Science.gov

Sample records for mapping interaction sites

  1. Interactive Maps

    Cancer.gov

    Close Window State Cancer Profiles Quick Reference Guides ? Quick Reference Guides Index Interactive Maps Send to Printer Text description of this image. Site Home Policies Accessibility Viewing Files FOIA Contact Us U.S. Department of Health and Human

  2. Site Map

    Cancer.gov

    Skip to Content The National Cancer Institute www.cancer.gov The National Institutes of Health Home About BBRB Mission and Goals BBRB Staff Biorepository Coordinating Committee (BCC) Interactive Timeline Related Initiatives International Initiatives Funding

  3. Interactive Maps

    Cancer.gov

    Provide maps of demographics, screening and risk factors, incidence and mortality statistics for use in assessing the burden and risk for a major cancer site for the US overall or for a selected state and its counties or parishes. The Healthy People 2020 objective for the US is provided in the legend when appropriate in order to give perspective on how favorably or unfavorably a location compares to this overall goal.

  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 success rate from different public web mapping sites was calculated and compared, and displayed by the means of diagram. And the answers from questionnaires were also classified and organized in this part. Moreover, based on the analysis, this paper expands the discussion about the layout, map visualization, map tools, search logic and etc. Finally, this paper closed with some valuable guidelines and suggestions for the design of public web mapping sites. Also, limitations for this research stated in the end.

  5. NCI: SBIR & STTR - Site Map

    Cancer.gov

    Skip to main content Sign Up for Updates | Follow us on Twitter | Connect with us on LinkedIn | Contact Us | Site Map Search About Program Information Program Structure Goals Eligibility Criteria Employment Opportunities Meet the Team Funding Opportunities Find

  6. mChIP-KAT-MS, a method to map protein interactions and acetylation sites for lysine acetyltransferases.

    PubMed

    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

    2013-04-23

    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

  7. 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

  8. 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

  9. 3D interactive pictorial maps 

    E-print Network

    Naz, Asma

    2005-02-17

    these maps interactive on the Web and have them accessible to a large number of viewers. The results show a number of interactive 3D pictorial maps of different countries and continents. These maps are initially built with Maya, a 3D modeling software... of simplififcation and exaggeration.. . . . . . . . . . . . . . 21 8 3D polygonal text in Maya. . . . . . . . . . . . . . . . . . . . . . . . 22 9 Final 3D model of Italy with text. . . . . . . . . . . . . . . . . . . . 23 10 Top view of 3D model of France...

  10. Site Map | Translational Research Program (TRP)

    Cancer.gov

    Skip to Content Search this site Last Updated: 11/11/13 Site Map Home SPOREs by Organ Location Bladder Brain Breast Cervical Endometrial GI Head & Neck Kidney Leukemia Lung Lymphoma Myeloma Ovarian Pancreatic Prostate Sarcoma Skin Thyroid SPOREs by

  11. Digital Soil Mapping: Interactions with

    E-print Network

    Grunwald, Sabine

    Chapter 21 Digital Soil Mapping: Interactions with and Applications for Hydropedology J.A. Thompson,1, * S. Roecker,2 S. Grunwald3 and P.R. Owens4 ABSTRACT Spatial information on soils, particularly hydrologic and hydromorphic soil properties, is used to understand and assess soil water retention, flooding

  12. Multimodal Interactive Maps: Designing for Human Performance.

    ERIC Educational Resources Information Center

    Oviatt, Sharon

    1997-01-01

    Analyzes interfaces supporting spoken, pen-based, and multimodal input for their effectiveness in interacting with interactive map systems. Results identified performance difficulties with speech-only map interactions that declined substantially when people could interact multimodally. Analyses also indicated that map displays can be structured to…

  13. Interactive Geophysical Mapping on the Web

    NASA Astrophysics Data System (ADS)

    Meertens, C.; Hamburger, M.; Estey, L.; Weingroff, M.; Deardorff, R.; Holt, W.

    2002-12-01

    We have developed a set of interactive, web-based map utilities that make geophysical results accessible to a large number and variety of users. These tools provide access to pre-determined map regions via a simple Html/JavaScript interface or to user-selectable areas using a Java interface to a Generic Mapping Tools (GMT) engine. Users can access a variety of maps, satellite images, and geophysical data at a range of spatial scales for the earth and other planets of the solar system. Developed initially by UNAVCO for study of global-scale geodynamic processes, users can choose from a variety of base maps (satellite mosaics, global topography, geoid, sea-floor age, strain rate and seismic hazard maps, and others) and can then add a number of geographic and geophysical overlays for example coastlines, political boundaries, rivers and lakes, NEIC earthquake and volcano locations, stress axes, and observed and model plate motion and deformation velocity vectors representing a compilation of 2933 geodetic measurements from around the world. The software design is flexible allowing for construction of special editions for different target audiences. Custom maps been implemented for UNAVCO as the "Jules Verne Voyager" and "Voyager Junior", for the International Lithosphere Project's "Global Strain Rate Map", and for EarthScope Education and Outreach as "EarthScope Voyager Jr.". For the later, a number of EarthScope-specific features have been added, including locations of proposed USArray (seismic), Plate Boundary Observatory (geodetic), and San Andreas Fault Observatory at Depth sites plus detailed maps and geographically referenced examples of EarthScope-related scientific investigations. In addition, we are developing a website that incorporates background materials and curricular activities that encourage users to explore Earth processes. A cluster of map processing computers and nearly a terabyte of disk storage has been assembled to power the generation of interactive maps and provide space for a very large collection of map data. A portal to these map tools can be found at: http://jules.unavco.ucar.edu.

  14. Mapping NEHRP VS30 site classes

    USGS Publications Warehouse

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

    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.

  15. 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.

  16. Golgi: Interactive Online Brain Mapping

    PubMed Central

    Brown, Ramsay A.; Swanson, Larry W.

    2015-01-01

    Golgi (http://www.usegolgi.com) is a prototype interactive brain map of the rat brain that helps researchers intuitively interact with neuroanatomy, connectomics, and cellular and chemical architecture. The flood of “-omic” data urges new ways to help researchers connect discrete findings to the larger context of the nervous system. Here we explore Golgi’s underlying reasoning and techniques and how our design decisions balance the constraints of building both a scientifically useful and usable tool. We demonstrate how Golgi can enhance connectomic literature searches with a case study investigating a thalamocortical circuit involving the Nucleus Accumbens and we explore Golgi’s potential and future directions for growth in systems neuroscience and connectomics. PMID:26635596

  17. Golgi: Interactive Online Brain Mapping.

    PubMed

    Brown, Ramsay A; Swanson, Larry W

    2015-01-01

    Golgi (http://www.usegolgi.com) is a prototype interactive brain map of the rat brain that helps researchers intuitively interact with neuroanatomy, connectomics, and cellular and chemical architecture. The flood of "-omic" data urges new ways to help researchers connect discrete findings to the larger context of the nervous system. Here we explore Golgi's underlying reasoning and techniques and how our design decisions balance the constraints of building both a scientifically useful and usable tool. We demonstrate how Golgi can enhance connectomic literature searches with a case study investigating a thalamocortical circuit involving the Nucleus Accumbens and we explore Golgi's potential and future directions for growth in systems neuroscience and connectomics. PMID:26635596

  18. NCORP :: Map

    Cancer.gov

    This interactive map application shows location and contact information of NCORP Research Bases, Community Sites, Minority Sites, Component Sites, and Subcomponent Sites in the United States. Click a Site Marker on the map to display additional information about these sites.

  19. Sense of Place Evoked by Interactive Maps 

    E-print Network

    Go, Hanyoung

    2012-07-16

    , spatial cognition, and virtual reality literature, this study constructed a conceptual framework to measure how different interactivity levels of a digital map interface affect potential tourists' experience when exploring maps. In addition, the study...

  20. Creating an Interactive Videodisc on Mapping.

    ERIC Educational Resources Information Center

    Andrews, Sona Karentz; Grozik, John

    1994-01-01

    Provides an overview of the University of Wisconsin-Milwaukee's Interactive Multimedia Cartography Project to create an interactive videodisc that would illustrate the topic of mapping and provide access to examples of cartography from the American Geographical Society Collection. (JLB)

  1. 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

  2. 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

  3. 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

  4. Interactive Multimedia, Concept Mapping, and Cultural Context.

    ERIC Educational Resources Information Center

    Henderson, L.; And Others

    Concept maps drawn by Aboriginal and Torres Strait Islander tertiary off-campus students were examined to determine the effectiveness of interactive multimedia as an instructional medium for teaching and learning in a multiple cultural context that integrates the requirements of academic culture and aspects of the students' cultures. Interactive

  5. 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 surface effects produced, and to learn about the organization and intended use of the map data contained in the archive.

  6. An improved map of conserved regulatory sites for Saccharomyces cerevisiae

    E-print Network

    Wang, Ting

    Background: The regulatory map of a genome consists of the binding sites for proteins that determine the transcription of nearby genes. An initial regulatory map for S. cerevisiae was recently published using six motif ...

