Nicolas L.; Guinot, Mégane; Lavergne, Jean-Pierre; Laguri, Cédric; Bougault, Catherine M.; VanNieuwenhze, Michael S.; Grangeasse, Christophe; Simorre, Jean-Pierre

    2016-01-01

    Accurate placement of the bacterial division site is a prerequisite for the generation of two viable and identical daughter cells. In Streptococcus pneumoniae, the positive regulatory mechanism involving the membrane protein MapZ positions precisely the conserved cell division protein FtsZ at the cell centre. Here we characterize the structure of the extracellular domain of MapZ and show that it displays a bi-modular structure composed of two subdomains separated by a flexible serine-rich linker. We further demonstrate in vivo that the N-terminal subdomain serves as a pedestal for the C-terminal subdomain, which determines the ability of MapZ to mark the division site. The C-terminal subdomain displays a patch of conserved amino acids and we show that this patch defines a structural motif crucial for MapZ function. Altogether, this structure–function analysis of MapZ provides the first molecular characterization of a positive regulatory process of bacterial cell division. PMID:27346279

  20. Savannah River Site, Liquid Waste Program, Savannah River Remediation American Recovery and Reinvestment Act Benefits and Lessons Learned - 12559

    SciTech Connect

    Schmitz, Mark A.; Crouse, Thomas N.

    2012-07-01

    Utilizing funding provided by the American Recovery and Reinvestment Act (ARRA), the Liquid Waste Program at Savannah River site successfully executed forty-one design, procurement, construction, and operating activities in the period from September 2009 through December 2011. Project Management of the program included noteworthy practices involving safety, integrated project teams, communication, and cost, schedule and risk management. Significant upgrades to plant capacity, progress toward waste tank closure and procurement of needed infrastructure were accomplished. Over 1.5 million hours were worked without a single lost work day case. Lessons Learned were continually identified and applied to enhance the program. Investment of Recovery Act monies into the Liquid Waste Program has ensured continued success in the disposition of radioactive wastes and the closure of high level waste tanks at SRS. The funding of a portion of the Liquid Waste Program at SRS by ARRA was a major success. Significant upgrades to plant capacity, progress toward waste tank closure and procurement of needed infrastructure was accomplished. Integrated Project Teams ensured quality products and services were provided to the Operations customers. Over 1.5 million hours were worked without a single lost work day case. Lessons Learned were continually reviewed and reapplied to enhance the program. Investment of Recovery Act monies into the Liquid Waste Program has ensured continued success in the disposition of radioactive wastes and the closure of high level waste tanks at SRS. (authors)

  1. The abandoned surface mining sites in the Czech Republic: mapping and creating a database with a GIS web application

    NASA Astrophysics Data System (ADS)

    Pokorný, Richard; Tereza Peterková, Marie

    2016-05-01

    Based on the vectorization of the 55-volume book series the Quarry Inventories of the Czechoslovak Republic/Czechoslovak Socialist Republic, published in the years 1932-1961, a new comprehensive database was built comprising 9958 surface mining sites of raw materials, which were active in the first half of the 20th century. The mapped area covers 40.9 % of the territory of the Czech Republic. For the purposes of visualization, a map application, the Quarry Inventories Online, was created that enables the data visualization.

  2. Construction of High-Density Genetic Map in Barley through Restriction-Site Associated DNA Sequencing.

    PubMed

    Zhou, Gaofeng; Zhang, Qisen; Zhang, Xiao-Qi; Tan, Cong; Li, Chengdao

    2015-01-01

    Genetic maps in barley are usually constructed from a limited number of molecular markers such as SSR (simple sequence repeat) and DarT (diversity arrays technology). These markers must be first developed before being used for genotyping. Here, we introduce a new strategy based on sequencing progeny of a doubled haploid population from Baudin × AC Metcalfe to construct a genetic map in barley. About 13,547 polymorphic SNP tags with >93% calling rate were selected to construct the genetic map. A total of 12,998 SNP tags were anchored to seven linkage groups which spanned a cumulative 967.6 cM genetic distance. The high-density genetic map can be used for QTL mapping and the assembly of WGS and BAC contigs. The genetic map was evaluated for its effectiveness and efficiency in QTL mapping and candidate gene identification. A major QTL for plant height was mapped at 105.5 cM on chromosome 3H. This QTL with LOD value of 13.01 explained 44.5% of phenotypic variation. This strategy will enable rapid and efficient establishment of high-density genetic maps in other species. PMID:26182149

  3. 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.

  4. A novel dipyridodiazepinone inhibitor of HIV-1 reverse transcriptase acts through a nonsubstrate binding site

    SciTech Connect

    Wu, J.C.; Warren, T.C.; Adams, J.; Proudfoot, J.; Skiles, J.; Raghavan, P.; Perry, C.; Potocki, I.; Farina, P.R.; Grob, P.M. )

    1991-02-26

    A novel dipyridodiazepinone, 6,11-dihydro-11-cyclopropyl-4-methyldipyrido(2,3-b:2{prime},3{prime}-e)-(1,4)diazepin-6-one (BI-RG-587), is a selective noncompetitive inhibitor of HIV-1 reverse transcriptase (RT-1). An azido photoaffinity analogue of BI-RG-587 was synthesized and found to irreversibly inhibit the enzyme upon UV irradiation. BI-RG-587 and close structural analogues competitively protected RT-1 from inactivation by the photoaffinity label. A thiobenzimidazolone (TIBO) derivative, a nonnucleoside inhibitor of RT-1, also protected the enzyme from photoinactivation, which suggests a common binding site for these compounds. Substrates dGTP, template-primer, and tRNA afforded no protection from enzyme inactivation. A tritiated photoaffinity probe was found to stoichiometrically and selectively label p66 such that 1 mol of probe inactivates 1 mol of RT-1.

  5. Characterization of inhibitors acting at the synthetase site of Escherichia coli asparagine synthetase B.

    PubMed

    Boehlein, S K; Nakatsu, T; Hiratake, J; Thirumoorthy, R; Stewart, J D; Richards, N G; Schuster, S M

    2001-09-18

    Asparagine synthetase catalyzes the ATP-dependent formation of L-asparagine from L-aspartate and L-glutamine, via a beta-aspartyl-AMP intermediate. Since interfering with this enzyme activity might be useful for treating leukemia and solid tumors, we have sought small-molecule inhibitors of Escherichia coli asparagine synthetase B (AS-B) as a model system for the human enzyme. Prior work showed that L-cysteine sulfinic acid competitively inhibits this enzyme by interfering with L-aspartate binding. Here, we demonstrate that cysteine sulfinic acid is also a partial substrate for E. coli asparagine synthetase, acting as a nucleophile to form the sulfur analogue of beta-aspartyl-AMP, which is subsequently hydrolyzed back to cysteine sulfinic acid and AMP in a futile cycle. While cysteine sulfinic acid did not itself constitute a clinically useful inhibitor of asparagine synthetase B, these results suggested that replacing this linkage by a more stable analogue might lead to a more potent inhibitor. A sulfoximine reported recently by Koizumi et al. as a competitive inhibitor of the ammonia-dependent E. coli asparagine synthetase A (AS-A) [Koizumi, M., Hiratake, J., Nakatsu, T., Kato, H., and Oda, J. (1999) J. Am. Chem. Soc. 121, 5799-5800] can be regarded as such a species. We found that this sulfoximine also inhibited AS-B, effectively irreversibly. Unlike either the cysteine sulfinic acid interaction with AS-B or the sulfoximine interaction with AS-A, only AS-B productively engaged in asparagine synthesis could be inactivated by the sulfoximine; free enzyme was unaffected even after extended incubation with the sulfoximine. Taken together, these results support the notion that sulfur-containing analogues of aspartate can serve as platforms for developing useful inhibitors of AS-B. PMID:11551215

  6. Construction of High-Density Linkage Maps of Populus deltoides × P. simonii Using Restriction-Site Associated DNA Sequencing

    PubMed Central

    Tong, Chunfa; Li, Huogen; Wang, Ying; Li, Xuran; Ou, Jiajia; Wang, Deyuan; Xu, Houxi; Ma, Chao; Lang, Xianye; Liu, Guangxin; Zhang, Bo; Shi, Jisen

    2016-01-01

    Although numerous linkage maps have been constructed in the genus Populus, they are typically sparse and thus have limited applications due to low throughput of traditional molecular markers. Restriction-site associated DNA sequencing (RADSeq) technology allows us to identify a large number of single nucleotide polymorphisms (SNP) across genomes of many individuals in a fast and cost-effective way, and makes it possible to construct high-density genetic linkage maps. We performed RADSeq for 299 progeny and their two parents in an F1 hybrid population generated by crossing the female Populus deltoides ‘I-69’ and male Populus simonii ‘L3’. A total of 2,545 high quality SNP markers were obtained and two parent-specific linkage maps were constructed. The female genetic map contained 1601 SNPs and 20 linkage groups, spanning 4,249.12 cM of the genome with an average distance of 2.69 cM between adjacent markers, while the male map consisted of 940 SNPs and also 20 linkage groups with a total length of 3,816.24 cM and an average marker interval distance of 4.15 cM. Finally, our analysis revealed that synteny and collinearity are highly conserved between the parental linkage maps and the reference genome of P. trichocarpa. We demonstrated that RAD sequencing is a powerful technique capable of rapidly generating a large number of SNPs for constructing genetic maps in outbred forest trees. The high-quality linkage maps constructed here provided reliable genetic resources to facilitate locating quantitative trait loci (QTLs) that control growth and wood quality traits in the hybrid population. PMID:26964097

  7. Geologic structure mapping database Spent Fuel Test - Climax, Nevada Test Site

    SciTech Connect

    Yow, J.L. Jr.

    1984-12-04

    Information on over 2500 discontinuities mapped at the SFT-C is contained in the geologic structure mapping database. Over 1800 of these features include complete descriptions of their orientations. This database is now available for use by other researchers. 6 references, 3 figures, 2 tables.

  8. Using JournalMap to link spatial information with ecological site descriptions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    JournalMap is a scientific literature search engine that empowers you to find relevant research based on location and biophysical variables as well as traditional keyword searches. All publications are geotagged based on reported location information and plotted on a world map showing where the rese...

  9. Dynamic prescription maps for site-specific variable rate irrigation of cotton

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A prescription map is a set of instructions that controls a variable rate irrigation (VRI) system. These maps, which may be based on prior yield, soil texture, topography, or soil electrical conductivity data, are often manually applied at the beginning of an irrigation season and remain static. The...

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  11. Orbital-science investigation: Part J: preliminary geologic map of the region around the candidate Proclus Apollo landing site

    USGS Publications Warehouse

    Wilhelms, Don E.

    1972-01-01

    The Proclus Crater region was mapped to test the value, for photogeologic mapping purposes, of Apollo 15 metric photographs and to estimate the scientific value of the area as a potential landing site. A metric photographic frame (fig. 25-67) serves as a base for a map of the region around the Proclus Crater (fig. 25-68), and adjacent frames were overlapped with the base frame to provide stereographic images. The excellent stereocoverage allows easy simultaneous observation of topography and albedo. The large forward overlap and the extensive areal photographic coverage provide the best photogeologic data available to date. Brief study has already refined earlier interpretations of the area (refs. 25-7 and 25-32). Although volcanic units have been shown to be extensive in this region, mass wasting apparently has been more important than volcanism in shaping terra landforms.

  12. Mapping the iron binding site(s) on the small tetraheme cytochrome of Shewanella oneidensis MR-1.

    PubMed

    Qian, Yufeng; Paquete, Catarina M; Louro, Ricardo O; Ross, Daniel E; Labelle, Edward; Bond, Daniel R; Tien, Ming

    2011-07-19

    In the model microbe Shewanella oneidensis, multi-heme proteins are utilized for respiratory metabolism where metals serve as the terminal electron acceptor. Among those is the periplasm-localized small tetraheme cytochrome (STC). STC has been extensively characterized structurally and electrochemically to which electron flow in and out of the protein has been modeled. However, until the present work, no kinetic studies have been performed to probe the route of electron flow or to determine the iron-binding site on STC. Using iron chelated by EDTA, NTA, or citrate, we have used chemical modification, site-directed mutagenesis along with isothermal titration calorimetry (ITC), and stopped-flow measurements to identify the iron binding site of STC. Chemical modifications of STC revealed that carboxyl groups on STC are involved in binding of EDTA-Fe(3+). Scanning mutagenesis was performed on Asp and Glu to probe the putative iron-binding site on STC. Two STC mutants (D21N; D80N) showed ∼70% decrease in observed electron transfer rate constant with EDTA-Fe(3+) from transient-state kinetic measurements. The impaired reactivity of STC (D80N/D21N) with EDTA-Fe(3+) was further confirmed by a significant decrease (>10-fold) in iron binding affinity.

  13. Mapping membrane protein backbone dynamics: a comparison of site-directed spin labeling with NMR 15N-relaxation measurements.

    PubMed

    Lo, Ryan H; Kroncke, Brett M; Solomon, Tsega L; Columbus, Linda

    2014-10-01

    The ability to detect nanosecond backbone dynamics with site-directed spin labeling (SDSL) in soluble proteins has been well established. However, for membrane proteins, the nitroxide appears to have more interactions with the protein surface, potentially hindering the sensitivity to backbone motions. To determine whether membrane protein backbone dynamics could be mapped with SDSL, a nitroxide was introduced at 55 independent sites in a model polytopic membrane protein, TM0026. Electron paramagnetic resonance spectral parameters were compared with NMR (15)N-relaxation data. Sequential scans revealed backbone dynamics with the same trends observed for the R1 relaxation rate, suggesting that nitroxide dynamics remain coupled to the backbone on membrane proteins.

  14. Risk map and spatial determinants of pancreas disease in the marine phase of Norwegian Atlantic salmon farming sites

    PubMed Central

    2012-01-01

    Background Outbreaks of pancreas disease (PD) greatly contribute to economic losses due to high mortality, control measures, interrupted production cycles, reduced feed conversion and flesh quality in the aquaculture industries in European salmon-producing countries. The overall objective of this study was to evaluate an effect of potential factors contributing to PD occurrence accounting for spatial congruity of neighboring infected sites, and then create quantitative risk maps for predicting PD occurrence. The study population included active Atlantic salmon farming sites located in the coastal area of 6 southern counties of Norway (where most of PD outbreaks have been reported so far) from 1 January 2009 to 31 December 2010. Results Using a Bayesian modeling approach, with and without spatial component, the final model included site latitude, site density, PD history, and local biomass density. Clearly, the PD infected sites were spatially clustered; however, the cluster was well explained by the covariates of the final model. Based on the final model, we produced a map presenting the predicted probability of the PD occurrence in the southern part of Norway. Subsequently, the predictive capacity of the final model was validated by comparing the predicted probabilities with the observed PD outbreaks in 2011. Conclusions The framework of the study could be applied for spatial studies of other infectious aquatic animal diseases. PMID:23006469

  15. The effect of administering long-acting oxytetracycline and tilmicosin either by dart gun or by hand on injection site lesions and drug residues in beef cattle.

    PubMed Central

    Van Donkersgoed, J; VanderKop, M; Salisbury, C; Sears, L; Holowath, J

    1999-01-01

    Forty yearling cattle were injected intramuscularly with long-acting oxytetracycline and subcutaneously with tilmicosin by dart gun or by hand in a chute 28 days prior to slaughter. The drugs caused injection site lesions and antibiotic residues in the neck and thigh that varied by technique, dose, and site. PMID:12001341

  16. Pharmacokinetics and the effect of application site on a novel, long-acting transdermal fentanyl solution in healthy laboratory Beagles.

    PubMed

    Freise, K J; Newbound, G C; Tudan, C; Clark, T P

    2012-08-01

    Application of transdermal drugs to different anatomical sites can result in different absorption characteristics. The pharmacokinetics (PKs) and bioequivalence of a single 2.6 mg/kg (50 μL/kg) dose of a novel, long-acting transdermal fentanyl solution were determined when applied topically to the ventral abdominal or dorsal interscapular skin of 40 healthy laboratory Beagles. The PKs were differentiated by a more rapid initial absorption of fentanyl from the dorsal application site. Mean plasma fentanyl concentrations remained above 0.6 ng/mL from 4 to 96 h in the dorsal application group and from 8 to 144 h in the ventral application group. Bioequivalence analysis demonstrated that the sites were not equivalent; the 90% confidence intervals of the ratio of the geometric means for both the maximum concentration (C(max)) and the area under the curve (AUC) were not contained within the 80-125% interval. The C(max) was 2.34 ± 1.29 (mean ± standard deviation) and 2.02 ± 0.84 ng/mL for the ventral and dorsal application groups, respectively. The terminal elimination half-lives (t(1/2)) for both groups were similar with values of 137 ± 58.9 and 117 ± 59.6 h for the ventral and dorsal application site groups, respectively. A mean absorption rate of ≥ 2 μg · kg/h was maintained from 2 to 144 h following dorsal application and from 2 to 264 h following ventral application. These results suggest that transdermal fentanyl solution could be applied as a single dose to the dorsal scapular area 2-4 h prior to surgery with analgesia lasting a minimum of 4 days.

  17. MAP4K family kinases act in parallel to MST1/2 to activate LATS1/2 in the Hippo pathway

    PubMed Central

    Meng, Zhipeng; Moroishi, Toshiro; Mottier-Pavie, Violaine; Plouffe, Steven W.; Hansen, Carsten G.; Hong, Audrey W.; Park, Hyun Woo; Mo, Jung-Soon; Lu, Wenqi; Lu, Shicong; Flores, Fabian; Yu, Fa-Xing; Halder, Georg; Guan, Kun-Liang

    2015-01-01

    The Hippo pathway plays a central role in tissue homoeostasis, and its dysregulation contributes to tumorigenesis. Core components of the Hippo pathway include a kinase cascade of MST1/2 and LATS1/2 and the transcription co-activators YAP/TAZ. In response to stimulation, LATS1/2 phosphorylate and inhibit YAP/TAZ, the main effectors of the Hippo pathway. Accumulating evidence suggests that MST1/2 are not required for the regulation of YAP/TAZ. Here we show that deletion of LATS1/2 but not MST1/2 abolishes YAP/TAZ phosphorylation. We have identified MAP4K family members—Drosophila Happyhour homologues MAP4K1/2/3 and Misshapen homologues MAP4K4/6/7—as direct LATS1/2-activating kinases. Combined deletion of MAP4Ks and MST1/2, but neither alone, suppresses phosphorylation of LATS1/2 and YAP/TAZ in response to a wide range of signals. Our results demonstrate that MAP4Ks act in parallel to and are partially redundant with MST1/2 in the regulation of LATS1/2 and YAP/TAZ, and establish MAP4Ks as components of the expanded Hippo pathway. PMID:26437443

  18. Pollution prevention opportunity assessment for the K-25 Site Toxic Substances Control Act Incinerator Operations, Level III

    SciTech Connect

    1995-09-01

    A Level III pollution prevention opportunity assessment (PPOA) was performed for the Oak Ridge K-25 Site Toxic Substances Control Act (TSCA) Incinerator to evaluate pollution prevention (P2) options for various waste streams: The main objective of this study was to identify and evaluate options to reduce the quantities of each waste stream generated by the TSCA Incinerator operations to realize significant environmental and/or economic benefits from P2. For each of the waste streams, P2 options were evaluated following the US Environmental Protection Agency (EPA) hierarchy to (1) reduce the quantity of waste generated, (2) recycle the waste, and/or (3) use alternate waste treatment or segregation methods. This report provides process descriptions, identification and evaluation of P2 options, and final recommendations.

  19. Mapping the heparin-binding site of the osteoinductive protein NELL1 by site-directed mutagenesis.

    PubMed

    Takahashi, Kaneyoshi; Imai, Arisa; Iijima, Masumi; Yoshimoto, Nobuo; Maturana, Andrés D; Kuroda, Shun'ichi; Niimi, Tomoaki

    2015-12-21

    Neural epidermal growth factor-like (NEL)-like 1 (NELL1) is a secretory osteogenic protein comprising an N-terminal thrombospondin-1-like (TSPN) domain, four von Willebrand factor type C domains, and six epidermal growth factor-like repeats. NELL1 shows heparin-binding activity; however, the biological significance remains to be explored. In this report, we demonstrate that NELL1 binds to cell surface proteoglycans through its TSPN domain. Major heparin-binding sites were identified on the three-dimensional structural model of the TSPN domain of NELL1. Mutant analysis of the heparin-binding sites indicated that the heparin-binding activity of the TSPN domain is involved in interaction of NELL1 with cell surface proteoglycans.

  20. Toward a physical map of Drosophila buzzatii. Use of randomly amplified polymorphic dna polymorphisms and sequence-tagged site landmarks.

    PubMed Central

    Laayouni, H; Santos, M; Fontdevila, A

    2000-01-01

    We present a physical map based on RAPD polymorphic fragments and sequence-tagged sites (STSs) for the repleta group species Drosophila buzzatii. One hundred forty-four RAPD markers have been used as probes for in situ hybridization to the polytene chromosomes, and positive results allowing the precise localization of 108 RAPDs were obtained. Of these, 73 behave as effectively unique markers for physical map construction, and in 9 additional cases the probes gave two hybridization signals, each on a different chromosome. Most markers (68%) are located on chromosomes 2 and 4, which partially agree with previous estimates on the distribution of genetic variation over chromosomes. One RAPD maps close to the proximal breakpoint of inversion 2z(3) but is not included within the inverted fragment. However, it was possible to conclude from this RAPD that the distal breakpoint of 2z(3) had previously been wrongly assigned. A total of 39 cytologically mapped RAPDs were converted to STSs and yielded an aggregate sequence of 28,431 bp. Thirty-six RAPDs (25%) did not produce any detectable hybridization signal, and we obtained the DNA sequence from three of them. Further prospects toward obtaining a more developed genetic map than the one currently available for D. buzzatii are discussed. PMID:11102375

  1. Groundwater contaminant plume maps and volumes, 100-K and 100-N Areas, Hanford Site, Washington

    USGS Publications Warehouse

    Johnson, Kenneth H.

    2016-09-27

    This study provides an independent estimate of the areal and volumetric extent of groundwater contaminant plumes which are affected by waste disposal in the 100-K and 100-N Areas (study area) along the Columbia River Corridor of the Hanford Site. The Hanford Natural Resource Trustee Council requested that the U.S. Geological Survey perform this interpolation to assess the accuracy of delineations previously conducted by the U.S. Department of Energy and its contractors, in order to assure that the Natural Resource Damage Assessment could rely on these analyses. This study is based on previously existing chemical (or radionuclide) sampling and analysis data downloaded from publicly available Hanford Site Internet sources, geostatistically selected and interpreted as representative of current (from 2009 through part of 2012) but average conditions for groundwater contamination in the study area. The study is limited in scope to five contaminants—hexavalent chromium, tritium, nitrate, strontium-90, and carbon-14, all detected at concentrations greater than regulatory limits in the past.All recent analytical concentrations (or activities) for each contaminant, adjusted for radioactive decay, non-detections, and co-located wells, were converted to log-normal distributions and these transformed values were averaged for each well location. The log-normally linearized well averages were spatially interpolated on a 50 × 50-meter (m) grid extending across the combined 100-N and 100-K Areas study area but limited to avoid unrepresentative extrapolation, using the minimum curvature geostatistical interpolation method provided by SURFER®data analysis software. Plume extents were interpreted by interpolating the log-normally transformed data, again using SURFER®, along lines of equal contaminant concentration at an appropriate established regulatory concentration . Total areas for each plume were calculated as an indicator of relative environmental damage. These plume

  2. A high-density genetic recombination map of sequence-tagged sites for sorghum, as a framework for comparative structural and evolutionary genomics of tropical grains and grasses.

    PubMed Central

    Bowers, John E; Abbey, Colette; Anderson, Sharon; Chang, Charlene; Draye, Xavier; Hoppe, Alison H; Jessup, Russell; Lemke, Cornelia; Lennington, Jennifer; Li, Zhikang; Lin, Yann-Rong; Liu, Sin-Chieh; Luo, Lijun; Marler, Barry S; Ming, Reiguang; Mitchell, Sharon E; Qiang, Dou; Reischmann, Kim; Schulze, Stefan R; Skinner, D Neil; Wang, Yue-Wen; Kresovich, Stephen; Schertz, Keith F; Paterson, Andrew H

    2003-01-01

    We report a genetic recombination map for Sorghum of 2512 loci spaced at average 0.4 cM ( approximately 300 kb) intervals based on 2050 RFLP probes, including 865 heterologous probes that foster comparative genomics of Saccharum (sugarcane), Zea (maize), Oryza (rice), Pennisetum (millet, buffelgrass), the Triticeae (wheat, barley, oat, rye), and Arabidopsis. Mapped loci identify 61.5% of the recombination events in this progeny set and reveal strong positive crossover interference acting across intervals of sites will foster many structural, functional and evolutionary genomic studies in major food, feed, and biomass crops. PMID:14504243

  3. Sequence-tagged site (STS) content mapping of human chromosomes: theoretical considerations and early experiences.

    PubMed

    Green, E D; Green, P

    1991-11-01

    The magnitude of the effort required to complete the human genome project will require constant refinements of the tools available for the large-scale study of DNA. Such improvements must include both the development of more powerful technologies and the reformulation of the theoretical strategies that account for the changing experimental capabilities. The two technological advances described here, PCR and YAC cloning, have rapidly become incorporated into the standard armamentarium of genome analysis and represent key examples of how technological developments continue to drive experimental strategies in molecular biology. Because of its high sensitivity, specificity, and potential for automation, PCR is transforming many aspects of DNA mapping. Similarly, by providing the means to isolate and study larger pieces of DNA, YAC cloning has made practical the achievement of megabase-level continuity in physical maps. Taken together, these two technologies can be envisioned as providing a powerful strategy for constructing physical maps of whole chromosomes. Undoubtedly, future technological developments will promote even more effective mapping strategies. Nonetheless, the theoretical projections and practical experience described here suggest that constructing YAC-based STS-content maps of whole human chromosomes is now possible. Random STSs can be efficiently generated and used to screen collections of YAC clones, and contiguous YAC coverage of regions exceeding 2 Mb can be readily obtained. While the predicted laboratory effort required for mapping whole human chromosomes remains daunting, it is clearly feasible.

  4. Groundwater contaminant plume maps and volumes, 100-K and 100-N Areas, Hanford Site, Washington

    USGS Publications Warehouse

    Johnson, Kenneth H.

    2016-09-27

    This study provides an independent estimate of the areal and volumetric extent of groundwater contaminant plumes which are affected by waste disposal in the 100-K and 100-N Areas (study area) along the Columbia River Corridor of the Hanford Site. The Hanford Natural Resource Trustee Council requested that the U.S. Geological Survey perform this interpolation to assess the accuracy of delineations previously conducted by the U.S. Department of Energy and its contractors, in order to assure that the Natural Resource Damage Assessment could rely on these analyses. This study is based on previously existing chemical (or radionuclide) sampling and analysis data downloaded from publicly available Hanford Site Internet sources, geostatistically selected and interpreted as representative of current (from 2009 through part of 2012) but average conditions for groundwater contamination in the study area. The study is limited in scope to five contaminants—hexavalent chromium, tritium, nitrate, strontium-90, and carbon-14, all detected at concentrations greater than regulatory limits in the past.All recent analytical concentrations (or activities) for each contaminant, adjusted for radioactive decay, non-detections, and co-located wells, were converted to log-normal distributions and these transformed values were averaged for each well location. The log-normally linearized well averages were spatially interpolated on a 50 × 50-meter (m) grid extending across the combined 100-N and 100-K Areas study area but limited to avoid unrepresentative extrapolation, using the minimum curvature geostatistical interpolation method provided by SURFER®data analysis software. Plume extents were interpreted by interpolating the log-normally transformed data, again using SURFER®, along lines of equal contaminant concentration at an appropriate established regulatory concentration . Total areas for each plume were calculated as an indicator of relative environmental damage. These plume

  5. Mapping the heparin-binding site of the BMP antagonist gremlin by site-directed mutagenesis based on predictive modelling.

    PubMed

    Tatsinkam, Arnold Junior; Mulloy, Barbara; Rider, Christopher C

    2015-08-15

    Gremlin is a member of the CAN (cerberus and DAN) family of secreted BMP (bone morphogenetic protein) antagonists and also an agonist of VEGF (vascular endothelial growth factor) receptor-2. It is critical in limb skeleton and kidney development and is re-expressed during tissue fibrosis. Gremlin binds strongly to heparin and heparan sulfate and, in the present study, we sought to investigate its heparin-binding site. In order to explore a putative non-contiguous binding site predicted by computational molecular modelling, we substituted a total of 11 key arginines and lysines located in three basic residue sequence clusters with homologous sequences from cerberus and DAN (differential screening selected gene abberative in neuroblastoma), CAN proteins which lack basic residues in these positions. A panel of six Myc-tagged gremlin mutants, MGR-1-MGR-6 (MGR, mutant gremlin), each containing different combinations of targeted substitutions, all showed markedly reduced affinity for heparin as demonstrated by their NaCl elution on heparin affinity chromatography, thus verifying our predictions. Both MGR-5 and MGR-6 retained BMP-4-binding activity comparable to that of wild-type gremlin. Low-molecular-mass heparin neither promoted nor inhibited BMP-4 binding. Finally, glutaraldehyde cross-linking demonstrated that gremlin forms non-covalent dimers, similar behaviour to that of DAN and also PRDC (protein related to cerberus and DAN), another CAN protein. The resulting dimer would possess two heparin-binding sites, each running along an exposed surface on the second β-strand finger loop of one of the monomers.

  6. Characterization of Airborne Microbial Communities at a High-Elevation Site and Their Potential To Act as Atmospheric Ice Nuclei▿

    PubMed Central

    Bowers, Robert M.; Lauber, Christian L.; Wiedinmyer, Christine; Hamady, Micah; Hallar, Anna G.; Fall, Ray; Knight, Rob; Fierer, Noah

    2009-01-01

    Bacteria and fungi are ubiquitous in the atmosphere. The diversity and abundance of airborne microbes may be strongly influenced by atmospheric conditions or even influence atmospheric conditions themselves by acting as ice nucleators. However, few comprehensive studies have described the diversity and dynamics of airborne bacteria and fungi based on culture-independent techniques. We document atmospheric microbial abundance, community composition, and ice nucleation at a high-elevation site in northwestern Colorado. We used a standard small-subunit rRNA gene Sanger sequencing approach for total microbial community analysis and a bacteria-specific 16S rRNA bar-coded pyrosequencing approach (4,864 sequences total). During the 2-week collection period, total microbial abundances were relatively constant, ranging from 9.6 × 105 to 6.6 × 106 cells m−3 of air, and the diversity and composition of the airborne microbial communities were also relatively static. Bacteria and fungi were nearly equivalent, and members of the proteobacterial groups Burkholderiales and Moraxellaceae (particularly the genus Psychrobacter) were dominant. These taxa were not always the most abundant in freshly fallen snow samples collected at this site. Although there was minimal variability in microbial abundances and composition within the atmosphere, the number of biological ice nuclei increased significantly during periods of high relative humidity. However, these changes in ice nuclei numbers were not associated with changes in the relative abundances of the most commonly studied ice-nucleating bacteria. PMID:19502432

  7. Case History of a Clean Water Act Compliance Agreement at the Rocky Flats Environmental Technology Site near Golden, Colorado

    SciTech Connect

    Thompson, J.S.

    1995-08-01

    A major Clean Water Act (CWA) Federal Facilities Compliance Agreement was signed on March 25, 1991 by the US Department of Energy, Rocky Flats Field Office (DOE, RFFO) and the Water Enforcement Division of the Environmental Protection Agency (EPA), Region VIII. The agreement revised the Rocky Flats Plant`s National Pollutant Discharge Elimination System (NPDES) permit and arose from pemittee-requested changes in effluent monitoring points and permit violations, most notably the February 22, 1989 Chromic Acid Incident. The Rocky Flats Plant, now called the Rocky Flats Environmental Technology Site (Site) near Golden Colorado was operated at that time by Rockwell International Corporation, who later plead guilty to six misdemeanor and felony counts of the CWA (the aforementioned NPDES permit violations) and paid a $4 million fine on March 26, 1992. The Compliance Agreement, hereafter referred to as the NPDES FFCA, called for three separate remedial action plans and contained a schedule for their submittal to the EPA. The compliance plans focussed on: (1) Waste Water Treatment Plant (WWTP) performance upgrades, (2) source control and surface water protection, and (3) characterization of the impacts from past sludge disposal practices. Projects that implemented the compliance plans were initiated soon after submittal to the EPA and are forecast to complete in 1997 at a total cost of over $35 million. This paper presents a case history of NPDES FFCA compliance projects and highlights the successes, failures, and lessons learned.

  8. Acoustic mapping of diffuse flow at a seafloor hydrothermal site: Monolith Vent, Juan de Fuca Ridge

    NASA Astrophysics Data System (ADS)

    Rona, P. A.; Jackson, D. R.; Wen, T.; Jones, C.; Mitsuzawa, K.; Bemis, K. G.; Dworski, J. G.

    Diffuse flow of hydrothermal solutions commonly occurs in patchy areas up to tens of meters in diameter in seafloor hydrothermal fields. It is recognized as a quantitatively significant component of thermal and chemical fluxes, yet is elusive to map. We report a new acoustic method to detect and map areas of diffuse flow using phase-coherent correlation techniques. The sonar system was modified to record phase information and mounted on DSV SEA CLIFF. The submersible occupied a stationary position on the seafloor and the transducer scanned the seafloor surrounding Monolith Vent, a sulfide edifice venting black smokers, at a nominal range of 17 m at a depth of 2249 m on the Juan de Fuca Ridge. Patchy areas of uncorrelated returns clearly stood out from a background of returns that exhibited ping-to-ping correlation. The areas of uncorrelated returns coincided with areas of diffuse flow as mapped by a video survey with the Navy's Advanced Tethered Vehicle (ATV). Correlated returns were backscattered from invariant seafloor. Uncorrelated returns were distorted by index of refraction inhomogeneities as they passed through diffuse flow between the seafloor and the transducer. The acoustic method presented can synoptically map areas of diffuse flow. When combined with standard in situ measurement and sampling methods the acoustic mapping will facilitate accurate determination of diffuse thermal and chemical fluxes in seafloor hydrothermal fields.

  9. Ithaca MAP3S regional precipitation chemistry site. Annual progress report, 1 November 1984-31 October 1985

    SciTech Connect

    Butler, T.J.; Likens, G.E.

    1986-07-01

    Samples were collected at the MAP3S Regional Precipitation Chemistry Site located 15 km southwest of Ithaca, New York (Lat. 42/sup 0/ 24', Long. 76/sup 0/ 39') at an elevation of 503 m. The surrounding area is rural in nature and consists of gently rolling terrain, vegetated by deciduous forest, abandoned fields, pasture and some agricultural land. Local point sources of combustion products include a 250 mw coal-fired power plant, 23 km NNE of the site and the Cornell University steam-generating plant 16 km ENE of the site. The latter produces emissions of SO/sub 2/ and particulates comparable to a 50 mw coal-fired power plant. Both of these plants are in a quadrant that is consistently downwind of the sampling station. Other local potential sources of particles are from agricultural activity, road dust, and road salt during the winter. Data are collected September 1984 through September 1985.

  10. Autoradiographic quantitation and anatomical mapping of 125I-galanin binding sites in the rat central nervous system.

    PubMed

    Melander, T; Köhler, C; Nilsson, S; Hökfelt, T; Brodin, E; Theodorsson, E; Bartfai, T

    1988-01-01

    The distribution of 125I-galanin binding sites in the rat central nervous system was studied by the use of autoradiography, and the amount of peptide bound was determined by the use of microdensitometry. The amount of 125I-galanin bound in various CNS regions ranged from non detectable to 0.40 pmol per gramme tissue at a concentration of 1.5 nM 125I-galanin. The anatomical mapping revealed high density of binding sites in the telencephalon, where labelling was seen in the entorhinal, perirhinal and piriform cortices, in most septal nuclei, in the amygdala and in the hippocampal formation. In the diencephalon binding sites were densely accumulated in the hypothalamus, including the median eminence and periventricular nucleus as well as in the dorsal and medial thalamic nuclei. In the mesencephalon binding sites were seen in many nuclei including the dorsal raphe nucleus, the periaqueductal central grey and pars compacta of the substantia nigra. The pons/medulla revealed high density of binding sites in the locus coeruleus, parabrachial nuclei and in the dorsal vagal complex, while binding in the spinal cord was seen in laminae I, II and X as well as in the intermediolateral horn. The distribution of 125I-galanin binding sites corresponded well to the localization of the peptide as revealed in several earlier immunohistochemical and radioimmunoassay studies, as well as to several previously reported effects of galanin on central autonomic functions.

  11. Mapping Sites of O-Glycosylation and Fringe Elongation on Drosophila Notch.

    PubMed

    Harvey, Beth M; Rana, Nadia A; Moss, Hillary; Leonardi, Jessica; Jafar-Nejad, Hamed; Haltiwanger, Robert S

    2016-07-29

    Glycosylation of the Notch receptor is essential for its activity and serves as an important modulator of signaling. Three major forms of O-glycosylation are predicted to occur at consensus sites within the epidermal growth factor-like repeats in the extracellular domain of the receptor: O-fucosylation, O-glucosylation, and O-GlcNAcylation. We have performed comprehensive mass spectral analyses of these three types of O-glycosylation on Drosophila Notch produced in S2 cells and identified peptides containing all 22 predicted O-fucose sites, all 18 predicted O-glucose sites, and all 18 putative O-GlcNAc sites. Using semiquantitative mass spectral methods, we have evaluated the occupancy and relative amounts of glycans at each site. The majority of the O-fucose sites were modified to high stoichiometries. Upon expression of the β3-N-acetylglucosaminyltransferase Fringe with Notch, we observed varying degrees of elongation beyond O-fucose monosaccharide, indicating that Fringe preferentially modifies certain sites more than others. Rumi modified O-glucose sites to high stoichiometries, although elongation of the O-glucose was site-specific. Although the current putative consensus sequence for O-GlcNAcylation predicts 18 O-GlcNAc sites on Notch, we only observed apparent O-GlcNAc modification at five sites. In addition, we performed mass spectral analysis on endogenous Notch purified from Drosophila embryos and found that the glycosylation states were similar to those found on Notch from S2 cells. These data provide foundational information for future studies investigating the mechanisms of how O-glycosylation regulates Notch activity.

  12. Mapping Sites of O-Glycosylation and Fringe Elongation on Drosophila Notch.

    PubMed

    Harvey, Beth M; Rana, Nadia A; Moss, Hillary; Leonardi, Jessica; Jafar-Nejad, Hamed; Haltiwanger, Robert S

    2016-07-29

    Glycosylation of the Notch receptor is essential for its activity and serves as an important modulator of signaling. Three major forms of O-glycosylation are predicted to occur at consensus sites within the epidermal growth factor-like repeats in the extracellular domain of the receptor: O-fucosylation, O-glucosylation, and O-GlcNAcylation. We have performed comprehensive mass spectral analyses of these three types of O-glycosylation on Drosophila Notch produced in S2 cells and identified peptides containing all 22 predicted O-fucose sites, all 18 predicted O-glucose sites, and all 18 putative O-GlcNAc sites. Using semiquantitative mass spectral methods, we have evaluated the occupancy and relative amounts of glycans at each site. The majority of the O-fucose sites were modified to high stoichiometries. Upon expression of the β3-N-acetylglucosaminyltransferase Fringe with Notch, we observed varying degrees of elongation beyond O-fucose monosaccharide, indicating that Fringe preferentially modifies certain sites more than others. Rumi modified O-glucose sites to high stoichiometries, although elongation of the O-glucose was site-specific. Although the current putative consensus sequence for O-GlcNAcylation predicts 18 O-GlcNAc sites on Notch, we only observed apparent O-GlcNAc modification at five sites. In addition, we performed mass spectral analysis on endogenous Notch purified from Drosophila embryos and found that the glycosylation states were similar to those found on Notch from S2 cells. These data provide foundational information for future studies investigating the mechanisms of how O-glycosylation regulates Notch activity. PMID:27268051

  13. 24 CFR 3285.103 - Site suitability with design zone maps.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... is to be installed. The design zone maps are those identified in part 3280 of this chapter. (a) Wind zone. Manufactured homes must not be installed in a wind zone that exceeds the design wind loads for which the home has been designed, as evidenced by the wind zone indicated on the home's data plate...