  7. Data visualization in interactive maps and time series

    NASA Astrophysics Data System (ADS)

    Maigne, Vanessa; Evano, Pascal; Brockmann, Patrick; Peylin, Philippe; Ciais, Philippe

    2014-05-01

    State-of-the-art data visualization has nothing to do with plots and maps we used few years ago. Many opensource tools are now available to provide access to scientific data and implement accessible, interactive, and flexible web applications. Here we will present a web site opened November 2013 to create custom global and regional maps and time series from research models and datasets. For maps, we explore and get access to data sources from a THREDDS Data Server (TDS) with the OGC WMS protocol (using the ncWMS implementation) then create interactive maps with the OpenLayers javascript library and extra information layers from a GeoServer. Maps become dynamic, zoomable, synchroneaously connected to each other, and exportable to Google Earth. For time series, we extract data from a TDS with the Netcdf Subset Service (NCSS) then display interactive graphs with a custom library based on the Data Driven Documents javascript library (D3.js). This time series application provides dynamic functionalities such as interpolation, interactive zoom on different axes, display of point values, and export to different formats. These tools were implemented for the Global Carbon Atlas (http://www.globalcarbonatlas.org): a web portal to explore, visualize, and interpret global and regional carbon fluxes from various model simulations arising from both human activities and natural processes, a work led by the Global Carbon Project.

  8. 47 CFR 73.4108 - FM transmitter site map submissions.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ...2010-10-01 2010-10-01 false FM transmitter site map submissions. 73.4108 Section 73.4108 Telecommunication...to All Broadcast Stations § 73.4108 FM transmitter site map submissions. See Memorandum Opinion and Order and...

  9. 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.

  10. Fundamentals of protein interaction network mapping.

    PubMed

    Snider, Jamie; Kotlyar, Max; Saraon, Punit; Yao, Zhong; Jurisica, Igor; Stagljar, Igor

    2015-01-01

    Studying protein interaction networks of all proteins in an organism ("interactomes") remains one of the major challenges in modern biomedicine. Such information is crucial to understanding cellular pathways and developing effective therapies for the treatment of human diseases. Over the past two decades, diverse biochemical, genetic, and cell biological methods have been developed to map interactomes. In this review, we highlight basic principles of interactome mapping. Specifically, we discuss the strengths and weaknesses of individual assays, how to select a method appropriate for the problem being studied, and provide general guidelines for carrying out the necessary follow-up analyses. In addition, we discuss computational methods to predict, map, and visualize interactomes, and provide a summary of some of the most important interactome resources. We hope that this review serves as both a useful overview of the field and a guide to help more scientists actively employ these powerful approaches in their research. PMID:26681426

  11. Interactive Web Interface to the Global Strain Rate Map Project

    NASA Astrophysics Data System (ADS)

    Meertens, C. M.; Estey, L.; Kreemer, C.; Holt, W.

    2004-05-01

    An interactive web interface allows users to explore the results of a global strain rate and velocity model and to compare them to other geophysical observations. The most recent model, an updated version of Kreemer et al., 2003, has 25 independent rigid plate-like regions separated by deformable boundaries covered by about 25,000 grid areas. A least-squares fit was made to 4900 geodetic velocities from 79 different geodetic studies. In addition, Quaternary fault slip rate data are used to infer geologic strain rate estimates (currently only for central Asia). Information about the style and direction of expected strain rate is inferred from the principal axes of the seismic strain rate field. The current model, as well as source data, references and an interactive map tool, are located at the International Lithosphere Program (ILP) "A Global Strain Rate Map (ILP II-8)" project website: http://www-world-strain-map.org. The purpose of the ILP GSRM project is to provide new information from this, and other investigations, that will contribute to a better understanding of continental dynamics and to the quantification of seismic hazards. A unique aspect of the GSRM interactive Java map tool is that the user can zoom in and make custom views of the model grid and results for any area of the globe selecting strain rate and style contour plots and principal axes, observed and model velocity fields in specified frames of reference, and geologic fault data. The results can be displayed with other data sets such Harvard CMT earthquake focal mechanisms, stress directions from the ILP World Stress Map Project, and topography. With the GSRM Java map tool, the user views custom maps generated by a Generic Mapping Tool (GMT) server. These interactive capabilities greatly extend what is possible to present in a published paper. A JavaScript version, using pre-constructed maps, as well as a related information site have also been created for broader education and outreach access. The GSRM map tool will be demonstrated and latest model GSRM 1.1 results, containing important new data for Asia, Iran, western Pacific, and Southern California, will be presented.

  12. 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. PMID:25666474

  13. 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).

  14. Ground water maps of Hanford Site Separations Areas, December 1989

    SciTech Connect

    Kasza, G.L.

    1990-06-01

    The Separations Areas consist 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 Areas by Westinghouse Hanford Company for the US Department of Energy-Richland Operations Office. This set of ground water maps consists of: (1) Separations Areas depth-to-water map, (2) Separations Areas 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 December 1989. 3 figs., 1 tab.

  15. 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.

  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. Groundwater maps of the Hanford Site, June 1992

    SciTech Connect

    Kasza, G.L.; Hartman, M.J.; Hodges, F.N.; Weekes, D.C.

    1992-12-01

    The Groundwater Maps of the Hanford Site, June 1992 is an update to the series of reports that document the configuration of the water table in the unconsolidated sediments beneath the Hanford Site (Figure 1). Water level measurements for these reports are collected from site groundwater monitoring wells each June and December. The groundwater data are portrayed on a series of maps to illustrate the hydrologic conditions at the Hanford Site and are also tabulated in an appendix. The purpose of this report series is to document the changes in the groundwater level at Hanford as the site transitions from a nuclear material production role to environmental restoration and remediation. In addition, these reports provide water level data in support of the site characterization and groundwater monitoring programs 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).

  18. Groudwater maps of the Hanford Site Separations Area, June 1989

    SciTech Connect

    Kasza, G.L.; Reidel, S.P.; Schatz, A.L.

    1989-09-01

    The groundwater maps of the Hanford Site Separations Area, recorded June 1989, are prepared by the Environmental Engineering and Technology Function, Environmental Division, Westinghouse Hanford Company. This set of groundwater maps consists of Separations Area depth-to-water map, Separations Area water table map, and 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 June 1989. The Separations Area depth-to-water map depicts the measurement well locations and the depths to the water table at these locations. This map supports engineering or environmental studies which may require the approximate depth from the ground surface to the water table. On the third map, the potentiometric surface of the Rattlesnake Ridge confined aquifer is compared with the water table of the unconfined aquifer in the vicinity of West Lake, Gable Mountain Pond, and the B Pond system. The purpose of this map is to monitor the potential for aquifer intercommunication in this area. 3 figs., 1 tab.

  19. 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.

  20. Groundwater maps of the Hanford Site, December 1994

    SciTech Connect

    Serkowski, J.A.; Hartman, M.J.; Sweeney, M.D.

    1995-06-01

    This report is a continuation of a series of reports (see Serkowski et al 1994) that 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 groundwater monitoring programs currently in progress on the Hanford Site.

  1. 24 CFR 3285.103 - Site suitability with design zone maps.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ...false Site suitability with design zone maps. 3285.103 Section 3285.103 ...103 Site suitability with design zone maps. Prior to the initial installation...home, as indicated on the design zone maps provided with the home, are...

  2. INTERACTIVE NAME PLACEMENT FOR PROVISIONAL MAPS.

    USGS Publications Warehouse

    Goldberg, Jeffrey L.; Miller, Thomas C.

    1983-01-01

    Computer generation and placement of map type has been refined into a production mode at Mid-Continent Mapping Center (MCMC) for USGS 1:24,000- and 1:25,000-scale Provisional maps. The map collar program is written in FORTRAN using batch processing that allows the program to work in the background.

  3. 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

  4. Hanford site Computer Automated Mapping Information System (CAMIS)

    SciTech Connect

    Rush, S.F.

    1995-09-01

    The Computer Automated Mapping Information System (CAMIS) provides sitewide, networked access to CAD based geographically referenced data. CAMIS allows multiple organizations to maintain and share their data. Information collected and managed according to site-wide standards, enables each organization to focus their limited resources on data issues tied to their own discipline without having to collect or manage reference data outside their respective domains. Sharing information also minimizes redundant data and helps improve the overall quality of the sites` data resources.

  5. Quantitative Genetic Interaction Mapping Using the E-MAP Approach

    PubMed Central

    Collins, Sean R.; Roguev, Assen; Krogan, Nevan J.

    2010-01-01

    Genetic interactions represent the degree to which the presence of one mutation modulates the phenotype of a second mutation. In recent years, approaches for measuring genetic interactions systematically and quantitatively have proven to be effective tools for unbiased characterization of gene function and have provided valuable data for analyses of evolution. Here, we present protocols for systematic measurement of genetic interactions with respect to organismal growth rate for two yeast species. PMID:20946812

  6. An interactive method for digitizing zone maps

    NASA Technical Reports Server (NTRS)

    Giddings, L. E.; Thompson, E. J.