  14. 24 CFR 3285.103 - Site suitability with design zone maps.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... § 3285.315 for Special Snow Load Conditions. (c) Thermal zone. Manufactured homes must not be installed in a thermal zone that exceeds the thermal zone for which the home has been designed, as evidenced by the thermal zone indicated on the heating/cooling certificate and insulation zone map and as...

  15. 24 CFR 3285.103 - Site suitability with design zone maps.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... § 3285.315 for Special Snow Load Conditions. (c) Thermal zone. Manufactured homes must not be installed in a thermal zone that exceeds the thermal zone for which the home has been designed, as evidenced by the thermal zone indicated on the heating/cooling certificate and insulation zone map and as...

  16. Geomorphic/Geologic Mapping, Localization, and Traverse Planning at the Opportunity Landing Site, Mars

    NASA Astrophysics Data System (ADS)

    Parker, T. J.; Golombek, M. P.; Powell, M. W.

    2010-03-01

    Mapping of the Opportunity traverse, using the project’s planning tool, “maestro”, and GIS software. Experience gained by the science and engineering teams will be invaluable for planning and conducting future mobile explorer missions to Mars and other planetary bodies.

  17. 24 CFR 3285.103 - Site suitability with design zone maps.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... § 3285.315 for Special Snow Load Conditions. (c) Thermal zone. Manufactured homes must not be installed in a thermal zone that exceeds the thermal zone for which the home has been designed, as evidenced by the thermal zone indicated on the heating/cooling certificate and insulation zone map and as...

  18. 24 CFR 3285.103 - Site suitability with design zone maps.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... § 3285.315 for Special Snow Load Conditions. (c) Thermal zone. Manufactured homes must not be installed in a thermal zone that exceeds the thermal zone for which the home has been designed, as evidenced by the thermal zone indicated on the heating/cooling certificate and insulation zone map and as...

  19. Use of IHF--mediated Achilles' heel cleavage (IHF-AC) method for mapping ihf sites.

    PubMed

    Kur, J

    1993-01-01

    We have shown that Integration Host Factor of E. coli can successfully be used in the IHF-mediated Achilles' Heel Cleavage (IHF-AC) technique (Kur et al., 1992b), for generating rare natural cleavage sites. The first step of this procedure is methylation of DNA in the presence of IHF, when the overlapping ihf/restriction sites are protected from methylation, and in the second step the DNA is cut by the cognate restriction enzyme. The extent of cleavage could be controlled by varying the IHF:DNA ratio and temperature. The aim of the present study is to demonstrate that IHF-AC procedure might serve as a useful tool for finding new protein-binding sites which overlap known restriction sites. I have used this approach in conjunction with several MTases to find several other unknown IHF-binding sites.

  20. Mapping of RNA accessible sites by extension of random oligonucleotide libraries with reverse transcriptase.

    PubMed Central

    Allawi, H T; Dong, F; Ip, H S; Neri, B P; Lyamichev, V I

    2001-01-01

    A rapid and simple method for determining accessible sites in RNA that is independent of the length of target RNA and does not require RNA labeling is described. In this method, target RNA is allowed to hybridize with sequence-randomized libraries of DNA oligonucleotides linked to a common tag sequence at their 5'-end. Annealed oligonucleotides are extended with reverse transcriptase and the extended products are then amplified by using PCR with a primer corresponding to the tag sequence and a second primer specific to the target RNA sequence. We used the combination of both the lengths of the RT-PCR products and the location of the binding site of the RNA-specific primer to determine which regions of the RNA molecules were RNA extendible sites, that is, sites available for oligonucleotide binding and extension. We then employed this reverse transcription with the random oligonucleotide libraries (RT-ROL) method to determine the accessible sites on four mRNA targets, human activated ras (ha-ras), human intercellular adhesion molecule-1 (ICAM-1), rabbit beta-globin, and human interferon-gamma (IFN-gamma). Our results were concordant with those of other researchers who had used RNase H cleavage or hybridization with arrays of oligonucleotides to identify accessible sites on some of these targets. Further, we found good correlation between sites when we compared the location of extendible sites identified by RT-ROL with hybridization sites of effective antisense oligonucleotides on ICAM-1 mRNA in antisense inhibition studies. Finally, we discuss the relationship between RNA extendible sites and RNA accessibility. PMID:11233988

  1. Geophysical logging and geologic mapping data in the vicinity of the GMH Electronics Superfund site near Roxboro, North Carolina

    USGS Publications Warehouse

    Chapman, Melinda J.; Clark, Timothy W.; Williams, John H.

    2013-01-01

    Geologic mapping, the collection of borehole geophysical logs and images, and passive diffusion bag sampling were conducted by the U.S. Geological Survey North Carolina Water Science Center in the vicinity of the GMH Electronics Superfund site near Roxboro, North Carolina, during March through October 2011. The study purpose was to assist the U.S. Environmental Protection Agency in the development of a conceptual groundwater model for the assessment of current contaminant distribution and future migration of contaminants. Data compilation efforts included geologic mapping of more than 250 features, including rock type and secondary joints, delineation of more than 1,300 subsurface features (primarily fracture orientations) in 15 open borehole wells, and the collection of passive diffusion-bag samples from 42 fracture zones at various depths in the 15 wells.

  2. Digital mapping of the Mars Pathfinder landing site: Design, acquisition, and derivation of cartographic products for science applications

    USGS Publications Warehouse

    Gaddis, L.R.; Kirk, R.L.; Johnson, J. R.; Soderblom, L.A.; Ward, A.W.; Barrett, J.; Becker, K.; Decker, T.; Blue, J.; Cook, D.; Eliason, E.; Hare, T.; Howington-Kraus, E.; Isbell, C.; Lee, E.M.; Redding, B.; Sucharski, R.; Sucharski, T.; Smith, P.H.; Britt, D.T.

    1999-01-01

    The Imager for Mars Pathfinder (IMP) acquired more than 16,000 images and provided panoramic views of the surface of Mars at the Mars Pathfinder landing site in Ares Vallis. This paper describes the stereoscopic, multispectral IMP imaging sequences and focuses on their use for digital mapping of the landing site and for deriving cartographic products to support science applications of these data. Two-dimensional cartographic processing of IMP data, as performed via techniques and specialized software developed for ISIS (the U.S.Geological Survey image processing software package), is emphasized. Cartographic processing of IMP data includes ingestion, radiometric correction, establishment of geometric control, coregistration of multiple bands, reprojection, and mosaicking. Photogrammetric processing, an integral part of this cartographic work which utilizes the three-dimensional character of the IMP data, supplements standard processing with geometric control and topographic information [Kirk et al., this issue]. Both cartographic and photogrammetric processing are required for producing seamless image mosaics and for coregistering the multispectral IMP data. Final, controlled IMP cartographic products include spectral cubes, panoramic (360?? azimuthal coverage) and planimetric (top view) maps, and topographic data, to be archived on four CD-ROM volumes. Uncontrolled and semicontrolled versions of these products were used to support geologic characterization of the landing site during the nominal and extended missions. Controlled products have allowed determination of the topography of the landing site and environs out to ???60 m, and these data have been used to unravel the history of large- and small-scale geologic processes which shaped the observed landing site. We conclude by summarizing several lessons learned from cartographic processing of IMP data. Copyright 1999 by the American Geophysical Union.

  3. Operation and research at the Ithaca MAP3S regional precipitation chemistry site: Annual progress report for 1988

    SciTech Connect

    Butler, T.J.; Likens, G.E.

    1988-07-01

    Ten complete years of precipitation chemistry data, 1977 to 1986, are summarized for the Ithaca MAP3S site. For comparison purposed selected data from the eight other MAP3S sites are included. Notable findings include the following: 1) Monthly concentrations of H/sup +/, SO/sub 4//sup 2/minus//, NO/sub 3//sup /minus//, and NH/sub 4//sup +/ show a high degree of variability from year to year. 2) The Ithaca Site shows a statistically significant (p = 0.05) decline, from 1977 to 1986, in annual volume-weighed H/sup +/ concentration. 3) A statistically significant (p = 0.05) increase in annual volume-weighted NH/sub 4//sup +/ concentration also occurs for this time period at the Ithaca site. 4) Ohio, from 1979 to 1986, shows a significant (p = 0.05) decline in volume-weighted H/sup +/ and SO/sub 4//sup 2/minus// concentration. 5) While there is not a significant (p = 0.05) linear relationship between emissions of SO/sub 2/ and SO/sub 4//sup /minus// concentrations, and emissions of NO/sub x/ and NO/sub 3//sup /minus// concentrations, there is a significant positive relationship for emissions of SO/sub 2/ plus NO/sub x/ versus H/sup +/ concentrations at Ithaca (p = 0.10) and Ohio (p = 0.05). 6) 15% to 30% of dry-deposited particles at the Ithaca site are anthropogenicly derived. On a mass basis, one third of the calcium species are CaSO/sub 4/, probably derived from the conversion of CaCO/sub 3/ interacting with SO/sub 2/ or acidic sulfate. Experimental results suggest this conversion can occur at rates from 0% to 20% per day in the Ithaca area. 13 refs., 23 figs., 2 tabs.

  4. Mapping of the leptin binding sites and design of a leptin antagonist.

    PubMed

    Peelman, Frank; Van Beneden, Katrien; Zabeau, Lennart; Iserentant, Hannes; Ulrichts, Peter; Defeau, Delphine; Verhee, Annick; Catteeuw, Dominiek; Elewaut, Dirk; Tavernier, Jan

    2004-09-24

    The leptin/leptin receptor system shows strong similarities to the long-chain cytokine interleukin-6 (IL-6) and granulocyte colony-stimulating factor cytokine/receptor systems. The IL-6 family cytokines interact with their receptors through three different binding sites I-III. The leptin structure was superposed on the crystal structures of several long-chain cytokines, and a series of leptin mutants was generated focusing on binding sites I-III. The effect of the mutations on leptin receptor (LR) signaling and on binding to the membrane proximal cytokine receptor homology domain (CRH2) of the LR was determined. Mutations in binding site I at the C terminus of helix D show a modest effect on signaling and do not affect binding to CRH2. Binding site II is composed of residues at the surface of helices A and C. Mutations in this site impair binding to CRH2 but have only limited effect on signaling. Site III mutations around the N terminus of helix D impair receptor activation without affecting binding to CRH2. We identified an S120A/T121A mutant in binding site III, which lacks any signaling capacity, but which still binds to CRH2 with wild type affinity. This leptin mutant behaves as a potent leptin antagonist both in vitro and in vivo. PMID:15213225

  5. Genetic Mapping and QTL Analysis of Growth-Related Traits in Pinctada fucata Using Restriction-Site Associated DNA Sequencing

    PubMed Central

    Li, Yaoguo; He, Maoxian

    2014-01-01

    The pearl oyster, Pinctada fucata (P. fucata), is one of the marine bivalves that is predominantly cultured for pearl production. To obtain more genetic information for breeding purposes, we constructed a high-density linkage map of P. fucata and identified quantitative trait loci (QTL) for growth-related traits. One F1 family, which included the two parents, 48 largest progeny and 50 smallest progeny, was sampled to construct a linkage map using restriction site-associated DNA sequencing (RAD-Seq). With low coverage data, 1956.53 million clean reads and 86,342 candidate RAD loci were generated. A total of 1373 segregating SNPs were used to construct a sex-average linkage map. This spanned 1091.81 centimorgans (cM), with 14 linkage groups and an average marker interval of 1.41 cM. The genetic linkage map coverage, Coa, was 97.24%. Thirty-nine QTL-peak loci, for seven growth-related traits, were identified using the single-marker analysis, nonparametric mapping Kruskal-Wallis (KW) test. Parameters included three for shell height, six for shell length, five for shell width, four for hinge length, 11 for total weight, eight for soft tissue weight and two for shell weight. The QTL peak loci for shell height, shell length and shell weight were all located in linkage group 6. The genotype frequencies of most QTL peak loci showed significant differences between the large subpopulation and the small subpopulation (P<0.05). These results highlight the effectiveness of RAD-Seq as a tool for generation of QTL-targeted and genome-wide marker data in the non-model animal, P. fucata, and its possible utility in marker-assisted selection (MAS). PMID:25369421

  6. Genetic mapping and QTL analysis of growth-related traits in Pinctada fucata using restriction-site associated DNA sequencing.

    PubMed

    Li, Yaoguo; He, Maoxian

    2014-01-01

    The pearl oyster, Pinctada fucata (P. fucata), is one of the marine bivalves that is predominantly cultured for pearl production. To obtain more genetic information for breeding purposes, we constructed a high-density linkage map of P. fucata and identified quantitative trait loci (QTL) for growth-related traits. One F1 family, which included the two parents, 48 largest progeny and 50 smallest progeny, was sampled to construct a linkage map using restriction site-associated DNA sequencing (RAD-Seq). With low coverage data, 1956.53 million clean reads and 86,342 candidate RAD loci were generated. A total of 1373 segregating SNPs were used to construct a sex-average linkage map. This spanned 1091.81 centimorgans (cM), with 14 linkage groups and an average marker interval of 1.41 cM. The genetic linkage map coverage, Coa, was 97.24%. Thirty-nine QTL-peak loci, for seven growth-related traits, were identified using the single-marker analysis, nonparametric mapping Kruskal-Wallis (KW) test. Parameters included three for shell height, six for shell length, five for shell width, four for hinge length, 11 for total weight, eight for soft tissue weight and two for shell weight. The QTL peak loci for shell height, shell length and shell weight were all located in linkage group 6. The genotype frequencies of most QTL peak loci showed significant differences between the large subpopulation and the small subpopulation (P<0.05). These results highlight the effectiveness of RAD-Seq as a tool for generation of QTL-targeted and genome-wide marker data in the non-model animal, P. fucata, and its possible utility in marker-assisted selection (MAS).

  7. Missouri aeromagnetic and gravity maps and data: a web site for distribution of data

    USGS Publications Warehouse

    Kucks, Robert P.; Hill, Patricia L.

    2005-01-01

    Magnetic anomalies are due to variations in the Earth's magnetic field caused by the uneven distribution of magnetic minerals (primarily magnetite) in the rocks that make up the upper part of the Earth's crust. The features and patterns of the magnetic anomalies can be used to delineate details of subsurface geology, including the locations of buried faults and magnetite-bearing rocks and the depth to the base of sedimentary basins. This information is valuable for mineral exploration, geologic mapping, and environmental studies. The Missouri magnetic map is constructed from grids that combine information collected in 25 separate magnetic surveys conducted between 1943 and 1987. The data from these surveys are of varying quality. The design and specifications (terrain clearance, sampling rates, line spacing, and reduction procedures) varied from survey to survey depending on the purpose of the project and the technology of that time. Every attempt was made to acquire the data in digital form.

  8. A Remote Characterization System for subsurface mapping of buried waste sites

    SciTech Connect

    Sandness, G.A.; Bennett, D.W.; Martinson, L.

    1992-06-01

    This paper describes a development project that will provide new technology for characterizing hazardous waste burial sites. The project is a collaborative effort by five of the national laboratories, involving the development and demonstration of a remotely controlled site characterization system. The Remote Characterization System (RCS) includes a unique low-signature survey vehicle, a base station, radio telemetry data links, satellite-based vehicle tracking, stereo vision, and sensors for non-invasive inspection of the surface and subsurface.

  9. Mineral Mapping of High Priority Landing Sites for MSL and Beyond Using Mars Express OMEGA and HRSC Data

    NASA Astrophysics Data System (ADS)

    Michalski, J.; Bibring, J.; Poulet, F.; Mangold, N.; Loizeau, D.; Hauber, E.; Altieri, F.; Carrozzo, G.

    2008-12-01

    High priority candidate landing sites for the Mars Science Laboratory (MSL) mission have been proposed by various researchers, their significance based largely on spectroscopic and geomorphic evidence for aqueous processes. Specifically, seven candidate landing sites are under consideration for MSL at the time of this writing: Mawrth Vallis, Nili Fossae, southern Meridiani Planum, Eberswalde Crater, Holden Crater, Gale Crater, and Miyamoto Crater. While only one of these sites can be visited by MSL, the other sites remain among the most compelling localities on Mars for future in-situ exploration by ESA's ExoMars mission or an international Mars sample return mission. We have produced regional scale mineral maps of these sites using data from the Mars Express Observatoire pour la Minéralogie, l'Eau, les Glaces, et l'Activité (OMEGA). Visible images from the High Resolution Stereo Camera (HRSC) are used as a map base. OMEGA infrared band parameters are used to identify and map pyroxene, olivine, oxides, sulfates, phyllosilicates, and other hydrated phases. OMEGA visible channel data also provide color information, which gives an estimate of dust cover and additional insights into the mineralogy of altered deposits. The dustiest site is Gale Crater and the least dusty is Nili Fossae. The strongest signature of phyllosilicates occurs in Mawrth Vallis, followed by Nili Fossae. However, Nili Fossae also has some of the strongest olivine signatures on the planet. One fundamental difference between the Nili Fossae and Mawrth Vallis sites is that in Mawrth Vallis, phyllosilicate-bearing, light-toned rocks contain no evidence for primary phases in OMEGA data, but in the Nili Fossae area, phyllosilicates, olivine, and pyroxene are mixed at the subpixel level. South Meridiani Planum shows hydrated plains in contact with ancient, pyroxene-bearing, slightly altered, older bedrock. Patchy deposits of phyllosilicates are found in Miyamoto Crater, but their geologic context is

  10. A solid waste disposal site selection procedure based on groundwater vulnerability mapping

    NASA Astrophysics Data System (ADS)

    Simsek, Celalettin; Kincal, Cem; Gunduz, Orhan

    2006-02-01

    In this study, a new, GIS-based solid waste site selection tool (DUPIT) is introduced to obtain a systematic and unbiased methodology during the evaluation phases of alternative solid waste disposal areas with regards to vulnerability to groundwater pollution. The proposed tool is an index technique based on the linear combination of five different hydrogeological parameters including Depth to groundwater table, Upper layer lithology, Permeability of the unsaturated zone, Impermeable layer thickness and Topographic slope. Five different categories are developed to classify each alternative based on the suitability of the site for a solid waste disposal area. As a result, each site is ranked according to the contamination risks for groundwater resources. The proposed technique is applied to the District of Torbali near Izmir, Turkey to determine the most appropriate solid waste disposal site location. The Torbali application is implemented by using a GIS database developed for the area. Based on the results of this application, the best alternative solid waste disposal site for Torbali is selected to be located in the northern portions of the city where the groundwater table is deep, the permeability is low and the topographic slope is mild.

  11. Hazard Ranking System evaluation of CERCLA (Comprehensive Environmental Response, Compensation, and Liability Act) inactive waste sites at Hanford: Volume 1, Evaluation methods and results

    SciTech Connect

    Stenner, R.D.; Cramer, K.H.; Higley, K.A.; Jette, S.J.; Lamar, D.A.; McLaughlin, T.J.; Sherwood, D.R.; Van Houten, N.C.

    1988-10-01

    The purpose of this report is to formally document the individual site Hazard Ranking System (HRS) evaluations conducted as part of the preliminary assessment/site inspection (PA/SI) activities at the US Department of Energy (DOE) Hanford Site. These activities were carried out pursuant to the DOE orders that describe the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) Program addressing the cleanup of inactive waste sites. These orders incorporate the US Environmental Protection Agency methodology, which is based on the Superfund Amendments and Reauthorization Act of 1986 (SARA). The methodology includes six parts: PA/SI, remedial investigation/feasibility study, record of decision, design and implementation of remedial action, operation and monitoring, and verification monitoring. Volume 1 of this report discusses the CERCLA inactive waste-site evaluation process, assumptions, and results of the HRS methodology employed. Volume 2 presents the data on the individual CERCLA engineered-facility sites at Hanford, as contained in the Hanford Inactive Site Surveillance (HISS) Data Base. Volume 3 presents the data on the individual CERCLA unplanned-release sites at Hanford, as contained in the HISS Data Base. 34 refs., 43 figs., 47 tabs.

  12. Evaluation of Different N-Glycopeptide Enrichment Methods for N-Glycosylation Sites Mapping in Mouse Brain.

    PubMed

    Zhang, Chengqian; Ye, Zilu; Xue, Peng; Shu, Qingbo; Zhou, Yue; Ji, Yanlong; Fu, Ying; Wang, Jifeng; Yang, Fuquan

    2016-09-01

    N-Glycosylation of proteins plays a critical role in many biological pathways. Because highly heterogeneous N-glycopeptides are present in biological sources, the enrichment procedure is a crucial step for mass spectrometry analysis. Five enrichment methods, including IP-ZIC-HILIC, hydrazide chemistry, lectin affinity, ZIC-HILIC-FA, and TiO2 affinity were evaluated and compared in the study of mapping N-glycosylation sites in mouse brain. On the basis of our results, the identified N-glycosylation sites were 1891, 1241, 891, 869, and 710 and the FDR values were 3.29, 5.62, 9.54, 9.54, and 20.02%, respectively. Therefore, IP-ZIC-HILIC enrichment method displayed the highest sensitivity and specificity. In this work, we identified a total of 3446 unique glycosylation sites conforming to the N-glycosylation consensus motif (N-X-T/S/C; X ≠ P) with (18)O labeling in 1597 N-glycoproteins. N-glycosylation site information was used to confirm or correct the transmembrane topology of the 57 novel transmembrane N-glycoproteins.

  13. Evaluation of Different N-Glycopeptide Enrichment Methods for N-Glycosylation Sites Mapping in Mouse Brain.

    PubMed

    Zhang, Chengqian; Ye, Zilu; Xue, Peng; Shu, Qingbo; Zhou, Yue; Ji, Yanlong; Fu, Ying; Wang, Jifeng; Yang, Fuquan

    2016-09-01

    N-Glycosylation of proteins plays a critical role in many biological pathways. Because highly heterogeneous N-glycopeptides are present in biological sources, the enrichment procedure is a crucial step for mass spectrometry analysis. Five enrichment methods, including IP-ZIC-HILIC, hydrazide chemistry, lectin affinity, ZIC-HILIC-FA, and TiO2 affinity were evaluated and compared in the study of mapping N-glycosylation sites in mouse brain. On the basis of our results, the identified N-glycosylation sites were 1891, 1241, 891, 869, and 710 and the FDR values were 3.29, 5.62, 9.54, 9.54, and 20.02%, respectively. Therefore, IP-ZIC-HILIC enrichment method displayed the highest sensitivity and specificity. In this work, we identified a total of 3446 unique glycosylation sites conforming to the N-glycosylation consensus motif (N-X-T/S/C; X ≠ P) with (18)O labeling in 1597 N-glycoproteins. N-glycosylation site information was used to confirm or correct the transmembrane topology of the 57 novel transmembrane N-glycoproteins. PMID:27480293

  14. Evaluation of a Single-Beam Sonar System to Map Seagrass at Two Sites in Northern Puget Sound, Washington

    USGS Publications Warehouse

    Stevens, Andrew W.; Lacy, Jessica R.; Finlayson, David P.; Gelfenbaum, Guy

    2008-01-01

    Seagrass at two sites in northern Puget Sound, Possession Point and nearby Browns Bay, was mapped using both a single-beam sonar and underwater video camera. The acoustic and underwater video data were compared to evaluate the accuracy of acoustic estimates of seagrass cover. The accuracy of the acoustic method was calculated for three classifications of seagrass observed in underwater video: bare (no seagrass), patchy seagrass, and continuous seagrass. Acoustic and underwater video methods agreed in 92 percent and 74 percent of observations made in bare and continuous areas, respectively. However, in patchy seagrass, the agreement between acoustic and underwater video was poor (43 percent). The poor agreement between the two methods in areas with patchy seagrass is likely because the two instruments were not precisely colocated. The distribution of seagrass at the two sites differed both in overall percent vegetated and in the distribution of percent cover versus depth. On the basis of acoustic data, seagrass inhabited 0.29 km2 (19 percent of total area) at Possession Point and 0.043 km2 (5 percent of total area) at the Browns Bay study site. The depth distribution at the two sites was markedly different. Whereas the majority of seagrass at Possession Point occurred between -0.5 and -1.5 m MLLW, most seagrass at Browns Bay occurred at a greater depth, between -2.25 and -3.5 m MLLW. Further investigation of the anthropogenic and natural factors causing these differences in distribution is needed.

  15. Point Cloud Mapping Methods for Documenting Cultural Landscape Features at the Wormsloe State Historic Site, Savannah, Georgia, USA

    NASA Astrophysics Data System (ADS)

    Jordana, T. R.; Goetcheus, C. L.; Madden, M.

    2016-06-01

    Documentation of the three-dimensional (3D) cultural landscape has traditionally been conducted during site visits using conventional photographs, standard ground surveys and manual measurements. In recent years, there have been rapid developments in technologies that produce highly accurate 3D point clouds, including aerial LiDAR, terrestrial laser scanning, and photogrammetric data reduction from unmanned aerial systems (UAS) images and hand held photographs using Structure from Motion (SfM) methods. These 3D point clouds can be precisely scaled and used to conduct measurements of features even after the site visit has ended. As a consequence, it is becoming increasingly possible to collect non-destructive data for a wide variety of cultural site features, including landscapes, buildings, vegetation, artefacts and gardens. As part of a project for the U.S. National Park Service, a variety of data sets have been collected for the Wormsloe State Historic Site, near Savannah, Georgia, USA. In an effort to demonstrate the utility and versatility of these methods at a range of scales, comparisons of the features mapped with different techniques will be discussed with regards to accuracy, data set completeness, cost and ease-of-use.

  16. Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne.

    PubMed

    Pfender, W F; Saha, M C; Johnson, E A; Slabaugh, M B

    2011-05-01

    A mapping population was created to detect quantitative trait loci (QTL) for resistance to stem rust caused by Puccinia graminis subsp. graminicola in Lolium perenne. A susceptible and a resistant plant were crossed to produce a pseudo-testcross population of 193 F(1) individuals. Markers were produced by the restriction-site associated DNA (RAD) process, which uses massively parallel and multiplexed sequencing of reduced-representation libraries. Additional simple sequence repeat (SSR) and sequence-tagged site (STS) markers were combined with the RAD markers to produce maps for the female (738 cM) and male (721 cM) parents. Stem rust phenotypes (number of pustules per plant) were determined in replicated greenhouse trials by inoculation with a field-collected, genetically heterogeneous population of urediniospores. The F(1) progeny displayed continuous distribution of phenotypes and transgressive segregation. We detected three resistance QTL. The most prominent QTL (qLpPg1) is located near 41 cM on linkage group (LG) 7 with a 2-LOD interval of 8 cM, and accounts for 30-38% of the stem rust phenotypic variance. QTL were detected also on LG1 (qLpPg2) and LG6 (qLpPg3), each accounting for approximately 10% of phenotypic variance. Alleles of loci closely linked to these QTL originated from the resistant parent for qLpPg1 and from both parents for qLpPg2 and qLpPg3. Observed quantitative nature of the resistance may be due to partial-resistance effects against all pathogen genotypes, or qualitative effects completely preventing infection by only some genotypes in the genetically mixed inoculum. RAD markers facilitated rapid construction of new genetic maps in this outcrossing species and will enable development of sequence-based markers linked to stem rust resistance in L. perenne. PMID:21344184

  17. Mapping molecular adhesion sites inside SMIL coated capillaries using atomic force microscopy recognition imaging.

    PubMed

    Leitner, Michael; Stock, Lorenz G; Traxler, Lukas; Leclercq, Laurent; Bonazza, Klaus; Friedbacher, Gernot; Cottet, Hervé; Stutz, Hanno; Ebner, Andreas

    2016-08-01

    Capillary zone electrophoresis (CZE) is a powerful analytical technique for fast and efficient separation of different analytes ranging from small inorganic ions to large proteins. However electrophoretic resolution significantly depends on the coating of the inner capillary surface. High technical efforts like Successive Multiple Ionic Polymer Layer (SMIL) generation have been taken to develop stable coatings with switchable surface charges fulfilling the requirements needed for optimal separation. Although the performance can be easily proven in normalized test runs, characterization of the coating itself remains challenging. Atomic force microscopy (AFM) allows for topographical investigation of biological and analytical relevant surfaces with nanometer resolution and yields information about the surface roughness and homogeneity. Upgrading the scanning tip to a molecular biosensor by adhesive molecules (like partly inverted charged molecules) allows for performing topography and recognition imaging (TREC). As a result, simultaneously acquired sample topography and adhesion maps can be recorded. We optimized this technique for electrophoresis capillaries and investigated the charge distribution of differently composed and treated SMIL coatings. By using the positively charged protein avidin as a single molecule sensor, we compared these SMIL coatings with respect to negative charges, resulting in adhesion maps with nanometer resolution. The capability of TREC as a functional investigation technique at the nanoscale was successfully demonstrated. PMID:27265903

  18. Iowa magnetic and gravity maps and data: a web site for distribution of data

    USGS Publications Warehouse

    Kucks, Robert P.; Hill, Patricia L.

    2005-01-01

    Magnetic anomalies are due to variations in the Earth's magnetic field caused by the uneven distribution of magnetic minerals (primarily magnetite) in the rocks that make up the upper part of the Earth's crust. The features and patterns of the magnetic anomalies can be used to delineate details of subsurface geology, including the locations of buried faults and magnetite-bearing rocks and the depth to the base of sedimentary basins. This information is valuable for mineral exploration, geologic mapping, and environmental studies. The Iowa magnetic map is constructed from grids that combine information collected in nine separate magnetic surveys conducted between 1953 and 1972. The data from these surveys are of varying quality. The design and specifications (terrain clearance, sampling rates, line spacing, and reduction procedures) varied from survey to survey depending on the purpose of the project and the technology of that time. Every attempt was made to acquire the data in digital form. All survey grids have been continued to 305 m (1,000 ft) above ground and merged together to form the State compilation.

  19. North Dakota aeromagnetic and gravity maps and data, a web site for distribution of data

    USGS Publications Warehouse

    Sweeney, Ronald E.; Hill, Patricia L.

    2003-01-01

    The North Dakota aeromagnetic grid is constructed from grids that combine information collected in 13 separate aeromagnetic surveys conducted between 1978 and 2001. The data from these surveys are of varying quality. The design and specifications (terrain clearance, sampling rates, line spacing, and reduction procedures) varied from survey to survey depending on the purpose of the project and the technology of that time. Every attempt was made to acquire the data in digital form. Most of the available digital data were obtained from aeromagnetic surveys flown by the U.S. Geological Survey (USGS), flown on contract with the USGS, or were obtained from other federal agencies and state universities. Some of the 1980 data are available only on hand-contoured maps and had to be digitized. These maps were digitized along flight-line/contour-line intersections, which is considered to be the most accurate method of recovering the original data. Digitized data are available as USGS Open File Report 99-557. All surveys have been continued to 304.8 meters (1000 feet) above ground and then blended or merged together.

  20. Mapping molecular adhesion sites inside SMIL coated capillaries using atomic force microscopy recognition imaging.

    PubMed

    Leitner, Michael; Stock, Lorenz G; Traxler, Lukas; Leclercq, Laurent; Bonazza, Klaus; Friedbacher, Gernot; Cottet, Hervé; Stutz, Hanno; Ebner, Andreas

    2016-08-01

    Capillary zone electrophoresis (CZE) is a powerful analytical technique for fast and efficient separation of different analytes ranging from small inorganic ions to large proteins. However electrophoretic resolution significantly depends on the coating of the inner capillary surface. High technical efforts like Successive Multiple Ionic Polymer Layer (SMIL) generation have been taken to develop stable coatings with switchable surface charges fulfilling the requirements needed for optimal separation. Although the performance can be easily proven in normalized test runs, characterization of the coating itself remains challenging. Atomic force microscopy (AFM) allows for topographical investigation of biological and analytical relevant surfaces with nanometer resolution and yields information about the surface roughness and homogeneity. Upgrading the scanning tip to a molecular biosensor by adhesive molecules (like partly inverted charged molecules) allows for performing topography and recognition imaging (TREC). As a result, simultaneously acquired sample topography and adhesion maps can be recorded. We optimized this technique for electrophoresis capillaries and investigated the charge distribution of differently composed and treated SMIL coatings. By using the positively charged protein avidin as a single molecule sensor, we compared these SMIL coatings with respect to negative charges, resulting in adhesion maps with nanometer resolution. The capability of TREC as a functional investigation technique at the nanoscale was successfully demonstrated.

  1. Identification and mapping of nucleotide binding site-leucine rich repeat resistance gene analogs in bermudagrass

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Thirty-one bermudagrass (Cynodon spp.) disease resistance gene homologs (BRGH) were cloned and sequenced from diploid, triploid, and hexaploid bermudagrass using degenerate primers to target the nucleotide binding site (NBS) of the NBS- leucine rich repeat (LRR) resistance gene family. Alignment of ...

  2. Multi-Site N-glycan mapping study 1: Capillary electrophoresis – laser induced fluorescence

    PubMed Central

    Szekrényes, Ákos; Park, SungAe Suhr; Santos, Marcia; Lew, Clarence; Jones, Aled; Haxo, Ted; Kimzey, Michael; Pourkaveh, Shiva; Szabó, Zoltán; Sosic, Zoran; Feng, Peng; Váradi, Csaba; de l'Escaille, François; Falmagne, Jean-Bernard; Sejwal, Preeti; Niedringhaus, Thomas; Michels, David; Freckleton, Gordon; Hamm, Melissa; Manuilov, Anastasiya; Schwartz, Melissa; Luo, Jiann-Kae; van Dyck, Jonathan; Leung, Pui-King; Olajos, Marcell; Gu, Yingmei; Gao, Kai; Wang, Wenbo; Wegstein, Jo; Tep, Samnang; Guttman, András

    2016-01-01

    An international team that included 20 independent laboratories from biopharmaceutical companies, universities, analytical contract laboratories and national authorities in the United States, Europe and Asia was formed to evaluate the reproducibility of sample preparation and analysis of N-glycans using capillary electrophoresis of 8-aminopyrene-1,3,6-trisulfonic acid (APTS)-labeled glycans with laser induced fluorescence (CE-LIF) detection (16 sites) and ultra high-performance liquid chromatography (UHPLC, 12 sites; results to be reported in a subsequent publication). All participants used the same lot of chemicals, samples, reagents, and columns/capillaries to run their assays. Migration time, peak area and peak area percent values were determined for all peaks with >0.1% peak area. Our results demonstrated low variability and high reproducibility, both, within any given site as well across all sites, which indicates that a standard N-glycan analysis platform appropriate for general use (clone selection, process development, lot release, etc.) within the industry can be established. PMID:26466659

  3. Multi-Site N-glycan mapping study 1: Capillary electrophoresis - laser induced fluorescence.

    PubMed

    Szekrényes, Ákos; Park, SungAe Suhr; Santos, Marcia; Lew, Clarence; Jones, Aled; Haxo, Ted; Kimzey, Michael; Pourkaveh, Shiva; Szabó, Zoltán; Sosic, Zoran; Feng, Peng; Váradi, Csaba; de l'Escaille, François; Falmagne, Jean-Bernard; Sejwal, Preeti; Niedringhaus, Thomas; Michels, David; Freckleton, Gordon; Hamm, Melissa; Manuilov, Anastasiya; Schwartz, Melissa; Luo, Jiann-Kae; van Dyck, Jonathan; Leung, Pui-King; Olajos, Marcell; Gu, Yingmei; Gao, Kai; Wang, Wenbo; Wegstein, Jo; Tep, Samnang; Guttman, András

    2016-01-01

    An international team that included 20 independent laboratories from biopharmaceutical companies, universities, analytical contract laboratories and national authorities in the United States, Europe and Asia was formed to evaluate the reproducibility of sample preparation and analysis of N-glycans using capillary electrophoresis of 8-aminopyrene-1,3,6-trisulfonic acid (APTS)-labeled glycans with laser induced fluorescence (CE-LIF) detection (16 sites) and ultra high-performance liquid chromatography (UHPLC, 12 sites; results to be reported in a subsequent publication). All participants used the same lot of chemicals, samples, reagents, and columns/capillaries to run their assays. Migration time, peak area and peak area percent values were determined for all peaks with >0.1% peak area. Our results demonstrated low variability and high reproducibility, both, within any given site as well across all sites, which indicates that a standard N-glycan analysis platform appropriate for general use (clone selection, process development, lot release, etc.) within the industry can be established.

  4. Mapping an antibody-binding site and a T-cell-stimulating site on the 1A protein of respiratory syncytial virus.

    PubMed Central

    Nicholas, J A; Mitchell, M A; Levely, M E; Rubino, K L; Kinner, J H; Harn, N K; Smith, C W

    1988-01-01

    A synthetic peptide modeled on residues 45 to 60 of the 1A protein of respiratory syncytial (RS) virus [1A(45-60)] was constructed and used for immunization of mice and rabbits. The immunoglobulin G fraction of the resulting rabbit antibody, purified on protein A-Sepharose, immunoprecipitated from RS-infected HEp-2 cells a protein with a molecular size of approximately 9.5 kilodaltons, which corresponds to the previously published molecular size of the 1A protein (Y. T. Huang, P. L. Collins, and G. W. Wertz, Virus Res. 2:157-173, 1985). To investigate the T-cell-inducing properties of 1A(45-60), six strains of mice were immunized and their popliteal lymph node cells were tested for proliferation upon restimulation with peptide in vitro. The lymph node cells of all six strains of mice were responsive to restimulation with 1A(45-60) and showed high- and low-responder strain variation. These peptide-primed lymph node cells also proliferated upon in vitro restimulation with RS virus-infected cells. Correlation of proliferation with interleukin 2 production suggested that the responding lymphocytes were T-helper cells. The antibody-binding and T-cell-stimulating sites of 1A were mapped by constructing a series of overlapping synthetic peptides and testing each for ability to react with antiserum prepared by immunization of BALB/C mice with free peptide 1A(45-60) or for ability to restimulate proliferation in 1A(45-60)-primed lymph node cells of BALB/C mice. Human antibody, obtained during confirmed RS virus infection, was similarly tested with the truncated peptides. Antibody-binding activity was reduced after truncation from the carboxy terminus, and a binding site was mapped to residues 51 through 60, the smallest peptide tested. T-cell-stimulating activity in mice was relatively resistant to truncation from the carboxy terminus and sensitive to truncation from the amino terminus. The smallest region which retained significant T-cell-stimulating activity mapped to

  5. Site characterization progress report: Yucca Mountain, Nevada, April 1, 1990--September 30, 1990, Number 3; Nuclear Waste Policy Act (Section 113)

    SciTech Connect

    1991-03-01

    In accordance with the requirements of Section 113(b)(3) of the Nuclear Waste Policy Act of 1982 (NWPA), as amended, the US Department of Energy has prepared this report on the progress of site characterization activities at Yucca Mountain, Nevada, for the period April 1 through September 30, 1990. This report is the third of a series of reports that are issued at intervals of approximately six months during site characterization. The report covers a number of new initiatives to improve the effectiveness of the site characterization program and covers continued efforts related to preparatory activities, study plans, and performance assessment. 85 refs., 2 figs., 3 tabs.

  6. A new approach to map transcription sites at the ultrastructural level.

    PubMed

    Testillano, P S; Gorab, E; Risueño, M C

    1994-01-01

    We describe a new ultrastructural method for locating transcription on ultra-thin sections. The use of anti-DNA/RNA hybrid antibodies provides specific labeling on precise structures of the nuclear compartments of several cell types. All mammalian and plant material studied (HeLa cells, lymphocytes, onion root meristematic cells) showed the same pattern of labeling: fibrillar structures in the interchromatin region and discrete regions of the dense fibrillar component at the periphery of the fibrillar centers in the nucleolus. The specificity of the immunogold labeling was tested by RNAse H digestion and by pre-blocking the antibody with synthetic DNA/RNA hybrids; in both cases no gold particles were observed. This method has considerable advantages compared with current techniques, constituting a very useful tool to map transcriptionally active loci in a variety of cells. PMID:7505298

  7. Acid-base site detection and mapping on solid surfaces by Kelvin force microscopy (KFM).

    PubMed

    Gouveia, Rubia F; Bernardes, Juliana S; Ducati, Telma R D; Galembeck, Fernando

    2012-12-01

    Electrostatic potential at the surface of acidic or basic solids changes under higher relative humidity (RH), as determined by using Kelvin force microscopy (KFM). The potential on acid surfaces becomes more negative as the water vapor pressure increases, while it becomes more positive on basic solids. These results verify the following hypothesis: OH(-) or H(+) ions associated with atmospheric water ion clusters are selectively adsorbed on solid surfaces, depending on the respective Brønsted acid or base character. Therefore, Kelvin microscopy, under variable humidity, is a rigorous but convenient alternative to determine the acid-base character of solid surfaces, with a great advantage: it uses only one amphoteric and simple reagent to determine both the acid and base sites. Moreover, this technique provides information on the spatial distribution of acid-base sites, which is currently inaccessible to any other method.