    1975-01-01

    A method is presented for digitizing maps that consist of zones, such as contour or climatic zone maps. A color-coded map is prepared by any convenient process. The map is then read into memory of an Image 100 computer by means of its table scanner, using colored filters. Zones are separated and stored in themes, using standard classification procedures. Thematic data are written on magnetic tape and these data, appropriately coded, are combined to make a digitized image on tape. Step-by-step procedures are given for digitization of crop moisture index maps with this procedure. In addition, a complete example of the digitization of a climatic zone map is given.

  7. 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.

  8. Access to Space Interactive Design Web Site

    NASA Technical Reports Server (NTRS)

    Leon, John; Cutlip, William; Hametz, Mark

    2000-01-01

    The Access To Space (ATS) Group at NASA's Goddard Space Flight Center (GSFC) supports the science and technology community at GSFC by facilitating frequent and affordable opportunities for access to space. Through partnerships established with access mode suppliers, the ATS Group has developed an interactive Mission Design web site. The ATS web site provides both the information and the tools necessary to assist mission planners in selecting and planning their ride to space. This includes the evaluation of single payloads vs. ride-sharing opportunities to reduce the cost of access to space. Features of this site include the following: (1) Mission Database. Our mission database contains a listing of missions ranging from proposed missions to manifested. Missions can be entered by our user community through data input tools. Data is then accessed by users through various search engines: orbit parameters, ride-share opportunities, spacecraft parameters, other mission notes, launch vehicle, and contact information. (2) Launch Vehicle Toolboxes. The launch vehicle toolboxes provide the user a full range of information on vehicle classes and individual configurations. Topics include: general information, environments, performance, payload interface, available volume, and launch sites.

  9. 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.

  10. 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 resolution GPS, LiDAR and hyperspectral imagery were also acquired. The LiDAR and hyperspectral data are being processed and will be added to the existing geo-referenced database as separate information layers for remote sensing analysis of surface features associated with the legacy test. By consolidating the various components of a VOB data point (coordinates, photo and item description) into a standalone database, searching or querying for other components or collects such as subsurface geophysical and/or airborne imagery is made much easier. Work by Los Alamos 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 Contract No. DE AC52 06NA25946 with the U.S. Department of Energy.

  11. Quantitative genetic-interaction mapping in mammalian cells

    PubMed Central

    Roguev, Assen; Talbot, Dale; Negri, Gian Luca; Shales, Michael; Cagney, Gerard; Bandyopadhyay, Sourav; Panning, Barbara; Krogan, Nevan J

    2013-01-01

    Mapping genetic interactions (GIs) by simultaneously perturbing pairs of genes is a powerful tool for understanding complex biological phenomena. Here we describe an experimental platform for generating quantitative GI maps in mammalian cells using a combinatorial RNA interference strategy. We performed ~11,000 pairwise knockdowns in mouse fibroblasts, focusing on 130 factors involved in chromatin regulation to create a GI map. Comparison of the GI and protein-protein interaction (PPI) data revealed that pairs of genes exhibiting positive GIs and/or similar genetic profiles were predictive of the corresponding proteins being physically associated. The mammalian GI map identified pathways and complexes but also resolved functionally distinct submodules within larger protein complexes. By integrating GI and PPI data, we created a functional map of chromatin complexes in mouse fibroblasts, revealing that the PAF complex is a central player in the mammalian chromatin landscape. PMID:23407553

  12. A proteome-wide protein interaction map for Campylobacter jejuni

    PubMed Central

    Parrish, Jodi R; Yu, Jingkai; Liu, Guozhen; Hines, Julie A; Chan, Jason E; Mangiola, Bernie A; Zhang, Huamei; Pacifico, Svetlana; Fotouhi, Farshad; DiRita, Victor J; Ideker, Trey; Andrews, Phillip; Finley, Russell L

    2007-01-01

    Background Data from large-scale protein interaction screens for humans and model eukaryotes have been invaluable for developing systems-level models of biological processes. Despite this value, only a limited amount of interaction data is available for prokaryotes. Here we report the systematic identification of protein interactions for the bacterium Campylobacter jejuni, a food-borne pathogen and a major cause of gastroenteritis worldwide. Results Using high-throughput yeast two-hybrid screens we detected and reproduced 11,687 interactions. The resulting interaction map includes 80% of the predicted C. jejuni NCTC11168 proteins and places a large number of poorly characterized proteins into networks that provide initial clues about their functions. We used the map to identify a number of conserved subnetworks by comparison to protein networks from Escherichia coli and Saccharomyces cerevisiae. We also demonstrate the value of the interactome data for mapping biological pathways by identifying the C. jejuni chemotaxis pathway. Finally, the interaction map also includes a large subnetwork of putative essential genes that may be used to identify potential new antimicrobial drug targets for C. jejuni and related organisms. Conclusion The C. jejuni protein interaction map is one of the most comprehensive yet determined for a free-living organism and nearly doubles the binary interactions available for the prokaryotic kingdom. This high level of coverage facilitates pathway mapping and function prediction for a large number of C. jejuni proteins as well as orthologous proteins from other organisms. The broad coverage also facilitates cross-species comparisons for the identification of evolutionarily conserved subnetworks of protein interactions. PMID:17615063

  13. Tools for Glycomics: Mapping Interactions of Carbohydrates in Biological Systems

    E-print Network

    Ratner, Daniel M.

    Tools for Glycomics: Mapping Interactions of Carbohydrates in Biological Systems Daniel M. Ratner of carbohydrates in biological processes.[1] This includes carbohydrate­carbohy- drate, carbohydrate­protein, and carbohydrate­nu- cleic acid interactions (see Figure 1). Carbohydrates, in the form of glycopeptides

  14. A Physical and Regulatory Map of Host-Influenza Interactions

    E-print Network

    A Physical and Regulatory Map of Host-Influenza Interactions Reveals Pathways in H1N1 Infection and pathways. Here, we present a systematic strategy to elucidate the dynamic interactions between H1N1 model of influenza-host interac- tions for the H1N1 strain A/PR/8/34 (``PR8''). Our experimental

  15. 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.

  16. Interactive computer methods for generating mineral-resource maps

    USGS Publications Warehouse

    Calkins, James Alfred; Crosby, A.S.; Huffman, T.E.; Clark, A.L.; Mason, G.T.; Bascle, R.J.

    1980-01-01

    Inasmuch as maps are a basic tool of geologists, the U.S. Geological Survey's CRIB (Computerized Resources Information Bank) was constructed so that the data it contains can be used to generate mineral-resource maps. However, by the standard methods used-batch processing and off-line plotting-the production of a finished map commonly takes 2-3 weeks. To produce computer-generated maps more rapidly, cheaply, and easily, and also to provide an effective demonstration tool, we have devised two related methods for plotting maps as alternatives to conventional batch methods. These methods are: 1. Quick-Plot, an interactive program whose output appears on a CRT (cathode-ray-tube) device, and 2. The Interactive CAM (Cartographic Automatic Mapping system), which combines batch and interactive runs. The output of the Interactive CAM system is final compilation (not camera-ready) paper copy. Both methods are designed to use data from the CRIB file in conjunction with a map-plotting program. Quick-Plot retrieves a user-selected subset of data from the CRIB file, immediately produces an image of the desired area on a CRT device, and plots data points according to a limited set of user-selected symbols. This method is useful for immediate evaluation of the map and for demonstrating how trial maps can be made quickly. The Interactive CAM system links the output of an interactive CRIB retrieval to a modified version of the CAM program, which runs in the batch mode and stores plotting instructions on a disk, rather than on a tape. The disk can be accessed by a CRT, and, thus, the user can view and evaluate the map output on a CRT immediately after a batch run, without waiting 1-3 days for an off-line plot. The user can, therefore, do most of the layout and design work in a relatively short time by use of the CRT, before generating a plot tape and having the map plotted on an off-line plotter.

  17. Mapping of Vps21 and HOPS Binding Sites in Vps8 and Effect of Binding Site Mutants on Endocytic Trafficking ?

    PubMed Central

    Pawelec, Agnes; Arsi?, Janja; Kölling, Ralf

    2010-01-01

    Vps8 is a subunit of the CORVET tethering complex, which is involved in early-to-late endosome fusion. Here, we examine the role of Vps8 in membrane fusion at late endosomes in Saccharomyces cerevisiae. We demonstrate that Vps8 associates with membranes and that this association is independent of the class C/HOPS core complex and, contrary to a previous report, also independent of the Rab GTPase Vps21. Our data indicate that Vps8 makes multiple contacts with membranes. One of these membrane binding regions could be mapped to the N-terminal part of the protein. By two-hybrid analysis, we obtained evidence for a physical interaction between Vps8 and the Rab5 homologue Vps21. In addition, the interaction with the HOPS core complex was confirmed by immunoprecipitation experiments. By deletion analysis, the Vps21 and HOPS binding sites were mapped in Vps8. Deletions that abrogated HOPS core complex binding had a strong effect on the turnover of the endocytic cargo protein Ste6 and on vacuolar sorting of carboxypeptidase Y. In contrast, deletions that abolished Vps21 binding showed only a modest effect. This suggests that the Vps21 interaction is not essential for endosomal trafficking but may be important for some other aspect of Vps8 function. PMID:20173035

  18. Galaxy Interactions with FIRE: Mapping Star Formation

    NASA Astrophysics Data System (ADS)

    Moreno, Jorge

    2016-01-01

    We utilize a suite of 75 simulations of galaxies in idealised major mergers (stellar mass ratio ~2.5:1), with a wide range of orbital parameters, to investigate the spatial extent of interaction-induced star formation. Two versions are used, one based on a Kennicult-like subgrid model (Gadget, Springel & Hernquist 2003); the other based on the new Feedback In Realistic Environments model (FIRE, Hopkins et al. 2014). Although the total star formation in galaxy encounters is generally elevated relative to isolated galaxies, we find that this elevation is a combination of intense enhancements within the central kpc and moderately suppressed activity at large galacto-centric radii. This effect appears to be stronger in the older Gadget model. Suppression is the disk is also found in the FIRE runs, but at larger scales. This is because tidal torques are weaker in the newer FIRE model, leading to a more extended nuclear starburt. Our predictions of the radial dependence of triggered star formation, and specifically the suppression of star formation beyond kpc-scales, will be testable with the next generation of integral-field spectroscopic surveys.