  8. Fine resolution mapping of double-strand break sites for human ribosomal DNA units.

    PubMed

    Pope, Bernard J; Mahmood, Khalid; Jung, Chol-Hee; Park, Daniel J

    2016-12-01

    DNA breakage arises during a variety of biological processes, including transcription, replication and genome rearrangements. In the context of disease, extensive fragmentation of DNA has been described in cancer cells and during early stages of neurodegeneration (Stephens et al., 2011 Stephens et al. (2011) [5]; Blondet et al., 2001 Blondet et al. (2001) [1]). Stults et al. (2009) Stults et al. (2009) [6] reported that human rDNA gene clusters are hotspots for recombination and that rDNA restructuring is among the most common chromosomal alterations in adult solid tumours. As such, analysis of rDNA regions is likely to have significant prognostic and predictive value, clinically. Tchurikov et al. (2015a, 2016) Tchurikov et al. (2015a, 2016) [7], [9] have made major advances in this direction, reporting that sites of human genome double-strand breaks (DSBs) occur frequently at sites in rDNA that are tightly linked with active transcription - the authors used a RAFT (rapid amplification of forum termini) protocol that selects for blunt-ended sites. They reported the relative frequency of these rDNA DSBs within defined co-ordinate 'windows' of varying size and made these data (as well as the relevant 'raw' sequencing information) available to the public (Tchurikov et al., 2015b). Assay designs targeting rDNA DSB hotspots will benefit greatly from the publication of break sites at greater resolution. Here, we re-analyse public RAFT data and make available rDNA DSB co-ordinates to the single-nucleotide level. PMID:27656414

  9. Target detection and mapping of aquatic hazardous waste sites in Massachusetts Bay utilizing sidescan sonar

    SciTech Connect

    Keith, D.J.; Capone, V.; Cook, G.S.; Casey, D.A.; Wiley, D.N.

    1992-01-01

    The oceans have frequently been used for disposal for a variety of industrial, chemical, and low-level radioactive wastes. In Massachusetts Bay, several areas have been used for the permitted and possible non-permitted disposal of waste containers with environmentally sensitive materials. During the Summer and Fall of 1991, the Industrial Waste Site (IWS) and the Boston Lightship Dumping Ground (BLDG) in Massachusetts Bay were the subject of intensive surveys to determine the areal extent, distribution and location of waste containers.

  10. Multi-level assessment protocol (MAP) for adoption in multi-site clinical trials

    PubMed Central

    Guydish, J.; Manser, S.T.; Jessup, M.; Tajima, B.; Sears, C.; Montini, T.

    2010-01-01

    The National Institute on Drug Abuse (NIDA) Clinical Trials Network (CTN) is intended to test promising drug abuse treatment models in multi-site clinical trials, and to support adoption of new interventions into clinical practice. Using qualitative research methods we asked: How might the technology of multi-site clinical trials be modified to better support adoption of tested interventions? A total of 42 participants, representing 8 organizational levels ranging from clinic staff to clinical trial leaders, were interviewed about their role in the clinical trial, its interactions with clinics, and intervention adoption. Among eight clinics participating in the clinical trial, we found adoption of the tested intervention in one clinic only. In analysis of interview data we identified four conceptual themes which are likely to affect adoption and may be informative in future multi-site clinical trials. We offer the conclusion that planning for adoption in the early stages of protocol development will better serve the aim of integrating new interventions into practice. PMID:20890376

  11. The intergenic region between the divergently transcribed niiA and niaD genes of Aspergillus nidulans contains multiple NirA binding sites which act bidirectionally.

    PubMed Central

    Punt, P J; Strauss, J; Smit, R; Kinghorn, J R; van den Hondel, C A; Scazzocchio, C

    1995-01-01

    The niaD and niiA genes of Aspergillus nidulans, which code, respectively, for nitrate and nitrite reductases, are divergently transcribed, and their ATGs are separated by 1,200 bp. The genes are under the control of the positively acting NirA transcription factor, which mediates nitrate induction. The DNA binding domain of NirA was expressed as a fusion protein with the glutathione S-transferase of Schistosoma japonicum. Gel shift and footprint experiments have shown that in the intergenic region there are four binding sites for the NirA transcription factor. These sites can be represented by the nonpalindromic consensus 5'CTCCGHGG3'. Making use of a bidirectional expression vector, we have analyzed the role of each of the sites in niaD and niiA expression. The sites were numbered from the niiA side. It appeared that site 1 is necessary for the inducibility of niiA only, while sites 2, 3, and to a lesser extent 4 (which is nearer to and strongly affects niaD) act bidirectionally. The results also suggest that of the 10 binding sites for the AreA protein, which mediates nitrogen metabolite repression, those which are centrally located are physiologically important. The insertion of an unrelated upstream activating sequence into the intergenic region strongly affected the expression of both genes, irrespective of the orientation in which the element was inserted. PMID:7565720

  12. Uav Surveying for a Complete Mapping and Documentation of Archaeological Findings. The Early Neolithic Site of Portonovo

    NASA Astrophysics Data System (ADS)

    Malinverni, E. S.; Conati Barbaro, C.; Pierdicca, R.; Bozzi, C. A.; Tassetti, A. N.

    2016-06-01

    The huge potential of 3D digital acquisition techniques for the documentation of archaeological sites, as well as the related findings, is almost well established. In spite of the variety of available techniques, a sole documentation pipeline cannot be defined a priori because of the diversity of archaeological settings. Stratigraphic archaeological excavations, for example, require a systematic, quick and low cost 3D single-surface documentation because the nature of stratigraphic archaeology compels providing documentary evidence of any excavation phase. Only within a destructive process each single excavation cannot be identified, documented and interpreted and this implies the necessity of a re- examination of the work on field. In this context, this paper describes the methodology, carried out during the last years, to 3D document the Early Neolithic site of Portonovo (Ancona, Italy) and, in particular, its latest step consisting in a photogrammetric aerial survey by means of UAV platform. It completes the previous research delivered in the same site by means of terrestrial laser scanning and close range techniques and sets out different options for further reflection in terms of site coverage, resolution and campaign cost. With the support of a topographic network and a unique reference system, the full documentation of the site is managed in order to detail each excavation phase; besides, the final output proves how the 3D digital methodology can be completely integrated with reasonable costs during the excavation and used to interpret the archaeological context. Further contribution of this work is the comparison between several acquisition techniques (i.e. terrestrial and aerial), which could be useful as decision support system for different archaeological scenarios. The main objectives of the comparison are: i) the evaluation of 3D mapping accuracy from different data sources, ii) the definition of a standard pipeline for different archaeological needs

  13. Integration of landslide hazard maps into probabilistic risk assessment in context of global changes: an alpine test site

    NASA Astrophysics Data System (ADS)

    Vandromme, Rosalie; Desramaut, Nicolas; Baills, Audrey; Fontaine, Mélanie; Hohmann, Audrey; Grandjean, Gilles; Sedan, Olivier; Puissant, Anne; Malet, Jean-Philippe

    2013-04-01

    The aim of this work is to develop a methodology to integrate global changes scenarios into quantitative risk assessment. This paper describes a methodology to take into account effects of changing climate on landslides activity and impacts of social changes on exposure to provide a complete evaluation of risk for given scenarios. This approach is applied for demonstration purpose on a southern alpine test site. Mechanical approaches represent a solution to quantify landslide susceptibility and to model hazard on unprecedented conditions, as it is likely to occur. However, as the quantity and the quality of data are generally very heterogeneous at a regional scale, it is necessary to take into account their uncertainty in the analysis. In this perspective, a new hazard modeling method has been developed and integrated in a GIS-based software called ALICE®. To go further, climate change scenarios have been computed for the alpine test site (Barcelonnette area, France) using the REMO-COSMO-LM. From the precipitation time series, a daily index of the soil water content has been computed thanks to a reservoir-based model (GARDENIA®). Hence, the program classifies hazard zones depending on the several spatial data (lithological, DEM, etc…) and different hydrological contexts varying in time. The probabilistically initiated landslides are then propagated thank to a semi-empirical model (BORA) to provide real hazard maps. Different scenarios of land-use have been developed using an automate cellular model to cover the probable range of development of potential elements at risks in the future. These exposure maps are then combined with the aforementioned hazard maps to obtain risk maps for the different periods and the different land-use development scenarios. Potential evolutions of landslide risks are then evaluated, with a general increase in the 7 communes. This methodology also allows the analysis of the contributions of both considered global changes (climate and

  14. Field-mapping and petrographic analysis of volcanoes surrounding the Lake Natron Homo sapiens footprint site, northern Tanzania

    NASA Astrophysics Data System (ADS)

    Hewitt, S. M.; Zimmer, B.; Liutkus, C.; Carmichael, S. K.; McGinnis, K.

    2010-12-01

    The Lake Natron Homo sapiens footprint site is located in northern Tanzania along the East African Rift escarpment. The site is positioned south of Lake Natron within an ephemeral channel of the Engare Sero River. The hominid footprints are preserved in a tuff, which originated from one of the volcanic centers surrounding the site. Two large volcanoes in the surrounding region, including the active carbonatite producing Oldoinyo L’engai and the now extinct Kerimasi are possible sources. This area also contains over 30 smaller tuff cones and tuff rings that have been poorly mapped and not analyzed in detail. The site is significant as it is the oldest modern human trackway in East Africa and one of the largest collections of hominid footprints in the world. Determining the source of the footprinted volcanic ash requires detailed field mapping, and both petrographic and geochemical analyses. Extensive field-mapping of the region revealed multiple regional beds that stratigraphically overlay the footprinted layer. Age dating as well as geochemical analysis is being conducted to relate these beds to the footprinted layer. Field-mapping showed that the footprinted tuff is over 35 cm thick, suggesting a large, sustained eruption. The bulk of the tuff cones examined in the field visibly varied in composition to the footprinted tuff and, based on proximity to the footprint site, are too small to produce the requisite volume of ash. Field analysis of samples collected from Oldoinyo L’engai reveal the most similar mineral assemblages to the footprinted layer, and the large volcano provides a source substantial enough to create a thick ash bed 10 km north of the summit. Preliminary research reveals that the footprinted tuff is a phonolite, characterized by silica depletion and the presence of sanidine, augite, and annite with interstitial calcite. XRD analysis of samples collected from Oldoinyo L’engai reveal a nepheline-rich phonolite with zeolites (ie. phillipsite

  15. Mapping an aggregate extraction site off the Eastern English Channel: A methodology in support of monitoring and management

    NASA Astrophysics Data System (ADS)

    Birchenough, Silvana N. R.; Boyd, Siân E.; Vanstaen, Koen; Coggan, Roger A.; Limpenny, David S.

    2010-04-01

    Each year approximately 23-28 million tonnes of sand and gravel are removed from offshore sediments around England and Wales. This study was located in a licensed marine aggregate extraction site off Shoreham in the Eastern English Channel (EEC thereafter). Results from the multibeam survey showed the presence of dredged pits created by suction hopper dredging and elongated furrows created by trailer suction hopper dredging in the area where sand and gravel had been excavated. Electronic Monitoring System (EMS) contained the dredging intensity recorded annually at the site; this information was combined with particle size data providing interpreted maps, which informed the status of the sediments at the site. The aim of the current study was to explore the presence of marine habitats over a smaller area known as the 'Shoreham Box' in the EEC. Results showed some differences in the community composition produced by the two methods of extraction. There was also indication of enhanced number of species in the area dredged by suction hopper method. Notably, slipper limpets were also observed inhabiting dredged pits and creating permanent habitats in areas cratered by the dredging activity. This study has generated ecological information on the status of species and habitats inhabiting the dredged and undredged area. Management considerations are also discussed to ensure that sound aggregate extraction practices are in place to minimised the effects of aggregate dredging over licensed areas.

  16. High-resolution mapping of transcription factor binding sites on native chromatin

    PubMed Central

    Kasinathan, Sivakanthan; Orsi, Guillermo A.; Zentner, Gabriel E.; Ahmad, Kami; Henikoff, Steven

    2014-01-01

    Sequence-specific DNA-binding proteins including transcription factors (TFs) are key determinants of gene regulation and chromatin architecture. Formaldehyde cross-linking and sonication followed by Chromatin ImmunoPrecipitation (X-ChIP) is widely used for profiling of TF binding, but is limited by low resolution and poor specificity and sensitivity. We present a simple protocol that starts with micrococcal nuclease-digested uncross-linked chromatin and is followed by affinity purification of TFs and paired-end sequencing. The resulting ORGANIC (Occupied Regions of Genomes from Affinity-purified Naturally Isolated Chromatin) profiles of Saccharomyces cerevisiae Abf1 and Reb1 provide highly accurate base-pair resolution maps that are not biased toward accessible chromatin, and do not require input normalization. We also demonstrate the high specificity of our method when applied to larger genomes by profiling Drosophila melanogaster GAGA Factor and Pipsqueak. Our results suggest that ORGANIC profiling is a widely applicable high-resolution method for sensitive and specific profiling of direct protein-DNA interactions. PMID:24336359

  17. Cloud fraction at the ARM SGP site: reducing uncertainty with self-organizing maps

    NASA Astrophysics Data System (ADS)

    Kennedy, Aaron D.; Dong, Xiquan; Xi, Baike

    2016-04-01

    Instrument downtime leads to uncertainty in the monthly and annual record of cloud fraction (CF), making it difficult to perform time series analyses of cloud properties and perform detailed evaluations of model simulations. As cloud occurrence is partially controlled by the large-scale atmospheric environment, this knowledge is used to reduce uncertainties in the instrument record. Synoptic patterns diagnosed from the North American Regional Reanalysis (NARR) during the period 1997-2010 are classified using a competitive neural network known as the self-organizing map (SOM). The classified synoptic states are then compared to the Atmospheric Radiation Measurement (ARM) Southern Great Plains (SGP) instrument record to determine the expected CF. A number of SOMs are tested to understand how the number of classes and the period of classifications impact the relationship between classified states and CFs. Bootstrapping is utilized to quantify the uncertainty of the instrument record when statistical information from the SOM is included. Although all SOMs significantly reduce the uncertainty of the CF record calculated in Kennedy et al. (Theor Appl Climatol 115:91-105, 2014), SOMs with a large number of classes and separated by month are required to produce the lowest uncertainty and best agreement with the annual cycle of CF. This result may be due to a manifestation of seasonally dependent biases in NARR. With use of the SOMs, the average uncertainty in monthly CF is reduced in half from the values calculated in Kennedy et al. (Theor Appl Climatol 115:91-105, 2014).

  18. Mapping topoisomerase sites in mitochondrial DNA with a poisonous mitochondrial topoisomerase I (Top1mt).

    PubMed

    Dalla Rosa, Ilaria; Huang, Shar-Yin N; Agama, Keli; Khiati, Salim; Zhang, Hongliang; Pommier, Yves

    2014-06-27

    Mitochondrial topoisomerase I (Top1mt) is a type IB topoisomerase present in vertebrates and exclusively targeted to mitochondria. Top1mt relaxes mitochondrial DNA (mtDNA) supercoiling by introducing transient cleavage complexes wherein the broken DNA strand swivels around the intact strand. Top1mt cleavage complexes (Top1mtcc) can be stabilized in vitro by camptothecin (CPT). However, CPT does not trap Top1mtcc efficiently in cells and is highly cytotoxic due to nuclear Top1 targeting. To map Top1mtcc on mtDNA in vivo and to overcome the limitations of CPT, we designed two substitutions (T546A and N550H) in Top1mt to stabilize Top1mtcc. We refer to the double-mutant enzyme as Top1mt*. Using retroviral transduction and ChIP-on-chip assays with Top1mt* in Top1mt knock-out murine embryonic fibroblasts, we demonstrate that Top1mt* forms high levels of cleavage complexes preferentially in the noncoding regulatory region of mtDNA, accumulating especially at the heavy strand replication origin OH, in the ribosomal genes (12S and 16S) and at the light strand replication origin OL. Expression of Top1mt* also caused rapid mtDNA depletion without affecting mitochondria mass, suggesting the existence of specific mitochondrial pathways for the removal of damaged mtDNA.

  19. Mapping and Monitoring Bedforms on the Mid-Continental Shelf : 23-Mile Site, Onslow Bay, NC

    NASA Astrophysics Data System (ADS)

    Head, M. E.; Grindlay, N. R.; Leonard, L. A.

    2002-12-01

    This study attempts to constrain the spatial and temporal variations in the seafloor morphology, as well as the relationship between sidescan sonar data and seafloor characteristics at the 23-Mile hardbottom area on the mid-continental shelf of Onslow Bay, NC. The 23-Mile site consists of an upper limestone hardbottom at 29-30m depth covered in a thin discontinuous veneer of sediments. The lower sand flats at 32-33m depth consist of concentrated areas of contrasting grain size. A dual-frequency sidescan sonar system was used to repeatedly image the seafloor of a 3.5 km by 2.1 km region at 23-mile site over a period of 2.5 years. Cruises were conducted in December 1999, December 2000, July 2001, and May 2002. During this time period no major tropical storms impacted the shelf, although at least three small (sustained winds <30 kts/hr) nor'easters were recorded in the region of study. Textural analysis of the sidescan sonar imagery was conducted using grey-level co-occurrence matrices. Two textural indices: entropy (acoustic roughness), and homogeneity (level of textural organization) were used. Following the textural analysis both unsupervised and supervised classification schemes were utilized. Four distinct seabed units were identified. Ground-truthing by divers indicates that these units show a strong positive correlation between backscatter intensity and sediment grain size. Further analysis will be conducted to determine if the classification system is capable of recognizing distinct benthic assemblages. A comparison of results between successive surveys shows a significant difference in the spatial orientation of the coarse-grained and fine-grained contacts of the lower sand flats. In some areas sediment movements in excess of 10 m are documented. This movement, however, shows no consistent trend in direction or magnitude. Flow data collected on-site by an acoustic Doppler profiler moored 2 m above the seabed suggest that mean bottom current velocities are

  20. Characterization, Validation and Intercomparison of Clumping Index Maps from POLDER, MODIS, and MISR Satellite Data Over Reference Sites

    NASA Astrophysics Data System (ADS)

    Pisek, J.; He, L.; Chen, J. M.; Govind, A.; Sprintsin, M.; Ryu, Y.; Arndt, S. K.; Hocking, D.; Wardlaw, T.; Kuusk, J.; Oliphant, A. J.; Korhonen, L.; Fang, H.; Matteucci, G.; Longdoz, B.; Raabe, K.

    2015-12-01

    Vegetation foliage clumping significantly alters its radiation environment and therefore affects vegetation growth as well as water and carbon cycles. The clumping index is useful in ecological and meteorological models because it provides new structural information in addition to the effective leaf area index (LAI) retrieved from mono-angle remote sensing and allows accurate separation of sunlit and shaded leaves in the canopy. Not accounting for the foliage clumping in LAI retrieval algorithms leads to substantial underestimation of actual LAI, especially for needleleaf forests. Normalized Difference between Hotspot and Darkspot (NDHD) index has been previously used to retrieve global clumping index maps from POLarization and Directionality of the Earth's Reflectances (POLDER) data at ~6 km resolution, from Moderate Resolution Imaging Spectroradiometer (MODIS) Bidirectional Reflectance Distribution Function (BRDF) product at 500 m resolution. Most recently the algorithm was applied with Multi-angle Imaging SpectroRadiometer (MISR) data at 275 m resolution over selected areas. In this presentation we characterize and intercompare the three products over a set of sites representing diverse biomes and different canopy structures. The products are also directly validated with both in-situ vertical profiles and seasonal trajectories of clumping index. We illustrate that the vertical distribution of foliage and especially the effect of understory needs to be taken into account while validating foliage clumping products from remote sensing products with values measured in the field. Satellite measurements respond to the structural effects near the top of canopies, while ground measurements may be biased by the lower vegetation layers. Additionally, caution should be taken regarding the misclassification in land cover maps as their errors can be propagated into the foliage clumping maps. Our results indicate that MODIS data and MISR data with 275 m resolution in

  1. Characterization, validation and intercomparison of clumping index maps from POLDER, MODIS, and MISR satellite data over reference sites

    NASA Astrophysics Data System (ADS)

    Pisek, Jan; He, Liming; Chen, Jing; Govind, Ajit; Sprintsin, Michael; Ryu, Youngryel; Arndt, Stefan; Hocking, Darren; Wardlaw, Timothy; Kuusk, Joel; Oliphant, Andrew; Korhonen, Lauri; Fang, Hongliang; Matteucci, Giorgio; Longdoz, Bernard; Raabe, Kairi

    2015-04-01

    Vegetation foliage clumping significantly alters its radiation environment and therefore affects vegetation growth as well as water and carbon cycles. The clumping index is useful in ecological and meteorological models because it provides new structural information in addition to the effective leaf area index (LAI) retrieved from mono-angle remote sensing and allows accurate separation of sunlit and shaded leaves in the canopy. Not accounting for the foliage clumping in LAI retrieval algorithms leads to substantial underestimation of actual LAI, especially for needleleaf forests. Normalized Difference between Hotspot and Darkspot (NDHD) index has been previously used to retrieve global clumping index maps from POLarization and Directionality of the Earth's Reflectances (POLDER) data at ~6 km resolution, from Moderate Resolution Imaging Spectroradiometer (MODIS) Bidirectional Reflectance Distribution Function (BRDF) product at 500 m resolution. Most recently the algorithm was applied with Multi-angle Imaging SpectroRadiometer (MISR) data at 275 m resolution over selected areas. In this presentation we characterize and intercompare the three products over a set of sites representing diverse biomes and different canopy structures. The products are also directly validated with both in-situ vertical profiles and seasonal trajectories of clumping index. We illustrate that the vertical distribution of foliage and especially the effect of understory needs to be taken into account while validating foliage clumping products from remote sensing products with values measured in the field. Satellite measurements respond to the structural effects near the top of canopies, while ground measurements may be biased by the lower vegetation layers. Additionally, caution should be taken regarding the misclassification in land cover maps as their errors can be propagated into the foliage clumping maps. Our results indicate that MODIS data and MISR data with 275 m in particular can

  2. Use of Bedrock and Geomorphic Mapping Compilations in Assessing Geologic Hazards at Recreation Sites on National Forests in NW California

    NASA Astrophysics Data System (ADS)

    de La Fuente, J. A.; Bell, A.; Elder, D.; Mowery, R.; Mikulovsky, R.; Klingel, H.; Stevens, M.

    2010-12-01

    coverage is a compilation of the best available mapping for all National Forests in California. The geomorphic coverage includes features such as active and dormant landslides, alluvial fans, headwall basins, glacial features, and valley inner gorge. Criteria will be developed which utilize elements of this data to evaluate geologic hazards in the vicinity of developed recreation sites. The second phase will be conducted later and involves site specific analyses focusing on areas identified as higher hazard in the first phase, along with verification and updating of phase 1 findings. The third phase will complete any site level geologic or hydrologic investigations, and wrap up the hazard assessment process. A summary report with hazard maps and recommendations will be prepared at the end of each phase. The overriding goal of this project is to provide sound geologic information to managers so they can use a science-based approach in recognizing and managing geologic hazards at recreation sites.

  3. 75 FR 60761 - Medical Device User Fee and Modernization Act; Notice to Public of Web site Location of Fiscal...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-01

    ... Public of Web site Location of Fiscal Year 2011 Proposed Guidance Development AGENCY: Food and Drug Administration, HHS. ACTION: Notice. ] SUMMARY: The Food and Drug Administration (FDA) is announcing the Web site... topics, or suggestions for new or different guidances. This notice announces the Web site location of...

  4. Characterization of FRA7B, a human common fragile site mapped at the 7p chromosome terminal region.

    PubMed

    Bosco, Nazario; Pelliccia, Franca; Rocchi, Angela

    2010-10-01

    Common fragile sites (CFS) are specific regions of the mammalian chromosomes that are particularly prone to gaps and breaks. They are a cause of genome instability, and the location of many CFS correlates with breakpoints of aberrations recurrent in some cancers. The molecular characterization of some CFS has not clarified the causes of their fragility. In this work, by using fluorescence in situ hybridization analysis with BAC and PAC clones, we determined the DNA sequence of the CFS FRA7B. The FRA7B sequence was then analyzed to identify coding sequences and some structural features possibly involved in fragility. FRA7B spans about 12.2 megabases, and is therefore one of the largest CFS analyzed. It maps at the 7p21.3-22.3 chromosome bands, therefore at the interface of G- and R-band regions that are probably difficult to replicate. A 90-kilobase long sequence that presents very high flexibility values was identified at the very beginning of the more fragile CFS region. Three large genes (THSD7A, SDK1, and MAD1L1) and two miRNA genes (MIRN589 and MIRN339) map in the fragile region. The chromosome band 7p22 is a recurrent breakpoint in chromosome abnormalities in different types of neoplasm. FRA7B is the first characterized CFS located in a chromosome terminal region.

  5. Mapping functional group free energy patterns at protein occluded sites: nuclear receptors and G-protein coupled receptors.

    PubMed

    Lakkaraju, Sirish Kaushik; Yu, Wenbo; Raman, E Prabhu; Hershfeld, Alena V; Fang, Lei; Deshpande, Deepak A; MacKerell, Alexander D

    2015-03-23

    Occluded ligand-binding pockets (LBP) such as those found in nuclear receptors (NR) and G-protein coupled receptors (GPCR) represent a significant opportunity and challenge for computer-aided drug design. To determine free energies maps of functional groups of these LBPs, a Grand-Canonical Monte Carlo/Molecular Dynamics (GCMC/MD) strategy is combined with the Site Identification by Ligand Competitive Saturation (SILCS) methodology. SILCS-GCMC/MD is shown to map functional group affinity patterns that recapitulate locations of functional groups across diverse classes of ligands in the LBPs of the androgen (AR) and peroxisome proliferator-activated-γ (PPARγ) NRs and the metabotropic glutamate (mGluR) and β2-adreneric (β2AR) GPCRs. Inclusion of protein flexibility identifies regions of the binding pockets not accessible in crystal conformations and allows for better quantitative estimates of relative ligand binding affinities in all the proteins tested. Differences in functional group requirements of the active and inactive states of the β2AR LBP were used in virtual screening to identify high efficacy agonists targeting β2AR in Airway Smooth Muscle (ASM) cells. Seven of the 15 selected ligands were found to effect ASM relaxation representing a 46% hit rate. Hence, the method will be of use for the rational design of ligands in the context of chemical biology and the development of therapeutic agents.

  6. Fluid expulsion sites on the Cascadia accretionary prism: mapping diagenetic deposits with processed GLORIA imagery

    USGS Publications Warehouse

    Carson, Bobb; Seke, Erol; Paskevich, Valerie F.; Holmes, Mark L.

    1994-01-01

     Point-discharge fluid expulsion on accretionary prisms is commonly indicated by diagenetic deposition of calcium carbonate cements and gas hydrates in near-surface (<10 m below seafloor; mbsf) hemipelagic sediment. The contrasting clastic and diagenetic lithologies should be apparent in side scan images. However, sonar also responds to variations in bottom slope, so unprocessed images mix topographic and lithologic information. We have processed GLORIA imagery from the Oregon continental margin to remove topographic effects. A synthetic side scan image was created initially from Sea Beam bathymetric data and then was subtracted iteratively from the original GLORIA data until topographic features disappeared. The residual image contains high-amplitude backscattering that we attribute to diagenetic deposits associated with fluid discharge, based on submersible mapping, Ocean Drilling Program drilling, and collected samples. Diagenetic deposits are concentrated (1) near an out-of-sequence thrust fault on the second ridge landward of the base of the continental slope, (2) along zones characterized by deep-seated strikeslip faults that cut transversely across the margin, and (3) in undeformed Cascadia Basin deposits which overlie incipient thrust faults seaward of the toe of the prism. There is no evidence of diagenetic deposition associated with the frontal thrust that rises from the dècollement. If the dècollement is an important aquifer, apparently the fluids are passed either to the strike-slip faults which intersect the dècollement or to the incipient faults in Cascadia Basin for expulsion. Diagenetic deposits seaward of the prism toe probably consist dominantly of gas hydrates

  7. Mapping of a cholinergic binding site by means of synthetic peptides, monoclonal antibodies, and. alpha. -bungarotoxin

    SciTech Connect

    Conti-Tronconi, B.M.; Tang, Fen; Diethelm, B.M.; Spencer, S.R. ); Reinhardt-Maelicke, S.; Maelicke, A. )

    1990-07-03

    Previous studies by several laboratories have identified a narrow sequence region of the nicotinic acetylcholine receptor (AChR) {alpha} subunit, flanking the cysteinyl residues at positions 192 and 193, as containing major elements of, if not all, the binding site for cholinergic ligands. In the present study, the authors used a panel of synthetic peptides as representative structural elements of the AChR to investigate whether additional segments of the AChR sequences are able to bind {alpha}-bungarotoxin ({alpha}-BTX) and several {alpha}-BTX-competitive monoclonal antibodies (mAbs). The mAbs used (WF6, WF5, and W2) were raised against native Torpedo AChR, specifically recognize the {alpha}-subunit, and bind to AChR in a mutually exclusive fashion with {alpha}-BTX. The binding of WF5 and W2 to Torpedo AChR is inhibited by all cholinergic ligands. WF6 competes with agonists, but not with low mol. wt. antagonists, for AChR binding. Peptides {alpha}181-200 and {alpha}55-74 both inhibited binding of {sup 125}I-{alpha}-BTX to native Torpedo AChR. None of the peptides corresponding to sequence segments from other subunits bound {alpha}-BTX or WF6, or interfered with their binding. Therefore, the cholinergic binding site is not a single narrow sequence region, but rather two or more discontinuous sequence segments within the N-terminal extracellular region of the AChR {alpha} subunit, folded together in the native structure of the receptor, contribute to form a cholinergic binding region.

  8. Mapping the Nucleotide Binding Site of Uncoupling Protein 1 Using Atomic Force Microscopy

    PubMed Central

    2013-01-01

    A tight regulation of proton transport in the inner mitochondrial membrane is crucial for physiological processes such as ATP synthesis, heat production, or regulation of the reactive oxygen species as proposed for the uncoupling protein family members (UCP). Specific regulation of proton transport is thus becoming increasingly important in the therapy of obesity and inflammatory, neurodegenerative, and ischemic diseases. We and other research groups have shown previously that UCP1- and UCP2-mediated proton transport is inhibited by purine nucleotides. Several hypotheses have been proposed to explain the inhibitory effect of ATP, although structural details are still lacking. Moreover, the unresolved mystery is how UCP operates in vivo despite the permanent presence of high (millimolar) concentrations of ATP in mitochondria. Here we use the topographic and recognition (TREC) mode of an atomic force microscope to visualize UCP1 reconstituted into lipid bilayers and to analyze the ATP–protein interaction at a single molecule level. The comparison of recognition patterns obtained with anti-UCP1 antibody and ATP led to the conclusion that the ATP binding site can be accessed from both sides of the membrane. Using cantilever tips with different cross-linker lengths, we determined the location of the nucleotide binding site inside the membrane with 1 Å precision. Together with the recently published NMR structure of a UCP family member (Berardi et al. Nature, 2011, 476, 109–113), our data provide a valuable insight into the mechanism of the nucleotide binding and pave the way for new pharmacological approaches against the diseases mentioned above. PMID:23414455

  9. Modeling LAI based on land cover map and NDVI using SPOT and Landsat data in two Mediterranean sites: preliminary results

    NASA Astrophysics Data System (ADS)

    Topaloglou, Charalampos; Monachou, Styliani; Strati, Stavroula; Alexandridis, Thomas; Stavridou, Domna; Silleos, Nikolaos; Misopolinos, Nikolaos; Nunes, Antonio; Araújo, Antonio

    2013-08-01

    Leaf Area Index (LAI) is considered to be a key parameter of ecosystem processes and it is widely used as input to biogeochemical process models that predict net primary production (NPP) or can be a useful parameter for crop yield prediction and crop stress assessment as well as estimation of the exchanges of carbon dioxide, water, and nutrients in forests. LAI can be derived from satellite optical data using models referred to physical-based approaches, which describe the physical processes of energy flow in the soil-vegetation-atmosphere system, and models using empirically derived regression relationships based on spectral vegetation indices (VIs). The first category of models are more general in application because they can account for the different sources of variability, although in many cases the information needed to constrain model inputs is not available. In contrast, empirical models depend on the site and time. The aim of this paper is to create a reliable semi-empirical method, applied in two Mediterranean sites, to estimate LAI with high spatial resolution images. The model uses a minimum dataset of a Landsat 5 TM or SPOT 4 XS image, land cover map and DEM for each area. Specifically, this model calculates the reflectance of initial bands implementing topographic correction with the aid of DEM and metadata of the images and afterwards uses a list of NDVI values that correspond to certain LAI values on different land cover types which has been proposed by the MODIS Land Team. This model has been applied in two areas; in the river basin of Nestos (Greece and Bulgaria) and in the river basin of Tamega (Portugal). The predicted LAI map was validated with ground truth data from hemispherical images showing high correlation, with r reaching 0.79 and RMSE less than 1 m2/m2.

  10. Contour Mapping

    NASA Technical Reports Server (NTRS)

    1995-01-01

    In the early 1990s, the Ohio State University Center for Mapping, a NASA Center for the Commercial Development of Space (CCDS), developed a system for mobile mapping called the GPSVan. While driving, the users can map an area from the sophisticated mapping van equipped with satellite signal receivers, video cameras and computer systems for collecting and storing mapping data. George J. Igel and Company and the Ohio State University Center for Mapping advanced the technology for use in determining the contours of a construction site. The new system reduces the time required for mapping and staking, and can monitor the amount of soil moved.

  11. 75 FR 26196 - Notice of Proposed New Recreation Fee Site; Federal Lands Recreation Enhancement Act, (Title VIII...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-11

    ..., (Title VIII, Pub. L. 108-447) AGENCY: National Forests in Mississippi, Forest Service, USDA. ACTION... 39269. SUPPLEMENTARY INFORMATION: The Federal Recreation Lands Enhancement Act (Title VII, Pub. L....

  12. High-throughput genomic mapping of vector integration sites in gene therapy studies.

    PubMed

    Beard, Brian C; Adair, Jennifer E; Trobridge, Grant D; Kiem, Hans-Peter

    2014-01-01

    Gene therapy has enormous potential to treat a variety of infectious and genetic diseases. To date hundreds of patients worldwide have received hematopoietic cell products that have been gene-modified with retrovirus vectors carrying therapeutic transgenes, and many patients have been cured or demonstrated disease stabilization as a result (Adair et al., Sci Transl Med 4:133ra57, 2012; Biffi et al., Science 341:1233158, 2013; Aiuti et al., Science 341:1233151, 2013; Fischer et al., Gene 525:170-173, 2013). Unfortunately, for some patients the provirus integration dysregulated the expression of nearby genes leading to clonal outgrowth and, in some cases, cancer. Thus, the unwanted side effect of insertional mutagenesis has become a major concern for retrovirus gene therapy. The careful study of retrovirus integration sites (RIS) and the contribution of individual gene-modified clones to hematopoietic repopulating cells is of crucial importance for all gene therapy studies. Supporting this, the US Food and Drug Administration (FDA) has mandated the careful monitoring of RIS in all clinical trials of gene therapy. An invaluable method was developed: linear amplification mediated-polymerase chain reaction (LAM-PCR) capable of analyzing in vitro and complex in vivo samples, capturing valuable genomic information directly flanking the site of provirus integration. Linking this method and similar methods to high-throughput sequencing has now made possible an unprecedented understanding of the integration profile of various retrovirus vectors, and allows for sensitive monitoring of their safety. It also allows for a detailed comparison of improved safety-enhanced gene therapy vectors. An important readout of safety is the relative contribution of individual gene-modified repopulating clones. One limitation of LAM-PCR is that the ability to capture the relative contribution of individual clones is compromised because of the initial linear PCR common to all current methods

  13. Baseline mapping study of the Steed Pond aquifer and vadose zone beneath A/M Area, Savannah River Site, Aiken, South Carolina

    SciTech Connect

    Jackson, D.G. Jr.

    2000-01-27

    This report presents the second phase of a baseline mapping project conducted for the Environmental Restoration Department (ERD) at Savannah River Site. The purpose of this second phase is to map the structure and distribution of mud (clay and silt-sized sediment) within the vadose zone beneath A/M Area. The results presented in this report will assist future characterization and remediation activities in the vadose zone and upper aquifer zones in A/M Area.

  14. Peroxyacetyl nitrate (PAN) at the urban core site of Seoul during 2015 MAPS / KORUS - AQ

    NASA Astrophysics Data System (ADS)

    Lee, J. S.; Lee, G.; Lee, M.; Lee, H.

    2015-12-01

    A few measurements of atmospheric PAN were made in Seoul for the last decade. One study showed the average and maximum PAN concentration in summer of 2004 and 2005 with 0.8 ppb and 10.4 ppb and another study specified 0.64 ppb and 5.03 ppb, respectively in 2011. In this study, the measurements of peroxyacetyl nitrate (PAN) have been conducted at an urban site situated in KIST campus (Korea Institute of Science and Technology, Seoul, 127° 2'E, 37° 36'N) from May 18 to June 12, 2015. PAN was measured every 2 minutes by a fast chromatography with luminol-based chemiluminescence detection. Concentration of PAN ranged from 0.15ppbv to 4.37ppbv, with the average of 0.57 ppbv. PAN revealed its peak between 2 and 4 pm matching with the photochemical activities and precursor emission. When comparing with historic data of PAN in urban Seoul during the past decade, it has decreased about 50%. The rather rapid decrease of summertime PAN level for last ten years in Seoul will be discussed further with the behaviors of its precursor species.

  15. High-Pressure EPR and Site-Directed Spin Labeling for Mapping Molecular Flexibility in Proteins.

    PubMed

    Lerch, Michael T; Yang, Zhongyu; Altenbach, Christian; Hubbell, Wayne L

    2015-01-01

    High hydrostatic pressure is a powerful probe of protein conformational flexibility. Pressurization reveals regions of elevated compressibility, and thus flexibility, within individual conformational states, but also shifts conformational equilibria such that "invisible" excited states become accessible for spectroscopic characterization. The central aim of this chapter is to describe recently developed instrumentation and methodologies that enable high-pressure site-directed spin labeling electron paramagnetic resonance (SDSL-EPR) experiments on proteins and to demonstrate the information content of these experiments by highlighting specific recent applications. A brief introduction to the thermodynamics of proteins under pressure is presented first, followed by a discussion of the principles underlying SDSL-EPR detection of pressure effects in proteins, and the suitability of SDSL-EPR for this purpose in terms of timescale and ability to characterize conformational heterogeneity. Instrumentation and practical considerations for variable-pressure continuous wave EPR and pressure-resolved double electron-electron resonance (PR DEER) experiments are reviewed, and finally illustrations of data analysis using recent applications are presented. Although high-pressure SDSL-EPR is in its infancy, the recent applications presented highlight the considerable potential of the method to (1) identify compressible (flexible) regions in a folded protein; (2) determine thermodynamic parameters that relate conformational states in equilibrium; (3) populate and characterize excited states of proteins undetected at atmospheric pressure; (4) reveal the structural heterogeneity of conformational ensembles and provide distance constraints on the global structure of pressure-populated states with PR DEER.

  16. International association for the study of lung cancer map, Wang lymph node map and rapid on-site evaluation in transbronchial needle aspiration

    PubMed Central

    Liu, Qing-Hua; Arias, Sixto

    2016-01-01

    The invaluable role of transbronchial needle aspiration (TBNA) in the diagnosis and staging of mediastinal adenopathy and lung cancer has been well established. Different lymph nodes regional nomenclatures and maps had been described over the years. The international association for the study of lung cancer (IASLC) and Wang’s maps complement each other benefiting patients with lung cancer. In this article we briefly reviewed the roles of IALSC, Wang’s maps and ROSE in TBNA. PMID:27747023

  17. Proteomic Quantification and Site-Mapping of S-Nitrosylated Proteins Using Isobaric iodoTMT Reagents

    PubMed Central

    2015-01-01

    S-Nitrosylation is a redox-based protein post-translational modification in response to nitric oxide signaling and is involved in a wide range of biological processes. Detection and quantification of protein S-nitrosylation have been challenging tasks due to instability and low abundance of the modification. Many studies have used mass spectrometry (MS)-based methods with different thiol-reactive reagents to label and identify proteins with S-nitrosylated cysteine (SNO-Cys). In this study, we developed a novel iodoTMT switch assay (ISA) using an isobaric set of thiol-reactive iodoTMTsixplex reagents to specifically detect and quantify protein S-nitrosylation. Irreversible labeling of SNO-Cys with the iodoTMTsixplex reagents enables immune-affinity detection of S-nitrosylated proteins, enrichment of iodoTMT-labeled peptides by anti-TMT resin, and importantly, unambiguous modification site-mapping and multiplex quantification by liquid chromatography–tandem MS. Additionally, we significantly improved anti-TMT peptide enrichment efficiency by competitive elution. Using ISA, we identified a set of SNO-Cys sites responding to lipopolysaccharide (LPS) stimulation in murine BV-2 microglial cells and revealed effects of S-allyl cysteine from garlic on LPS-induced protein S-nitrosylation in antioxidative signaling and mitochondrial metabolic pathways. ISA proved to be an effective proteomic approach for quantitative analysis of S-nitrosylation in complex samples and will facilitate the elucidation of molecular mechanisms of nitrosative stress in disease. PMID:24926564

  18. Mapping and Imaging Methodologies within the Comprehensive Test Ban Treaty's On-Site Inspection Framework

    NASA Astrophysics Data System (ADS)

    Hawkins, W.; Sussman, A. J.; Kelley, R. E.; Wohletz, K. H.; Schultz-Fellenz, E. S.

    2013-12-01

    On-site inspection (OSI) is the final verification measure of the Comprehensive Nuclear Test Ban Treaty (CTBT). OSIs rely heavily on geologic and geophysical investigations. The objective is to apply methods that are effective, efficient and minimally intrusive. We present a general overview of the OSI as provisioned in the CTBT, specifying the allowed techniques and the timeline for their application. A CTBT OSI relies on many geological, geophysical and radiological methods. The search area for an OSI is mostly defined by uncertainty in the location of a suspect event detected by the International Monitoring System (IMS) and reported through the International Data Center and can be as large as 1000 km2. Thus OSI methods are fundamentally divided into general survey methods that narrow the search area and more focused, detailed survey methods to look for evidence of a potential underground explosion and try to find its location within an area of several km2. The purpose and goal of a CTBT OSI, as specified in the Article IV of the Treaty, is 'to clarify whether a nuclear explosion has been carried out in violation of the Treaty' and to 'gather any facts which might assist in identifying any possible violator.' Through the use of visual, geophysical, and radiological techniques, OSIs can detect and characterize anomalies and artifacts related to the event that triggered the inspection. In the context of an OSI, an 'observable' is a physical property that is important to recognize and document because of its relevance to the purpose of the inspection. Potential observables include: (1) visual observables such as ground/environmental disturbances and manmade features, (2) geophysical techniques that provide measurements of altered and damaged ground and buried artifacts, and (3) radiological measurements on samples. Information provided in this presentation comes from observations associated with historical testing activities that were not intended to go undetected

  19. Mapping of the RNA recognition site of Escherichia coli ribosomal protein S7.

    PubMed Central

    Robert, F; Gagnon, M; Sans, D; Michnick, S; Brakier-Gingras, L

    2000-01-01

    Bacterial ribosomal protein S7 initiates the folding of the 3' major domain of 16S ribosomal RNA by binding to its lower half. The X-ray structure of protein S7 from thermophilic bacteria was recently solved and found to be a modular structure, consisting of an alpha-helical domain with a beta-ribbon extension. To gain further insights into its interaction with rRNA, we cloned the S7 gene from Escherichia coli K12 into a pET expression vector and introduced 4 deletions and 12 amino acid substitutions in the protein sequence. The binding of each mutant to the lower half of the 3' major domain of 16S rRNA was assessed by filtration on nitrocellulose membranes. Deletion of the N-terminal 17 residues or deletion of the B hairpins (residues 72-89) severely decreased S7 affinity for the rRNA. Truncation of the C-terminal portion (residues 138-178), which includes part of the terminal alpha-helix, significantly affected S7 binding, whereas a shorter truncation (residues 148-178) only marginally influenced its binding. Severe effects were also observed with several strategic point mutations located throughout the protein, including Q8A and F17G in the N-terminal region, and K35Q, G54S, K113Q, and M115G in loops connecting the alpha-helices. Our results are consistent with the occurrence of several sites of contact between S7 and the 16S rRNA, in line with its role in the folding of the 3' major domain. PMID:11105763

  20. Mapping the Putative G Protein-coupled Receptor (GPCR) Docking Site on GPCR Kinase 2

    PubMed Central

    Beautrait, Alexandre; Michalski, Kevin R.; Lopez, Thomas S.; Mannix, Katelynn M.; McDonald, Devin J.; Cutter, Amber R.; Medina, Christopher B.; Hebert, Aaron M.; Francis, Charnelle J.; Bouvier, Michel; Tesmer, John J. G.; Sterne-Marr, Rachel

    2014-01-01

    G protein-coupled receptor kinases (GRKs) phosphorylate agonist-occupied receptors initiating the processes of desensitization and β-arrestin-dependent signaling. Interaction of GRKs with activated receptors serves to stimulate their kinase activity. The extreme N-terminal helix (αN), the kinase small lobe, and the active site tether (AST) of the AGC kinase domain have previously been implicated in mediating the allosteric activation. Expanded mutagenesis of the αN and AST allowed us to further assess the role of these two regions in kinase activation and receptor phosphorylation in vitro and in intact cells. We also developed a bioluminescence resonance energy transfer-based assay to monitor the recruitment of GRK2 to activated α2A-adrenergic receptors (α2AARs) in living cells. The bioluminescence resonance energy transfer signal exhibited a biphasic response to norepinephrine concentration, suggesting that GRK2 is recruited to Gβγ and α2AAR with EC50 values of 15 nm and 8 μm, respectively. We show that mutations in αN (L4A, V7E, L8E, V11A, S12A, Y13A, and M17A) and AST (G475I, V477D, and I485A) regions impair or potentiate receptor phosphorylation and/or recruitment. We suggest that a surface of GRK2, including Leu4, Val7, Leu8, Val11, and Ser12, directly interacts with receptors, whereas residues such as Asp10, Tyr13, Ala16, Met17, Gly475, Val477, and Ile485 are more important for kinase domain closure and activation. Taken together with data on GRK1 and GRK6, our data suggest that all three GRK subfamilies make conserved interactions with G protein-coupled receptors, but there may be unique interactions that influence selectivity. PMID:25049229

  1. Mapping of the RNA recognition site of Escherichia coli ribosomal protein S7.

    PubMed

    Robert, F; Gagnon, M; Sans, D; Michnick, S; Brakier-Gingras, L

    2000-11-01

    Bacterial ribosomal protein S7 initiates the folding of the 3' major domain of 16S ribosomal RNA by binding to its lower half. The X-ray structure of protein S7 from thermophilic bacteria was recently solved and found to be a modular structure, consisting of an alpha-helical domain with a beta-ribbon extension. To gain further insights into its interaction with rRNA, we cloned the S7 gene from Escherichia coli K12 into a pET expression vector and introduced 4 deletions and 12 amino acid substitutions in the protein sequence. The binding of each mutant to the lower half of the 3' major domain of 16S rRNA was assessed by filtration on nitrocellulose membranes. Deletion of the N-terminal 17 residues or deletion of the B hairpins (residues 72-89) severely decreased S7 affinity for the rRNA. Truncation of the C-terminal portion (residues 138-178), which includes part of the terminal alpha-helix, significantly affected S7 binding, whereas a shorter truncation (residues 148-178) only marginally influenced its binding. Severe effects were also observed with several strategic point mutations located throughout the protein, including Q8A and F17G in the N-terminal region, and K35Q, G54S, K113Q, and M115G in loops connecting the alpha-helices. Our results are consistent with the occurrence of several sites of contact between S7 and the 16S rRNA, in line with its role in the folding of the 3' major domain.

  2. Image Analysis for Facility Siting: a Comparison of Lowand High-altitude Image Interpretability for Land Use/land Cover Mapping

    NASA Technical Reports Server (NTRS)

    Borella, H. M.; Estes, J. E.; Ezra, C. E.; Scepan, J.; Tinney, L. R.

    1982-01-01

    For two test sites in Pennsylvania the interpretability of commercially acquired low-altitude and existing high-altitude aerial photography are documented in terms of time, costs, and accuracy for Anderson Level II land use/land cover mapping. Information extracted from the imagery is to be used in the evaluation process for siting energy facilities. Land use/land cover maps were drawn at 1:24,000 scale using commercially flown color infrared photography obtained from the United States Geological Surveys' EROS Data Center. Detailed accuracy assessment of the maps generated by manual image analysis was accomplished employing a stratified unaligned adequate class representation. Both 'area-weighted' and 'by-class' accuracies were documented and field-verified. A discrepancy map was also drawn to illustrate differences in classifications between the two map scales. Results show that the 1:24,000 scale map set was more accurate (99% to 94% area-weighted) than the 1:62,500 scale set, especially when sampled by class (96% to 66%). The 1:24,000 scale maps were also more time-consuming and costly to produce, due mainly to higher image acquisition costs.

  3. Active site mapping, biochemical properties and subcellular localization of rhodesain, the major cysteine protease of Trypanosoma brucei rhodesiense.

    PubMed

    Caffrey, C R; Hansell, E; Lucas, K D; Brinen, L S; Alvarez Hernandez, A; Cheng, J; Gwaltney, S L; Roush, W R; Stierhof, Y D; Bogyo, M; Steverding, D; McKerrow, J H

    2001-11-01

    Cysteine protease activity of African trypanosome parasites is a target for new chemotherapy using synthetic protease inhibitors. To support this effort and further characterize the enzyme, we expressed and purified rhodesain, the target protease of Trypanosoma brucei rhodesiense (MVAT4 strain), in reagent quantities from Pichia pastoris. Rhodesain was secreted as an active, mature protease. Site-directed mutagenesis of a cryptic glycosylation motif not previously identified allowed production of rhodesain suitable for crystallization. An invariable ER(A/V)FNAA motif in the pro-peptide sequence of rhodesain was identified as being unique to the genus Trypanosoma. Antibodies to rhodesain localized the protease in the lysosome and identified a 40-kDa protein in long slender forms of T. b. rhodesiense and all life-cycle stages of T. b. brucei. With the latter parasite, protease expression was five times greater in short stumpy trypanosomes than in the other stages. Radiolabeled active site-directed inhibitors identified brucipain as the major cysteine protease in T. b. brucei. Peptidomimetic vinyl sulfone and epoxide inhibitors designed to interact with the S2, S1 and S' subsites of the active site cleft revealed differences between rhodesain and the related trypanosome protease cruzain. Using fluorogenic dipeptidyl substrates, rhodesain and cruzain had acid pH optima, but unlike some mammalian cathepsins retained significant activity and stability up to pH 8.0, consistent with a possible extracellular function. S2 subsite mapping of rhodesain and cruzain with fluorogenic peptidyl substrates demonstrates that the presence of alanine rather than glutamate at S2 prevents rhodesain from cleaving substrates in which P2 is arginine. PMID:11704274

  4. migS, a cis-acting site that affects bipolar positioning of oriC on the Escherichia coli chromosome.

    PubMed

    Yamaichi, Yoshiharu; Niki, Hironori

    2004-01-14

    During replication of the Escherichia coli chromosome, the replicated Ori domains migrate towards opposite cell poles, suggesting that a cis-acting site for bipolar migration is located in this region. To identify this cis-acting site, a series of mutants was constructed by splitting subchromosomes from the original chromosome. One mutant, containing a 720 kb subchromosome, was found to be defective in the bipolar positioning of oriC. The creation of deletion mutants allowed the identification of migS, a 25 bp sequence, as the cis-acting site for the bipolar positioning of oriC. When migS was located at the replication terminus, the chromosomal segment showed bipolar positioning. migS was able to rescue bipolar migration of plasmid DNA containing a mutation in the SopABC partitioning system. Interestingly, multiple copies of the migS sequence on a plasmid in trans inhibited the bipolar positioning of oriC. Taken together, these findings indicate that migS plays a crucial role in the bipolar positioning of oriC. In addition, real-time analysis of the dynamic morphological changes of nucleoids in wild-type and migS mutants suggests that bipolar positioning of the replicated oriC contributes to nucleoid organization.

  5. Entrainment mapping in patients with sustained atrioventricular nodal reentrant tachycardia: insights into the sites of conduction slowing in the slow atrioventricular nodal pathway.

    PubMed

    Haines, D E; Nath, S; DiMarco, J P; Lobban, J H

    1997-10-01

    The inferoposterior region of the triangle of Koch is hypothesized to be the location of the atrial insertion of the slow atrioventricular (AV) nodal pathway. However, the actual site of conduction slowing in the slow AV nodal pathway is unknown. Entrainment mapping during AV nodal reentry can localize the reentrant pathway as follows: the AH interval measured from the mapping catheter = A'H (where A' is the exit site of the reentrant circuit) minus A'A (the conduction time from A' to the site of mapping); the SH interval during entrainment = SA' (the conduction time from stimulus into the reentry circuit) plus A'H. Thus, in all cases, the SH interval should be greater than or equal to the AH interval, and the deltaAH-SH should increase as distance and conduction time (SA' and A'A) from the reentry circuit increases. Fourteen patients with typical AV nodal reentry (cycle length 346 +/- 62 ms) and 1 with fast-slow (cycle length 430 ms) underwent activation and entrainment mapping from 8 to 12 sites in the triangle of Koch and coronary sinus. Pacing was performed at 2 to 3 mA above threshold, at a cycle length 10 ms shorter than tachycardia. A mapping site was defined as being in close proximity to the circuit if the deltaAH-SH was within 120% of the shortest 20th percentile deltaAH-SH value from all measured sites. In the 14 typical cases, 45 of 83 sites (54%) in the anatomic slow pathway region fulfilled criteria for close proximity to the reentry circuit compared with 13 of 50 sites (26%) outside of this region (p = 0.005). For these patients, the shortest SH interval measured from any entrainment site was 294 +/- 58 ms (89 +/- 10% of tachycardia cycle length, range 70% to 119%), indicating that the site of slow conduction in the slow pathway during AV nodal reentrant tachycardia was distal to all mapped sites. Thus, during typical AV nodal reentry, the "slow" pathway does not conduct slowly, and its insertion is located at or within the inferoposterior or

  6. 77 FR 74266 - Review of National Environmental Policy Act Categorical Exclusion Survey Posted on DOT/FHWA Web Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-13

    ... applicable (72 FR 44038 (Aug. 7, 2007), Docket No. FTA-2006-26604 and 77 FR 15310 (Mar. 15, 2012), Docket No... Categorical Exclusion Survey Posted on DOT/FHWA Web Site AGENCY: Federal Highway Administration (FHWA... notice to advise the public that the CE survey review is now available on the FHWA Web site,...

  7. 75 FR 21583 - Notice of Proposed New Fee Site; Federal Lands Recreation Enhancement Act (Title VIII, Pub. L...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-26

    ...-unit Pioneer Campground and at the Buckeye Group Site within the Buckeye Recreation Area Paradox, Colorado. The proposed fee for the Pioneer Campground units is $10 per site per night. The proposed fee for... to the public and on a first come basis. Fees are assessed based on the level of amenities...

  8. A Temporospatial Map That Defines Specific Steps at Which Critical Surfaces in the Gag MA and CA Domains Act during Immature HIV-1 Capsid Assembly in Cells

    PubMed Central

    Robinson, Bridget A.; Reed, Jonathan C.; Geary, Clair D.; Swain, J. Victor

    2014-01-01

    ABSTRACT During HIV-1 assembly, Gag polypeptides target to the plasma membrane, where they multimerize to form immature capsids that undergo budding and maturation. Previous mutational analyses identified residues within the Gag matrix (MA) and capsid (CA) domains that are required for immature capsid assembly, and structural studies showed that these residues are clustered on four exposed surfaces in Gag. Exactly when and where the three critical surfaces in CA function during assembly are not known. Here, we analyzed how mutations in these four critical surfaces affect the formation and stability of assembly intermediates in cells expressing the HIV-1 provirus. The resulting temporospatial map reveals that critical MA residues act during membrane targeting, residues in the C-terminal CA subdomain (CA-CTD) dimer interface are needed for the stability of the first membrane-bound assembly intermediate, CA-CTD base residues are necessary for progression past the first membrane-bound intermediate, and residues in the N-terminal CA subdomain (CA-NTD) stabilize the last membrane-bound intermediate. Importantly, we found that all four critical surfaces act while Gag is associated with the cellular facilitators of assembly ABCE1 and DDX6. When correlated with existing structural data, our findings suggest the following model: Gag dimerizes via the CA-CTD dimer interface just before or during membrane targeting, individual CA-CTD hexamers form soon after membrane targeting, and the CA-NTD hexameric lattice forms just prior to capsid release. This model adds an important new dimension to current structural models by proposing the potential order in which key contacts within the immature capsid lattice are made during assembly in cells. IMPORTANCE While much is known about the structure of the completed HIV-1 immature capsid and domains of its component Gag proteins, less is known about the sequence of events leading to formation of the HIV-1 immature capsid. Here we used

  9. Hoxb-2 transcriptional activation in rhombomeres 3 and 5 requires an evolutionarily conserved cis-acting element in addition to the Krox-20 binding site.

    PubMed Central

    Vesque, C; Maconochie, M; Nonchev, S; Ariza-McNaughton, L; Kuroiwa, A; Charnay, P; Krumlauf, R

    1996-01-01

    Segmentation is a key feature of the development of the vertebrate hindbrain where it involves the generation of repetitive morphological units termed rhombomeres (r). Hox genes are likely to play an essential role in the specification of segmental identity and we have been investigating their regulation. We show here that the mouse and chicken Hoxb-2 genes are dependent for their expression in r3 and r5 on homologous enhancer elements and on binding to this enhancer of the r3/r5-specific transcriptional activator Krox-20. Among the three Krox-20 binding sites of the mouse Hoxb-2 enhancer, only the high-affinity site is absolutely necessary for activity. In contrast, we have identified an additional cis-acting element, Box1, essential for r3/r5 enhancer activity. It is conserved both in sequence and in position respective to the high-affinity Krox-20 binding site within the mouse and chicken enhancers. Furthermore, a short 44 bp sequence spanning the Box1 and Krox-20 sites can act as an r3/r5 enhancer when oligomerized. Box1 may therefore constitute a recognition sequence for another factor cooperating with Krox-20. Taken together, these data demonstrate the conservation of Hox gene regulation and of Krox-20 function during vertebrate evolution. Images PMID:8895582

  10. Geologic resource evaluation of Pu‘ukoholā Heiau National Historic Site, Hawai‘i, part II: benthic habitat mapping

    USGS Publications Warehouse

    Cochran, Susan A.; Gibbs, Ann E.; Logan, Joshua B.

    2006-01-01

    In cooperation with the U.S. National Park Service (NPS), the U.S. Geological Survey (USGS) has mapped the underwater environment in and adjacent to three parks along the Kona coast on the island of Hawai‘i. This report is the second of two produced for the NPS on the geologic resource evaluation of Pu‘ukoholā Heiau National Historic Site (PUHE) and presents benthic habitat mapping of the waters of Kawaihae Bay offshore of PUHE. See Part I (Richmond and others, 2006) for an overview of the regional geology, local volcanics, and a detailed description of coastal landforms in the park. PUHE boundaries do not officially extend into the marine environment; however, impacts downslope of any activity in the park are of concern to management. The area of Kawaihae Bay mapped for this report extends from the north edge of the U.S. Coast Guard Reservation north of Kawaihae Harbor approximately 3.5 km south to the north edge of the Mauna Kea Golf Course and Beach Resort at Waikoloa and from the shoreline to depths of approximately 40 m (130 ft), where the fore reef drops off to the sandy shelf. The waters of smaller Pelekane Bay directly offshore of the park, while not formally under NPS jurisdiction, are managed by the park under an agreement with the State. This embayment is described in greater detail because of its special resource status. PUHE lies within the Kawaihae watershed, which contributes ~75 percent of the drainage in the northern portion of the study area; the Waikoloa/Waiulaula watershed contributes ~25 percent in the southern portion of the study area. Drainages from these watersheds into the study area include Makahuna, Makeāhua, Pohaukole, Kukui, and Waikoloa/Waiulaula Gulches. The Waikoloa/Waiulaula Gulch is the only perennial stream with a year-round water flow. Only during periods of extreme rainfall will water flow in the Makeāhua and Pohaukole gulches, merge together in the park, and empty directly into Pelekane Bay. In the late 1950s the reef

  11. 78 FR 41783 - Notice of Proposed New Fee Sites; Federal Lands Recreation Enhancement Act, (Title VIII, Pub. L...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-11

    ... continued operation and maintenance of these recreation sites. Two campgrounds on the Challis-Yankee Fork... and are conveniently located near the Historic Custer Townsite and the Yankee Fork of the Salmon...

  12. Quantification and site-specification of the support practice factor when mapping soil erosion risk associated with olive plantations in the Mediterranean island of Crete.

    PubMed

    Karydas, Christos G; Sekuloska, Tijana; Silleos, Georgios N

    2009-02-01

    Due to inappropriate agricultural management practices, soil erosion is becoming one of the most dangerous forms of soil degradation in many olive farming areas in the Mediterranean region, leading to significant decrease of soil fertility and yield. In order to prevent further soil degradation, proper measures are necessary to be locally implemented. In this perspective, an increase in the spatial accuracy of remote sensing datasets and advanced image analysis are significant tools necessary and efficient for mapping soil erosion risk on a fine scale. In this study, the Revised Universal Soil Loss Equation (RUSLE) was implemented in the spatial domain using GIS, while a very high resolution satellite image, namely a QuickBird image, was used for deriving cover management (C) and support practice (P) factors, in order to map the risk of soil erosion in Kolymvari, a typical olive farming area in the island of Crete, Greece. The results comprised a risk map of soil erosion when P factor was taken uniform (conventional approach) and a risk map when P factor was quantified site-specifically using object-oriented image analysis. The results showed that the QuickBird image was necessary in order to achieve site-specificity of the P factor and therefore to support fine scale mapping of soil erosion risk in an olive cultivation area, such as the one of Kolymvari in Crete. Increasing the accuracy of the QB image classification will further improve the resulted soil erosion mapping.

  13. Raman chemical mapping reveals site of action of HIV protease inhibitors in HPV16 E6 expressing cervical carcinoma cells.

    PubMed

    Kim, Dong-Hyun; Jarvis, Roger M; Allwood, J William; Batman, Gavin; Moore, Rowan E; Marsden-Edwards, Emma; Hampson, Lynne; Hampson, Ian N; Goodacre, Royston

    2010-12-01

    It has been shown that the HIV protease inhibitors indinavir and lopinavir may have activity against the human papilloma virus (HPV) type 16 inhibiting HPV E6-mediated proteasomal degradation of p53 in cultured cervical carcinoma cells. However, their mode and site of action is unknown. HPV-negative C33A cervical carcinoma cells and the same cells stably transfected with E6 (C33AE6) were exposed to indinavir and lopinavir at concentrations of 1 mM and 30 μM, respectively. The intracellular distribution of metabolites and metabolic changes induced by these treatments were investigated by Raman microspectroscopic imaging combined with the analysis of cell fractionation products by liquid chromatography-mass spectrometry (LC-MS). A uniform cellular distribution of proteins was found in drug-treated cells irrespective of cell type. Indinavir was observed to co-localise with nucleic acid in the nucleus, but only in E6 expressing cells. Principal components analysis (PCA) score maps generated on the full Raman hypercube and the corresponding PCA loadings plots revealed that the majority of metabolic variations influenced by the drug exposure within the cells were associated with changes in nucleic acids. Analysis of cell fractionation products by LC-MS confirmed that the level of indinavir in nuclear extracts was approximately eight-fold greater than in the cytoplasm. These data demonstrate that indinavir undergoes enhanced nuclear accumulation in E6-expressing cells, which suggests that this is the most likely site of action for this compound against HPV.

  14. Rapid Reconnaissance Mapping of Volatile Organic Compounds by Photoionization Detection at the USGS Amargosa Desert Research Site

    NASA Astrophysics Data System (ADS)

    Thordsen, J. J.; Stonestrom, D. A.; Conaway, C. H.; Luo, W.; Baker, R. J.; Andraski, B. J.

    2015-12-01

    Two types of handheld photoionization detectors were evaluated in April 2015 for reconnaissance mapping of volatile organic compounds (VOCs) in the unsaturated zone surrounding legacy disposal trenches for commercial low-level radioactive waste near Beatty, Nevada (USA). This method is rapid and cost effective when compared to the more conventional procedure used ate the site, where VOCs are collected on sorbent cartridges in the field followed by thermal desorption, gas chromatographic separation, and quantitation by mass spectroscopy in the laboratory (TD-GC-MS analysis). Using the conventional method, more than sixty distinct compounds have been identified in the 110-m deep unsaturated zone vapor phase, and the changing nature of the VOC mix over a 15-yr timeframe has been recorded. Analyses to date have identified chlorofluorocarbons (CFCs), chlorinated ethenes, chlorinated ethanes, gasoline-range hydrocarbons, chloroform, and carbon tetrachloride as the main classes of VOCs present. The VOC plumes emanating from the various subgroups of trenches are characterized by different relative abundances of the compound classes, and total VOC concentrations that cover several orders of magnitude. One of the photoionization detectors, designed for industrial compliance testing, lacked sufficient dynamic range and sensitivity to be useful. The other, a wide range (1 ppb-20,000 ppm) research-grade instrument with a 10.6 eV photoionization detector (PID) lamp, produced promising results, detecting roughly half of the non-CFC VOCs present. The rapid and inexpensive photoionization method is envisioned as a screening tool to supplement, expedite, and direct the collection of additional samples for TD-GC-MS analyses at this and other VOC-contaminated sites.

  15. Digital photogrammetric analysis of the IMP camera images: Mapping the Mars Pathfinder landing site in three dimensions

    USGS Publications Warehouse

    Kirk, R.L.; Howington-Kraus, E.; Hare, T.; Dorrer, E.; Cook, D.; Becker, K.; Thompson, K.; Redding, B.; Blue, J.; Galuszka, D.; Lee, E.M.; Gaddis, L.R.; Johnson, J. R.; Soderblom, L.A.; Ward, A.W.; Smith, P.H.; Britt, D.T.

    1999-01-01

    This paper describes our photogrammetric analysis of the Imager for Mars Pathfinder data, part of a broader program of mapping the Mars Pathfinder landing site in support of geoscience investigations. This analysis, carried out primarily with a commercial digital photogrammetric system, supported by our in-house Integrated Software for Imagers and Spectrometers (ISIS), consists of three steps: (1) geometric control: simultaneous solution for refined estimates of camera positions and pointing plus three-dimensional (3-D) coordinates of ???103 features sitewide, based on the measured image coordinates of those features; (2) topographic modeling: identification of ???3 ?? 105 closely spaced points in the images and calculation (based on camera parameters from step 1) of their 3-D coordinates, yielding digital terrain models (DTMs); and (3) geometric manipulation of the data: combination of the DTMs from different stereo pairs into a sitewide model, and reprojection of image data to remove parallax between the different spectral filters in the two cameras and to provide an undistorted planimetric view of the site. These processes are described in detail and example products are shown. Plans for combining the photogrammetrically derived topographic data with spectrophotometry are also described. These include photometric modeling using surface orientations from the DTM to study surface microtextures and improve the accuracy of spectral measurements, and photoclinometry to refine the DTM to single-pixel resolution where photometric properties are sufficiently uniform. Finally, the inclusion of rover images in a joint photogrammetric analysis with IMP images is described. This challenging task will provide coverage of areas hidden to the IMP, but accurate ranging of distant features can be achieved only if the lander is also visible in the rover image used. Copyright 1999 by the American Geophysical Union.

  16. Shear-wave velocity characterization of the USGS Hawaiian strong-motion network on the Island of Hawaii and development of an NEHRP site-class map

    USGS Publications Warehouse

    Wong, Ivan G.; Stokoe, Kenneth; Cox, Brady R.; Yuan, Jiabei; Knudsen, Keith L.; Terra, Fabia; Okubo, Paul G.; Lin, Yin-Cheng

    2011-01-01

    To assess the level and nature of ground shaking in Hawaii for the purposes of earthquake hazard mitigation and seismic design, empirical ground-motion prediction models are desired. To develop such empirical relationships, knowledge of the subsurface site conditions beneath strong-motion stations is critical. Thus, as a first step to develop ground-motion prediction models for Hawaii, spectral-analysis-of-surface-waves (SASW) profiling was performed at the 22 free-field U.S. Geological Survey (USGS) strong-motion sites on the Big Island to obtain shear-wave velocity (VS) data. Nineteen of these stations recorded the 2006 Kiholo Bay moment magnitude (M) 6.7 earthquake, and 17 stations recorded the triggered M 6.0 Mahukona earthquake. VS profiling was performed to reach depths of more than 100 ft. Most of the USGS stations are situated on sites underlain by basalt, based on surficial geologic maps. However, the sites have varying degrees of weathering and soil development. The remaining strong-motion stations are located on alluvium or volcanic ash. VS30 (average VS in the top 30 m) values for the stations on basalt ranged from 906 to 1908 ft/s [National Earthquake Hazards Reduction Program (NEHRP) site classes C and D], because most sites were covered with soil of variable thickness. Based on these data, an NEHRP site-class map was developed for the Big Island. These new VS data will be a significant input into an update of the USGS statewide hazard maps and to the operation of ShakeMap on the island of Hawaii.

  17. High Resolution Mapping of an Alleged Chemical Weapons Dump Site in the Santa Cruz Basin, offshore California

    NASA Astrophysics Data System (ADS)

    Brewer, P. G.; Peltzer, E. T.; Walz, P. M.; Caress, D. W.; Thomas, H. J.

    2013-12-01

    Nautical charts record seven locations off the coast of California labeled as 'Chemical Munitions Dumping Area, Disused' that together cover some 12,000 km2 of sea floor. However only one such chemical munitions site is officially documented and no record exists of any chemical munitions disposed of at other locations, thus creating confusion. We have executed a one day AUV mapping survey of a corner of one such site in the Santa Cruz Basin, south of Port Hueneme, to examine and investigate the debris field. The region is covered with soft sediment and the overlying water is very low in oxygen at ~10 μmol/kg. The processed 110 kHz sidescan data revealed some 754 targets in 25.6 km2 for an average of 29 targets per km2. This was followed by two ROV dives to investigate the targets identified. We found but one false positives among the over 40 targets visited, and found items ranging from two distinct lines of unmarked or labeled and now empty barrels, two target drones, and much miscellaneous debris including 4-packs of cat food cans and a large ships mast over 30m in length. There was zero evidence of chemical weapons materiel as expected given the lack of official records. Almost all of the targets were covered in dense and colorful assemblages of invertebrates: sponges, anemones, and crabs. Where barrels were sufficiently open for full visual inspection, the interior sea floor appeared to have become fully anoxic and was covered in white and yellow bacterial mat. The area chosen for our survey (centered at 33.76 deg N 119.56 deg W) was across the north western boundary of the marked site, and represents only ~ 10% percent of the designated area. Our expectation, that human nature would drive the disposal activities to the nearest corner of the chosen area rather than the center of the field appears to have been confirmed. Objects were found both within and outside of the boundary of the dump site. We have not surveyed the full marked area but there appears to be

  18. Genome-Wide Mapping of Collier In Vivo Binding Sites Highlights Its Hierarchical Position in Different Transcription Regulatory Networks

    PubMed Central

    Dubois, Laurence; Bataillé, Laetitia; Painset, Anaïs; Le Gras, Stéphanie; Jost, Bernard; Crozatier, Michèle; Vincent, Alain

    2015-01-01

    Collier, the single Drosophila COE (Collier/EBF/Olf-1) transcription factor, is required in several developmental processes, including head patterning and specification of muscle and neuron identity during embryogenesis. To identify direct Collier (Col) targets in different cell types, we used ChIP-seq to map Col binding sites throughout the genome, at mid-embryogenesis. In vivo Col binding peaks were associated to 415 potential direct target genes. Gene Ontology analysis revealed a strong enrichment in proteins with DNA binding and/or transcription-regulatory properties. Characterization of a selection of candidates, using transgenic CRM-reporter assays, identified direct Col targets in dorso-lateral somatic muscles and specific neuron types in the central nervous system. These data brought new evidence that Col direct control of the expression of the transcription regulators apterous and eyes-absent (eya) is critical to specifying neuronal identities. They also showed that cross-regulation between col and eya in muscle progenitor cells is required for specification of muscle identity, revealing a new parallel between the myogenic regulatory networks operating in Drosophila and vertebrates. Col regulation of eya, both in specific muscle and neuronal lineages, may illustrate one mechanism behind the evolutionary diversification of Col biological roles. PMID:26204530

  19. Nanobodies: site-specific labeling for super-resolution imaging, rapid epitope-mapping and native protein complex isolation

    PubMed Central

    Pleiner, Tino; Bates, Mark; Trakhanov, Sergei; Lee, Chung-Tien; Schliep, Jan Erik; Chug, Hema; Böhning, Marc; Stark, Holger; Urlaub, Henning; Görlich, Dirk

    2015-01-01

    Nanobodies are single-domain antibodies of camelid origin. We generated nanobodies against the vertebrate nuclear pore complex (NPC) and used them in STORM imaging to locate individual NPC proteins with <2 nm epitope-label displacement. For this, we introduced cysteines at specific positions in the nanobody sequence and labeled the resulting proteins with fluorophore-maleimides. As nanobodies are normally stabilized by disulfide-bonded cysteines, this appears counterintuitive. Yet, our analysis showed that this caused no folding problems. Compared to traditional NHS ester-labeling of lysines, the cysteine-maleimide strategy resulted in far less background in fluorescence imaging, it better preserved epitope recognition and it is site-specific. We also devised a rapid epitope-mapping strategy, which relies on crosslinking mass spectrometry and the introduced ectopic cysteines. Finally, we used different anti-nucleoporin nanobodies to purify the major NPC building blocks – each in a single step, with native elution and, as demonstrated, in excellent quality for structural analysis by electron microscopy. The presented strategies are applicable to any nanobody and nanobody-target. DOI: http://dx.doi.org/10.7554/eLife.11349.001 PMID:26633879

  20. Development and testing of a contamination potential mapping system for a portion of the General Separations Area, Savannah River Site, South Carolina

    USGS Publications Warehouse

    Rine, J.M.; Berg, R.C.; Shafer, J.M.; Covington, E.R.; Reed, J.K.; Bennett, C.B.; Trudnak, J.E.

    1998-01-01

    A methodology was developed to evaluate and map the contamination potential or aquifer sensitivity of the upper groundwater flow system of a portion of the General Separations Area (GSA) at the Department of Energy's Savannah River Site (SRS) in South Carolina. A Geographic Information System (GIS) was used to integrate diverse subsurface geologic data, soils data, and hydrology utilizing a stack-unit mapping approach to construct mapping layers. This is the first time that such an approach has been used to delineate the hydrogeology of a coastal plain environment. Unit surface elevation maps were constructed for the tops of six Tertiary units derived from over 200 boring logs. Thickness or isopach maps were created for five hydrogeologic units by differencing top and basal surface elevations. The geologic stack-unit map was created by stacking the five isopach maps and adding codes for each stack-unit polygon. Stacked-units were rated according to their hydrogeologic properties and ranked using a logarithmic approach (utility theory) to establish a contamination potential index. Colors were assigned to help display relative importance of stacked-units in preventing or promoting transport of contaminants. The sensitivity assessment included the effects of surface soils on contaminants which are particularly important for evaluating potential effects from surface spills. Hydrogeologic/hydrologic factors did not exhibit sufficient spatial variation to warrant incorporation into contamination potential assessment. Development of this contamination potential mapping system provides a useful tool for site planners, environmental scientists, and regulatory agencies.A methodology was developed to evaluate and map the contamination potential or aquifer sensitivity of the upper groundwater flow system of a portion of the General Separations Area (GSA) at the Department of Energy's Savannah River Site (SRS) in South Carolina. A Geographic Information System (GIS) was used to

  1. Genome-wide mapping of human DNA-replication origins: levels of transcription at ORC1 sites regulate origin selection and replication timing.

    PubMed

    Dellino, Gaetano Ivan; Cittaro, Davide; Piccioni, Rossana; Luzi, Lucilla; Banfi, Stefania; Segalla, Simona; Cesaroni, Matteo; Mendoza-Maldonado, Ramiro; Giacca, Mauro; Pelicci, Pier Giuseppe

    2013-01-01

    We report the genome-wide mapping of ORC1 binding sites in mammals, by chromatin immunoprecipitation and parallel sequencing (ChIP-seq). ORC1 binding sites in HeLa cells were validated as active DNA replication origins (ORIs) using Repli-seq, a method that allows identification of ORI-containing regions by parallel sequencing of temporally ordered replicating DNA. ORC1 sites were universally associated with transcription start sites (TSSs) of coding or noncoding RNAs (ncRNAs). Transcription levels at the ORC1 sites directly correlated with replication timing, suggesting the existence of two classes of ORIs: those associated with moderate/high transcription levels (≥1 RNA copy/cell), firing in early S and mapping to the TSSs of coding RNAs; and those associated with low transcription levels (<1 RNA copy/cell), firing throughout the entire S and mapping to TSSs of ncRNAs. These findings are compatible with a scenario whereby TSS expression levels influence the efficiency of ORC1 recruitment at G(1) and the probability of firing during S.

  2. Novel bis-(−)-nor-meptazinol derivatives act as dual binding site AChE inhibitors with metal-complexing property

    SciTech Connect

    Zheng, Wei; Li, Juan; Qiu, Zhuibai; Xia, Zheng; Li, Wei; Yu, Lining; Chen, Hailin; Chen, Jianxing; Chen, Yan; Hu, Zhuqin; Zhou, Wei; Shao, Biyun; Cui, Yongyao; Xie, Qiong; Chen, Hongzhuan

    2012-10-01

    The strategy of dual binding site acetylcholinesterase (AChE) inhibition along with metal chelation may represent a promising direction for multi-targeted interventions in the pathophysiological processes of Alzheimer's disease (AD). In the present study, two derivatives (ZLA and ZLB) of a potent dual binding site AChE inhibitor bis-(−)-nor-meptazinol (bis-MEP) were designed and synthesized by introducing metal chelating pharmacophores into the middle chain of bis-MEP. They could inhibit human AChE activity with IC{sub 50} values of 9.63 μM (for ZLA) and 8.64 μM (for ZLB), and prevent AChE-induced amyloid-β (Aβ) aggregation with IC{sub 50} values of 49.1 μM (for ZLA) and 55.3 μM (for ZLB). In parallel, molecular docking analysis showed that they are capable of interacting with both the catalytic and peripheral anionic sites of AChE. Furthermore, they exhibited abilities to complex metal ions such as Cu(II) and Zn(II), and inhibit Aβ aggregation triggered by these metals. Collectively, these results suggest that ZLA and ZLB may act as dual binding site AChEIs with metal-chelating potency, and may be potential leads of value for further study on disease-modifying treatment of AD. -- Highlights: ► Two novel bis-(−)-nor-meptazinol derivatives are designed and synthesized. ► ZLA and ZLB may act as dual binding site AChEIs with metal-chelating potency. ► They are potential leads for disease-modifying treatment of Alzheimer's disease.