  19. CONTIG EXPLORER: Interactive marker-content map assembly

    SciTech Connect

    Nadkarni, P.M.; Miller, P.; Banks, A.

    1996-02-01

    In STS-content mapping of a region, multiple optimal or near-optimal putative orders of markers exist. Determining which of the markers lack sufficient evidence to be placed requires software that facilitates exploratory sensitivity analysis and interactive reassembly with different subsets of the input data and that also assists the evaluation of any arbitrary (user-specified) marker order. We describe CONTIG EXPLORER, a package for interactive assembly of STS-content maps that provides the user with various ways of performing such analysis, thereby facilitating the design of laboratory experiments aimed at reducing ambiguity in STS order. We then compare the output of CONTIG EXPLORER with two other assembly programs, SEGMAP and CONTIGMAKER, for a region of chromosome 12p between 21 and 38 cM on the sex-averaged CEPH/Genethon linkage map. 18 refs., 4 figs.

  20. Picture Browsing and Map Interaction using a Projector Phone

    E-print Network

    Picture Browsing and Map Interaction using a Projector Phone Andrew Greaves1 , Alina Hang2 , Enrico that projector phones (mobile phones with built-in pico projectors) will hit the market by 2010. Such phones in this paper allows the simulation of these projector phones as the real devices are not yet available. Through

  1. Interactive Maps from the Great Basin Center for Geothermal Energy

    DOE Data Explorer

    The Great Basin Center for Geothermal Energy, part of the University of Nevada, Reno, conducts research towards the establishment of geothermal energy as an economically viable energy source within the Great Basin. The Center specializes in collecting and synthesizing geologic, geochemical, geodetic, geophysical, and tectonic data, and using Geographic Information System (GIS) technology to view and analyze this data and to produce favorability maps of geothermal potential. The interactive maps are built with layers of spatial data that are also available as direct file downloads (see DDE00299). The maps allow analysis of these many layers, with various data sets turned on or off, for determining potential areas that would be favorable for geothermal drilling or other activity. They provide information on current exploration projects and leases, Bureau of Land Management land status, and map presentation of each type of scientific spatial data: geothermal, geophysical, geologic, geodetic, groundwater, and geochemical.

  2. Prediction protein--protein interaction sites heterocomplexes with neural networks

    E-print Network

    Pazos, Florencio

    % residues involved protein interactions in a selected database comprising 226 heterodimers. analysis. propose the predictor significantly complement results structural and func­ tional proteomics. Keywords--protein interaction through isolation protein complexes under way, and map proteomics adds a to efficiently study

  3. Interaction sites of DivIVA and RodA from Corynebacterium glutamicum.

    PubMed

    Sieger, Boris; Bramkamp, Marc

    2014-01-01

    Elongation growth in actinobacteria is localized at the cell poles. This is in contrast to many classical model organisms where insertion of new cell wall material is localized around the lateral site. We previously described a role of RodA from Corynebacterium glutamicum in apical cell growth and morphogenesis. Deletion of rodA had drastic effects on morphology and growth, likely a result from misregulation of penicillin-binding proteins and cell wall precursor delivery. We identified the interaction of RodA with the polar scaffold protein DivIVA, thus explaining subcellular localization of RodA to the cell poles. In this study, we describe this interaction in detail and map the interaction sites of DivIVA and RodA. A single amino acid residue in the N-terminal domain of DivIVA was found to be crucial for the interaction with RodA. The interaction site of RodA was mapped to its cytoplasmic, C-terminal domain, in a region encompassing the last 10 amino acids (AAs). Deletion of these 10 AAs significantly decreased the interaction efficiency with DivIVA. Our results corroborate the interaction of DivIVA and RodA, underscoring the important role of DivIVA as a spatial organizer of the elongation machinery in Corynebacterineae. PMID:25709601

  4. 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 anomalies. On contrary, the shape of the magnetic anomalies implies to propose magnetized or non-magnetized structures with a width of several meters. To fit completely the shape of the magnetic anomaly, an iterative algorithm is used consisting of modifying the shape of the top of the magnetized layer.

  5. Mapping protein binding sites on the biomolecular corona of nanoparticles

    NASA Astrophysics Data System (ADS)

    Kelly, Philip M.; Ĺberg, Christoffer; Polo, Ester; O'Connell, Ann; Cookman, Jennifer; Fallon, Jonathan; Krpeti?, Željka; Dawson, Kenneth A.

    2015-05-01

    Nanoparticles in a biological milieu are known to form a sufficiently long-lived and well-organized ‘corona’ of biomolecules to confer a biological identity to the particle. Because this nanoparticle-biomolecule complex interacts with cells and biological barriers, potentially engaging with different biological pathways, it is important to clarify the presentation of functional biomolecular motifs at its interface. Here, we demonstrate that by using antibody-labelled gold nanoparticles, differential centrifugal sedimentation and various imaging techniques it is possible to identify the spatial location of proteins, their functional motifs and their binding sites. We show that for transferrin-coated polystyrene nanoparticles only a minority of adsorbed proteins exhibit functional motifs and the spatial organization appears random, which is consistent, overall, with a stochastic and irreversible adsorption process. Our methods are applicable to a wide array of nanoparticles and can offer a microscopic molecular description of the biological identity of nanoparticles.

  6. Methods for Mapping of Interaction Networks Involving Membrane Proteins

    SciTech Connect

    Hooker, Brian S.; Bigelow, Diana J.; Lin, Chiann Tso

    2007-11-23

    Numerous approaches have been taken to study protein interactions, such as tagged protein complex isolation followed by mass spectrometry, yeast two-hybrid methods, fluorescence resonance energy transfer, surface plasmon resonance, site-directed mutagenesis, and crystallography. Membrane protein interactions pose significant challenges due to the need to solubilize membranes without disrupting protein-protein interactions. Traditionally, analysis of isolated protein complexes by high-resolution 2D gel electrophoresis has been the main method used to obtain an overall picture of proteome constituents and interactions. However, this method is time consuming, labor intensive, detects only abundant proteins and is not suitable for the coverage required to elucidate large interaction networks. In this review, we discuss the application of various methods to elucidate interactions involving membrane proteins. These techniques include methods for the direct isolation of single complexes or interactors as well as methods for characterization of entire subcellular and cellular interactomes.

  7. Large Scale Wind Turbine Siting Map Report NJ Department of Environmental Protection

    E-print Network

    Holberton, Rebecca L.

    Large Scale Wind Turbine Siting Map Report NJ Department of Environmental Protection September 8 Jersey Department of Environmental Protection's (NJDEP) "Large Scale Wind Turbine Siting Map Management rules to address the development and permitting of wind turbines in the coastal zone

  8. 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 Contract No. DE AC52 06NA25946 with the U.S. Department of Energy. Sandia National Laboratories, is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  9. GEO 599 Web Mapping & Human Computer Interaction (Credits 4) GEO 568 Interactive Cartography and Geovisualization (Credits 4)

    E-print Network

    Jenny, Bernhard

    GEO 599 Web Mapping & Human Computer Interaction (Credits 4) soon to be GEO 568 Interactive of the course, students are introduced to a working knowledge of programming for web or mobile devices of JavaScript programming, HTML & CSS Web Mapping Frameworks: MapBox & Leaflet www.leafletjs.com Charts

  10. Genome-wide map of regulatory interactions in the human genome.

    PubMed

    Heidari, Nastaran; Phanstiel, Douglas H; He, Chao; Grubert, Fabian; Jahanbani, Fereshteh; Kasowski, Maya; Zhang, Michael Q; Snyder, Michael P

    2014-12-01

    Increasing evidence suggests that interactions between regulatory genomic elements play an important role in regulating gene expression. We generated a genome-wide interaction map of regulatory elements in human cells (ENCODE tier 1 cells, K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. Bound regions covered 80% of DNase I hypersensitive sites including 99.7% of TSS and 98% of enhancers. Correlating this map with ChIP-seq and RNA-seq data sets revealed cohesin, CTCF, and ZNF143 as key components of three-dimensional chromatin structure and revealed how the distal chromatin state affects gene transcription. Comparison of interactions between cell types revealed that enhancer-promoter interactions were highly cell-type-specific. Construction and comparison of distal and proximal regulatory networks revealed stark differences in structure and biological function. Proximal binding events are enriched at genes with housekeeping functions, while distal binding events interact with genes involved in dynamic biological processes including response to stimulus. This study reveals new mechanistic and functional insights into regulatory region organization in the nucleus. PMID:25228660

  11. Genome-wide map of regulatory interactions in the human genome

    PubMed Central

    Heidari, Nastaran; Phanstiel, Douglas H.; He, Chao; Grubert, Fabian; Jahanbani, Fereshteh; Kasowski, Maya; Zhang, Michael Q.