  3. Mapping the Binding Site of a Cross-Reactive Plasmodium falciparum PfEMP1 Monoclonal Antibody Inhibitory of ICAM-1 Binding

    PubMed Central

    Lennartz, Frank; Bengtsson, Anja; Olsen, Rebecca W.; Joergensen, Louise; Brown, Alan; Remy, Louise; Man, Petr; Forest, Eric; Barfod, Lea K.; Adams, Yvonne

    2015-01-01

    The virulence of Plasmodium falciparum is linked to the ability of infected erythrocytes (IE) to adhere to the vascular endothelium, mediated by P. falciparum erythrocyte membrane protein 1 (PfEMP1). In this article, we report the functional characterization of an mAb that recognizes a panel of PfEMP1s and inhibits ICAM-1 binding. The 24E9 mouse mAb was raised against PFD1235w DBLβ3_D4, a domain from the group A PfEMP1s associated with severe malaria. 24E9 recognizes native PfEMP1 expressed on the IE surface and shows cross-reactivity with and cross-inhibition of the ICAM-1 binding capacity of domain cassette 4 PfEMP1s. 24E9 Fab fragments bind DBLβ3_D4 with nanomolar affinity and inhibit ICAM-1 binding of domain cassette 4–expressing IE. The antigenic regions targeted by 24E9 Fab were identified by hydrogen/deuterium exchange mass spectrometry and revealed three discrete peptides that are solvent protected in the complex. When mapped onto a homology model of DBLβ3_D4, these cluster to a defined, surface-exposed region on the convex surface of DBLβ3_D4. Mutagenesis confirmed that the site most strongly protected is necessary for 24E9 binding, which is consistent with a low-resolution structure of the DBLβ3_D4::24E9 Fab complex derived from small-angle x-ray scattering. The convex surface of DBLβ3_D4 has previously been shown to contain the ICAM-1 binding site of DBLβ domains, suggesting that the mAb acts by occluding the ICAM-1 binding surface. Conserved epitopes, such as those targeted by 24E9, are promising candidates for the inclusion in a vaccine interfering with ICAM-1–specific adhesion of group A PfEMP1 expressed by P. falciparum IE during severe malaria. PMID:26320251

  4. 77 FR 62215 - Notice of Proposed New Fee Site; Federal Lands Recreation Enhancement Act, (Title VIII, Pub. L...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-12

    ... Cabin from June 1 to October 15 and a $65 fee from October 16 to June 1 with no water available; a $65 fee at the Paddy Flat Rental Cabin; and a $65 fee at the Lake Fork Rental Cabin. Fees are assessed... are reasonable and typical of similar sites in the area. DATES: Comments will be accepted...

  5. 78 FR 19445 - Notice of Proposed New Fee Sites; Federal Lands Recreation Enhancement Act, (Title VIII, Pub. L...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-01

    ... maintenance, market assessment, and public comment. Funds from fees would be used for the continued operation and maintenance of these recreation sites. Lake Canyon Recreation Area is a fee campground with 54... West Price River Drive, Price, Utah 84501. FOR FURTHER INFORMATION CONTACT: Ann King, Public...

  6. Post-Closure Report for Closed Resource Conservation and Recovery Act Corrective Action Units, Nevada National Security Site, Nevada, for Fiscal Year 2014

    SciTech Connect

    Silvas, Alissa J.

    2015-01-01

    This report serves as the combined annual report for post-closure activities for several Corrective Action Units (CAUs). The locations of the sites are shown in Figure 1. This report covers fiscal year 2014 (October 2013–September 2014). The post-closure requirements for these sites are described in Resource Conservation and Recovery Act Permit Number NEV HW0101 and summarized in each CAU-specific section in Section 1.0 of this report. The results of the inspections, a summary of maintenance activities, and an evaluation of monitoring data are presented in this report. Site inspections are conducted semiannually at CAUs 90 and 91 and quarterly at CAUs 92, 110, 111, and 112. Additional inspections are conducted at CAU 92 if precipitation occurs in excess of 0.50 inches (in.) in a 24-hour period and at CAU 111 if precipitation occurs in excess of 1.0 in. in a 24-hour period. Inspections include an evaluation of the condition of the units, including covers, fences, signs, gates, and locks. In addition to visual inspections, soil moisture monitoring, vegetation evaluations, and subsidence surveys are conducted at CAU 110. At CAU 111, soil moisture monitoring, vegetation evaluations, subsidence surveys, direct radiation monitoring, air monitoring, radon flux monitoring, and groundwater monitoring are conducted. The results of the vegetation surveys and an analysis of the soil moisture monitoring data at CAU 110 are presented in this report. Results of additional monitoring at CAU 111 are documented annually in the Nevada National Security Site Waste Management Monitoring Report Area 3 and Area 5 Radioactive Waste Management Sites and in the Nevada National Security Site Data Report: Groundwater Monitoring Program Area 5 Radioactive Waste Management Site, which will be prepared in approximately June 2015. All required inspections, maintenance, and monitoring were conducted in accordance with the post-closure requirements of the permit. It is recommended to continue

  7. "Homosexuality/Homophobia Is Un-African"?: Un-Mapping Transnational Discourses in the Context of Uganda's Anti-Homosexuality Bill/Act.

    PubMed

    Wahab, Amar

    2016-01-01

    This article un-maps the recent impasse between pro- and antigay mobilization around Uganda's Anti-Homosexuality Act (AHA, 2009-2014). Drawing on scholarly and social media sources, it summarizes the increasing influence of (U.S.) transnational evangelism that has precipitated a state-religious complex of "anticipatory political homophobia" in Uganda. If transnational evangelism against same-sex sexuality in Uganda has generated a strong reaction from global LGBT human-rights advocates, this article critiques this Western homotransnationalist response by analyzing its limited terms of operation, focusing on the ways in which Uganda is hailed into the biopolitical project of a Western queer modernity. The author focuses on the copresence between homotransnationalist mobilization and "homophobic anticipatory countermobilization" as (re)organizing/suturing a global ordering project that is deeply invested in biopolitics and necropolitics. This suggests that the global flashpointing of Uganda in the context of the AHA incites further questions concerning the transnationality of "gay human rights" discourse under neoliberalism.

  8. "Homosexuality/Homophobia Is Un-African"?: Un-Mapping Transnational Discourses in the Context of Uganda's Anti-Homosexuality Bill/Act.

    PubMed

    Wahab, Amar

    2016-01-01

    This article un-maps the recent impasse between pro- and antigay mobilization around Uganda's Anti-Homosexuality Act (AHA, 2009-2014). Drawing on scholarly and social media sources, it summarizes the increasing influence of (U.S.) transnational evangelism that has precipitated a state-religious complex of "anticipatory political homophobia" in Uganda. If transnational evangelism against same-sex sexuality in Uganda has generated a strong reaction from global LGBT human-rights advocates, this article critiques this Western homotransnationalist response by analyzing its limited terms of operation, focusing on the ways in which Uganda is hailed into the biopolitical project of a Western queer modernity. The author focuses on the copresence between homotransnationalist mobilization and "homophobic anticipatory countermobilization" as (re)organizing/suturing a global ordering project that is deeply invested in biopolitics and necropolitics. This suggests that the global flashpointing of Uganda in the context of the AHA incites further questions concerning the transnationality of "gay human rights" discourse under neoliberalism. PMID:26503528

  9. Developing of a VS30 map for addressing site effects for Portugal: evaluation of the effectiveness of using VS30-proxies for stable continental regions.

    NASA Astrophysics Data System (ADS)

    Vilanova, Susana; Narciso, Joao; Carvalho, Joao; Pinto, Carlos; Lopes, Isabel; Nemser, Eliza; Borges, Jose; Oliveira, Carlos

    2014-05-01

    The need to perform first-order estimates for site amplification in a regional sense has been strongly emphasized in recent years. The use site-amplification maps is of major importance for addressing both land-use planning (seismic-hazard maps) and emergency planning (instrumental intensity maps). Project SCENE, funded by the Portuguese Foundation for Science and Technology (FCT), aimed at gathering and acquiring shear-wave velocity profiles in diverse lithological and geological formations in Portugal, in order to develop a regional site conditions map to be used for including first-order site-effects into seismic hazard assessment maps. Within the scope of project SCENE thirty sites where strong motion stations are installed were characterized using shear-wave seismic refraction. The project SCENE shear-wave database also includes a significant amount of shear-wave refraction data available from FCT project NEFITAG and from previously performed CAPSA and ERSTA campaigns. Few sites characterised by using other methods (multichannel analysis of surface waves and invasive profiles) were also included in the database. The shear-wave database currently includes 85 shear-wave depth sections or profiles from a variety of lithological/geological formations. In addition to the shear-wave profile database we compiled geotechnical and geological profiles in the vicinity of the sites analysed. We performed a careful evaluation of the geological conditions for each site in the database using the largest scale available (usually 1:50 000). A smaller scale map (1:500000) was also used in order to evaluate the bias introduced by the scale-dependent map accuracy. We grouped the sites into six generalized geological units: S1 - igneous and metamorphic rocks; S2 - old sedimentary rocks (Limestones, marly limestones, dolomites, conglomerates and sandstones); S3 - Sand, sandstones, clays and conglomerates of Miocene age; S4 - Sandstones, gravels, sands and clays of Pliocene age; S5

  10. The transcription initiation sites of eggplant latent viroid strands map within distinct motifs in their in vivo RNA conformations.

    PubMed

    López-Carrasco, Amparo; Gago-Zachert, Selma; Mileti, Giuseppe; Minoia, Sofia; Flores, Ricardo; Delgado, Sonia

    2016-01-01

    Eggplant latent viroid (ELVd), like other members of family Avsunviroidae, replicates in plastids through a symmetric rolling-circle mechanism in which elongation of RNA strands is most likely catalyzed by a nuclear-encoded polymerase (NEP) translocated to plastids. Here we have addressed where NEP initiates transcription of viroid strands. Because this step is presumably directed by sequence/structural motifs, we have previously determined the conformation of the monomeric linear (+) and (-) RNAs of ELVd resulting from hammerhead-mediated self-cleavage. In silico predictions with 3 softwares led to similar bifurcated conformations for both ELVd strands. In vitro examination by non-denaturing PAGE showed that they migrate as prominent single bands, with the ELVd (+) RNA displaying a more compact conformation as revealed by its faster electrophoretic mobility. In vitro SHAPE analysis corroborated the ELVd conformations derived from thermodynamics-based predictions in silico. Moreover, sequence analysis of 94 full-length natural ELVd variants disclosed co-variations, and mutations converting canonical into wobble pairs or vice versa, which confirmed in vivo most of the stems predicted in silico and in vitro, and additionally helped to introduce minor structural refinements. Therefore, results from the 3 experimental approaches were essentially consistent among themselves. Application to RNA preparations from ELVd-infected tissue of RNA ligase-mediated rapid amplification of cDNA ends, combined with pretreatments to modify the 5' ends of viroid strands, mapped the transcription initiation sites of ELVd (+) and (-) strands in vivo at different sequence/structural motifs, in contrast with the situation previously observed in 2 other members of the family Avsunviroidae. PMID:26618399

  11. Sequestration of Polo kinase to microtubules by phosphopriming-independent binding to Map205 is relieved by phosphorylation at a CDK site in mitosis

    PubMed Central

    Archambault, Vincent; D’Avino, Pier Paolo; Deery, Michael J.; Lilley, Kathryn S.; Glover, David M.

    2008-01-01

    The conserved Polo kinase controls multiple events in mitosis and cytokinesis. Although Polo-like kinases are regulated by phosphorylation and proteolysis, control of subcellular localization plays a major role in coordinating their mitotic functions. This is achieved largely by the Polo-Box Domain, which binds prephosphorylated targets. However, it remains unclear whether and how Polo might interact with partner proteins when priming mitotic kinases are inactive. Here we show that Polo associates with microtubules in interphase and cytokinesis, through a strong interaction with the microtubule-associated protein Map205. Surprisingly, this interaction does not require priming phosphorylation of Map205, and the Polo-Box Domain of Polo is required but not sufficient for this interaction. Moreover, phosphorylation of Map205 at a CDK site relieves this interaction. Map205 can stabilize Polo and inhibit its cellular activity in vivo. In syncytial embryos, the centrosome defects observed in polo hypomorphs are enhanced by overexpression of Map205 and suppressed by its deletion. We propose that Map205-dependent targeting of Polo to microtubules provides a stable reservoir of Polo that can be rapidly mobilized by the activity of Cdk1 at mitotic entry. PMID:18832073

  12. Cross-validated methods for promoter/transcription start site mapping in SL trans-spliced genes, established using the Ciona intestinalis troponin I gene

    PubMed Central

    Khare, Parul; Mortimer, Sandra I.; Cleto, Cynthia L.; Okamura, Kohji; Suzuki, Yutaka; Kusakabe, Takehiro; Nakai, Kenta; Meedel, Thomas H.; Hastings, Kenneth E. M.

    2011-01-01

    In conventionally-expressed eukaryotic genes, transcription start sites (TSSs) can be identified by mapping the mature mRNA 5′-terminal sequence onto the genome. However, this approach is not applicable to genes that undergo pre-mRNA 5′-leader trans-splicing (SL trans-splicing) because the original 5′-segment of the primary transcript is replaced by the spliced leader sequence during the trans-splicing reaction and is discarded. Thus TSS mapping for trans-spliced genes requires different approaches. We describe two such approaches and show that they generate precisely agreeing results for an SL trans-spliced gene encoding the muscle protein troponin I in the ascidian tunicate chordate Ciona intestinalis. One method is based on experimental deletion of trans-splice acceptor sites and the other is based on high-throughput mRNA 5′-RACE sequence analysis of natural RNA populations in order to detect minor transcripts containing the pre-mRNA’s original 5′-end. Both methods identified a single major troponin I TSS located ∼460 nt upstream of the trans-splice acceptor site. Further experimental analysis identified a functionally important TATA element 31 nt upstream of the start site. The two methods employed have complementary strengths and are broadly applicable to mapping promoters/TSSs for trans-spliced genes in tunicates and in trans-splicing organisms from other phyla. PMID:21109525

  13. VS30 – A site-characterization parameter for use in building Codes, simplified earthquake resistant design, GMPEs, and ShakeMaps

    USGS Publications Warehouse

    Borcherdt, Roger D.

    2012-01-01

    VS30, defined as the average seismic shear-wave velocity from the surface to a depth of 30 meters, has found wide-spread use as a parameter to characterize site response for simplified earthquake resistant design as implemented in building codes worldwide. VS30 , as initially introduced by the author for the US 1994 NEHRP Building Code, provides unambiguous definitions of site classes and site coefficients for site-dependent response spectra based on correlations derived from extensive borehole logging and comparative ground-motion measurement programs in California. Subsequent use of VS30 for development of strong ground motion prediction equations (GMPEs) and measurement of extensive sets of VS borehole data have confirmed the previous empirical correlations and established correlations of SVS30 with VSZ at other depths. These correlations provide closed form expressions to predict S30 V at a large number of additional sites and further justify S30 V as a parameter to characterize site response for simplified building codes, GMPEs, ShakeMap, and seismic hazard mapping.

  14. Caught in the act: the crystal structure of cleaved cathepsin L bound to the active site of Cathepsin L.

    PubMed

    Sosnowski, Piotr; Turk, Dušan

    2016-04-01

    Cathepsin L is a ubiquitously expressed papain-like cysteine protease involved in the endosomal degradation of proteins and has numerous roles in physiological and pathological processes, such as arthritis, osteoporosis, and cancer. Insight into the specificity of cathepsin L is important for elucidating its physiological roles and drug discovery. To study interactions with synthetic ligands, we prepared a presumably inactive mutant and crystallized it. Unexpectedly, the crystal structure determined at 1.4 Å revealed that the cathepsin L molecule is cleaved, with the cleaved region trapped in the active site cleft of the neighboring molecule. Hence, the catalytic mutant demonstrated low levels of catalytic activity. PMID:26992470

  15. Caught in the act: the crystal structure of cleaved cathepsin L bound to the active site of Cathepsin L.

    PubMed

    Sosnowski, Piotr; Turk, Dušan

    2016-04-01

    Cathepsin L is a ubiquitously expressed papain-like cysteine protease involved in the endosomal degradation of proteins and has numerous roles in physiological and pathological processes, such as arthritis, osteoporosis, and cancer. Insight into the specificity of cathepsin L is important for elucidating its physiological roles and drug discovery. To study interactions with synthetic ligands, we prepared a presumably inactive mutant and crystallized it. Unexpectedly, the crystal structure determined at 1.4 Å revealed that the cathepsin L molecule is cleaved, with the cleaved region trapped in the active site cleft of the neighboring molecule. Hence, the catalytic mutant demonstrated low levels of catalytic activity.

  16. CArG boxes in the human cardiac. cap alpha. -actin gene are core binding sites for positive trans-acting regulatory factors

    SciTech Connect

    Miwa, T.; Boxer, L.M.; Kedes, L.

    1987-10-01

    Positively acting, rate-limiting regulatory factors that influence tissue-specific expression of the human cardiac ..cap alpha..-actin gene in a mouse muscle cell line are shown by in vivo competition and gel mobility-shift assays to bind to upstream regions of its promoter but to neither vector DNA not a ..beta..-globin promoter. Although the two binding regions are distinctly separated, each corresponds to a cis region required for muscle-specific transcriptional stimulation, and each contains a core CC(A+T-rich)/sub 6/GC sequence (designated CArG box), which is found in the promoter regions of several muscle-associated genes. Each site has an apparently different binding affinity for trans-acting factors, which may explain the different transcriptional stimulation activities of the two cis regions. Therefore, the authors conclude that the two CArG box regions are responsible for muscle-specific transcriptional activity of the cardiac ..cap alpha..-actin gene through a mechanism that involves their binding of a positive trans-acting factor in muscle cells.

  17. Process for Transition of Uranium Mill Tailings Radiation Control Act Title II Disposal Sites to the U.S. Department of Energy Office of Legacy Management for Long-Term Surveillance and Maintenance

    SciTech Connect

    2012-03-01

    This document presents guidance for implementing the process that the U.S. Department of Energy (DOE) Office of Legacy Management (LM) will use for assuming perpetual responsibility for a closed uranium mill tailings site. The transition process specifically addresses sites regulated under Title II of the Uranium Mill Tailings Radiation Control Act (UMTRCA) but is applicable in principle to the transition of sites under other regulatory structures, such as the Formerly Utilized Sites Remedial Action Program.

  18. Baseline Mapping Study of the Steed Pond Aquifer and Crouch Branch Confining Unit Beneath A/M Area, Savannah River Site, Aiken, South Carolina

    SciTech Connect

    JACKSON, DENNISG.

    1998-09-01

    This report presents the results of a baseline mapping project conducted for the Environmental Restoration Department at Savannah River Site. The purpose of this report is to map the distribution of mud (clay and silt-sized material) within each hydrogeologic unit from the surface down to the top of the Crouch Branch aquifer beneath the A/M Area. The distribution of mud layers and variations in the percentage of clay and silt within the strata is extremely important in order to fully characterize the extent of DNAPL beneath the A/M Area and determine the geometry of the contaminant plumes emanating from them. Precision mapping of these layers can aid in locating areas where contamination is most likely to have migrated into the saturated zone. In addition, this information can be used to refine the current remediation systems or assist in designing new remedial systems.

  19. Mapping, Characterizing, and Interpreting Mineral Fabrics in Mafic and Ultramafic Rock Samples from Mars Analog Sites in Samail, Oman Using the Ultra-Compact Imaging Spectrometer (UCIS)

    NASA Astrophysics Data System (ADS)

    Sanders, C. B.; Ehlmann, B. L.; Sellar, R.; Van Gorp, B.; Mouroulis, P.; Blaney, D. L.; Green, R. O.

    2013-12-01

    The Ultra-Compact Imaging Spectrometer (UCIS) is a hyperspectral instrument that enables an autonomous geologist, such as Mars 2020 or future missions of planetary exploration, to determine the mineral fabric and composition of rock samples. In this investigation, UCIS was used in a micro-imaging configuration in a laboratory environment to image the reflectance spectra of solid rock samples in the visible through shortwave-infrared wavelengths (0.50 to 2.50 μm.) These data were used both to evaluate the capabilities of UCIS at the micro-scale and to analyze the spectral and mineralogical diversity of rocks from Mars-analog sites. The primary site of interest for this investigation was the Samail Ophiolite in Oman, where subsurface serpentinization and subsurface/subaerial carbonate deposition mimic some of the processes undergone by a Noachian Mars. Data were processed with the IDL-based image analysis software ENVI to generate detailed parameter maps distinguishing carbonate and serpentine minerals in varying modes of aqueous alteration. Close inspection of these maps yielded new spectral parameters, including the strength of absorption bands at 1.39, 1.90, 2.12, and 2.34 μm, continuum shapes including slopes about 1.08 μm, and feature shifting, which reliably identify and map serpentines and carbonates with distinct cation contents, water contents, and internal textures. These spectral parameters were combined to produce detailed color composite maps which informed our understanding of the relationships between phases and the extent of aqueous alteration in the Oman samples. Areal maps of mineral phases were used to quantitatively estimate the mineralogy of samples nondestructively, comparing to standard techniques such as x-ray diffraction and electron microprobe analysis, which require processing or destruction of rock samples. Our maps and measurements will provide a means for comparison between these techniques and the imaging spectroscopy performed by

  20. Sequence, structure, and active site analyses of p38 MAP kinase: exploiting DFG-out conformation as a strategy to design new type II leads.

    PubMed

    Badrinarayan, Preethi; Sastry, G Narahari

    2011-01-24

    A new knowledge, structure, and sequence based strategy involving the effective exploitation of the DFG-out conformation is delineated. A comprehensive analysis of the structure, sequence, cocrystals, and active sites of p38 MAP kinase crystal structures present in Protein Data Bank (PDB) and the FDA approved MAP kinase drugs has been done, and the information is used for the design of type II leads. The 98 crystal structures, 138 cocrystals, and 31 FDA drugs comprise of 7 different sequences of 2 organisms viz., Homo sapiens and Mus musculus differing in sequence length, constituting both homo- and heterochains. Multiple sequence alignment with ClustalW showed >95% sequence similarity with highly conserved domains and a high propensity for mutations in the activation loop. The bound ligands were extracted, and their interactions with DFG in and out conformations were studied. These cocrystals and FDA drugs were fragmented on the basis of their binding interactions and their affinity to ATP and allosteric sites. The fragment library thus generated contains 106 fragments with overlapping drug fragments. A blue print constituting three main parts viz., head (ATP region), linker (DFG region), and tail (allosteric region) has thus been formulated and used to design 64 type II p38 MAP kinase inhibitors. The above strategy has been employed to design potent type II p38 MAP kinase inhibitors, which are shown to be very promising. PMID:21141877

  1. YUCCA MOUNTAIN PROJECT RECOMMENDATION BY THE SECRETARY OF ENERGY REGARDING THE SUITABILITY OF THE YUCCA MOUNTAIN SITE FOR A REPOSITORY UNDER THE NUCLEAR WASTE POLICY ACT OF 1982

    SciTech Connect

    NA

    2002-03-26

    For more than half a century, since nuclear science helped us win World War II and ring in the Atomic Age, scientists have known that !he Nation would need a secure, permanent facility in which to dispose of radioactive wastes. Twenty years ago, when Congress adopted the Nuclear Waste Policy Act of 1982 (NWPA or ''the Act''), it recognized the overwhelming consensus in the scientific community that the best option for such a facility would be a deep underground repository. Fifteen years ago, Congress directed the Secretary of Energy to investigate and recommend to the President whether such a repository could be located safely at Yucca Mountain, Nevada. Since then, our country has spent billions of dollars and millions of hours of research endeavoring to answer this question. I have carefully reviewed the product of this study. In my judgment, it constitutes sound science and shows that a safe repository can be sited there. I also believe that compelling national interests counsel in favor of proceeding with this project. Accordingly, consistent with my responsibilities under the NWPA, today I am recommending that Yucca Mountain be developed as the site for an underground repository for spent fuel and other radioactive wastes. The first consideration in my decision was whether the Yucca Mountain site will safeguard the health and safety of the people, in Nevada and across the country, and will be effective in containing at minimum risk the material it is designed to hold. Substantial evidence shows that it will. Yucca Mountain is far and away the most thoroughly researched site of its kind in the world. It is a geologically stable site, in a closed groundwater basin, isolated on thousands of acres of Federal land, and farther from any metropolitan area than the great majority of less secure, temporary nuclear waste storage sites that exist in the country today. This point bears emphasis. We are not confronting a hypothetical problem. We have a staggering amount of

  2. The Role of the Environmental Management Site Specific Advisory Board under the Federal Advisory Committee Act, With Emphasis on the Northern New Mexico Citizens' Advisory Board - 12482

    SciTech Connect

    Santistevan, Menice B.

    2012-07-01

    The Environmental Management Site Specific Advisory Board (EM SSAB) is comprised of eight Citizens' Advisory Boards, chartered under the Federal Advisory Committee Act (FACA) by the Assistant Secretary for Environmental Management for the U. S. Department of Energy (DOE). The purpose of the EM SSAB is to provide the DOE with recommendations regarding Environmental Management issues from legacy waste produced at major sites across the DOE Complex. The Northern New Mexico Citizens' Advisory Board (NNMCAB) is the site specific advisory board to the DOE on issues of environmental monitoring, remediation, waste management and long-term stewardship at Los Alamos National Laboratory (LANL). The other boards are located at: Hanford, Idaho, Nevada, Paducah, Portsmouth, Oak Ridge and Savannah River. Using broad citizen outreach and input, the SSAB provides an official mechanism for the citizenry at each of these sites to monitor current activities affecting the region and also to have input into the prioritization of future activities. 'The mission of the EM SSAB is to more directly involve stakeholders in EM Planning and decision-making processes for the nuclear weapons complex cleanup. DOE has various means of involving the public in its planning and decision-making processes; the EM SSAB is only one component of EM's public participation program, and is not intended to be an exclusive means of public participation. It is the policy of DOE and EM to conduct it programs in an open and responsive manner, thereby encouraging and providing the opportunity for public participation in its planning and decision-making processes. EM SSAB members are appointed to a two year term and may serve up to three terms. During this time, members are able to hear many presentation from subject matter experts, attend several site tours at their site and across the DOE complex and are able to express their concerns and give input to the prioritization of clean up at each site. It is an

  3. cis-Acting sequences in addition to donor and acceptor sites are required for template switching during synthesis of plus-strand DNA for duck hepatitis B virus.

    PubMed Central

    Havert, M B; Loeb, D D

    1997-01-01

    A characteristic of all hepadnaviruses is the relaxed-circular conformation of the DNA genome within an infectious virion. Synthesis of the relaxed-circular genome by reverse transcription requires three template switches. These template switches, as for the template switches or strand transfers of other reverse-transcribing genetic elements, require repeated sequences (the donor and acceptor sites) between which a complementary strand of nucleic acid is transferred. The mechanism for each of the template switches in hepadnaviruses is poorly understood. To determine whether sequences other than the donor and acceptor sites are involved in the template switches of duck hepatitis B virus (DHBV), a series of molecular clones which express viral genomes bearing deletion mutations were analyzed. We found that three regions of the DHBV genome, which are distinct from the donor and acceptor sites, are required for the synthesis of relaxed-circular DNA. One region, located near the 3' end of the minus-strand template, is required for the template switch that circularizes the genome. The other two regions, located in the middle of the genome and near DR2, appear to be required for plus-strand primer translocation. We speculate that these cis-acting sequences may play a role in the organization of the minus-strand DNA template within the capsid particle so that it supports efficient template switching during plus-strand DNA synthesis. PMID:9188603

  4. Single-site access robot-assisted epicardial mapping with a snake robot: preparation and first clinical experience.

    PubMed

    Neuzil, Petr; Cerny, Stepan; Kralovec, Stepan; Svanidze, Oleg; Bohuslavek, Jan; Plasil, Petr; Jehlicka, Pavel; Holy, Frantisek; Petru, Jan; Kuenzler, Richard; Sediva, Lucie

    2013-06-01

    CardioARM, a highly flexible "snakelike" medical robotic system (Medrobotics, Raynham, MA), has been developed to allow physicians to view, access, and perform complex procedures intrapericardially on the beating heart through a single-access port. Transthoracic epicardial catheter mapping and ablation has emerged as a strategy to treat arrhythmias, particularly ventricular arrhythmias, originating from the epicardial surface. The aim of our investigation was to determine whether the CardioARM could be used to diagnose and treat ventricular tachycardia (VT) of epicardial origin. Animal and clinical studies of the CardioARM flexible robot were performed in hybrid surgical-electrophysiology settings. In a porcine model study, single-port pericardial access, navigation, mapping, and ablation were performed in nine animals. The device was then used in a small, single-center feasibility clinical study. Three patients, all with drug-refractory VT and multiple failed endocardial ablation attempts, underwent epicardial mapping with the flexible robot. In all nine animals, navigation, mapping, and ablation were successful without hemodynamic compromise. In the human study, all three patients demonstrated a favorable safety profile, with no major adverse events through a 30-day follow-up. Two cases achieved technical success, in which an electroanatomic map of the epicardial ventricle surface was created; in the third case, blood obscured visualization. These results, although based on a limited number of experimental animals and patients, show promise and suggest that further clinical investigation on the use of the flexible robot in patients requiring epicardial mapping of VT is warranted.

  5. Meta-diamide insecticides acting on distinct sites of RDL GABA receptor from those for conventional noncompetitive antagonists.

    PubMed

    Nakao, Toshifumi; Banba, Shinich; Nomura, Michikazu; Hirase, Kangetsu

    2013-04-01

    The RDL GABA receptor is an attractive target of insecticides. Here we demonstrate that meta-diamides [3-benzamido-N-(4-(perfluoropropan-2-yl)phenyl)benzamides] are a distinct class of RDL GABA receptor antagonists showing high insecticidal activity against Spodoptera litura. We also suggest that the mode of action of the meta-diamides is distinct from that of conventional noncompetitive antagonists (NCAs), such as fipronil, picrotoxin, lindane, dieldrin, and α-endosulfan. Using a membrane potential assay, we examined the effects of the meta-diamide 3-benzamido-N-(2-bromo-4-(perfluoropropan-2-yl)-6-(trifluoromethyl)phenyl)-2-fluorobenzamide (meta-diamide 7) and NCAs on mutant Drosophila RDL GABA receptors expressed in Drosophila Mel-2 cells. NCAs had little or no inhibitory activity against at least one of the three mutant receptors (A2'S, A2'G, and A2'N), which were reported to confer resistance to NCAs. In contrast, meta-diamide 7 inhibited all three A2' mutant receptors, at levels comparable to its activity with the wild-type receptor. Furthermore, the A2'S·T6'V mutation almost abolished the inhibitory effects of all NCAs. However, meta-diamide 7 inhibited the A2'S・T6'S mutant receptor at the same level as its activity with the wild-type receptor. In contrast, a G336M mutation in the third transmembrane domain of the RDL GABA receptor abolished the inhibitory activities of meta-diamide 7, although the G336M mutation had little effect on the inhibitory activities of conventional NCAs. Molecular modeling studies also suggested that the binding site of meta-diamides was different from those of NCAs. Meta-diamide insecticides are expected to be prominent insecticides effective against A2' mutant RDL GABA receptors with a different mode of action.

  6. Improved binding site assignment by high-resolution mapping of RNA-protein interactions using iCLIP.

    PubMed

    Hauer, Christian; Curk, Tomaz; Anders, Simon; Schwarzl, Thomas; Alleaume, Anne-Marie; Sieber, Jana; Hollerer, Ina; Bhuvanagiri, Madhuri; Huber, Wolfgang; Hentze, Matthias W; Kulozik, Andreas E

    2015-08-11

    Individual-nucleotide resolution crosslinking and immunoprecipitation (iCLIP) allows the determination of crosslinking sites of RNA-binding proteins (RBPs) on RNAs. iCLIP is based on ultraviolet light crosslinking of RBPs to RNA, reverse transcription and high-throughput sequencing of fragments terminating at the site of crosslinking. As a result, start sites of iCLIP fragments are expected to cluster with a narrow distribution, typically representing the site of direct interaction between the RBP and the RNA. Here we show that for several RBPs (eIF4A3, PTB, SRSF3, SRSF4 and hnRNP L), the start sites of iCLIP fragments show a fragment length-dependent broader distribution that can be shifted to positions upstream of the known RNA-binding site. We developed an analysis tool that identifies these shifts and can improve the positioning of RBP binding sites.

  7. Rivastigmine Alleviates Experimentally Induced Colitis in Mice and Rats by Acting at Central and Peripheral Sites to Modulate Immune Responses

    PubMed Central

    Shifrin, Helena; Nadler-Milbauer, Mirela; Shoham, Shai; Weinstock, Marta

    2013-01-01

    The cholinergic anti-inflammatory system and α7 nicotinic receptors in macrophages have been proposed to play a role in neuroimmunomodulation and in the etiology of ulcerative colitis. We investigated the ability of a cholinesterase (ChE) inhibitor rivastigmine, to improve the pathology of ulcerative colitis by increasing the concentration of extracellular acetylcholine in the brain and periphery. In combination with carbachol (10 µM), rivastigmine (1 µM) significantly decreased the release of nitric oxide, TNF-α, IL-1β and IL-6 from lipopolysaccharide-activated RAW 264.7 macrophages and this effect was abolished by α7 nicotinic receptor blockade by bungarotoxin. Rivastigmine (1 mg/kg) but not (0.5 mg/kg), injected subcutaneously once daily in BALB/c mice with colitis induced by 4% dextran sodium sulphate (DSS), reduced the disease activity index (DAI) by 60% and damage to colon structure. Rivastigmine (1 mg/kg) also reduced myeloperoxidase activity and IL-6 by >60%, and the infiltration of CD11b expressing cells by 80%. These effects were accompanied by significantly greater ChE inhibition in cortex, brain stem, plasma and colon than that after 0.5 mg/kg. Co-administration of rivastigmine (1 mg/kg) with the muscarinic antagonist scopolamine significantly increased the number of CD11b expressing cells in the colon but did not change DAI compared to those treated with rivastigmine alone. Rivastigmine 1 and 2 mg given rectally to rats with colitis induced by rectal administration of 30 mg dintrobezene sulfonic acid (DNBS) also caused a dose related reduction in ChE activity in blood and colon, the number of ulcers and area of ulceration, levels of TNF-α and in MPO activity. The study revealed that the ChE inhibitor rivastigmine is able to reduce gastro-intestinal inflammation by actions at various sites at which it preserves ACh. These include ACh released from vagal nerve endings that activates alpha7 nicotinic receptors on circulating macrophages and in

  8. Mapping the RNA binding sites for human immunodeficiency virus type-1 gag and NC proteins within the complete HIV-1 and -2 untranslated leader regions.

    PubMed Central

    Damgaard, C K; Dyhr-Mikkelsen, H; Kjems, J

    1998-01-01

    Encapsidation of HIV-1 genomic RNA is mediated by specific interactions between the RNA packaging signal and the Gag protein. During maturation of the virion, the Gag protein is processed into smaller fragments, including the nucleocapsid (NC) domain which remains associated with the viral genomic RNA. We have investigated the binding of glutathione- S -transferase (GST) Gag and NC fusion proteins from HIV-1, to the entire HIV-1 and -2 leader RNAencompassing the packaging signal. We have mapped the binding sites at conditions where only about two complexes are formed and find that GST-Gag and GST-NC fusion proteins bind specifically to discrete sites within the leader. Analysis of the HIV-1 leader indicated that GST-Gag strongly associates with the PSI stem-loop and to a lesser extent with regions near the primer binding site. GST-NC binds the same regions but with reversed preferences. The HIV-1 proteins also interact specifically with the 5'-leader of HIV-2 and the major site of interaction mapped to a stem-loop, with homology to the HIV-1 PSI stem-loop structure. The different specificities of Gag and NC may reflect functionally distinct roles in the viral replication, and suggest that the RNA binding specificity of NC is modulated by its structural context. PMID:9685481

  9. Post-Closure Report for Closed Resource Conservation and Recovery Act Corrective Action Units, Nevada National Security Site, Nevada, For Fiscal Year 2010

    SciTech Connect

    NSTec Environmental Management

    2011-01-26

    This report serves as the combined annual report for post-closure activities for the following closed Corrective Action Units (CAUs): (1) CAU 90, Area 2 Bitcutter Containment; (2) CAU 91, Area 3 U-3fi Injection Well; (3) CAU 92, Area 6 Decon Pond Facility; (4) CAU 110, Area 3 WMD U-3ax/bl Crater; and (5) CAU 112, Area 23 Hazardous Waste Trenches. The locations of the sites are shown in Figure 1. This report covers fiscal year 2010 (October 2009-September 2010). The post-closure requirements for these sites are described in Resource Conservation and Recovery Act Permit Number NEV HW0021 and summarized in each CAU-specific section in Section 1.0 of this report. Site inspections are conducted semiannually at CAUs 90 and 91 and quarterly at CAUs 92, 110, and 112. Additional inspections are conducted at CAU 92 if precipitation occurs in excess of 0.50 inches in a 24-hour period. Inspections include an evaluation of the condition of the units and identification of any deficiencies that may compromise the integrity of the units. The condition of covers, fencing, signs, gates, and locks is documented. In addition, soil moisture monitoring and subsidence surveys are conducted at CAU 110. The results of the inspections, summary of maintenance activities, results of vegetations surveys, and analysis of monitoring data are presented in this report. Copies of the inspection checklists are included as Appendix A. Field notes completed during each inspection are included in Appendix B. Photographs taken during the site inspections are included in Appendix C.

  10. Role of cis-acting sites in stimulation of the phage λ P(RM) promoter by CI-mediated looping.

    PubMed

    Michalowski, Christine B; Little, John W

    2013-08-01

    The lysogenic state of phage λ is maintained by the CI repressor. CI binds to three operators each in the right operator (O(R)) and left operator (O(L)) regions, which lie 2.4 kb apart. At moderate CI levels, the predominant binding pattern is two dimers of CI bound cooperatively at each regulatory region. The resulting tetramers can then interact, forming an octamer and a loop of the intervening DNA. CI is expressed from the P(RM) promoter, which lies in the O(R) region and is subjected to multiple regulatory controls. Of these, the most recently discovered is stimulation by loop formation. In this work, we have investigated the mechanism by which looping stimulates P(RM). We find that two cis-acting sites lying in the O(L) region are involved. One site, an UP element, is required for stimulation. Based on the behavior of other promoters with UP elements located upstream of the -35 region, we suggest that a subunit of RNA polymerase (RNAP) bound at P(RM) binds to the UP element located in the O(L) region. In addition, adjacent to the UP element lies a binding site for integration host factor (IHF); this site plays a less critical role but is required for stimulation of the weak prm240 allele. A loop with CI at the O(L)2 and O(L)3 operators does not stimulate P(RM), while one with CI only at O(L)2 provides some stimulation. We discuss possible mechanisms for stimulation. PMID:23708136

  11. Post-Closure Report for Closed Resource Conservation and Recovery Act Corrective Action Units, Nevada Test Site, Nevada, For Fiscal Year 2008 (October 2007-September 2008)

    SciTech Connect

    NSTec Environmental Restoration

    2008-12-23

    This report is the first combined annual report for post-closure activities for the following closed Corrective Action Units (CAUs): • CAU 90, Area 2 Bitcutter Containment • CAU 91, Area 3 U-3fi Injection Well • CAU 92, Area 6 Decon Pond Facility • CAU 110, Area 3 WMD U-3ax/bl Crater • CAU 112, Area 23 Hazardous Waste Trenches The locations of the sites are shown in Figure 1. This report covers fiscal year (FY) 2008 (October 2007–September 2008). Because this is the first combined annual report for these CAUs, this report only covers the period not covered in the previous annual report for each CAU. For example, the last report submitted for CAU 91 covered the period January 2007–December 2007; therefore, this report only covers the remainder of FY2008 (January 2008–September 2008) for CAU 91. The post-closure requirements for these sites are described in Resource Conservation and Recovery Act Permit Number NEV HW0021 and summarized in each CAU-specific section in Section 1.0 of this report. Site inspections are conducted semiannually at CAUs 90 and 91 and quarterly at CAUs 92, 110, and 112. Additional inspections are conducted at CAU 92 if precipitation occurs in excess of 0.50 inches in a 24-hour period. Inspections include an evaluation of the condition of the units and identification of any deficiencies that may compromise the integrity of the units. The condition of covers, fencing, signs, gates, and locks is documented. In addition, soil moisture monitoring and subsidence surveys are conducted at CAU 110. The results of the inspections, summary of maintenance activities, results of vegetations surveys, and analysis of monitoring data are presented in this report. Copies of the inspection checklists are included as Appendix A. Field notes completed during each inspection are included in Appendix B. Photographs taken during the site inspections are included in Appendix C.