    2014-01-01

    Increasing evidence suggests that interactions between regulatory genomic elements play an important role in regulating gene expression. We generated a genome-wide interaction map of regulatory elements in human cells (ENCODE tier 1 cells, K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. Bound regions covered 80% of DNase I hypersensitive sites including 99.7% of TSS and 98% of enhancers. Correlating this map with ChIP-seq and RNA-seq data sets revealed cohesin, CTCF, and ZNF143 as key components of three-dimensional chromatin structure and revealed how the distal chromatin state affects gene transcription. Comparison of interactions between cell types revealed that enhancer–promoter interactions were highly cell-type-specific. Construction and comparison of distal and proximal regulatory networks revealed stark differences in structure and biological function. Proximal binding events are enriched at genes with housekeeping functions, while distal binding events interact with genes involved in dynamic biological processes including response to stimulus. This study reveals new mechanistic and functional insights into regulatory region organization in the nucleus. PMID:25228660

  12. Prediction of proteinprotein interaction sites in heterocomplexes with neural networks

    E-print Network

    Pazos, Florencio

    involved in protein interactions in a selected database comprising 226 heterodimers. Our analysis confirms that the predictor can significantly complement results from structural and func- tional proteomics. Keywords, and cell- map proteomics adds a route to efficiently study the genome at the protein level [3

  13. A protein interaction map of the LSU processome

    PubMed Central

    McCann, Kathleen L.; Charette, J. Michael; Vincent, Nicholas G.

    2015-01-01

    Maturation of the large ribosomal subunit (LSU) in eukaryotes is a complex and highly coordinated process that requires the concerted action of a large, dynamic, ribonucleoprotein complex, the LSU processome. While we know that >80 ribosome biogenesis factors are required throughout the course of LSU assembly, little is known about how these factors interact with each other within the LSU processome. To interrogate its organization and architecture, we took a systems biology approach and performed a semi-high-throughput, array-based, directed yeast two-hybrid assay. Assaying 4800 protein–protein interactions, we identified 232 high-confidence, binary-interacting protein pairs, representing a fourfold increase from current knowledge. The resulting LSU processome interactome map has enhanced our understanding of the organization and function of the biogenesis factors within the LSU processome, revealing both novel and previously identified subcomplexes and hub proteins, including Nop4. PMID:25877921

  14. 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.

  15. Mapping of mutation-sensitive sites in proteinlike chains M. Skorobogatiy1

    E-print Network

    Skorobogatiy, Maksim

    Mapping of mutation-sensitive sites in proteinlike chains M. Skorobogatiy1 and G. Tiana2 1 sensitive to point mutations ``hot'' sites in proteinlike chains. It has been found that this pattern is responsible for the distribution pattern of sites sensitive to point mutations in a heteropolymeric chain

  16. Mapping of lamin A- and progerin-interacting genome regions.

    PubMed

    Kubben, Nard; Adriaens, Michiel; Meuleman, Wouter; Voncken, Jan Willem; van Steensel, Bas; Misteli, Tom

    2012-10-01

    Mutations in the A-type lamins A and C, two major components of the nuclear lamina, cause a large group of phenotypically diverse diseases collectively referred to as laminopathies. These conditions often involve defects in chromatin organization. However, it is unclear whether A-type lamins interact with chromatin in vivo and whether aberrant chromatin-lamin interactions contribute to disease. Here, we have used an unbiased approach to comparatively map genome-wide interactions of gene promoters with lamin A and progerin, the mutated lamin A isoform responsible for the premature aging disorder Hutchinson-Gilford progeria syndrome (HGPS) in mouse cardiac myoytes and embryonic fibroblasts. We find that lamin A-associated genes are predominantly transcriptionally silent and that loss of lamin association leads to the relocation of peripherally localized genes, but not necessarily to their activation. We demonstrate that progerin induces global changes in chromatin organization by enhancing interactions with a specific subset of genes in addition to the identified lamin A-associated genes. These observations demonstrate disease-related changes in higher order genome organization in HGPS and provide novel insights into the role of lamin-chromatin interactions in chromatin organization. PMID:22610065

  17. Final report for the project "Improving the understanding of surface-atmosphere radiative interactions by mapping surface reflectance over the ARM CART site" (award DE-FG02-02ER63351)

    SciTech Connect

    Alexander P. Trishchenko; Yi Luo; Konstantin V. Khlopenkov, William M. Park; Zhanqing Li; Maureen Cribb

    2008-11-28

    Surface spectral reflectance (albedo) is a fundamental variable affecting the transfer of solar radiation and the Earth’s climate. It determines the proportion of solar energy absorbed by the surface and reflected back to the atmosphere. The International Panel on Climate Change (IPCC) identified surface albedo among key factors influencing climate radiative forcing. Accurate knowledge of surface reflective properties is important for advancing weather forecasting and climate change impact studies. It is also important for determining radiative impact and acceptable levels of greenhouse gases in the atmosphere, which makes this work strongly linked to major scientific objectives of the Climate Change Research Division (CCRD) and Atmospheric Radiation Measurement (ARM) Program. Most significant accomplishments of eth project are listed below. I) Surface albedo/BRDF datasets from 1995 to the end of 2004 have been produced. They were made available to the ARM community and other interested users through the CCRS public ftp site ftp://ftp.ccrs.nrcan.gc.ca/ad/CCRS_ARM/ and ARM IOP data archive under “PI data Trishchenko”. II) Surface albedo properties over the ARM SGP area have been described for 10-year period. Comparison with ECMWF data product showed some deficiencies in the ECMWF surface scheme, such as missing some seasonal variability and no dependence on sky-conditions which biases surface energy budget and has some influence of the diurnal cycle of upward radiation and atmospheric absorption. III) Four surface albedo Intensive Observation Period (IOP) Field Campaigns have been conducted for every season (August, 2002, May 2003, February 2004 and October 2004). Data have been prepared, documented and transferred to ARM IOP archive. Nine peer-reviewed journal papers and 26 conference papers have been published.

  18. Extended three-dimensional impedance map methods for identifying ultrasonic scattering sites

    E-print Network

    Illinois at Urbana-Champaign, University of

    Extended three-dimensional impedance map methods for identifying ultrasonic scattering sites, the anatomic microstructure details responsible for ultrasonic scattering remain unidentified. However from ultrasonic backscatter measurements. Recently, three-dimensional 3D acoustic models of tissue

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

    DOE Data Explorer

    Jaffe, Todd

    2012-01-01

    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.

  20. Response mapping interacts with perceptual thresholds and stimulus processing speed.

    PubMed

    Shalev, Nir; Humphreys, Glyn; Demeyere, Nele

    2015-09-01

    Traditionally, response selection is considered to reflect a separate stage of processing to visual perception. An alternative view proposes action and perception to be closely linked; however the processing stage where any cross-modal interaction would then occur remains unclear. In this study, we investigated the influence of response-mapping on a simple classification task. We presented an array of eight frames arranged in a square around a fixation point, followed by a brief presentation of an arrow in one of them (varying SOAs of 10,30,50,80 and 100ms masked). The arrow could appear in a congruent, incongruent or a neutral location with respect to its direction. Participants indicated the direction of the arrow using a response-box organized in a corresponding configuration: eight response-buttons, arranged in a square; an arrow appeared on each button. In Exp 1, the directions of the buttons matched their locations (e.g., arrow pointing right appearing on the right side); In Exp 2, the arrows and the locations were mismatched (arrow appearing on the left side, pointing right). Subsequently we manipulated the response-mapping between the locations and directions of the arrows. We changed the task to respond to locations instead of direction, in a single (Exp 3) and a dual task (Exp 5); and replicated our original experiment with different exposure times (Exp 4). In our first experiment, we observed a robust congruency effect on accuracy for arrows appearing in their matching locations. Crucially, in our following experiments, we managed to invert and manipulate this effect by changing the motor-response mapping. Using mathematical modelling according to the Theory of Visual Attention, we demonstrate that motor-mapping modulates two low-level processes independently: perceptual threshold and stimulus processing speed. We discuss the implications of multi-modal integration within a general framework of attention as a proactive cognitive function, which predicts and formulates visual percepts. Meeting abstract presented at VSS 2015. PMID:26326673

  1. 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.

  2. 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.

  3. 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.

  4. Structural mapping of nucleotide binding sites on chloroplast coupling factor

    SciTech Connect

    Cerione, R.A.; Hammes, G.G.

    1982-02-16

    Fluorescence resonance energy transfer was used to measure the distances between three nucleotide binding sites on solubilized chloroplast coupling factor from spinach and between each nucleotide site and two tyrosine residues which are important for catalytic activity. The nucleotide energy donor was 1,N/sup 6/-ethernoadenosine di- or triphosphate, and the nucleotide energy acceptor was 2'(3')-(trinitrophenyl)adenosine diphosphate. The tyrosine residues were specifically labeled with 7-chloro-4-nitro-2,1,3-benzoxadiazole, which served as an energy acceptor. The results obtained indicate the three nucleotide binding sites form a triangle with sides of 44, 48, and 36 angstron. (The assumption has been made in calculating these distances that the energy donor and acceptor rotate rapidly relative to the fluorescence lifetime.) Two of the nucleotide sites are approximately equidistant from each of the two tyrosines: one of the nucleotide sites is about 37 angstron and the other about 41 angstron from each tyrosine. The third nucleotide site is about 41 angstron from one of the tyrosines and greater than or equalto 41 angstron from the other tyrosine.

  5. 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.

  6. Mapping epitopes and antigenicity by site-directed masking

    PubMed Central

    Paus, Didrik; Winter, Greg

    2006-01-01

    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. PMID:16754878

  7. 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.

  8. Distinguishing time-delayed causal interactions using convergent cross mapping

    NASA Astrophysics Data System (ADS)

    Ye, Hao; Deyle, Ethan R.; Gilarranz, Luis J.; Sugihara, George

    2015-10-01

    An important problem across many scientific fields is the identification of causal effects from observational data alone. Recent methods (convergent cross mapping, CCM) have made substantial progress on this problem by applying the idea of nonlinear attractor reconstruction to time series data. Here, we expand upon the technique of CCM by explicitly considering time lags. Applying this extended method to representative examples (model simulations, a laboratory predator-prey experiment, temperature and greenhouse gas reconstructions from the Vostok ice core, and long-term ecological time series collected in the Southern California Bight), we demonstrate the ability to identify different time-delayed interactions, distinguish between synchrony induced by strong unidirectional-forcing and true bidirectional causality, and resolve transitive causal chains.

  9. Distinguishing time-delayed causal interactions using convergent cross mapping

    PubMed Central

    Ye, Hao; Deyle, Ethan R.; Gilarranz, Luis J.; Sugihara, George

    2015-01-01

    An important problem across many scientific fields is the identification of causal effects from observational data alone. Recent methods (convergent cross mapping, CCM) have made substantial progress on this problem by applying the idea of nonlinear attractor reconstruction to time series data. Here, we expand upon the technique of CCM by explicitly considering time lags. Applying this extended method to representative examples (model simulations, a laboratory predator-prey experiment, temperature and greenhouse gas reconstructions from the Vostok ice core, and long-term ecological time series collected in the Southern California Bight), we demonstrate the ability to identify different time-delayed interactions, distinguish between synchrony induced by strong unidirectional-forcing and true bidirectional causality, and resolve transitive causal chains. PMID:26435402

  10. Groundwater vulnerability: Interactions of chemical and site properties

    USGS Publications Warehouse

    Worrall, F.; Besien, T.; Kolpin, D.W.

    2002-01-01

    This study brings together extensive, multi-annual groundwater monitoring datasets from the UK and Midwestern US to test the relative importance of site (e.g. land use, soil and aquifer type) and chemical factors (e.g. solubility in water) and between and within year variations in controlling groundwater contamination by pesticides. ANOVA (general linear modelling) was used to test the significance and proportion of variation explained by each factor and their interactions. Results from both the UK and US datasets show that: (i) Chemical and site factors both have a statistically significant influence on groundwater pollution; (ii) Site factors on their own explain a greater proportion of data variance than chemical factors on their own; (iii) Interaction between site and chemical factors represents the most important control on the occurrence of pesticides in groundwater; (iv) Variation within the year was slight but still significant while there was no significant difference between data from consecutive years. The combination of factors analysed in this study were sufficient to explain the majority of the variation in the data save for that ascribable to the analytical detection limit. The results provide statistical evidence that it is viable to develop both molecular methods and groundwater vulnerability as tools to understanding pollution, but that a greater emphasis should be placed on their interaction to fully understand pesticide contamination. ?? 2002 Elsevier Science B.V. All rights reserved.

  11. Current approaches to fine mapping of antigen–antibody interactions

    PubMed Central

    Abbott, W Mark; Damschroder, Melissa M; Lowe, David C

    2014-01-01

    A number of different methods are commonly used to map the fine details of the interaction between an antigen and an antibody. Undoubtedly the method that is now most commonly used to give details at the level of individual amino acids and atoms is X-ray crystallography. The feasibility of undertaking crystallographic studies has increased over recent years through the introduction of automation, miniaturization and high throughput processes. However, this still requires a high level of sophistication and expense and cannot be used when the antigen is not amenable to crystallization. Nuclear magnetic resonance spectroscopy offers a similar level of detail to crystallography but the technical hurdles are even higher such that it is rarely used in this context. Mutagenesis of either antigen or antibody offers the potential to give information at the amino acid level but suffers from the uncertainty of not knowing whether an effect is direct or indirect due to an effect on the folding of a protein. Other methods such as hydrogen deuterium exchange coupled to mass spectrometry and the use of short peptides coupled with ELISA-based approaches tend to give mapping information over a peptide region rather than at the level of individual amino acids. It is quite common to use more than one method because of the limitations and even with a crystal structure it can be useful to use mutagenesis to tease apart the contribution of individual amino acids to binding affinity. PMID:24635566

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

    NASA Astrophysics Data System (ADS)

    Reppert, Mike; Tokmakoff, Andrei

    2015-08-01

    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-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.

  13. 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.

  14. Halogenated naphthyl methoxy piperidines for mapping serotonin transporter sites

    DOEpatents

    Goodman, Mark M. (Atlanta, GA); Faraj, Bahjat (Lithonia, GA)

    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.

  15. 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.

  16. Mapping Functional Interactions in a Heterodimeric Phospholipid Pump*

    PubMed Central

    Puts, Catheleyne F.; Panatala, Radhakrishnan; Hennrich, Hanka; Tsareva, Alina; Williamson, Patrick; Holthuis, Joost C. M.

    2012-01-01

    Type 4 P-type ATPases (P4-ATPases) catalyze phospholipid transport to generate phospholipid asymmetry across membranes of late secretory and endocytic compartments, but their kinship to cation-transporting P-type transporters raised doubts about whether P4-ATPases alone are sufficient to mediate flippase activity. P4-ATPases form heteromeric complexes with Cdc50 proteins. Studies of the enzymatic properties of purified P4-ATPase·Cdc50 complexes showed that catalytic activity depends on direct and specific interactions between Cdc50 subunit and transporter, whereas in vivo interaction assays suggested that the binding affinity for each other fluctuates during the transport reaction cycle. The structural determinants that govern this dynamic association remain to be established. Using domain swapping, site-directed, and random mutagenesis approaches, we here show that residues throughout the subunit contribute to forming the heterodimer. Moreover, we find that a precise conformation of the large ectodomain of Cdc50 proteins is crucial for the specificity and functionality to transporter/subunit interactions. We also identified two highly conserved disulfide bridges in the Cdc50 ectodomain. Functional analysis of cysteine mutants that disrupt these disulfide bridges revealed an inverse relationship between subunit binding and P4-ATPase-catalyzed phospholipid transport. Collectively, our data indicate that a dynamic association between subunit and transporter is crucial for the transport reaction cycle of the heterodimer. PMID:22791719

  17. Spatial games with cyclic interactions: the response of empty sites

    NASA Astrophysics Data System (ADS)

    Brown, Bart; Pleimling, Michel

    2015-03-01

    Predator-prey models of the May-Leonard family employ empty sites in a spatial setting as an intermediate step in the reproduction process. This requirement makes the number and arrangement of empty sites important to the formation of space-time patterns. We study the density of empty sites in a stochastic predator-prey model in which the species compete in a cyclic way in two dimensions. In some cases systems of this type quickly form domains of neutral species after which all predation, and therefore, reproduction occur near the interface of competing domains. Using Monte Carlo simulations we investigate the relationship of this density of empty sites to the time-dependent domain length. We further explore the dynamics by introducing perturbations to the interaction rates of the system after which we measure the perturbed density, i.e. the response of empty sites, as the system relaxes. A dynamical scaling behavior is observed in the response of empty sites. This work is supported by the US National Science Foundation through Grant DMR-1205309.