  12. Functional polarization of the Escherichia coli chromosome terminus: the dif site acts in chromosome dimer resolution only when located between long stretches of opposite polarity.

    PubMed

    Pérals, K; Cornet, F; Merlet, Y; Delon, I; Louarn, J M

    2000-04-01

    In Escherichia coli, chromosome dimers are generated by recombination between circular sister chromosomes. Dimers are lethal unless resolved by a system that involves the XerC, XerD and FtsK proteins acting at a site (dif) in the terminus region. Resolution fails if dif is moved from its normal position. To analyse this positional requirement, dif was transplaced to a variety of positions, and deletions and inversions of portions of the dif region were constructed. Resolution occurs only when dif is located at the convergence of multiple, oppositely polarized DNA sequence elements, inferred to lie in the terminus region. These polar elements may position dif at the cell septum and be general features of chromosome organization with a role in nucleoid dynamics.

  13. P-SAMS: a web site for plant artificial microRNA and synthetic trans-acting small interfering RNA design

    PubMed Central

    Fahlgren, Noah; Hill, Steven T.; Carrington, James C.; Carbonell, Alberto

    2016-01-01

    Summary: The Plant Small RNA Maker Site (P-SAMS) is a web tool for the simple and automated design of artificial miRNAs (amiRNAs) and synthetic trans-acting small interfering RNAs (syn-tasiRNAs) for efficient and specific targeted gene silencing in plants. P-SAMS includes two applications, P-SAMS amiRNA Designer and P-SAMS syn-tasiRNA Designer. The navigation through both applications is wizard-assisted, and the job runtime is relatively short. Both applications output the sequence of designed small RNA(s), and the sequence of the two oligonucleotides required for cloning into ‘B/c’ compatible vectors. Availability and implementation: The P-SAMS website is available at http://p-sams.carringtonlab.org. Contact: acarbonell@ibmcp.upv.es or nfahlgren@danforthcenter.org PMID:26382195

  14. Predicted hexameric structure of the Agrobacterium VirB4 C terminus suggests VirB4 acts as a docking site during type IV secretion

    PubMed Central

    Middleton, Rebecca; Sjölander, Kimmen; Krishnamurthy, Nandini; Foley, Jonathan; Zambryski, Patricia

    2005-01-01

    The Agrobacterium T-DNA transporter belongs to a growing class of evolutionarily conserved transporters, called type IV secretion systems (T4SSs). VirB4, 789 aa, is the largest T4SS component, providing a rich source of possible structural domains. Here, we use a variety of bioinformatics methods to predict that the C-terminal domain of VirB4 (including the Walker A and B nucleotide-binding motifs) is related by divergent evolution to the cytoplasmic domain of TrwB, the coupling protein required for conjugative transfer of plasmid R388 from Escherichia coli. This prediction is supported by detailed sequence and structure analyses showing conservation of functionally and structurally important residues between VirB4 and TrwB. The availability of a solved crystal structure for TrwB enables the construction of a comparative model for VirB4 and the prediction that, like TrwB, VirB4 forms a hexamer. These results lead to a model in which VirB4 acts as a docking site at the entrance of the T4SS channel and acts in concert with VirD4 and VirB11 to transport substrates (T-strand linked to VirD2 or proteins such as VirE2, VirE3, or VirF) through the T4SS. PMID:15668378

  15. Geologic map of the southern Funeral Mountains including nearby groundwater discharge sites in Death Valley National Park, California and Nevada

    USGS Publications Warehouse

    Fridrich, C.J.; Thompson, R.A.; Slate, J.L.; Berry, M.E.; Machette, M.N.

    2012-01-01

    This 1:50,000-scale geologic map covers the southern part of the Funeral Mountains, and adjoining parts of four structural basins—Furnace Creek, Amargosa Valley, Opera House, and central Death Valley—in California and Nevada. It extends over three full 7.5-minute quadrangles, and parts of eleven others—an area of about 1,000 square kilometers (km2). The boundaries of this map were drawn to include all of the known proximal hydrogeologic features that may affect the flow of groundwater that discharges from springs of the Furnace Creek basin, in the west-central part of the map. These springs provide the main potable water supply for Death Valley National Park. Major hydrogeologic features shown on this map include: (1) springs of the Furnace Creek basin, (2) a large Pleistocene groundwater discharge mound in the northeastern part of the map, (3) the exposed extent of limestones and dolomites that constitute the Paleozoic carbonate aquifer, and (4) the exposed extent of the alluvial conglomerates that constitute the Funeral Formation aquifer.

  16. Wingless-type MMTV integration site family member 2 (WNT2) gene is associated with resistance to MAP in faecal culture and antibody response in Holstein cattle.

    PubMed

    Pauciullo, A; Küpper, J; Brandt, H; Donat, K; Iannuzzi, L; Erhardt, G

    2015-04-01

    Mycobacterium avium subspecies paratuberculosis (MAP) is a pathogenic bacterium responsible for the lethal Johne's disease in cattle. So far, several genome-wide association studies (GWAS) have been carried out to identify chromosomal regions highly associated with Johne's disease. The aim of this study was to investigate the genetic variability within a pool of seven genes (LAMB1, DLD, WNT2, PRDM1, SOCS5, PTGER4 and IL10) indicated by former GWAS/RNA-Seq studies as putatively associated with MAP infections and to achieve a confirmation study of association with paratuberculosis susceptibility in a population of 324 German Holstein cattle (162 cases MAP positive and 162 controls MAP negative) using ELISA and fecal cultural tests. SNP validation and genotyping information are provided, quick methods for allelic discrimination were set up and transcription factor binding analyses were performed. The rs43390642:G>TSNP in the WNT2 promoter region is associated with paratuberculosis susceptibility (P = 0.013), suggesting a protective role of the T allele (P = 0.043; odds ratio 0.50 [0.25-0.97]). The linkage disequilibrium with the DLD rs134692583:A>T might suggest a combined mechanism of action of these neighboring genes in resistance to MAP infection, which is also supported by a significant effect shown by the haplotype DLD(T) /WNT2(T) (P = 0.047). In silico analysis predicted rs43390642:G>T and rs134692583:A>T as essential parts of binding sites for the transcription factors GR, C/EBPβ and GATA-1, hence suggesting a potential influence on WNT2 and DLD gene expression. This study confirmed the region on BTA 4 (UMD 3.1: 50639460-51397892) as involved in tolerance/resistance to Johne's disease. In addition, this study clarifies the involvement of the investigated genes in MAP infection and contributes to the understanding of genetic variability involved in Johne's disease susceptibility.

  17. Hydrothermal Plume Mapping Along the Hotspot-affected Galapagos Spreading Center Finds High-Temperature Vent Sites are Anomalously Scarce

    NASA Astrophysics Data System (ADS)

    Baker, E. T.; Resing, J. A.; Walker, S. L.; Lebon, G. T.; Nakamura, K.; Haymon, R. M.; White, S. M.; MacDonald, K. C.

    2006-12-01

    Systematic searches for hydrothermal activity along midocean ridges (MORs) demonstrate that the spatial density of hydrothermal activity is a robust linear function of spreading rate. This trend argues that the availability of mantle heat is the first order control on the distribution of seafloor vent fields. However, some crustal thermal models predict that the thicker, hotter, more ductile crust associated with hotspots substantially reduces convective hydrothermal cooling, explaining observations of axial magma chambers (AMC) at shallower depths than found on normal MORs. In Dec-Jan 2006 we tested this hypothesis by mapping hydrothermal plumes overlying the hotspot-affected Galapagos Spreading Center (GSC) from 95°-89.6°W, using a dual-pass, side-scan deep tow with an array of plume sensors spanning 50- 250 m above bottom. The western GSC near 91°-92.5°W has axial-high morphology, shallow and quasi-continuous AMC, and thick (8 km) crust, changing to a transitional morphology, deeper and more discontinuous AMC, and normal (6 km) crust from 93° to 95°W. The eastern GSC, 90.5°- 89.6°W is also an axial high and presumably has crustal characteristics similar to the western GSC at 91°-92.5°W. We identified hydrothermal plumes by anomalies in light backscattering (NTU) from a vertical array of MAPR sensors along the tow line, plus redox potential (Eh) measured continuously in-situ on the tow body at a nominal elevation of 100 m. Many plumes were subsequently confirmed by CTD tows and sampling. Only three areas of extensive and intense plumes were observed: 90.52°-90.63°W, 91.78°- 91.96°W, and 94°-94.1°W. Maximum plume rise at the latter two sites exceeded 200 m, indicative of high-temperature venting that was confirmed by camera tows. Some 25 other NTU and Eh anomalies were detected along ~1000 km of trackline, but none were >5 km in length. The primary result of our survey is that hydrothermal plumes were scarce for a ridge spreading at ~60 mm

  18. Genome wide association mapping of grain arsenic, copper, molybdenum and zinc in rice (Oryza sativa L.) grown at four international field sites.

    PubMed

    Norton, Gareth J; Douglas, Alex; Lahner, Brett; Yakubova, Elena; Guerinot, Mary Lou; Pinson, Shannon R M; Tarpley, Lee; Eizenga, Georgia C; McGrath, Steve P; Zhao, Fang-Jie; Islam, M Rafiqul; Islam, Shofiqul; Duan, Guilan; Zhu, Yongguan; Salt, David E; Meharg, Andrew A; Price, Adam H

    2014-01-01

    The mineral concentrations in cereals are important for human health, especially for individuals who consume a cereal subsistence diet. A number of elements, such as zinc, are required within the diet, while some elements are toxic to humans, for example arsenic. In this study we carry out genome-wide association (GWA) mapping of grain concentrations of arsenic, copper, molybdenum and zinc in brown rice using an established rice diversity panel of ∼ 300 accessions and 36.9 k single nucleotide polymorphisms (SNPs). The study was performed across five environments: one field site in Bangladesh, one in China and two in the US, with one of the US sites repeated over two years. GWA mapping on the whole dataset and on separate subpopulations of rice revealed a large number of loci significantly associated with variation in grain arsenic, copper, molybdenum and zinc. Seventeen of these loci were detected in data obtained from grain cultivated in more than one field location, and six co-localise with previously identified quantitative trait loci. Additionally, a number of candidate genes for the uptake or transport of these elements were located near significantly associated SNPs (within 200 kb, the estimated global linkage disequilibrium previously employed in this rice panel). This analysis highlights a number of genomic regions and candidate genes for further analysis as well as the challenges faced when mapping environmentally-variable traits in a highly genetically structured diversity panel. PMID:24586963

  19. Genome Wide Association Mapping of Grain Arsenic, Copper, Molybdenum and Zinc in Rice (Oryza sativa L.) Grown at Four International Field Sites

    PubMed Central

    Norton, Gareth J.; Douglas, Alex; Lahner, Brett; Yakubova, Elena; Guerinot, Mary Lou; Pinson, Shannon R. M.; Tarpley, Lee; Eizenga, Georgia C.; McGrath, Steve P.; Zhao, Fang-Jie; Islam, M. Rafiqul; Islam, Shofiqul; Duan, Guilan; Zhu, Yongguan; Salt, David E.; Meharg, Andrew A.; Price, Adam H.

    2014-01-01

    The mineral concentrations in cereals are important for human health, especially for individuals who consume a cereal subsistence diet. A number of elements, such as zinc, are required within the diet, while some elements are toxic to humans, for example arsenic. In this study we carry out genome-wide association (GWA) mapping of grain concentrations of arsenic, copper, molybdenum and zinc in brown rice using an established rice diversity panel of ∼300 accessions and 36.9 k single nucleotide polymorphisms (SNPs). The study was performed across five environments: one field site in Bangladesh, one in China and two in the US, with one of the US sites repeated over two years. GWA mapping on the whole dataset and on separate subpopulations of rice revealed a large number of loci significantly associated with variation in grain arsenic, copper, molybdenum and zinc. Seventeen of these loci were detected in data obtained from grain cultivated in more than one field location, and six co-localise with previously identified quantitative trait loci. Additionally, a number of candidate genes for the uptake or transport of these elements were located near significantly associated SNPs (within 200 kb, the estimated global linkage disequilibrium previously employed in this rice panel). This analysis highlights a number of genomic regions and candidate genes for further analysis as well as the challenges faced when mapping environmentally-variable traits in a highly genetically structured diversity panel. PMID:24586963

  20. The Abandoned E-Waste Recycling Site Continued to Act As a Significant Source of Polychlorinated Biphenyls: An in Situ Assessment Using Fugacity Samplers.

    PubMed

    Wang, Yan; Luo, Chunling; Wang, Shaorui; Cheng, Zhineng; Li, Jun; Zhang, Gan

    2016-08-16

    The recycling of e-waste has attracted significant attention due to emissions of polychlorinated biphenyls (PCBs) and other contaminants into the environment. We measured PCB concentrations in surface soils, air equilibrated with the soil, and air at 1.5-m height using a fugacity sampler in an abandoned electronic waste (e-waste) recycling site in South China. The total concentrations of PCBs in the soils were 39.8-940 ng/g, whereas the concentrations in air equilibrated with the soil and air at 1.5 m height were 487-8280 pg/m(3) and 287-7380 pg/m(3), respectively. The PCB concentrations displayed seasonal variation; they were higher in winter in the soils and higher in summer in the air, indicating that the emission of PCBs from the soil was enhanced during hot seasons for the relatively high temperature or additional sources, especially for low-chlorinated PCBs. We compared two methods (traditional fugacity model and fugacity sampler) for assessing the soil-air partition coefficients (Ksa) and the fugacity fractions of PCBs. The results suggested that the fugacity sampler provided more instructive and practical estimation on Ksa values and trends in air-soil exchange, especially for low-chlorinated PCBs. The abandoned e-waste burning site still acted as a significant source of PCBs many years after the prohibition on open burning. PMID:27427439

  1. Orbital-science investigation: Part H: sketch map of the region around the candidate Littrow Apollo landing sites

    USGS Publications Warehouse

    Carr, M.H.

    1972-01-01

    The photograph in figure 25-59 and the corresponding map (fig. 25-60) show the geology of part of the lunar surface just east of the Littrow rilles at the eastern edge of Mare Serenitatis. The most striking feature of the region is the extremely low albedo of the area mapped as Eld in the western half of the map. The low albedo is believed to be caused by a thin layer of pyroclastic volcanic material at the surface. Another notable feature is the fresh-appearing ridges that cross the mare and the adjacent terra. The fine-braided texture of these ridges contrasts markedly with the rounded, subdued topography more common to such features, an indication that the ridges here may be unusually young. Also evident is a well-exposed succession of marelike plains units, which probably represent different stages in the filling of the Serenitatis basin. Several sets of rilles are present; most are roughly tangential to the basin and terminate against the different plains units according to the relative ages. In the northwest corner of the map is a relatively fresh volcanic crater chain (Cch) from which material appears to have been ejected over the surrounding terrain, forming rays of volcanic ejecta. The area thus includes an unusually wide variety of lunar features.

  2. Hydrologic index development and application to selected Coastwide Reference Monitoring System sites and Coastal Wetlands Planning, Protection and Restoration Act projects

    USGS Publications Warehouse

    Snedden, Gregg A.; Swenson, Erick M.

    2012-01-01

    Hourly time-series salinity and water-level data are collected at all stations within the Coastwide Reference Monitoring System (CRMS) network across coastal Louisiana. These data, in addition to vegetation and soils data collected as part of CRMS, are used to develop a suite of metrics and indices to assess wetland condition in coastal Louisiana. This document addresses the primary objectives of the CRMS hydrologic analytical team, which were to (1) adopt standard time-series analytical techniques that could effectively assess spatial and temporal variability in hydrologic characteristics across the Louisiana coastal zone on site, project, basin, and coastwide scales and (2) develop and apply an index based on wetland hydrology that can describe the suitability of local hydrology in the context of maximizing the productivity of wetland plant communities. Approaches to quantifying tidal variability (least squares harmonic analysis) and partitioning variability of time-series data to various time scales (spectral analysis) are presented. The relation between marsh elevation and the tidal frame of a given hydrograph is described. A hydrologic index that integrates water-level and salinity data, which are collected hourly, with vegetation data that are collected annually is developed. To demonstrate its utility, the hydrologic index is applied to 173 CRMS sites across the coast, and variability in index scores across marsh vegetation types (fresh, intermediate, brackish, and saline) is assessed. The index is also applied to 11 sites located in three Coastal Wetlands Planning, Protection and Restoration Act projects, and the ability of the index to convey temporal hydrologic variability in response to climatic stressors and restoration measures, as well as the effect that this community may have on wetland plant productivity, is illustrated.

  3. Post-Closure Report for Closed Resource Conservation and Recovery Act Corrective Action Units, Nevada Test Site, Nevada, for Fiscal Year 2009

    SciTech Connect

    NSTec Environmental Restoration

    2010-01-31

    This report serves as the combined annual report for post-closure activities for the following closed Corrective Action Units (CAUs): · CAU 90, Area 2 Bitcutter Containment · CAU 91, Area 3 U-3fi Injection Well · CAU 92, Area 6 Decon Pond Facility · CAU 110, Area 3 WMD U-3ax/bl Crater · CAU 112, Area 23 Hazardous Waste Trenches This report covers fiscal year 2009 (October 2008–September 2009). The post-closure requirements for these sites are described in Resource Conservation and Recovery Act Permit Number NEV HW0021 and summarized in each CAU-specific section in Section 1.0 of this report. Site inspections are conducted semiannually at CAUs 90 and 91 and quarterly at CAUs 92, 110, and 112. Additional inspections are conducted at CAU 92 if precipitation occurs in excess of 0.50 inches in a 24-hour period. Inspections include an evaluation of the condition of the units and identification of any deficiencies that may compromise the integrity of the units. The condition of covers, fencing, signs, gates, and locks is documented. In addition, soil moisture monitoring and subsidence surveys are conducted at CAU 110. The results of the inspections, summary of maintenance activities, results of vegetations surveys, and analysis of monitoring data are presented in this report. Copies of the inspection checklists are included as Appendix A. Field notes completed during each inspection are included in Appendix B. Photographs taken during the site inspections are included in Appendix C.

  4. Classification and comparison of ligand-binding sites derived from grid-mapped knowledge-based potentials.

    PubMed

    Hoppe, Christian; Steinbeck, Christoph; Wohlfahrt, Gerd

    2006-03-01

    We describe the application of knowledge-based potentials implemented in the MOE program to compare the ligand-binding sites of several proteins. The binding probabilities for a polar and a hydrophobic probe are calculated on a grid to allow easy comparison of binding sites of superimposed related proteins. The method is fast and simple enough to simultaneously use structural information of multiple proteins of a target family. The method can be used to rapidly cluster proteins into subfamilies according to the similarity of hydrophobic and polar fields of their ligand-binding sites. Regions of the binding site which are common within a protein family can be identified and analysed for the design of family-targeted libraries or those which differ for improvement of ligand selectivity. The field-based hierarchical clustering is demonstrated for three protein families: the ligand-binding domains of nuclear receptors, the ATP-binding sites of protein kinases and the substrate binding sites of proteases. More detailed comparisons are presented for serine proteases of the chymotrypsin family, for the peroxisome proliferator-activated receptor subfamily of nuclear receptors and for progesterone and androgen receptor. The results are in good accordance with structure-based analysis and highlight important differences of the binding sites, which have been also described in the literature.

  5. Comprehensive mapping of the human papillomavirus (HPV) DNA integration sites in cervical carcinomas by HPV capture technology

    PubMed Central

    Xu, Ruiping; Ke, Yang

    2016-01-01

    Integration of human papillomavirus (HPV) DNA into the host genome can be a driver mutation in cervical carcinoma. Identification of HPV integration at base resolution has been a longstanding technical challenge, largely due to sensitivity masking by HPV in episomes or concatenated forms. The aim was to enhance the understanding of the precise localization of HPV integration sites using an innovative strategy. Using HPV capture technology combined with next generation sequencing, HPV prevalence and the exact integration sites of the HPV DNA in 47 primary cervical cancer samples and 2 cell lines were investigated. A total of 117 unique HPV integration sites were identified, including HPV16 (n = 101), HPV18 (n = 7), and HPV58 (n = 9). We observed that the HPV16 integration sites were broadly located across the whole viral genome. In addition, either single or multiple integration events could occur frequently for HPV16, ranging from 1 to 19 per sample. The viral integration sites were distributed across almost all the chromosomes, except chromosome 22. All the cervical cancer cases harboring more than four HPV16 integration sites showed clinical diagnosis of stage III carcinoma. A significant enrichment of overlapping nucleotides shared between the human genome and HPV genome at integration breakpoints was observed, indicating that it may play an important role in the HPV integration process. The results expand on knowledge from previous findings on HPV16 and HPV18 integration sites and allow a better understanding of the molecular basis of the pathogenesis of cervical carcinoma. PMID:26735580

  6. "Where On Mars?": A Web Map Visualisation of the ExoMars 2018 Rover Candidate Landing Sites

    NASA Astrophysics Data System (ADS)

    Manaud, N.; Boix, O.; Vago, J.; Hill, A.; Iriberri, C.; Carrión, D.

    2015-10-01

    The ExoMars 2018 mission will deliver a European rover and a Russian surface platform to the surface of Mars. Armed with a drill that can bore 2 metres into rock, the ExoMars rover will travel across the Martian surface to search for signs of life, past or present. But where on Mars to land? - The search for a suitable ExoMars rover landing site began in December 2013, when the planetary science community was asked to propose candidates. Eight proposals were considered during a workshop held by the ExoMars Landing Site Selection Working Group (LSSWG). By the end of the workshop, there were four clear front-runners. Following additional review, the four sites have now been formally recommended for further detailed analysis [1]: Mawrth Vallis, Oxia Planum, Hypanis Vallis and Aram Dorsum. Scientists will continue working on the characterisation of these four sites until they provide their final recommendation in October 2017.

  7. Digital Isostatic Gravity Map of the Nevada Test Site and Vicinity, Nye, Lincoln, and Clark Counties, Nevada, and Inyo County, California

    USGS Publications Warehouse

    Ponce, David A.; Mankinen, E.A.; Davidson, J.G.; Morin, R.L.; Blakely, R.J.

    2000-01-01

    An isostatic gravity map of the Nevada Test Site area was prepared from publicly available gravity data (Ponce, 1997) and from gravity data recently collected by the U.S. Geological Survey (Mankinen and others, 1999; Morin and Blakely, 1999). Gravity data were processed using standard gravity data reduction techniques. Southwest Nevada is characterized by gravity anomalies that reflect the distribution of pre-Cenozoic carbonate rocks, thick sequences of volcanic rocks, and thick alluvial basins. In addition, regional gravity data reveal the presence of linear features that reflect large-scale faults whereas detailed gravity data can indicate the presence of smaller-scale faults.

  8. Preliminary mapping of surficial geology of Midway Valley Yucca Mountain Project, Nye County, Nevada; Yucca Mountain Site Characterization Project

    SciTech Connect

    Wesling, J.R.; Bullard, T.F.; Swan, F.H.; Perman, R.C.; Angell, M.M.; Gibson, J.D.

    1992-04-01

    The tectonics program for the proposed high-level nuclear waste repository at Yucca Mountain in southwestern Nevada must evaluate the potential for surface faulting beneath the prospective surface facilities. To help meet this goal, Quaternary surficial mapping studies and photolineament analyses were conducted to provide data for evaluating the location, recency, and style of faulting with Midway Valley at the eastern base of Yucca Mountain, the preferred location of these surface facilities. This interim report presents the preliminary results of this work.

  9. Genome-Wide Mapping of the Binding Sites and Structural Analysis of Kaposi's Sarcoma-Associated Herpesvirus Viral Interferon Regulatory Factor 2 Reveal that It Is a DNA-Binding Transcription Factor

    PubMed Central

    Hu, Haidai; Dong, Jiazhen; Liang, Deguang; Gao, Zengqiang; Bai, Lei; Sun, Rui; Hu, Hao; Zhang, Heng

    2015-01-01

    ABSTRACT The oncogenic herpesvirus Kaposi's sarcoma-associated herpesvirus (KSHV) is known to encode four viral interferon regulatory factors (vIRF1 to -4) to subvert the host antiviral immune response, but their detailed DNA-binding profiles as transcription factors in the host remain uncharacterized. Here, we first performed genome-wide vIRF2-binding site mapping in the human genome using chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq). vIRF2 was capable of binding to the promoter regions of 100 putative target genes. Importantly, we confirmed that vIRF2 can specifically interact with the promoters of the genes encoding PIK3C3, HMGCR, and HMGCL, which are associated with autophagosome formation or tumor progression and metastasis, and regulate their transcription in vivo. The crystal structure of the vIRF2 DNA-binding domain (DBD) (referred to here as vIRF2DBD) showed variable loop conformations and positive-charge distributions different from those of vIRF1 and cellular IRFs that are associated with DNA-binding specificities. Structure-based mutagenesis revealed that Arg82 and Arg85 are required for the in vitro DNA-binding activity of vIRF2DBD and can abolish the transcription regulation function of vIRF2 on the promoter reporter activity of PIK3C3, HMGCR, and HMGCL. Collectively, our study provided unique insights into the DNA-binding potency of vIRF2 and suggested that vIRF2 could act as a transcription factor of its target genes in the host antiviral immune response. IMPORTANCE The oncogenic herpesvirus KSHV is the etiological agent of Kaposi's sarcoma, primary effusion lymphoma, and multicentric Castleman's disease. KSHV has developed a unique mechanism to subvert the host antiviral immune responses by encoding four homologues of cellular interferon regulatory factors (vIRF1 to -4). However, none of their DNA-binding profiles in the human genome have been characterized until now, and the structural basis for their diverse

  10. The use of body surface potential map for identifying sites of accessory pathway in patients with Wolff-Parkinson-White syndrome.

    PubMed

    Tseng, Y Z; Hsu, K L; Chiang, F T; Lo, H M; Tseng, C D; Lin, J L

    1998-07-01

    The body surface potential map (BSPM) may reflect regional myocardial electrical activity. This technique can thus provide information regarding the excitation of ventricles. This study is an attempt to evaluate the usefulness of BSPM in determining the sites of the atrioventricular (AV) accessory pathway (AP) in patients with Wolff-Parkinson-White (W-P-W) syndrome. The BSPMs were obtained from 40 consecutive patients with W-P-W syndrome in a fasting state, using the heart potential map system designed by Toyama et al. Unipolar electrocardiograms were recorded simultaneously from 87 lead points on the chest surface, including 59 lead points on the anterior chest and 28 on the back. Wilson's central terminal was used as a voltage reference and BSPMs in an isopotential distribution pattern were made every millisecond throughout ventricular activation from these unipolar ECGs with the use of a microcomputer system. All patients underwent an electrophysiologic study (EPS) at cardiac catheterization. We analyzed the potential distribution during ventricular depolarization and compared the results between EPS and BSPM findings. The following results were obtained: (1) seven types of BSPM pattern were identified in accordance with the sites of the AV AP confirmed by EPS; (2) the location of the potential minimum of ventricular depolarization and the direction of the excitation wavefront during early ventricular depolarization, the reversal pattern of ventricular potential distribution, the epicardial right ventricular breakthrough and the dynamic change of ventricular potential distribution were useful for the detection of the ventricular pre-excitation site; (3) epicardial right ventricular breakthrough occurred in nearly all patients with left ventricular free wall accessory AV connections; (4) the abnormal early reversal pattern of ventricular potential distribution did not occur in patients with left ventricular AV connections but did appear in most patients with

  11. High-resolution genome-wide mapping of HIF-binding sites by ChIP-seq

    PubMed Central

    Schödel, Johannes; Oikonomopoulos, Spyros; Ragoussis, Jiannis; Pugh, Christopher W.; Ratcliffe, Peter J.

    2011-01-01

    Hypoxia-inducible factor (HIF) regulates the major transcriptional cascade central to the response of all mammalian cells to alterations in oxygen tension. Expression arrays indicate that many hundreds of genes are regulated by this pathway, controlling diverse processes that in turn orchestrate both oxygen delivery and utilization. However, the extent to which HIF exerts direct versus indirect control over gene expression together with the factors dictating the range of HIF-regulated genes remains unclear. Using chromatin immunoprecipitation linked to high throughput sequencing, we identify HIF-binding sites across the genome, independently of gene architecture. Using gene set enrichment analysis, we demonstrate robust associations with the regulation of gene expression by HIF, indicating that these sites operate over long genomic intervals. Analysis of HIF-binding motifs demonstrates sequence preferences outside of the core RCGTG-binding motif but does not reveal any additional absolute sequence requirements. Across the entire genome, only a small proportion of these potential binding sites are bound by HIF, although occupancy of potential sites was enhanced approximately 20-fold at normoxic DNAse1 hypersensitivity sites (irrespective of distance from promoters), suggesting that epigenetic regulation of chromatin may have an important role in defining the response to hypoxia. PMID:21447827

  12. Chromosome Mapping of 18S Ribosomal RNA Genes in Eleven Hypostomus Species (Siluriformes, Loricariidae): Diversity Analysis of the Sites.

    PubMed

    Rubert, Marceléia; da Rosa, Renata; Zawadzki, Claudio H; Mariotto, Sandra; Moreira-Filho, Orlando; Giuliano-Caetano, Lucia

    2016-08-01

    We investigated the chromosomal distribution of 18S ribosomal DNA (rDNA) in different populations of 11 species of Hypostomus collected in important Brazilian basins, namely South Atlantic, Upper Paraná, and Paraguay applying the fluorescence in situ hybridization (FISH). Hypostomus cochliodon, Hypostomus commersoni, Hypostomus hermanni, Hypostomus regani, Hypostomus albopunctatus, Hypostomus paulinus, Hypostomus aff. paulinus, Hypostomus iheringii, and Hypostomus mutucae presented multiple 18S rDNA sites while Hypostomus strigaticeps and Hypostomus nigromaculatus exhibited a single pair of chromosomes with 18S rDNA sites. The studied species presented variations in the number and position of these sites. The results accomplished were similar to those obtained by the analysis of AgNORs, revealing the same interspecific variability. Each species exhibited distinctive patterns of AgNOR and 18S rDNA distribution, which can be considered cytogenetic markers in each species of the genus and help improve the discussions on the phylogeny of the group.

  13. Employing a portable X-Ray fluorescence (P-XRF) analyser and GIS to identify and map heavy metal pollution in soils of a traditional bonfire site

    NASA Astrophysics Data System (ADS)

    Dao, Ligang; Zhang, Chaosheng; Morrison, Liam

    2010-05-01

    Soils in the vicinity of bonfires are recipients of metal contaminants from burning of metal-containing materials. In order to better understand the impacts of bonfires on soils, a total of 218 surface soil samples were collected from a traditional bonfire site in Galway City, Ireland. Concentrations of Cu, Pb and Zn were determined using a portable X-ray Fluorescence (P-XRF) analyser. Strong variations were observed for these metals, and several samples contained elevated Zn concentrations which exceeded the intervention threshold of the Dutch criteria (720 mg kg-1). Spatial clusters and spatial outliers were detected using the local Moran's I index and were mapped using GIS. Two clear high value spatial clusters could be observed on the upper left side and centre part of the study area for Cu, Pb and Zn. Results of variogram analyses showed high nugget-sill-ratios for Cu, Pb and Zn, indicating strong spatial variation over short distances which could be resulted from anthropogenic activities. The spatial interpolation method of ordinary kriging was applied to produce the spatial interpolation maps for Cu, Pb and Zn, and the areas with elevated concentrations were in line with historical locations of the bonfires. The hazard maps showed small parts of the study area with Zn concentrations exceeding the Dutch intervention values. In order to prevent further contamination from bonfires, it is advised that tyres and other metal-containing wastes should not be burnt. The results in this study provide useful information for management of bonfires.

  14. Application of the High Resolution Melting analysis for genetic mapping of Sequence Tagged Site markers in narrow-leafed lupin (Lupinus angustifolius L.).

    PubMed

    Kamel, Katarzyna A; Kroc, Magdalena; Święcicki, Wojciech

    2015-01-01

    Sequence tagged site (STS) markers are valuable tools for genetic and physical mapping that can be successfully used in comparative analyses among related species. Current challenges for molecular markers genotyping in plants include the lack of fast, sensitive and inexpensive methods suitable for sequence variant detection. In contrast, high resolution melting (HRM) is a simple and high-throughput assay, which has been widely applied in sequence polymorphism identification as well as in the studies of genetic variability and genotyping. The present study is the first attempt to use the HRM analysis to genotype STS markers in narrow-leafed lupin (Lupinus angustifolius L.). The sensitivity and utility of this method was confirmed by the sequence polymorphism detection based on melting curve profiles in the parental genotypes and progeny of the narrow-leafed lupin mapping population. Application of different approaches, including amplicon size and a simulated heterozygote analysis, has allowed for successful genetic mapping of 16 new STS markers in the narrow-leafed lupin genome.

  15. Combining solvent thermodynamic profiles with functionality maps of the Hsp90 binding site to predict the displacement of water molecules.

    PubMed

    Haider, Kamran; Huggins, David J

    2013-10-28

    Intermolecular interactions in the aqueous phase must compete with the interactions between the two binding partners and their solvating water molecules. In biological systems, water molecules in protein binding sites cluster at well-defined hydration sites and can form strong hydrogen-bonding interactions with backbone and side-chain atoms. Displacement of such water molecules is only favorable when the ligand can form strong compensating hydrogen bonds. Conversely, water molecules in hydrophobic regions of protein binding sites make only weak interactions, and the requirements for favorable displacement are less stringent. The propensity of water molecules for displacement can be identified using inhomogeneous fluid solvation theory (IFST), a statistical mechanical method that decomposes the solvation free energy of a solute into the contributions from different spatial regions and identifies potential binding hotspots. In this study, we employed IFST to study the displacement of water molecules from the ATP binding site of Hsp90, using a test set of 103 ligands. The predicted contribution of a hydration site to the hydration free energy was found to correlate well with the observed displacement. Additionally, we investigated if this correlation could be improved by using the energetic scores of favorable probe groups binding at the location of hydration sites, derived from a multiple copy simultaneous search (MCSS) method. The probe binding scores were not highly predictive of the observed displacement and did not improve the predictivity when used in combination with IFST-based hydration free energies. The results show that IFST alone can be used to reliably predict the observed displacement of water molecules in Hsp90. However, MCSS can augment IFST calculations by suggesting which functional groups should be used to replace highly displaceable water molecules. Such an approach could be very useful in improving the hit-to-lead process for new drug targets.

  16. Isolation of DNA from agarose gels using DEAE-paper. Application to restriction site mapping of adenovirus type 16 DNA.

    PubMed Central

    Winberg, G; Hammarskjöld, M L

    1980-01-01

    A new method for isolating DNA from agarose gels is described. The method involves the simultaneous transfer of all DNA-fragments from an agarose slab gel onto DEAE-cellulose paper and the elution of the individual fragments from the paper with 1 M NaCl. DNA isolated from agarose gels in this way is susceptible to cleavage with several restriction endonucleases, and can be labeled in vitro with E coli DNA-polymerase I, T4 DNA-polymerase and T4 polynucleotide kinase. We have used the method to construct restriction endonuclease maps of adenovirus type 16 DNA. Images PMID:6252542

  17. Activity of the human immunodeficiency virus type 1 cell cycle-dependent internal ribosomal entry site is modulated by IRES trans-acting factors

    PubMed Central

    Vallejos, Maricarmen; Deforges, Jules; Plank, Terra-Dawn M.; Letelier, Alejandro; Ramdohr, Pablo; Abraham, Christopher G.; Valiente-Echeverría, Fernando; Kieft, Jeffrey S.; Sargueil, Bruno; López-Lastra, Marcelo

    2011-01-01

    The 5′ leader of the human immunodeficiency virus type 1 (HIV-1) genomic RNA harbors an internal ribosome entry site (IRES) that is functional during the G2/M phase of the cell cycle. Here we show that translation initiation mediated by the HIV-1 IRES requires the participation of trans-acting cellular factors other than the canonical translational machinery. We used ‘standard’ chemical and enzymatic probes and an ‘RNA SHAPE’ analysis to model the structure of the HIV-1 5′ leader and we show, by means of a footprinting assay, that G2/M extracts provide protections to regions previously identified as crucial for HIV-1 IRES activity. We also assessed the impact of mutations on IRES function. Strikingly, mutations did not significantly affect IRES activity suggesting that the requirement for pre-formed stable secondary or tertiary structure within the HIV-1 IRES may not be as strict as has been described for other viral IRESes. Finally, we used a proteomic approach to identify cellular proteins within the G2/M extracts that interact with the HIV-1 5′ leader. Together, data show that HIV-1 IRES-mediated translation initiation is modulated by cellular proteins. PMID:21482538

  18. RNA-interacting proteins act as site-specific repressors of ADAR2-mediated RNA editing and fluctuate upon neuronal stimulation

    PubMed Central

    Tariq, Aamira; Garncarz, Wojciech; Handl, Cornelia; Balik, Ales; Pusch, Oliver; Jantsch, Michael F.

    2013-01-01

    RNA editing by adenosine deaminases that act on RNA (ADARs) diversifies the transcriptome by changing adenosines to inosines. In mammals, editing levels vary in different tissues, during development, and also in pathogenic conditions. From a screen for repressors of editing we have isolated three proteins that repress ADAR2-mediated RNA editing. The three proteins RPS14, SFRS9 and DDX15 interact with RNA. Overexpression or depletion of these proteins can decrease or increase editing levels by 15%, thus allowing a modulation of RNA editing up to 30%. Interestingly, the three proteins alter RNA editing in a substrate-specific manner that correlates with their RNA binding preferences. In mammalian cells, SFRS9 significantly affects editing of the two substrates CFLAR and cyFIP2, while the ribosomal protein RPS14 mostly inhibits editing of cyFIP2 messenger RNA. The helicase DDX15, in turn, has a strong effect on editing in Caenorhabditis elegans. Expression of the three factors decreases during mouse brain development. Moreover, expression levels of SFRS9 and DDX15 respond strongly to neuronal stimulation or repression, showing an inverse correlation with editing levels. Colocalization and immunoprecipitation studies demonstrate a direct interaction of SFRS9 and RPS14 with ADAR2, while DDX15 associates with other helicases and splicing factors. Our data show that different editing sites can be specifically altered in their editing pattern by changing the local RNP landscape. PMID:23275536

  19. Genome-Wide Mapping of Binding Sites Reveals Multiple Biological Functions of the Transcription Factor Cst6p in Saccharomyces cerevisiae

    PubMed Central

    Bergenholm, David

    2016-01-01

    ABSTRACT In the model eukaryote Saccharomyces cerevisiae, the transcription factor Cst6p has been reported to play important roles in several biological processes. However, the genome-wide targets of Cst6p and its physiological functions remain unknown. Here, we mapped the genome-wide binding sites of Cst6p at high resolution. Cst6p binds to the promoter regions of 59 genes with various biological functions when cells are grown on ethanol but hardly binds to the promoter at any gene when cells are grown on glucose. The retarded growth of the CST6 deletion mutant on ethanol is attributed to the markedly decreased expression of NCE103, encoding a carbonic anhydrase, which is a direct target of Cst6p. The target genes of Cst6p have a large overlap with those of stress-responsive transcription factors, such as Sko1p and Skn7p. In addition, a CST6 deletion mutant growing on ethanol shows hypersensitivity to oxidative stress and ethanol stress, assigning Cst6p as a new member of the stress-responsive transcriptional regulatory network. These results show that mapping of genome-wide binding sites can provide new insights into the function of transcription factors and highlight the highly connected and condition-dependent nature of the transcriptional regulatory network in S. cerevisiae. PMID:27143390

  20. Tracing the path of DNA substrates in active Tetrahymena telomerase holoenzyme complexes: mapping of DNA contact sites in the RNA subunit.

    PubMed

    Goldin, Svetlana; Kertesz Rosenfeld, Karin; Manor, Haim

    2012-08-01

    Telomerase, the enzyme that extends single-stranded telomeric DNA, consists of an RNA subunit (TER) including a short template sequence, a catalytic protein (TERT) and accessory proteins. We used site-specific UV cross-linking to map the binding sites for DNA primers in TER within active Tetrahymena telomerase holoenzyme complexes. The mapping was performed at single-nucleotide resolution by a novel technique based on RNase H digestion of RNA-DNA hybrids made with overlapping complementary oligodeoxynucleotides. These data allowed tracing of the DNA path through the telomerase complexes from the template to the TERT binding element (TBE) region of TER. TBE is known to bind TERT and to be involved in the template 5'-boundary definition. Based on these findings, we propose that upstream sequences of each growing telomeric DNA chain are involved in regulation of its growth arrest at the 5'-end of the RNA template. The upstream DNA-TBE interaction may also function as an anchor for the subsequent realignment of the 3'-end of the DNA with the 3'-end of the template to enable initiation of synthesis of a new telomeric repeat.

  1. Nebraska, Kansas, and Oklahoma aeromagnetic and gravity maps and data: a web site for distribution of data

    USGS Publications Warehouse

    Sweeney, Ronald E.; Hill, Patricia L.

    2005-01-01

    The Nebraska, Kansas, and Oklahoma aeromagnetic grid is constructed from grids that combine information collected in 28 separate aeromagnetic surveys conducted between 1954 and 1985. The data from these surveys are of varying quality. The design and specifications (terrain clearance, sampling rates, line spacing, and reduction procedures) varied from survey to survey depending on the purpose of the project and the technology of that time. Every attempt was made to acquire the data in digital form. Most of the available digital data were obtained from aeromagnetic surveys flown by the U.S. Geological Survey (USGS), flown on contract with the USGS, or were obtained from other Federal agencies and State universities. The Kansas data were flown by and acquired from the Kansas Geological Survey. Some of the 1954, 1963, and 1964 data are available only on hand-contoured maps and had to be digitized. These maps were digitized along flight-line/contour-line intersections, which is considered to be the most accurate method of recovering the original data. All surveys have been continued to 304.8 m (1,000 ft) above ground and then blended or merged together.

  2. Epicardial and endocardial mapping determine most successful site of ablation for ventricular tachyarrhythmias originating from left ventricular summit.

    PubMed

    Iijima, Kenichi; Chinushi, Masaomi; Furushima, Hiroshi; Aizawa, Yoshifusa

    2012-06-01

    A 34-year-old woman presented with idiopathic premature ventricular complex (PVC) and ventricular tachycardia (VT) originating from the area called the left ventricular summit. Radiofrequency (RF) application both through the coronary sinus and to the epicardial surface transiently suppressed the VT/PVC. Radiofrequency with sufficient energy was only applicable from the endocardial site, and the VT/PVC was successfully eliminated.

  3. Mapping Cannabinoid 1 Receptor Allosteric Site(s): Critical Molecular Determinant and Signaling Profile of GAT100, a Novel, Potent, and Irreversibly Binding Probe.

    PubMed

    Laprairie, Robert B; Kulkarni, Abhijit R; Kulkarni, Pushkar M; Hurst, Dow P; Lynch, Diane; Reggio, Patricia H; Janero, David R; Pertwee, Roger G; Stevenson, Lesley A; Kelly, Melanie E M; Denovan-Wright, Eileen M; Thakur, Ganesh A

    2016-06-15

    agonism associated with Org27569 and PSNCBAM-1. Computational docking studies implicate C7.38(382) as a key feature of GAT100 ligand-binding motif. These data help inform the engineering of newer-generation, druggable CB1R allosteric modulators and demonstrate the utility of GAT100 as a covalent probe for mapping structure-function correlates characteristic of the druggable CB1R allosteric space.

  4. A Remote Characterization System and a fault-tolerant tracking system for subsurface mapping of buried waste sites

    SciTech Connect

    Sandness, G.A.; Bennett, D.W. ); Martinson, L. ); Bingham, D.N.; Anderson, A.A. )

    1992-08-01

    This paper describes two closely related projects that will provide new technology for characterizing hazardous waste burial sites. The first project, a collaborative effort by five of the national laboratories, involves the development and demonstration of a remotely controlled site characterization system. The Remote Characterization System (RCS) includes a unique low-signature survey vehicle, a base station, radio telemetry data links, satellite-based vehicle tracking, stereo vision, and sensors for noninvasive inspection of the surface and subsurface. The second project, conducted by the Idaho National Engineering Laboratory (INEL), involves the development of a position sensing system that can track a survey vehicle or instrument in the field. This system can coordinate updates at a rate of 200/s with an accuracy better than 0.1% of the distance separating the target and the sensor. It can employ acoustic or electromagnetic signals in a wide range of frequencies and can be operated as a passive or active device.

  5. Mapping and Characterizing Selected Canopy Tree Species at the Angkor World Heritage Site in Cambodia Using Aerial Data

    PubMed Central

    Singh, Minerva; Evans, Damian; Tan, Boun Suy; Nin, Chan Samean

    2015-01-01

    At present, there is very limited information on the ecology, distribution, and structure of Cambodia’s tree species to warrant suitable conservation measures. The aim of this study was to assess various methods of analysis of aerial imagery for characterization of the forest mensuration variables (i.e., tree height and crown width) of selected tree species found in the forested region around the temples of Angkor Thom, Cambodia. Object-based image analysis (OBIA) was used (using multiresolution segmentation) to delineate individual tree crowns from very-high-resolution (VHR) aerial imagery and light detection and ranging (LiDAR) data. Crown width and tree height values that were extracted using multiresolution segmentation showed a high level of congruence with field-measured values of the trees (Spearman’s rho 0.782 and 0.589, respectively). Individual tree crowns that were delineated from aerial imagery using multiresolution segmentation had a high level of segmentation accuracy (69.22%), whereas tree crowns delineated using watershed segmentation underestimated the field-measured tree crown widths. Both spectral angle mapper (SAM) and maximum likelihood (ML) classifications were applied to the aerial imagery for mapping of selected tree species. The latter was found to be more suitable for tree species classification. Individual tree species were identified with high accuracy. Inclusion of textural information further improved species identification, albeit marginally. Our findings suggest that VHR aerial imagery, in conjunction with OBIA-based segmentation methods (such as multiresolution segmentation) and supervised classification techniques are useful for tree species mapping and for studies of the forest mensuration variables. PMID:25902148

  6. Mapping and characterizing selected canopy tree species at the Angkor World Heritage site in Cambodia using aerial data.

    PubMed

    Singh, Minerva; Evans, Damian; Tan, Boun Suy; Nin, Chan Samean

    2015-01-01

    At present, there is very limited information on the ecology, distribution, and structure of Cambodia's tree species to warrant suitable conservation measures. The aim of this study was to assess various methods of analysis of aerial imagery for characterization of the forest mensuration variables (i.e., tree height and crown width) of selected tree species found in the forested region around the temples of Angkor Thom, Cambodia. Object-based image analysis (OBIA) was used (using multiresolution segmentation) to delineate individual tree crowns from very-high-resolution (VHR) aerial imagery and light detection and ranging (LiDAR) data. Crown width and tree height values that were extracted using multiresolution segmentation showed a high level of congruence with field-measured values of the trees (Spearman's rho 0.782 and 0.589, respectively). Individual tree crowns that were delineated from aerial imagery using multiresolution segmentation had a high level of segmentation accuracy (69.22%), whereas tree crowns delineated using watershed segmentation underestimated the field-measured tree crown widths. Both spectral angle mapper (SAM) and maximum likelihood (ML) classifications were applied to the aerial imagery for mapping of selected tree species. The latter was found to be more suitable for tree species classification. Individual tree species were identified with high accuracy. Inclusion of textural information further improved species identification, albeit marginally. Our findings suggest that VHR aerial imagery, in conjunction with OBIA-based segmentation methods (such as multiresolution segmentation) and supervised classification techniques are useful for tree species mapping and for studies of the forest mensuration variables. PMID:25902148

  7. Mapping elevations of tidal wetland restoration sites in San Francisco Bay: Comparing accuracy of aerial lidar with a singlebeam echosounder

    USGS Publications Warehouse

    Athearn, N.D.; Takekawa, J.Y.; Jaffe, B.; Hattenbach, B.J.; Foxgrover, A.C.

    2010-01-01

    The southern edge of San Francisco Bay is surrounded by former salt evaporation ponds, where tidal flow has been restricted since the mid to late 1890s. These ponds are now the focus of a large wetland restoration project, and accurate measurement of current pond bathymetry and adjacent mud flats has been critical to restoration planning. Aerial light detection and ranging (lidar) has become a tool for mapping surface elevations, but its accuracy had rarely been assessed for wetland habitats. We used a singlebeam echosounder system we developed for surveying shallow wetlands to map submerged pond bathymetry in January of 2004 and compared those results with aerial lidar surveys in two ponds that were dry in May of 2004. From those data sets, we compared elevations for 5164 (Pond E9, 154 ha) and 2628 (Pond E14, 69 ha) echosounder and lidar points within a 0.375-m radius of each other (0.750-m diameter lidar spot size). We found that mean elevations of the lidar points were lower than the echosounder results by 5 ?? 0.1 cm in Pond E9 and 2 ?? 0.2 cm in Pond E14. Only a few points (5% in Pond E9, 2% in Pond E14) differed by more than 20 cm, and some of these values may be explained by residual water in the ponds during the lidar survey or elevation changes that occurred between surveys. Our results suggest that aerial lidar may be a very accurate and rapid way to assess terrain elevations for wetland restoration projects. ?? 2010 Coastal Education and Research Foundation.

  8. Mapping and characterizing selected canopy tree species at the Angkor World Heritage site in Cambodia using aerial data.

    PubMed

    Singh, Minerva; Evans, Damian; Tan, Boun Suy; Nin, Chan Samean

    2015-01-01

    At present, there is very limited information on the ecology, distribution, and structure of Cambodia's tree species to warrant suitable conservation measures. The aim of this study was to assess various methods of analysis of aerial imagery for characterization of the forest mensuration variables (i.e., tree height and crown width) of selected tree species found in the forested region around the temples of Angkor Thom, Cambodia. Object-based image analysis (OBIA) was used (using multiresolution segmentation) to delineate individual tree crowns from very-high-resolution (VHR) aerial imagery and light detection and ranging (LiDAR) data. Crown width and tree height values that were extracted using multiresolution segmentation showed a high level of congruence with field-measured values of the trees (Spearman's rho 0.782 and 0.589, respectively). Individual tree crowns that were delineated from aerial imagery using multiresolution segmentation had a high level of segmentation accuracy (69.22%), whereas tree crowns delineated using watershed segmentation underestimated the field-measured tree crown widths. Both spectral angle mapper (SAM) and maximum likelihood (ML) classifications were applied to the aerial imagery for mapping of selected tree species. The latter was found to be more suitable for tree species classification. Individual tree species were identified with high accuracy. Inclusion of textural information further improved species identification, albeit marginally. Our findings suggest that VHR aerial imagery, in conjunction with OBIA-based segmentation methods (such as multiresolution segmentation) and supervised classification techniques are useful for tree species mapping and for studies of the forest mensuration variables.

  9. Mapping the Binding Site of the Inhibitor Tariquidar That Stabilizes the First Transmembrane Domain of P-glycoprotein*

    PubMed Central

    Loo, Tip W.; Clarke, David M.

    2015-01-01

    ABC (ATP-binding cassette) transporters are clinically important because drug pumps like P-glycoprotein (P-gp, ABCB1) confer multidrug resistance and mutant ABC proteins are responsible for many protein-folding diseases such as cystic fibrosis. Identification of the tariquidar-binding site has been the subject of intensive molecular modeling studies because it is the most potent inhibitor and corrector of P-gp. Tariquidar is a unique P-gp inhibitor because it locks the pump in a conformation that blocks drug efflux but activates ATPase activity. In silico docking studies have identified several potential tariquidar-binding sites. Here, we show through cross-linking studies that tariquidar most likely binds to sites within the transmembrane (TM) segments located in one wing or at the interface between the two wings (12 TM segments form 2 divergent wings). We then introduced arginine residues at all positions in the 12 TM segments (223 mutants) of P-gp. The rationale was that a charged residue in the drug-binding pocket would disrupt hydrophobic interaction with tariquidar and inhibit its ability to rescue processing mutants or stimulate ATPase activity. Arginines introduced at 30 positions significantly inhibited tariquidar rescue of a processing mutant and activation of ATPase activity. The results suggest that tariquidar binds to a site within the drug-binding pocket at the interface between the TM segments of both structural wings. Tariquidar differed from other drug substrates, however, as it stabilized the first TM domain. Stabilization of the first TM domain appears to be a key mechanism for high efficiency rescue of ABC processing mutants that cause disease. PMID:26507655

  10. mChIP-KAT-MS, a method to map protein interactions and acetylation sites for lysine acetyltransferases

    PubMed Central

    Mitchell, Leslie; Huard, Sylvain; Cotrut, Michael; Pourhanifeh-Lemeri, Roghayeh; Steunou, Anne-Lise; Hamza, Akil; Lambert, Jean-Philippe; Zhou, Hu; Ning, Zhibin; Basu, Amrita; Côté, Jacques; Figeys, Daniel A.; Baetz, Kristin

    2013-01-01

    Recent global proteomic and genomic studies have determined that lysine acetylation is a highly abundant posttranslational modification. The next challenge is connecting lysine acetyltransferases (KATs) to their cellular targets. We hypothesize that proteins that physically interact with KATs may not only predict the cellular function of the KATs but may be acetylation targets. We have developed a mass spectrometry-based method that generates a KAT protein interaction network from which we simultaneously identify both in vivo acetylation sites and in vitro acetylation sites. This modified chromatin-immunopurification coupled to an in vitro KAT assay with mass spectrometry (mChIP-KAT-MS) was applied to the Saccharomyces cerevisiae KAT nucleosome acetyltransferase of histone H4 (NuA4). Using mChIP-KAT-MS, we define the NuA4 interactome and in vitro-enriched acetylome, identifying over 70 previously undescribed physical interaction partners for the complex and over 150 acetyl lysine residues, of which 108 are NuA4-specific in vitro sites. Through this method we determine NuA4 acetylation of its own subunit Epl1 is a means of self-regulation and identify a unique link between NuA4 and the spindle pole body. Our work demonstrates that this methodology may serve as a valuable tool in connecting KATs with their cellular targets. PMID:23572591

  11. Systematic Mapping of Posttranslational Modifications in Human Estrogen Receptor-α with Emphasis on Novel Phosphorylation Sites*S⃞

    PubMed Central

    Atsriku, Christian; Britton, David J.; Held, Jason M.; Schilling, Birgit; Scott, Gary K.; Gibson, Bradford W.; Benz, Christopher C.; Baldwin, Michael A.

    2009-01-01

    A systematic study of posttranslational modifications of the estrogen receptor isolated from the MCF-7 human breast cancer cell line is reported. Proteolysis with multiple enzymes, mass spectrometry, and tandem mass spectrometry achieved very high sequence coverage for the full-length 66-kDa endogenous protein from estradiol-treated cell cultures. Nine phosphorylated serine residues were identified, three of which were previously unreported and none of which were previously observed by mass spectrometry by any other laboratory. Two additional modified serine residues were identified in recombinant protein, one previously reported but not observed here in endogenous protein and the other previously unknown. Although major emphasis was placed on identifying new phosphorylation sites, N-terminal loss of methionine accompanied by amino acetylation and a lysine side chain acetylation (or possibly trimethylation) were also detected. The use of both HPLC-ESI and MALDI interfaced to different mass analyzers gave higher sequence coverage and identified more sites than could be achieved by either method alone. The estrogen receptor is critical in the development and progression of breast cancer. One previously unreported phosphorylation site identified here was shown to be strongly dependent on estradiol, confirming its potential significance to breast cancer. Greater knowledge of this array of posttranslational modifications of estrogen receptor, particularly phosphorylation, will increase our understanding of the processes that lead to estradiol-induced activation of this protein and may aid the development of therapeutic strategies for management of hormone-dependent breast cancer. PMID:18984578

  12. Mapping the ribosomal protein S7 regulatory binding site on mRNA of the E. coli streptomycin operon.

    PubMed

    Surdina, A V; Rassokhin, T I; Golovin, A V; Spiridonova, V A; Kopylov, A M

    2010-07-01

    In this work it is shown by deletion analysis that an intercistronic region (ICR) approximately 80 nucleotides in length is necessary for interaction with recombinant E. coli S7 protein (r6hEcoS7). A model is proposed for the interaction of S7 with two ICR sites-region of hairpin bifurcations and Shine-Dalgarno sequence of cistron S7. A de novo RNA binding site for heterologous S7 protein of Thermus thermophilus (r6hTthS7) was constructed by selection of a combinatorial RNA library based on E. coli ICR: it has only a single supposed protein recognition site in the region of bifurcation. The SERW technique was used for selection of two intercistronic RNA libraries in which five nucleotides of a double-stranded region, adjacent to the bifurcation, had the randomized sequence. One library contained an authentic AG (-82/-20) pair, while in the other this pair was replaced by AU. A serwamer capable of specific binding to r6hTthS7 was selected; it appeared to be the RNA68 mutant with eight nucleotide mutations. The serwamer binds to r6hTthS7 with the same affinity as homologous authentic ICR of str mRNA binds to r6hEcoS7; apparent dissociation constants are 89 +/- 43 and 50 +/- 24 nM, respectively.

  13. Mapping DNA cleavage by the Type ISP restriction-modification enzymes following long-range communication between DNA sites in different orientations.

    PubMed

    van Aelst, Kara; Saikrishnan, Kayarat; Szczelkun, Mark D

    2015-12-01

    The prokaryotic Type ISP restriction-modification enzymes are single-chain proteins comprising an Mrr-family nuclease, a superfamily 2 helicase-like ATPase, a coupler domain, a methyltransferase, and a DNA-recognition domain. Upon recognising an unmodified DNA target site, the helicase-like domain hydrolyzes ATP to cause site release (remodeling activity) and to then drive downstream translocation consuming 1-2 ATP per base pair (motor activity). On an invading foreign DNA, double-strand breaks are introduced at random wherever two translocating enzymes form a so-called collision complex following long-range communication between a pair of target sites in inverted (head-to-head) repeat. Paradoxically, structural models for collision suggest that the nuclease domains are too far apart (>30 bp) to dimerise and produce a double-strand DNA break using just two strand-cleavage events. Here, we examined the organisation of different collision complexes and how these lead to nuclease activation. We mapped DNA cleavage when a translocating enzyme collides with a static enzyme bound to its site. By following communication between sites in both head-to-head and head-to-tail orientations, we could show that motor activity leads to activation of the nuclease domains via distant interactions of the helicase or MTase-TRD. Direct nuclease dimerization is not required. To help explain the observed cleavage patterns, we also used exonuclease footprinting to demonstrate that individual Type ISP domains can swing off the DNA. This study lends further support to a model where DNA breaks are generated by multiple random nicks due to mobility of a collision complex with an overall DNA-binding footprint of ∼30 bp.

  14. On-site Consultation Hearings, Occupational Safety and Health Act. Hearings before the Subcommittee on Manpower, Compensation, and Health and Safety of the Committee on Education and Labor, House of Representatives, Ninety-fourth Congress.

    ERIC Educational Resources Information Center

    Congress of the U.S., Washington, DC. House Committee on Education and Labor.

    The hearings consider a bill, H.R. 8618, to amend the Occupational Safety and Health Act of 1970 (OSHA) which would provide on-site consultative services to employers desiring to comply with OSHA standards. H.R. 8616 was introduced to strengthen OSHA by providing an additional program that would encourage employers to voluntarily comply with…

  15. Operation and research at the Ithaca MAP3S Regional Precipitation Chemistry Site: Annual progress report for 1 December 1986-30 November 1987

    SciTech Connect

    Butler, T.J.; Likens, G.E.

    1987-07-01

    Data at the MAP3S Site for 1 June 1986 to 31 May 1987 show average conditions in terms of precipitation amount (100 cm/yr), H/sup +/ concentration (63.9 ..mu..eq/liter), and H/sup +/ deposition (641 eq/ha-yr). H/sup +/ (lab) and Cl/sup -/ show significant (0.05 level) downward trends from 1977 to 1984. Trends for all sites were examined for SO/sub 4//sup =/ (anthropogenic source), and Ca/sup + +/ (crustal source). SO/sub 4//sup =/ generally shows insignificant but downward trends. Ca/sup + +/ shows insignificant trends, both upward and downward. Frequency diagrams of storm sizes show an exponential decay with increasing storm volume at all sites. Composition of dry deposition consists of 15% to 30% anthropogenic particles and calcium species consists of 33% to 50% CaSO/sub 4/. Conversation of CaCO/sub 3/ to CaSO/sub 4/ by absorption of SO/sub 2/ occurs at a rate of 0% to 20% per day. 1 ref., 9 figs., 1 tab.

  16. Post-Closure Report for Closed Resource Conservation and Recovery Act Corrective Action Units, Nevada National Security Site, Nevada for Fiscal Year 2011 (October 2010-September 2011)

    SciTech Connect

    NSTec Environmental Restoration

    2012-01-18

    This report serves as the combined annual report for post-closure activities for the following closed Corrective Action Units (CAUs): (1) CAU 90, Area 2 Bitcutter Containment; (2) CAU 91, Area 3 U-3fi Injection Well; (3) CAU 92, Area 6 Decon Pond Facility; (4) CAU 110, Area 3 WMD U-3ax/bl Crater; and (5) CAU 112, Area 23 Hazardous Waste Trenches. This report covers fiscal year 2011 (October 2010-September 2011). The post-closure requirements for these sites are described in Resource Conservation and Recovery Act Permit Number NEV HW0101 and summarized in each CAU-specific section in Section 1.0 of this report. Site inspections are conducted semiannually at CAUs 90 and 91 and quarterly at CAUs 92, 110, and 112. Additional inspections are conducted at CAU 92 if precipitation occurs in excess of 0.50 inches in a 24-hour period. Inspections include an evaluation of the condition of the units and identification of any deficiencies that may compromise the integrity of the units. The condition of covers, fencing, signs, gates, and locks is documented. In addition, soil moisture monitoring and subsidence surveys are conducted at CAU 110. The results of the inspections, summary of maintenance activities, results of vegetations surveys, and analysis of monitoring data are presented in this report. Copies of the inspection checklists are included as Appendix A. Field notes completed during each inspection are included in Appendix B. Photographs taken during the inspections are included in Appendix C. It is recommended to continue semiannual inspections at CAUs 90 and 91; quarterly inspections at CAUs 92, 110, and 112; and additional inspections at CAU 92 if precipitation occurs in excess of 0.50 inches in a 24-hour period. At CAU 92, it is recommended to remove the wave barriers, as they have not proven to be necessary to protect the cover. At CAU 110, it is recommended to continue annual vegetation monitoring and soil moisture monitoring, and to reduce the frequency of

  17. Site-condition map for Portugal, Western Iberia: methodology and constraints on the performance of Vs30 proxies for stable continental regions in Europe.

    NASA Astrophysics Data System (ADS)

    Vilanova, S. P.; Narciso, J.; Carvalho, J. P.; Cancela, C.; Lopes, I.; Nemser, E. S.; Borges, J.

    2014-12-01

    Information on the amplification characteristics of the near-surface formations in a regional sense is essential to adequately represent both seismic hazard maps and ground shaking maps. Due to the scarceness of shear-wave velocity data in most regions, several methods have been proposed in order to obtain first order representations of Vs30. These include the surface geology method and the topographic slope method. The latter method has become the standard way for incorporating site effects into regional studies worldwide given the convenience provided by the global Vs30 Internet server. In the framework of project SCENE we developed a shear wave velocity database for Portugal. The database consists of 87 shear-wave velocity depth profiles from a variety of lithological and geological formations. We used an iterative three-step procedure to develop the Vs30 based site-condition map: 1) to define a preliminary set of geologically defined units based on the literature; 2) to calculate the distribution of Vs30 for each unit; and 3) to perform statistical tests in order to estimate the significance of the difference in the Vs30 distribution characteristics between the units. The units were merged according to the results of the statistical tests and the procedure was repeated. We started by classifying the sites into six generalized geological units. The final set consists of three units only: F1 (igneous, metamorphic and old sedimentary rocks); F2 (Neogene and Pleistocene formations); and F3 (Holocene deposits). We used the database to evaluate the performance of Vs30 proxies. The use of proxies based either on geological units or on correlations with the topographic slope shows relatively unbiased total residual distributions of the logarithm of Vs30. However, the performance of the methods varies significantly with the generalized geological unit analyzed. Both methods are biased towards lower values of Vs30 for rock formations. The topographic-slope method is

  18. Putting English Language Learners on the Educational Map: The No Child Left Behind Act Implemented. Education in Focus: Urban Institute Policy Brief

    ERIC Educational Resources Information Center

    de Cohen, Clemencia Cosentino; Clewell, Beatriz Chu

    2007-01-01

    To expand knowledge about young immigrant populations and to document how the No Child Left Behind Act (NCLB) affects the education of English language learner (ELL) and limited English proficient (LEP) students, the Urban Institute was funded by the Foundation for Child Development to undertake a series of reports. This policy brief draws on this…

  19. Resistivity Profiling for Mapping Gravel Layers That May Control Contaminant Migration at the Amargosa Desert Research Site, Nevada

    USGS Publications Warehouse

    Lucius, Jeffrey E.; Abraham, Jared D.; Burton, Bethany L.

    2008-01-01

    Gaseous contaminants, including CFC 113, chloroform, and tritiated compounds, move preferentially in unsaturated subsurface gravel layers away from disposal trenches at a closed low-level radioactive waste-disposal facility in the Amargosa Desert about 17 kilometers south of Beatty, Nevada. Two distinct gravel layers are involved in contaminant transport: a thin, shallow layer between about 0.5 and 2.2 meters below the surface and a layer of variable thickness between about 15 and 30 meters below land surface. From 2003 to 2005, the U.S. Geological Survey used multielectrode DC and AC resistivity surveys to map these gravel layers. Previous core sampling indicates the fine-grained sediments generally have higher water content than the gravel layers or the sediments near the surface. The relatively higher electrical resistivity of the dry gravel layers, compared to that of the surrounding finer sediments, makes the gravel readily mappable using electrical resistivity profiling. The upper gravel layer is not easily distinguished from the very dry, fine-grained deposits at the surface. Two-dimensional resistivity models, however, clearly identify the resistive lower gravel layer, which is continuous near the facility except to the southeast. Multielectrode resistivity surveys provide a practical noninvasive method to image hydrogeologic features in the arid environment of the Amargosa Desert.

  20. History of the clay-rich unit at Mawrth Vallis, Mars: High-resolution mapping of a candidate landing site

    NASA Astrophysics Data System (ADS)

    Loizeau, D.; Mangold, N.; Poulet, F.; Bibring, J.-P.; Bishop, J. L.; Michalski, J.; Quantin, C.

    2015-11-01

    The Mawrth Vallis region is covered by some of the largest phyllosilicate-rich outcrops on Mars, making it a unique window into the past history of Mars in terms of water alteration, potential habitability, and the search for past life. A landing ellipse had been proposed for the Curiosity rover. This area has been extensively observed by the High Resolution Imaging Science Experiment and the Compact Reconnaissance Imaging Spectrometer for Mars, offering the possibility to produce geologic, structural, and topographic maps at very high resolution. These observations provide an unprecedented detailed context of the rocks at Mawrth Vallis, in terms of deposition, alteration, erosion, and mechanical constraints. Our analyses demonstrate the presence of a variety of alteration environments on the surface and readily accessible to a rover, the presence of flowing water at the surface postdating the formation of the clay-rich units, and evidence for probable circulation of fluids in the rocks at different depths. These rocks undergo continuous erosion, creating fresh outcrops where potential biomarkers may have been preserved. The diversity of aqueous environments over geological time coupled to excellent preservation properties make the area a very strong candidate for future robotic investigation on Mars, like the NASA Mars 2020 mission.

  1. Nuclear Localization Signal and p53 Binding Site in MAP/ERK Kinase Kinase 1 (MEKK1).

    PubMed

    Chipps, Elizabeth; Protzman, April; Muhi, M Zubayed; Ando, Shoko; Calvet, James P; Islam, M Rafiq

    2015-12-01

    Previously, we showed that Mekk1 translocates to the nucleus, interacts with tumor suppressor protein p53, and co-represses PKD1 transcription via an atypical p53 binding site on the minimal PKD1 promoter (JBC 285:38,818-38,831, 2010). In this study, we report the mechanisms of Mekk1 nuclear transport and p53 binding. Using GFP-linked constitutively active-Mekk1 (CA-Mekk1) and a deletion strategy, we identified a nuclear localization signal (HRDVK) located at amino acid (aa) residues 1,349-1,353 in the C-terminal Mekk1 catalytic domain. Deletion of this sequence in CA-Mekk1 and full-length Mekk1 significantly reduced their nuclear translocation in both HEK293T and COS-1 cells. Using co-immunoprecipitation, we identified an adjacent sequence (GANLID, aa 1,354-1,360) in Mekk1 responsible for p53 binding. Deletion of this sequence markedly reduced the interaction of Mekk1 with p53. Mekk1 does not appear to affect phosphorylation of Ser15, located in the Mdm2 interaction site, or other Ser residues in p53. However, Mekk1 mediates p53 protein stability in the presence of Mdm2 and reduces p53 ubiquitination, suggesting an interference with Mdm2-mediated degradation of p53 by the ubiquitin-proteasome pathway.

  2. Geographic distribution, age pattern and sites of lesions in a cohort of Buruli ulcer patients from the Mapé Basin of Cameroon.

    PubMed

    Bratschi, Martin W; Bolz, Miriam; Minyem, Jacques C; Grize, Leticia; Wantong, Fidèle G; Kerber, Sarah; Njih Tabah, Earnest; Ruf, Marie-Thérèse; Mou, Ferdinand; Noumen, Djeunga; Um Boock, Alphonse; Pluschke, Gerd

    2013-01-01

    Buruli ulcer (BU), a neglected tropical disease of the skin, caused by Mycobacterium ulcerans, occurs most frequently in children in West Africa. Risk factors for BU include proximity to slow flowing water, poor wound care and not wearing protective clothing. Man-made alterations of the environment have been suggested to lead to increased BU incidence. M. ulcerans DNA has been detected in the environment, water bugs and recently also in mosquitoes. Despite these findings, the mode of transmission of BU remains poorly understood and both transmission by insects or direct inoculation from contaminated environment have been suggested. Here, we investigated the BU epidemiology in the Mapé basin of Cameroon where the damming of the Mapé River since 1988 is believed to have increased the incidence of BU. Through a house-by-house survey in spring 2010, which also examined the local population for leprosy and yaws, and continued surveillance thereafter, we identified, till June 2012, altogether 88 RT-PCR positive cases of BU. We found that the age adjusted cumulative incidence of BU was highest in young teenagers and in individuals above the age of 50 and that very young children (<5) were underrepresented among cases. BU lesions clustered around the ankles and at the back of the elbows. This pattern neither matches any of the published mosquito biting site patterns, nor the published distribution of small skin injuries in children, where lesions on the knees are much more frequent. The option of multiple modes of transmission should thus be considered. Analyzing the geographic distribution of cases in the Mapé Dam area revealed a closer association with the Mbam River than with the artificial lake. PMID:23785529

  3. Geographic Distribution, Age Pattern and Sites of Lesions in a Cohort of Buruli Ulcer Patients from the Mapé Basin of Cameroon

    PubMed Central

    Bratschi, Martin W.; Bolz, Miriam; Minyem, Jacques C.; Grize, Leticia; Wantong, Fidèle G.; Kerber, Sarah; Njih Tabah, Earnest; Ruf, Marie-Thérèse; Mou, Ferdinand; Noumen, Djeunga; Um Boock, Alphonse; Pluschke, Gerd

    2013-01-01

    Buruli ulcer (BU), a neglected tropical disease of the skin, caused by Mycobacterium ulcerans, occurs most frequently in children in West Africa. Risk factors for BU include proximity to slow flowing water, poor wound care and not wearing protective clothing. Man-made alterations of the environment have been suggested to lead to increased BU incidence. M. ulcerans DNA has been detected in the environment, water bugs and recently also in mosquitoes. Despite these findings, the mode of transmission of BU remains poorly understood and both transmission by insects or direct inoculation from contaminated environment have been suggested. Here, we investigated the BU epidemiology in the Mapé basin of Cameroon where the damming of the Mapé River since 1988 is believed to have increased the incidence of BU. Through a house-by-house survey in spring 2010, which also examined the local population for leprosy and yaws, and continued surveillance thereafter, we identified, till June 2012, altogether 88 RT-PCR positive cases of BU. We found that the age adjusted cumulative incidence of BU was highest in young teenagers and in individuals above the age of 50 and that very young children (<5) were underrepresented among cases. BU lesions clustered around the ankles and at the back of the elbows. This pattern neither matches any of the published mosquito biting site patterns, nor the published distribution of small skin injuries in children, where lesions on the knees are much more frequent. The option of multiple modes of transmission should thus be considered. Analyzing the geographic distribution of cases in the Mapé Dam area revealed a closer association with the Mbam River than with the artificial lake. PMID:23785529

  4. Correlation between the compact regions predicted by the average distance map (ADM) and the biologically active sites in atrial natriuretic peptide.

    PubMed

    Kikuchi, T

    1992-10-01

    The prediction of the short-range compact regions of human atrial natriuretic peptide (alpha-hANP), one of the biologically active peptides, has been made by means of the Average Distance Map(ADM). We found out that the location of the predicted short-range compact regions is consistent with the structural units determined by the NMR analysis (Kobayashi et al., 1988). Furthermore, the short-range compact regions correspond well to the biologically active areas of atriopeptin (103-125)-amide (which is homologous peptide to alpha-hANP), detected by the glycine substitution technique (Konishi et al., 1987). The results suggest that a predicted short-range compact region can be regarded as a possible active site in a biologically active peptide.

  5. Sodium ions, acting at high-affinity extracellular sites, inhibit sodium-ATPase activity of the sodium pump by slowing dephosphorylation.

    PubMed Central

    Beaugé, L A; Glynn, I M

    1979-01-01

    1. It is known that extracellular Na+ ions, in low concentrations, inhibit Na+-ATPase activity in resealed red cell ghosts and that this inhibition is reversed by high concentrations of extracellular Na+. We have attempted to elucidate these actions of extracellular Na+ by investigating the dependence on Na+ concentration of (a) ATP-ADP exchange and Na+-ATPase activity both in native and in N-ethylmaleimide (NEM)-treated (Na+ + K+)-ATPase from pig kidney, and (b) the rate of hydrolysis of the phosphorylated kidney enzyme in the absence of K+ ions. 2. With the native enzyme, ATP-ADP exchange and Na+-ATPase activity showed similar responses to changes in Na+ concentration: a steep but S-shaped rise between 0 and 2.5 mM, a slight fall (exchange) or a plateau (ATPase) between 2.5 and 10 mM, and a roughly linear rise between 10 and 150 mM. With NEM-treated enzyme, the ATP-ADP exchange, which was greatly accelerated, showed no sign either of inhibition at intermediate Na+ concentrations or of the reversal of that inhibition at higher concentrations. The exchange rate increased with Na+ concentration in a smooth curve and was half-maximal at about 7 mM. 3. The effects, on ATP-ADP exchange, of changing the concentrations of ATP, ADP and Mg have also been investigated. With both native and NEM-treated enzyme, the interactions of ATP, ADP and Mg are complicated; they show that, for the reaction leading to ATP formation, either free ADP rather than MgADP is the substrate, or Mg2+ ions are inhibitory (or both). 4. Since NEM, in the conditions in which we have used it, is believed to act by inhibiting the conversion of an ADP-sensitive form of the phosphoenzyme (E1P) to an ADP-insensitive form (E2P), the absence of Na+ inhibition of ATP-ADP exchange in NEM-treated enzyme, together with the parallel effects of Na+ ions on the ATP-ADP exchange activity and on the Na+-ATPase activity of native enzyme, suggests that the inhibitory effect of external Na+ occurs after the conversion

  6. Mutational Analysis of Escherichia coli MoeA: Two Functional Activities Map to the Active Site Cleft

    SciTech Connect

    Nichols,J.; Xiang, S.; Schindelin, H.; Rajagopalan, K.

    2007-01-01

    The molybdenum cofactor is ubiquitous in nature, and the pathway for Moco biosynthesis is conserved in all three domains of life. Recent work has helped to illuminate one of the most enigmatic steps in Moco biosynthesis, ligation of metal to molybdopterin (the organic component of the cofactor) to form the active cofactor. In Escherichia coli, the MoeA protein mediates ligation of Mo to molybdopterin while the MogA protein enhances this process in an ATP-dependent manner. The X-ray crystal structures for both proteins have been previously described as well as two essential MogA residues, Asp49 and Asp82. Here we describe a detailed mutational analysis of the MoeA protein. Variants of conserved residues at the putative active site of MoeA were analyzed for a loss of function in two different, previously described assays, one employing moeA{sup -} crude extracts and the other utilizing a defined system. Oddly, no correlation was observed between the activity in the two assays. In fact, our results showed a general trend toward an inverse relationship between the activity in each assay. Moco binding studies indicated a strong correlation between a variant's ability to bind Moco and its activity in the purified component assay. Crystal structures of the functionally characterized MoeA variants revealed no major structural changes, indicating that the functional differences observed are not due to disruption of the protein structure. On the basis of these results, two different functional areas were assigned to regions at or near the MoeA active site cleft.

  7. High-resolution mapping of the HyHEL-10 epitope of chicken lysozyme by site-directed mutagenesis

    SciTech Connect

    Kam-Morgan, L.N.; Taylor, M.G.; Kirsch, J.F. ); Smith-Gill, S.J. ); Wilson, A.C.

    1993-05-01

    The complex formed between hen egg white lysozyme (HEL) and the monoclonal antibody HyHEL-10 Fab fragment has an interface composed of van der Waals interactions, hydrogen bonds, and a single ion pair. The antibody overlaps part of the active site cleft. Putative critical residues within the epitope region of HEL, identified from the x-ray crystallographic structure of the complex, were replaced by site-directed mutagenesis to probe their relative importance in determining affinity of the antibody for HEL. Twenty single mutations of HEL at three contact residues (Arg-21[sub HEL], Asp-101[sub HEL], and Gly-102[sub HEL]) and at a partially buried residue (Asn-19[sub HEL]) in the epitope were made, and the effects on the free energies of dissociation were measured. A correlation between increased amino acid side-chain volume and reduced affinity for HELs with mutations at position 101 was observed. The D101G[sub HEL] mutant is bound to HyHEL-10 as tightly as wild-type enzyme, but the [delta][delta]G[sub dissoc] is increased by about 2.2 kcal (9.2 kJ)/mol for the larger residues in this position. HEL variants with lysine or histidine replacements for arginine at position 21 are bound 1.4-2.7 times more tightly than those with neutral or negatively charged amino acids in this position. These exhibit 1/40 the affinity for HyHEL-10 Fab compared with wild type. There is no side-chain volume correlation with [delta][delta]G[sub dissoc] at position 21. Although Gly-102[sub HEL] and Asn-19[sub HEL] are in the epitope, replacements at these positions have no effect on the affinity of HEL for the antibody. 34 refs., 2 figs., 3 tabs.