  18. Quantifying the ?-Stacking Interactions in Nitroarene Binding Sites of Proteins.

    PubMed

    An, Yi; Bloom, Jacob W G; Wheeler, Steven E

    2015-11-12

    Stacking interactions in nitroarene binding sites of proteins were studied through analyses of structures in the protein data bank (PDB), as well as DFT and ab initio computations applied to model systems. Stacked dimers of mono-, di-, and trinitrobenzene with the amino acid side chains histidine (His), phenylalanine (Phe), tyrosine (Tyr), and tryptophan (Trp) were optimized at the B97-D/TZV(2d,2p) level of theory. Binding energies for the global minimum dimer geometries were further refined at the estimated CCSD(T)/aug-cc-pVTZ level of theory. The results show that the interactions between aromatic amino acids and nitroarenes are very strong (up to -14.6 kcal mol(-1)), and the regiochemistry of the nitro substituents plays a significant role in the relative monomer orientations and strength of the interaction. In contrast to model stacked benzene dimers, effects of nitro substituents in stacking complexes with aromatic amino acid side chains are not perfectly additive. This is attributed to direct interactions of the nitro substituents with functional groups in the amino acid side chain. Overall, the strength of stacking interactions with these nitrobenzenes follows the order Trp > Tyr > Phe ? His. We also analyzed nitroarene binding sites in the PDB. Out of 216 selected crystal structures containing nitroarene ligands, 191 have nearby aromatic residues, providing 65 examples of ?-stacking interactions involving a nitroarene. Of these, the representations of the different aromatic amino acids (Trp > Tyr > Phe > His) are correlated with the strength of model complexes of nitroarenes, with the exception of His. B97-D computations applied to complexes extracted from these crystal structures reveal that ?-stacking interactions between the nitroarene and aromatic amino acid side chains exhibit a broad range of strengths, with many contributing significantly to binding. PMID:26491883

  19. A Web-Based Interactive Mapping System of State Wide School Performance: Integrating Google Maps API Technology into Educational Achievement Data

    ERIC Educational Resources Information Center

    Wang, Kening; Mulvenon, Sean W.; Stegman, Charles; Anderson, Travis

    2008-01-01

    Google Maps API (Application Programming Interface), released in late June 2005 by Google, is an amazing technology that allows users to embed Google Maps in their own Web pages with JavaScript. Google Maps API has accelerated the development of new Google Maps based applications. This article reports a Web-based interactive mapping system…

  20. HABITAT AND BIODIVERSITY MAPPING, FOR THE DETERMINATION OF ALGAL BIOMASS AQUACULTURE SITES IN THE COSTAL AREAS OF PUERTO RICO

    E-print Network

    Gilbes, Fernando

    HABITAT AND BIODIVERSITY MAPPING, FOR THE DETERMINATION OF ALGAL BIOMASS AQUACULTURE SITES production. Here we analyze and map coastal habitats and biodiversity for the optimum the territorial water of Puerto Rico using several factors: benthic habitats, water depth, critical habitat

  1. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) interacts with apurinic/apyrimidinic sites in DNA.

    PubMed

    Kosova, Anastasiya A; Khodyreva, Svetlana N; Lavrik, Olga I

    2015-09-01

    Apurinic/apyrimidinic (AP) sites are some of the most frequent DNA damages and the key intermediates of base excision repair. Certain proteins can interact with the deoxyribose of the AP site to form a Schiff base, which can be stabilized by NaBH4 treatment. Several types of DNA containing the AP site were used to trap proteins in human cell extracts by this method. In the case of single-stranded AP DNA and AP DNA duplex with both 5' and 3' dangling ends, the major crosslinking product had an apparent molecular mass of 45 kDa. Using peptide mass mapping based on mass spectrometry data, we identified the protein forming this adduct as an isoform of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) called "uracil-DNA glycosylase". GAPDH is a glycolytic enzyme with many additional putative functions, which include interaction with nucleic acids, different DNA damages and DNA repair enzymes. We investigated interaction of GAPDH purified from HeLa cells and rabbit muscles with different AP DNAs. In spite of the ability to form a Schiff-base intermediate with the deoxyribose of the AP site, GAPDH does not display the AP lyase activity. In addition, along with the borohydride-dependent adducts with AP DNAs containing single-stranded regions, GAPDH was also shown to form the stable borohydride-independent crosslinks with these AP DNAs. GAPDH was proven to crosslink preferentially to AP DNAs cleaved via the ?-elimination mechanism (spontaneously or by AP lyases) as compared to DNAs containing the intact AP site. The level of GAPDH-AP DNA adduct formation depends on oxidation of the protein SH-groups; disulfide bond reduction in GAPDH leads to the loss of its ability to form the adducts with AP DNA. A possible role of formation of the stable adducts with AP sites by GAPDH is discussed. PMID:26203648

  2. Environmental Research Translation: Enhancing Interactions with Communities at Contaminated Sites

    PubMed Central

    Ramirez-Andreotta, Monica D.; Brusseau, Mark L.; Artiola, Janick F.; Maier, Raina M.; Gandolfi, A. Jay

    2014-01-01

    The characterization and remediation of contaminated sites are complex endeavors fraught with numerous challenges. One particular challenge that is receiving increased attention is the development and encouragement of full participation by communities and community members affected by a given site in all facets of decision-making. Many disciplines have been grappling with the challenges associated with environmental and risk communication, public participation in environmental data generation, and decision-making and increasing community capacity. The concepts and methods developed by these disciplines are reviewed, with a focus on their relevance to the specific dynamics associated with environmental contamination sites. The contributions of these disciplines are then synthesized and integrated to help develop Environmental Research Translation (ERT), a proposed framework for environmental scientists to promote interaction and communication among involved parties at contaminated sites. This holistic approach is rooted in public participation approaches to science, which includes: a transdisciplinary team, effective collaboration, information transfer, public participation in environmental projects, and a cultural model of risk communication. Although there are challenges associated with the implementation of ERT, it is anticipated that application of this proposed translational science method could promote more robust community participation at contaminated sites. PMID:25173762

  3. Conserved sequence-tagged sites: a phylogenetic approach to genome mapping.

    PubMed Central

    Mazzarella, R; Montanaro, V; Kere, J; Reinbold, R; Ciccodicola, A; D'Urso, M; Schlessinger, D

    1992-01-01

    Cognate sites in genomes that diverged approximately 100 million years ago can be detected by PCR assays based on primer pairs from unique sequences. The great majority of such syntenically equivalent sequence-tagged sites (STSs) from human DNA can be used to assemble and format corresponding maps for other primates, and some based on gene sequences are shown to be useful for mouse and rat as well. Universal genomic mapping strategies may be possible by using sets of STSs common to many mammalian species. Images PMID:1570287

  4. 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.

  5. 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.

  6. Map model for nonlinear alpha particle interaction with toroidal Alfven waves

    SciTech Connect

    Berk, H.L.; Breizman, B.N.; Ye, H.

    1992-09-01

    A map model has been developed for studying the nonlinear interaction of alpha particles with the toroidal Alfven eigenmodes. The map is constructed by assuming a linear interaction during a single poloidal transit, which allows the study of the nonlinear interaction over many transits. By using this map, analytic expressions are obtained for the particle nonlinear bounce frequency, and the wave amplitude threshold for the onset of particle orbit stochasticity. The map model can also facilitate self-consistent simulations which incorporate the time variation of the waves.

  7. A Universal Map for Fractal Structures in Weak Solitary Wave Interactions

    E-print Network

    Yi Zhu; Richard Haberman; Jianke Yang

    2008-02-25

    Fractal scatterings in weak solitary wave interactions is analyzed for generalized nonlinear Schr\\"odiger equations (GNLS). Using asymptotic methods, these weak interactions are reduced to a universal second-order map. This map gives the same fractal scattering patterns as those in the GNLS equations both qualitatively and quantitatively. Scaling laws of these fractals are also derived.

  8. 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

  9. 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

  10. Protein surface hydration mapped by site-specific mutations

    PubMed Central

    Qiu, Weihong; Kao, Ya-Ting; Zhang, Luyuan; Yang, Yi; Wang, Lijuan; Stites, Wesley E.; Zhong, Dongping; Zewail, Ahmed H.

    2006-01-01

    Water motion at protein surfaces is fundamental to protein structure, stability, dynamics, and function. By using intrinsic tryptophans as local optical probes, and with femtosecond resolution, it is possible to probe surface-water motions in the hydration layer. Here, we report our studies of local hydration dynamics at the surface of the enzyme Staphylococcus nuclease using site-specific mutations. From these studies of the WT and four related mutants, which change local charge distribution and structure, we are able to ascertain the contribution to solvation by protein side chains as relatively insignificant. We determined the time scales of hydration to be 3–5 ps and 100–150 ps. The former is the result of local librational/rotational motions of water near the surface; the latter is a direct measure of surface hydration assisted by fluctuations of the protein. Experimentally, these hydration dynamics of the WT and the four mutants are also consistent with results of the total dynamic Stokes shifts and fluorescence emission maxima and are correlated with their local charge distribution and structure. We discuss the role of protein fluctuation on the time scale of labile hydration and suggest reexamination of recent molecular dynamics simulations. PMID:16968773

  11. Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping.