  8. Mapping Calcium-Sensitive Regions in the Neuronal Calcium Sensor GCAP2 by Site-Specific Fluorescence Labeling.

    PubMed

    Sulmann, Stefan; Wallisch, Melanie; Scholten, Alexander; Christoffers, Jens; Koch, Karl-Wilhelm

    2016-05-10

    Myristoylation of most neuronal calcium sensor proteins, a group of EF-hand calcium-binding proteins mainly expressed in neuronal tissue, can have a strong impact on protein dynamics and functional properties. Intracellular oscillations of the free Ca(2+) concentration can trigger conformational changes in Ca(2+) sensors. The position and possible movements of the myristoyl group in the photoreceptor cell-specific Ca(2+) sensor GCAP2 are not well-defined but appear to be different from those of the highly homologous cognate GCAP1. We designed and applied a new group of diaminoterephthalate-derived fluorescent probes to label GCAP2 at a covalently attached 12-azido-dodecanoic acid (a myristoyl substitute) and at cysteine residues in critical positions. Fluorescence emission of dye-labeled GCAP2 decreased when going from low (10(-9) M) to high [Ca(2+)] (10(-3) M), reaching a half-maximal effect of fluorescence emission at 0.44 ± 0.07 μM. The modified acyl group can therefore monitor changes in the protein conformation during binding and dissociation of Ca(2+) in the physiological range of free [Ca(2+)]. However, fluorescence quenching studies showed that the dye-acyl chain was shielded from the quencher by an adjacent polypeptide region. Further probing three cysteine positions (C35, C111, and C131) by dye labeling revealed that all positions were also sensitive to a change in [Ca(2+)], but only one (C131) was sensitive to a change in [Mg(2+)]. We suggest a scenario during illumination of the photoreceptor cell in which Ca(2+) dissociates first from low and medium affinity binding sites. These steps are sensed by dyes in cysteines at positions 35 and 111. Release of Ca(2+) from high affinity sites is sensed by regions adjacent to the dye-labeled fatty acid and involves the critical conformational change leading to activating guanylate cyclase.

  9. Mapping of sites facing aqueous environment of voltage-gated proton channel at resting state: a study with PEGylation protection.

    PubMed

    Kurokawa, Tatsuki; Okamura, Yasushi

    2014-01-01

    Hv1 (also named, voltage-sensor only protein, VSOP) lacks an authentic pore domain, and its voltage sensor domain plays both roles in voltage sensing and proton permeation. The activities of a proton channel are intrinsic to protomers of Hv1, while Hv1 is dimeric in biological membranes; cooperative gating is exerted by interaction between two protomers. As the signature pattern conserved among voltage-gated channels and voltage-sensing phosphatase, Hv1 has multiple arginines intervened by two hydrophobic residues on the fourth transmembrane segment, S4. S4 moves upward relative to other helices upon depolarization, causing conformational change possibly leading to the formation of a proton-selective conduction pathway. However, detailed mechanisms of proton-selectivity and gating of Hv1 are unknown. Here we took an approach of PEGylation protection assay to define residues facing the aqueous environment of mouse Hv1 (mHv1). Accessibilities of two maleimide molecules, N-ethylmaleimide (NEM) and 4-acetamido-4'-maleimidylstilbene-2,2'-disulfonic acid (AMS), were examined on cysteine introduced into individual sites. Only the first arginine on S4 (R1: R201) was inaccessible by NEM and AMS in mHv1. This is consistent with previous results of electrophysiology on the resting state channel, suggesting that the accessibility profile represents the resting state of mHv1. D108, critical for proton selectivity, was accessible by AMS and NEM, suggesting that D108 faces the vestibule. F146, a site critical for blocking by a guanidinium-reagent, was accessible by NEM, suggesting that F146 also faces the inner vestibule. These findings suggest an inner vestibule lined by several residues on S2 including F146, D108 on S1, and the C-terminal half of S4.

  10. Antigenic mapping of an H9N2 avian influenza virus reveals two discrete antigenic sites and a novel mechanism of immune escape

    PubMed Central

    Peacock, Thomas; Reddy, Kolli; James, Joe; Adamiak, Beata; Barclay, Wendy; Shelton, Holly; Iqbal, Munir

    2016-01-01

    H9N2 avian influenza virus is a major cause of poultry production loss across Asia leading to the wide use of vaccines. Efficacy of vaccines is often compromised due to the rapid emergence of antigenic variants. To improve the effectiveness of vaccines in the field, a better understanding of the antigenic epitopes of the major antigen, hemagglutinin, is required. To address this, a panel of nine monoclonal antibodies were generated against a contemporary Pakistani H9N2 isolate, which represents a major Asian H9N2 viral lineage. Antibodies were characterized in detail and used to select a total of 26 unique ‘escape’ mutants with substitutions across nine different amino acid residues in hemagglutinin including seven that have not been described as antigenic determinants for H9N2 viruses before. Competition assays and structural mapping revealed two novel, discrete antigenic sites “H9-A” and “H9-B”. Additionally, a second subset of escape mutants contained amino acid deletions within the hemagglutinin receptor binding site. This constitutes a novel method of escape for group 1 hemagglutinins and could represent an alternative means for H9N2 viruses to overcome vaccine induced immunity. These results will guide surveillance efforts for arising antigenic variants as well as evidence based vaccine seed selection and vaccine design. PMID:26738561

  11. Crystal structure and mapping by site-directed mutagenesis of the collagen-binding epitope of an activated form of BM-40/SPARC/osteonectin.

    PubMed Central

    Sasaki, T; Hohenester, E; Göhring, W; Timpl, R

    1998-01-01

    The extracellular calcium-binding domain (positions 138-286) of the matrix protein BM-40 possesses a binding epitope of moderate affinity for several collagen types. This epitope was predicted to reside in helix alphaA and to be partially masked by helix alphaC. Here we show that deletion of helix alphaC produces a 10-fold increase in collagen affinity similar to that seen after proteolytic cleavage of this helix. The predicted removal of the steric constraint was clearly demonstrated by the crystal structure of the mutant at 2.8 A resolution. This constitutively activated mutant was used to map the collagen-binding site following alanine mutagenesis at 13 positions. Five residues were crucial for binding, R149 and N156 in helix alphaA, and L242, M245 and E246 in a loop region connecting the two EF hands of BM-40. These residues are spatially close and form a flat ring of 15 A diameter which matches the diameter of a triple-helical collagen domain. The mutations showed similar effects on binding to collagens I and IV, indicating nearly identical binding sites on both collagens. Selected mutations in the non-activated mutant DeltaI also reduced collagen binding, consistent with the same location of the epitope but in a more cryptic form in intact BM-40. PMID:9501084

  12. Application of Earth Sciencés Technology in Mapping the of Brazilian Coast: Localization, Analysis & Monitoring of the Archaeological Sites with Remote Sensing & LiDAR

    NASA Astrophysics Data System (ADS)

    Thompson Alves de Souza, Carlos Eduardo

    Application of Earth Sciencés Technology in Mapping the of Brazilian Coast: Localization, Analysis & Monitoring of the Archaeological Sites with Remote Sensing & LiDAR Carlos Eduardo Thompson Alves de Souza cethompsoniii@hotmail.com Archaeologist Member of the European Association of Archaeologists B.A.Archaeology MA.Remote Sensing Abstract The Archaeological Research in Urban Environment with the Air Light Detection and Ranging is problematic for the Overlay Layers mixed with contexts concerning the Interpretation of Archaeological Data. However, in the Underwater Archaeology the results are excellent. This paper considers the application of Remote Sensing and Air Light Detection and Ranging (LIDAR) as separate things as well as Land Archaeology and the Underwater Archaeology. European Archaeologists know very little about Brazil and the article presents an Overview of Research in Brazil with Remote Sensing in Archaeology and Light Detection and Ranging in Land Archaeology and Underwater Archaeology, because Brazil has Continental Dimensions. Braziliańs Methodology for Location, Analysis and Monitoring of Archaeological Sites is necessarily more Complex and Innovative and therefore can serve as a New Paradigm for other archaeologists involved in the Advanced Management Heritage.

  13. Mapping protein conformational heterogeneity under pressure with site-directed spin labeling and double electron-electron resonance.

    PubMed

    Lerch, Michael T; Yang, Zhongyu; Brooks, Evan K; Hubbell, Wayne L

    2014-04-01

    The dominance of a single native state for most proteins under ambient conditions belies the functional importance of higher-energy conformational states (excited states), which often are too sparsely populated to allow spectroscopic investigation. Application of high hydrostatic pressure increases the population of excited states for study, but structural characterization is not trivial because of the multiplicity of states in the ensemble and rapid (microsecond to millisecond) exchange between them. Site-directed spin labeling in combination with double electron-electron resonance (DEER) provides long-range (20-80 Å) distance distributions with angstrom-level resolution and thus is ideally suited to resolve conformational heterogeneity in an excited state populated under high pressure. DEER currently is performed at cryogenic temperatures. Therefore, a method was developed for rapidly freezing spin-labeled proteins under pressure to kinetically trap the high-pressure conformational ensemble for subsequent DEER data collection at atmospheric pressure. The methodology was evaluated using seven doubly-labeled mutants of myoglobin designed to monitor selected interhelical distances. For holomyoglobin, the distance distributions are narrow and relatively insensitive to pressure. In apomyoglobin, on the other hand, the distributions reveal a striking conformational heterogeneity involving specific helices in the pressure range of 0-3 kbar, where a molten globule state is formed. The data directly reveal the amplitude of helical fluctuations, information unique to the DEER method that complements previous rate determinations. Comparison of the distance distributions for pressure- and pH-populated molten globules shows them to be remarkably similar despite a lower helical content in the latter. PMID:24707053

  14. Mapping general anesthetic binding site(s) in human α1β3 γ-aminobutyric acid type A receptors with [³H]TDBzl-etomidate, a photoreactive etomidate analogue.

    PubMed

    Chiara, David C; Dostalova, Zuzana; Jayakar, Selwyn S; Zhou, Xiaojuan; Miller, Keith W; Cohen, Jonathan B

    2012-01-31

    The γ-aminobutyric acid type A receptor (GABA(A)R) is a target for general anesthetics of diverse chemical structures, which act as positive allosteric modulators at clinical doses. Previously, in a heterogeneous mixture of GABA(A)Rs purified from bovine brain, [³H]azietomidate photolabeling of αMet-236 and βMet-286 in the αM1 and βM3 transmembrane helices identified an etomidate binding site in the GABA(A)R transmembrane domain at the interface between the β and α subunits [Li, G. D., et.al. (2006) J. Neurosci. 26, 11599-11605]. To further define GABA(A)R etomidate binding sites, we now use [³H]TDBzl-etomidate, an aryl diazirine with broader amino acid side chain reactivity than azietomidate, to photolabel purified human FLAG-α1β3 GABA(A)Rs and more extensively identify photolabeled GABA(A)R amino acids. [³H]TDBzl-etomidate photolabeled in an etomidate-inhibitable manner β3Val-290, in the β3M3 transmembrane helix, as well as α1Met-236 in α1M1, a residue photolabeled by [³H]azietomidate, while no photolabeling of amino acids in the αM2 and βM2 helices that also border the etomidate binding site was detected. The location of these photolabeled amino acids in GABA(A)R homology models derived from the recently determined structures of prokaryote (GLIC) or invertebrate (GluCl) homologues and the results of computational docking studies predict the orientation of [³H]TDBzl-etomidate bound in that site and the other amino acids contributing to this GABA(A)R intersubunit etomidate binding site. Etomidate-inhibitable photolabeling of β3Met-227 in βM1 by [³H]TDBzl-etomidate and [³H]azietomidate also provides evidence of a homologous etomidate binding site at the β3-β3 subunit interface in the α1β3 GABA(A)R.

  15. Progress report on the scientific investigation program for the Nevada Yucca Mountain site, September 15, 1988--September 30, 1989; Nuclear Waste Policy Act (Section 113), Number 1

    SciTech Connect

    1990-02-01

    The Department of Energy (DOE) has prepared this report on the progress of site characterization activities at Yucca Mountain in southern Nevada. This report is the first of a series of reports that will hereafter be issued at intervals of approximately 6-months during site characterization. The DOE`s plans for site characterization are described in the Site Characterization Plan (SCP) for the Yucca Mountain site. The SCP has been reviewed and commented on by the NRC, the State of Nevada, the affected units of local government, other interested parties, and the public. More detailed information on plans for site characterization is being presented in study plans for the various site characterization activities. This progress report presents short summaries of the status of site characterization activities and cites technical reports and research products that provide more detailed information on the activities. The report provides highlights of work started during the reporting period, work in progress, and work completed and documented during the reporting period. In addition, the report is the vehicle for discussing major changes, if any, to the DOE`s site characterization program resulting from ongoing collection and evaluation of site information; the development of repository and waste-package designs; receipt of performance-assessment results; and changes, if any, that occur in response to external comments on the site characterization programs. 80 refs.

  16. Substantial prevalence of microdeletions of the Y-chromosome in infertile men with idiopathic azoospermia and oligozoospermia detected using a sequence-tagged site-based mapping strategy

    SciTech Connect

    Najmabadi, H.; Huang, V.; Bhasin, D.

    1996-04-01

    Genes on the long arm of Y (Yq), particularly within interval 6, are believed to play a critical role in human spermatogenesis. Cytogenetically detectable deletions of this region are associated with azoospermia in men, but are relatively uncommon. The objective of this study was to validate a sequence-tagged site (STS)-mapping strategy for the detection of Yq microdeletions and to use this method to determine the proportion of men with idiopathic azoospermia or severe oligozoospermia who carry microdeletions in Yq. STS mapping of a sufficiently large sample of infertile men should also help further localize the putative gene(s) involved in the pathogenesis of male infertility. Genomic DNA was extracted from peripheral leukocytes of 16 normal fertile men, 7 normal fertile women, 60 infertile men, and 15 patients with the X-linked disorder, ichthyosis. PCR primers were synthesized for 26 STSs that span Yq interval 6. None of the 16 normal men of known fertility had microdeletions. Seven normal fertile women failed to amplify any of the 26 STSs, providing evidence of their Y specificity. No microdeletions were detected in any of the 15 patients with ichthyosis. Of the 60 infertile men typed with 26 STSs, 11 (18%; 10 azoospermic and 1 oligozoospermic) failed to amplify 1 or more STS. Interestingly, 4 of the 11 patients had microdeletions in a region that is outside the Yq region from which the DAZ (deleted in azoospermia gene region) gene was cloned. In an additional 3 patients, microdeletions were present both inside and outside the DAZ region. The physical locations of these microdeletions provide further support for the concept that a gene(s) on Yq deletion interval 6 plays an important role in spermatogenesis. The presence of deletions that do not overlap with the DAZ region suggests that genes other than the DAZ gene may also be implicated in the pathogenesis of some subsets of male infertility. 48 refs., 2 figs., 2 tabs.

  17. A genomic library-based amplification approach (GL-PCR) for the mapping of multiple IS6110 insertion sites and strain differentiation of Mycobacterium tuberculosis.

    PubMed

    Namouchi, Amine; Mardassi, Helmi

    2006-11-01

    Evidence suggests that insertion of the IS6110 element is not without consequence to the biology of Mycobacterium tuberculosis complex strains. Thus, mapping of multiple IS6110 insertion sites in the genome of biomedically relevant clinical isolates would result in a better understanding of the role of this mobile element, particularly with regard to transmission, adaptability and virulence. In the present paper, we describe a versatile strategy, referred to as GL-PCR, that amplifies IS6110-flanking sequences based on the construction of a genomic library. M. tuberculosis chromosomal DNA is fully digested with HincII and then ligated into a plasmid vector between T7 and T3 promoter sequences. The ligation reaction product is transformed into Escherichia coli and selective PCR amplification targeting both 5' and 3' IS6110-flanking sequences are performed on the plasmid library DNA. For this purpose, four separate PCR reactions are performed, each combining an outward primer specific for one IS6110 end with either T7 or T3 primer. Determination of the nucleotide sequence of the PCR products generated from a single ligation reaction allowed mapping of 21 out of the 24 IS6110 copies of two 12 banded M. tuberculosis strains, yielding an overall sensitivity of 87,5%. Furthermore, by simply comparing the migration pattern of GL-PCR-generated products, the strategy proved to be as valuable as IS6110 RFLP for molecular typing of M. tuberculosis complex strains. Importantly, GL-PCR was able to discriminate between strains differing by a single IS6110 band. PMID:16725220

  18. A Laser Absorption Spectroscopy System for 2D Mapping of CO2 Over Large Spatial Areas for Monitoring, Reporting and Verification of Ground Carbon Storage Sites

    NASA Astrophysics Data System (ADS)

    Dobler, J. T.; Braun, M.; Blume, N.; McGregor, D.; Zaccheo, T. S.; Pernini, T.; Botos, C.

    2014-12-01

    We will present the development of the Greenhouse gas Laser Imaging Tomography Experiment (GreenLITE). GreenLITE consists of two laser based transceivers and a number of retro-reflectors to measure differential transmission (DT) of a number of overlapping chords in a plane over the site being monitored. The transceivers use the Intensity Modulated Continuous Wave (IM-CW) approach, which is a technique that allows simultaneous transmission/reception of multiple fixed wavelength lasers and a lock-in, or matched filter, to measure amplitude and phase of the different wavelengths in the digital domain. The technique was developed by Exelis and has been evaluated using an airborne demonstrator for the past 10 years by NASA Langley Research Center. The method has demonstrated high accuracy and high precision measurements as compared to an in situ monitor tracable to WMO standards, agreeing to 0.65 ppm +/-1.7 ppm. The GreenLITE system is coupled to a cloud-based data storage and processing system that takes the measured chord data, along with auxiliary data to retrieve an average CO2 concentration per chord and which combines the chords to provide an estimate of the spatial distribution of CO2 concentration in the plane. A web-based interface allows users to view real-time CO2 concentrations and 2D concentration maps of the area being monitored. The 2D maps can be differenced as a function of time for an estimate of the flux across the plane measured by the system. The system is designed to operate autonomously from semi-remote locations with a very low maintenance cycle. Initial instrument tests, conducted in June, showed signal to noise in the measured ratio of >3000 for 10 s averages. Additional local field testing and a quantifiable field testing at the Zero Emissions Research and Technology (ZERT) site in Bozeman, MT are planned for this fall. We will present details on the instrument and software tools that have been developed, along with results from the local

  19. AthaMap web tools for database-assisted identification of combinatorial cis-regulatory elements and the display of highly conserved transcription factor binding sites in Arabidopsis thaliana.

    PubMed

    Steffens, Nils Ole; Galuschka, Claudia; Schindler, Martin; Bülow, Lorenz; Hehl, Reinhard

    2005-07-01

    The AthaMap database generates a map of cis-regulatory elements for the Arabidopsis thaliana genome. AthaMap contains more than 7.4 x 10(6) putative binding sites for 36 transcription factors (TFs) from 16 different TF families. A newly implemented functionality allows the display of subsets of higher conserved transcription factor binding sites (TFBSs). Furthermore, a web tool was developed that permits a user-defined search for co-localizing cis-regulatory elements. The user can specify individually the level of conservation for each TFBS and a spacer range between them. This web tool was employed for the identification of co-localizing sites of known interacting TFs and TFs containing two DNA-binding domains. More than 1.8 x 10(5) combinatorial elements were annotated in the AthaMap database. These elements can also be used to identify more complex co-localizing elements consisting of up to four TFBSs. The AthaMap database and the connected web tools are a valuable resource for the analysis and the prediction of gene expression regulation at http://www.athamap.de. PMID:15980498

  20. Proposal for a study of computer mapping of terrain using multispectral data from ERTS-A for the Yellowstone National Park test site

    NASA Technical Reports Server (NTRS)

    Smedes, H. W. (Principal Investigator); Root, R. R.; Roller, N. E. G.; Despain, D.

    1978-01-01

    The author has identified the following significant results. A terrain map of Yellowstone National Park showed plant community types and other classes of ground cover in what is basically a wild land. The map comprised 12 classes, six of which were mapped with accuracies of 70 to 95%. The remaining six classes had spectral reflectances that overlapped appreciably, and hence, those were mapped less accurately. Techniques were devised for quantitatively comparing the recognition map of the park with control data acquired from ground inspection and from analysis of sidelooking radar images, a thermal IR mosaic, and IR aerial photos of several scales. Quantitative analyses were made in ten 40 sq km test areas. Comparison mechanics were performed by computer with the final results displayed on line printer output. Forested areas were mapped by computer using ERTS data for less than 1/4 the cost of the conventional forest mapping technique for topographic base maps.

  1. Negotiation and Decision Making with Collaborative Software: How MarineMap `Changed the Game' in California's Marine Life Protected Act Initiative

    NASA Astrophysics Data System (ADS)

    Cravens, Amanda E.

    2016-02-01

    Environmental managers and planners have become increasingly enthusiastic about the potential of decision support tools (DSTs) to improve environmental decision-making processes as information technology transforms many aspects of daily life. Discussions about DSTs, however, rarely recognize the range of ways software can influence users' negotiation, problem-solving, or decision-making strategies and incentives, in part because there are few empirical studies of completed processes that used technology. This mixed-methods study—which draws on data from approximately 60 semi-structured interviews and an online survey—examines how one geospatial DST influenced participants' experiences during a multi-year marine planning process in California. Results suggest that DSTs can facilitate communication by creating a common language, help users understand the geography and scientific criteria in play during the process, aid stakeholders in identifying shared or diverging interests, and facilitate joint problem solving. The same design features that enabled the tool to aid in decision making, however, also presented surprising challenges in certain circumstances by, for example, making it difficult for participants to discuss information that was not spatially represented on the map-based interface. The study also highlights the importance of the social context in which software is developed and implemented, suggesting that the relationship between the software development team and other participants may be as important as technical software design in shaping how DSTs add value. The paper concludes with considerations to inform the future use of DSTs in environmental decision-making processes.

  2. Negotiation and Decision Making with Collaborative Software: How MarineMap 'Changed the Game' in California's Marine Life Protected Act Initiative.

    PubMed

    Cravens, Amanda E

    2016-02-01

    Environmental managers and planners have become increasingly enthusiastic about the potential of decision support tools (DSTs) to improve environmental decision-making processes as information technology transforms many aspects of daily life. Discussions about DSTs, however, rarely recognize the range of ways software can influence users' negotiation, problem-solving, or decision-making strategies and incentives, in part because there are few empirical studies of completed processes that used technology. This mixed-methods study-which draws on data from approximately 60 semi-structured interviews and an online survey--examines how one geospatial DST influenced participants' experiences during a multi-year marine planning process in California. Results suggest that DSTs can facilitate communication by creating a common language, help users understand the geography and scientific criteria in play during the process, aid stakeholders in identifying shared or diverging interests, and facilitate joint problem solving. The same design features that enabled the tool to aid in decision making, however, also presented surprising challenges in certain circumstances by, for example, making it difficult for participants to discuss information that was not spatially represented on the map-based interface. The study also highlights the importance of the social context in which software is developed and implemented, suggesting that the relationship between the software development team and other participants may be as important as technical software design in shaping how DSTs add value. The paper concludes with considerations to inform the future use of DSTs in environmental decision-making processes. PMID:26429362

  3. Negotiation and Decision Making with Collaborative Software: How MarineMap 'Changed the Game' in California's Marine Life Protected Act Initiative.

    PubMed

    Cravens, Amanda E

    2016-02-01

    Environmental managers and planners have become increasingly enthusiastic about the potential of decision support tools (DSTs) to improve environmental decision-making processes as information technology transforms many aspects of daily life. Discussions about DSTs, however, rarely recognize the range of ways software can influence users' negotiation, problem-solving, or decision-making strategies and incentives, in part because there are few empirical studies of completed processes that used technology. This mixed-methods study-which draws on data from approximately 60 semi-structured interviews and an online survey--examines how one geospatial DST influenced participants' experiences during a multi-year marine planning process in California. Results suggest that DSTs can facilitate communication by creating a common language, help users understand the geography and scientific criteria in play during the process, aid stakeholders in identifying shared or diverging interests, and facilitate joint problem solving. The same design features that enabled the tool to aid in decision making, however, also presented surprising challenges in certain circumstances by, for example, making it difficult for participants to discuss information that was not spatially represented on the map-based interface. The study also highlights the importance of the social context in which software is developed and implemented, suggesting that the relationship between the software development team and other participants may be as important as technical software design in shaping how DSTs add value. The paper concludes with considerations to inform the future use of DSTs in environmental decision-making processes.

  4. Mapping structural landmarks, ligand binding sites and missense mutations to the collagen IV heterotrimers predicts major functional domains, novel interactions and variation in phenotypes in inherited diseases affecting basement membranes

    PubMed Central

    Des Parkin, J.; San Antonio, James D.; Pedchenko, Vadim; Hudson, Billy; Jensen, Shane T.; Savige, Judy

    2016-01-01

    Collagen IV is the major protein found in basement membranes. It comprises 3 heterotrimers (α1α1α2, α3α4α5, and α5α5α6) that form distinct networks, and are responsible for membrane strength and integrity. We constructed linear maps of the collagen IV heterotrimers (‘interactomes’) that indicated major structural landmarks, known and predicted ligand-binding sites, and missense mutations, in order to identify functional and disease-associated domains, potential interactions between ligands, and genotype-phenotype relationships. The maps documented more than 30 known ligand-binding sites as well as motifs for integrins, heparin, von Willebrand factor (VWF), decorin and bone morphogenetic protein (BMP). They predicted functional domains for angiogenesis and haemostasis, and disease domains for autoimmunity, tumor growth and inhibition, infection and glycation. Cooperative ligand interactions were indicated by binding site proximity, for example, between integrins, matrix metalloproteinases and heparin. The maps indicated that mutations affecting major ligand-binding sites, for example for Von Hippel Lindau (VHL) protein in the α1 chain or integrins in the α5 chain, resulted in distinctive phenotypes (Hereditary Angiopathy, Nephropathy, Aneurysms and muscle Cramps (HANAC) syndrome, and early onset Alport syndrome respectively). These maps further our understanding of basement membrane biology and disease, and suggest novel membrane interactions, functions, and therapeutic targets. PMID:21280145

  5. Mapping the Interaction Sites between AMPA Receptors and TARPs Reveals a Role for the Receptor N-Terminal Domain in Channel Gating

    PubMed Central

    Cais, Ondrej; Herguedas, Beatriz; Krol, Karolina; Cull-Candy, Stuart G.; Farrant, Mark; Greger, Ingo H.

    2014-01-01

    Summary AMPA-type glutamate receptors (AMPARs) mediate fast neurotransmission at excitatory synapses. The extent and fidelity of postsynaptic depolarization triggered by AMPAR activation are shaped by AMPAR auxiliary subunits, including the transmembrane AMPAR regulatory proteins (TARPs). TARPs profoundly influence gating, an effect thought to be mediated by an interaction with the AMPAR ion channel and ligand binding domain (LBD). Here, we show that the distal N-terminal domain (NTD) contributes to TARP modulation. Alterations in the NTD-LBD linker result in TARP-dependent and TARP-selective changes in AMPAR gating. Using peptide arrays, we identify a TARP interaction region on the NTD and define the path of TARP contacts along the LBD surface. Moreover, we map key binding sites on the TARP itself and show that mutation of these residues mediates gating modulation. Our data reveal a TARP-dependent allosteric role for the AMPAR NTD and suggest that TARP binding triggers a drastic reorganization of the AMPAR complex. PMID:25373908

  6. High resolution genetic mapping uncovers chitin synthase-1 as the target-site of the structurally diverse mite growth inhibitors clofentezine, hexythiazox and etoxazole in Tetranychus urticae

    PubMed Central

    Demaeght, Peter; Osborne, Edward J.; Odman-Naresh, Jothini; Grbić, Miodrag; Nauen, Ralf; Merzendorfer, Hans

    2014-01-01

    The acaricides clofentezine, hexythiazox and etoxazole are commonly referred to as ‘mite growth inhibitors’, and clofentezine and hexythiazox have been used successfully for the integrated control of plant mite pests for decades. Although they are still important today, their mode of action has remained elusive. Recently, a mutation in chitin synthase 1 (CHS1) was linked to etoxazole resistance. In this study, we identified and investigated a T. urticae strain (HexR) harboring recessive, monogenic resistance to each of hexythiazox, clofentezine, and etoxazole. To elucidate if there is a common genetic basis for the observed cross-resistance, we adapted a previously developed bulk segregant analysis method to map with high resolution a single, shared resistance locus for all three compounds. This finding indicates that the underlying molecular basis for resistance to all three compounds is identical. This locus is centered on the CHS1 gene, and as supported by additional genetic and biochemical studies, a non-synonymous variant (I1017F) in CHS1 associates with resistance to each of the tested acaricides in HexR. Our findings thus demonstrate a shared molecular mode of action for the chemically diverse mite growth inhibitors clofentezine, hexythiazox and etoxazole as inhibitors of an essential, non-catalytic activity of CHS1. Given the previously documented cross-resistance between clofentezine, hexythiazox and the benzyolphenylurea compounds flufenoxuron and cycloxuron, CHS1 should be also considered as a potential target-site of insecticidal BPUs. PMID:24859419

  7. Rock slope stability analysis along the North Carolina section of the Blue Ridge Parkway: Using a geographic information system (GIS) to integrate site data and digital geologic maps

    USGS Publications Warehouse

    Latham, R.S.; Wooten, R.M.; Cattanach, B.L.; Merschat, C.E.; Bozdog, G.N.

    2009-01-01

    In 2008, the North Carolina Geological Survey (NCGS) completed a five-year geologic and geohazards inventory of the 406-km long North Carolina segment of the Blue Ridge Parkway (BRP). The ArcGIS??? format deliverables for rock slopes include a slope movement and slope movement deposit database and maps and site-specific rock slope stability assessments at 158 locations. Database entries for known and potential rock slope failures include: location data, failure modes and dimensions, activity dates and levels, structural and lithologic data, the occurrence of sulfide minerals and acid-producing potential test results. Rock slope stability assessments include photographs of the rock cuts and show locations and orientations of rock data, seepage zones, and kinematic stability analyses. Assigned preliminary geologic hazard ratings of low, moderate and high indicate the generalized relative probability of rock fall and/or rock slide activity at a given location. Statistics compiled based on the database indicate some general patterns within the data. This information provides the National Park Service with tools that can aid in emergency preparedness, and in budgeting mitigation, maintenance and repair measures. Copyright 2009 ARMA, American Rock Mechanics Association.

  8. Gene for the catalytic subunit of the human DNA-activated protein kinase maps to the site of the XRCC7 gene on chromosome 8

    SciTech Connect

    Sipley, J.D.; Anderson, C.W.; Menninger, J.C.

    1995-08-01

    The DNA-activated serine/threonine protein kinase (DNA-PK) is composed for a large ({approximately}460 kDa) catalytic polypeptide (DNA-PK{sub cs}) and Ku, a heterodimeric DNA-binding component (p70/p80) that targets DNA-PK{sub cs} to DNA. A 41-kbp segment of the DNA-PK{sub cs} gene was isolated, and a 7902-bp segment was sequenced. The sequence contains a polymorphic Pvu II restriction enzyme site, and comparing the sequence with that of the cDNA revealed the positions of nine exons. The DNA-PK{sub cs} gene was mapped to band q11 of chromosome 8 by in situ hybridization. This location is coincident with that of XRCC7, the gene that complements the DNA double-strand break repair and V(D)J recombination defects (where V is variable, D is diversity, and J is joining) of hamster V3 and murine severe combined immunodeficient (scid) cells. 50 refs., 4 figs., 2 tabs.

  9. Geologic Maps and Cross Sections of the Tuba City Open Dump Site and Vicinity, With Implications for the Occurrence and Flow of Ground Water

    USGS Publications Warehouse

    Otton, James K.; Johnson, Ray H.; Horton, Robert J.

    2008-01-01

    This report is designed to make available to interested parties geologic and limited hydrologic and geochemical information about the Tuba City Open Dump (TCOD) site. This information has been gathered during studies of the site from January to September 2008. Mapping by the authors and construction of cross sections show that a section of gently northeast-dipping Jurassic sedimentary rocks underlies the TCOD and vicinity. Low mesas in the area are capped by variably cemented gravels and siliceous limestones. Surficial sediments are composed of eolian sand and fluvially reworked eolian sand that overlie bedrock underneath the TCOD. Nearby Pasture Canyon is underlain by fluvial and floodplain sediment consisting of sand and silt. Shallow ground water of the water-table aquifer at the TCOD moves westward through the surficial sediment and the underlying weathered bedrock to Pasture Canyon then southward along the canyon. A fracture zone extends up the wash that passes just to the north of the TCOD and brings deeper ground water of the N-aquifer to the water-table aquifer. Bedrock consists of the Jurassic Navajo Sandstone composed of thick sections of eolian crossbedded sandstone with lesser laterally discontinuous layers of silty sandstone, siltstone, and limestone. Below the Navajo Sandstone is a section informally known as the Kayenta Formation-Navajo Sandstone transition zone. It is composed of calcareous sandstone, silty sandstone, siltstone, and limestone beds that intertongue with crossbedded sandstone. The finer grained rocks in both major bedrock units form aquitards that limit downward movement of ground water. The water-table aquifer is perched on these aquitards, which locally occurs beneath the two open dumps that form the TCOD site. A monocline occupies the position of Pasture Canyon west of the TCOD. Fractures likely related to the monocline are exposed in several localities. Deep ground waters consist of dilute calcium-bicarbonate waters low in all

  10. Site characterization progress report: Yucca Mountain, Nevada, April 1, 1991--September 30, 1991, Number 5; Nuclear Waste Policy Act (Section 113)

    SciTech Connect

    1992-06-01

    The Site Characterization Progress Report of Yucca Mountain (PR) presents brief summaries of the status of site characterization activities and cites the technical reports and research products that provide more detailed information on the activities. The report provides highlights of work started during the reporting period, work in progress, and work completed and documented during the reporting period. In addition, the report is the vehicle for the discussion of changes to the DOE`s site characterization program resulting from ongoing collection and evaluation of site information; the development of repository and waste-package designs; the results of performance assessments; and any changes that occur in response to external comments. Information covered includes geochemistry, hydrology, geology, climate, and radiation dose estimate calculations.

  11. Sub-crop geologic map of pre-Tertiary rocks in the Yucca Flat and northern Frenchman Flat areas, Nevada Test Site, southern Nevada

    SciTech Connect

    Cole, J.C.; Harris, A.G.; Wahl, R.R.

    1997-10-02

    This map displays interpreted structural and stratigraphic relations among the Paleozoic and older rocks of the Nevada Test Site region beneath the Miocene volcanic rocks and younger alluvium in the Yucca Flat and northern Frenchman Flat basins. These interpretations are based on a comprehensive examination and review of data for more than 77 drillholes that penetrated part of the pre-Tertiary basement beneath these post-middle Miocene structural basins. Biostratigraphic data from conodont fossils were newly obtained for 31 of these holes, and a thorough review of all prior microfossil paleontologic data is incorporated in the analysis. Subsurface relationships are interpreted in light of a revised regional geologic framework synthesized from detailed geologic mapping in the ranges surrounding Yucca Flat, from comprehensive stratigraphic studies in the region, and from additional detailed field studies on and around the Nevada Test Site. All available data indicate the subsurface geology of Yucca Flat is considerably more complicated than previous interpretations have suggested. The western part of the basin, in particular, is underlain by relics of the eastward-vergent Belted Range thrust system that are folded back toward the west and thrust by local, west-vergent contractional structures of the CP thrust system. Field evidence from the ranges surrounding the north end of Yucca Flat indicate that two significant strike-slip faults track southward beneath the post-middle Miocene basin fill, but their subsurface traces cannot be closely defined from the available evidence. In contrast, the eastern part of the Yucca Flat basin is interpreted to be underlain by a fairly simple north-trending, broad syncline in the pre-Tertiary units. Far fewer data are available for the northern Frenchman Flat basin, but regional analysis indicates the pre-Tertiary structure there should also be relatively simple and not affected by thrusting. This new interpretation has implications

  12. ACT: Acting Out Central Theme.

    ERIC Educational Resources Information Center

    Kise, Joan Duff

    1982-01-01

    The author describes ACT (Acting Out Central Theme), a method for dealing with psychomotor, cognitive, and affective domains in slow readers. The ACT approach involves three sessions which focus on discussion of a theme such as friendship, presentaton of the theme as a skit, and assignment of topics to individual students. (SW)

  13. Mapping the homotypic binding sites in CD31 and the role of CD31 adhesion in the formation of interendothelial cell contacts

    PubMed Central

    1995-01-01

    CD31 is a member of the immunoglobulin superfamily consisting of six Ig- related domains. It is constitutively expressed by platelets, monocytes, and some lymphocytes, but at tenfold higher levels on vascular endothelial cells. CD31 has both homotypic and heterotypic adhesive properties. We have mapped the homotypic binding sites using a deletion series of CD31-Fc chimeras and a panel of anti-CD31 monoclonal antibodies. An extensive surface of CD31 is involved in homotypic binding with domains 2 and 3 and domains 5 and 6 playing key roles. A model consistent with the experimental data is that CD31 on one cell binds to CD31 on an apposing cell in an antiparallel interdigitating mode requiring full alignment of the six domains of each molecule. In addition to establishing intercellular homotypic contacts. CD31 binding leads to augmented adhesion via beta 1 integrins. The positive cooperation between CD31 and beta 1 integrins can occur in heterologous primate cells (COS cells). The interaction is specific to both CD31 and beta 1 integrins. Neither intercellular adhesion molecule-1 (ICAM- 1)/leukocyte function-associated antigen-1 (LCAM-1) nor neural cell adhesion molecule (NCAM)/NCAM adhesion leads to recruitment of beta 1 integrin adhesion pathways. Establishment of CD31 contacts have effects on the growth and morphology of endothelial cells. CD31(D1-D6)Fc inhibits the growth of endothelial cells in culture. In addition, papain fragments of anti-CD31 antibodies (Fab fragments) disrupt interendothelial contact formation and monolayer integrity when intercellular contacts are being formed. The same reagents are without effect once these contacts have been established, suggesting that CD31- CD31 interactions are critically important only in the initial phases of intercellular adhesion. PMID:7534767

  14. Two mutations in the locus control region hypersensitivity site-2 (5' HS-2) of haplotype 19 beta s chromosomes alter binding of trans-acting factors.

    PubMed

    Morgan, J C; Scott, D F; Lanclos, K D

    1996-01-01

    There are five major haplotypes associated with sickle cell anemia (SS). Individuals homozygous for haplotypes 3 (Senegal) and 31 (Saudi Arabian) have high fetal hemoglobin (HbF) levels (15 to 30% of total hemoglobin) whereas individuals homozygous for haplotypes 17 (Cameroon), 19 (Benin), and 20 (Bantu) have low HbF levels (1 to 10%). We previously identified several point mutations in the LCR 5'HS-2 that were specific for haplotype 19 beta s chromosomes (compared to the GenBank HUMHBB reference sequence, T-->G at position 8580, A-->G at position 8598, and A-->T at position 9114). We postulated that one or more of these mutations may alter the binding of specific trans-acting factors and ultimately affect the expression of HbF in these sickle cell patients. We performed gel mobility shift assays using 32P-end-labeled double-stranded 19mers corresponding to each of the LCR 5'HS-2 normal (GenBank) and mutant sequences. Nuclear extracts prepared from HeLa and HEL cells were used in our experiments and neither the normal nor mutant sequence at position 8580 bound trans-acting factors in either nuclear extract. The 8598 mutant increased binding of Sp1; using purified protein and both nuclear extracts. HEL extracts were used to quantify the increase in Sp1 binding to the 8598 mutation and we found an increase in binding of 66 and 47%, respectively, in two shifted bands. The 9114 mutation sharply decreased binding of an unknown trans-acting factor by 74%. This factor was present in both HeLa and HEL nuclear extracts.

  15. Site characterization progress report: Yucca Mountain, Nevada, October 1, 1994--March 31, 1995, Number 12. Nuclear Waste Policy Act (Section 113)

    SciTech Connect

    1995-08-01

    During the first half of fiscal year 1995, most activities at the Yucca Mountain Site Characterization Project were directed at implementing the Program Plan developed by the Office of Civilian Radioactive Waste Management. The Plan is designed to enable the Office to make measurable and significant progress toward key objectives over the next five years within the financial resources that can be realistically expected. Activities this period focused on the immediate goal of determining by 1998 whether Yucca Mountain, Nevada, is technically suitable as a possible site for a geologic repository for the permanent disposal of spent nuclear fuel and high-level radioactive waste. Work on the Project advanced in several critical areas, including programmatic activities such as issuing the Program Plan, completing the first technical basis report to support the assessment of three 10 CFR 960 guidelines, developing the Notice of Intent for the Environmental Impact Statement, submitting the License Application Annotated Outline, and beginning a rebaselining effort to con