    PubMed

    Zeng, Xin; Li, Bo; Welch, Rene; Rojo, Constanza; Zheng, Ye; Dewey, Colin N; Kele?, Sündüz

    2015-10-01

    Segmental duplications and other highly repetitive regions of genomes contribute significantly to cells' regulatory programs. Advancements in next generation sequencing enabled genome-wide profiling of protein-DNA interactions by chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq). However, interactions in highly repetitive regions of genomes have proven difficult to map since short reads of 50-100 base pairs (bps) from these regions map to multiple locations in reference genomes. Standard analytical methods discard such multi-mapping reads and the few that can accommodate them are prone to large false positive and negative rates. We developed Perm-seq, a prior-enhanced read allocation method for ChIP-seq experiments, that can allocate multi-mapping reads in highly repetitive regions of the genomes with high accuracy. We comprehensively evaluated Perm-seq, and found that our prior-enhanced approach significantly improves multi-read allocation accuracy over approaches that do not utilize additional data types. The statistical formalism underlying our approach facilitates supervising of multi-read allocation with a variety of data sources including histone ChIP-seq. We applied Perm-seq to 64 ENCODE ChIP-seq datasets from GM12878 and K562 cells and identified many novel protein-DNA interactions in segmental duplication regions. Our analysis reveals that although the protein-DNA interactions sites are evolutionarily less conserved in repetitive regions, they share the overall sequence characteristics of the protein-DNA interactions in non-repetitive regions. PMID:26484757

  12. Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping

    PubMed Central

    Zeng, Xin; Li, Bo; Welch, Rene; Rojo, Constanza; Zheng, Ye; Dewey, Colin N.; Kele?, Sündüz

    2015-01-01

    Segmental duplications and other highly repetitive regions of genomes contribute significantly to cells’ regulatory programs. Advancements in next generation sequencing enabled genome-wide profiling of protein-DNA interactions by chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq). However, interactions in highly repetitive regions of genomes have proven difficult to map since short reads of 50–100 base pairs (bps) from these regions map to multiple locations in reference genomes. Standard analytical methods discard such multi-mapping reads and the few that can accommodate them are prone to large false positive and negative rates. We developed Perm-seq, a prior-enhanced read allocation method for ChIP-seq experiments, that can allocate multi-mapping reads in highly repetitive regions of the genomes with high accuracy. We comprehensively evaluated Perm-seq, and found that our prior-enhanced approach significantly improves multi-read allocation accuracy over approaches that do not utilize additional data types. The statistical formalism underlying our approach facilitates supervising of multi-read allocation with a variety of data sources including histone ChIP-seq. We applied Perm-seq to 64 ENCODE ChIP-seq datasets from GM12878 and K562 cells and identified many novel protein-DNA interactions in segmental duplication regions. Our analysis reveals that although the protein-DNA interactions sites are evolutionarily less conserved in repetitive regions, they share the overall sequence characteristics of the protein-DNA interactions in non-repetitive regions. PMID:26484757

  13. NeuroMap: A Spline-Based Interactive Open-Source Software for Spatiotemporal Mapping of 2D and 3D MEA Data

    PubMed Central

    Abdoun, Oussama; Joucla, Sébastien; Mazzocco, Claire; Yvert, Blaise

    2010-01-01

    A major characteristic of neural networks is the complexity of their organization at various spatial scales, from microscopic local circuits to macroscopic brain-scale areas. Understanding how neural information is processed thus entails the ability to study them at multiple scales simultaneously. This is made possible using microelectrodes array (MEA) technology. Indeed, high-density MEAs provide large-scale coverage (several square millimeters) of whole neural structures combined with microscopic resolution (about 50??m) of unit activity. Yet, current options for spatiotemporal representation of MEA-collected data remain limited. Here we present NeuroMap, a new interactive Matlab-based software for spatiotemporal mapping of MEA data. NeuroMap uses thin plate spline interpolation, which provides several assets with respect to conventional mapping methods used currently. First, any MEA design can be considered, including 2D or 3D, regular or irregular, arrangements of electrodes. Second, spline interpolation allows the estimation of activity across the tissue with local extrema not necessarily at recording sites. Finally, this interpolation approach provides a straightforward analytical estimation of the spatial Laplacian for better current sources localization. In this software, coregistration of 2D MEA data on the anatomy of the neural tissue is made possible by fine matching of anatomical data with electrode positions using rigid-deformation-based correction of anatomical pictures. Overall, NeuroMap provides substantial material for detailed spatiotemporal analysis of MEA data. The package is distributed under GNU General Public License and available at http://sites.google.com/site/neuromapsoftware. PMID:21344013

  14. WW Denham Alyawarra Interactive Map Methods D R A F T 30-Oct-10 Alyawarra Interactive Map Visualization Methods

    E-print Network

    White, Douglas R.

    ..................................................................................................................... 20 Abstract Keywords Methods, map, Google Earth, layers, language groups, Alyawarra, Aranda, Country to that understanding. This is an experiment in using Google Earth to visualize multiple layers of maps and supporting..................................................................................................................... 2 Google Earth and the AIM Visualization

  15. Mapping History: A Web Map for the Study of Archaeological Sites in Turkey and Syria 

    E-print Network

    Hyde, Everet

    2015-11-26

    to the political climate and the current conflict. This has created the need for a tool which will allow researchers to visualise and study the archaeological sites in eastern Turkey and Syria. Web applications have been used by archaeologists for a number...

  16. THE POTENTIAL FOR MAPPING NEMATODE DISTRIBUTIONS FOR SITE-SPECIFIC MANAGEMENT

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 assess...

  17. Identifying and Mapping Factors Used in Siting Offshore Wind Farms Kayleah Griffen

    E-print Network

    Mountziaris, T. J.

    Milman; Graduate Student: Wind Goodale Offshore Wind Energy has great potential to be an energy source offshore wind energy build out scenarios for the East Coast of the United States. #12;Identifying and Mapping Factors Used in Siting Offshore Wind Farms Kayleah Griffen Professor Anita

  18. Microsystems Technology Laboratories | i-stepperThursday, October 27, 2005 / site map / contact

    E-print Network

    Reif, Rafael

    Microsystems Technology Laboratories | i-stepperThursday, October 27, 2005 / site map / contact Machine Chart Equipment SOPs ICL TRL EML Other Lab SOPs Training Chart PTC Process Matrix CORAL Administration Computation I-stepper STANDARD OPERATING PROCEDURE CORAL Name: i-stepper Model Number: Nikon NSR

  19. Home | Register | Home Delivery | Site Map | Archives | Print Edition | Advertise | Feedback jobs * cars * homes * rentals

    E-print Network

    Elkan, Charles

    Home | Register | Home Delivery | Site Map | Archives | Print Edition | Advertise | Feedback jobs County The Valley Ventura County Columnists Steve Harvey Peter H. King Steve Lopez Patt Morrison George Workplace/Jobs Editions Print Edition National Wireless Extras Discussion Boards Crossword Horoscope Lottery

  20. Web GIS in practice III: creating a simple interactive map of England's Strategic Health Authorities using Google Maps API, Google Earth KML, and MSN Virtual Earth Map Control

    PubMed Central

    Boulos, Maged N Kamel

    2005-01-01

    This eye-opener article aims at introducing the health GIS community to the emerging online consumer geoinformatics services from Google and Microsoft (MSN), and their potential utility in creating custom online interactive health maps. Using the programmable interfaces provided by Google and MSN, we created three interactive demonstrator maps of England's Strategic Health Authorities. These can be browsed online at – Google Maps API (Application Programming Interface) version, – Google Earth KML (Keyhole Markup Language) version, and – MSN Virtual Earth Map Control version. Google and MSN's worldwide distribution of "free" geospatial tools, imagery, and maps is to be commended as a significant step towards the ultimate "wikification" of maps and GIS. A discussion is provided of these emerging online mapping trends, their expected future implications and development directions, and associated individual privacy, national security and copyrights issues. Although ESRI have announced their planned response to Google (and MSN), it remains to be seen how their envisaged plans will materialize and compare to the offerings from Google and MSN, and also how Google and MSN mapping tools will further evolve in the near future. PMID:16176577

  1. 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.

  2. High-resolution melt analysis to identify and map sequence-tagged site anchor points onto linkage maps: a white lupin (Lupinus albus) map as an exemplar.

    PubMed

    Croxford, Adam E; Rogers, Tom; Caligari, Peter D S; Wilkinson, Michael J

    2008-01-01

    * The provision of sequence-tagged site (STS) anchor points allows meaningful comparisons between mapping studies but can be a time-consuming process for nonmodel species or orphan crops. * Here, the first use of high-resolution melt analysis (HRM) to generate STS markers for use in linkage mapping is described. This strategy is rapid and low-cost, and circumvents the need for labelled primers or amplicon fractionation. * Using white lupin (Lupinus albus, x = 25) as a case study, HRM analysis was applied to identify 91 polymorphic markers from expressed sequence tag (EST)-derived and genomic libraries. Of these, 77 generated STS anchor points in the first fully resolved linkage map of the species. The map also included 230 amplified fragment length polymorphisms (AFLP) loci, spanned 1916 cM (84.2% coverage) and divided into the expected 25 linkage groups. * Quantitative trait loci (QTL) analyses performed on the population revealed genomic regions associated with several traits, including the agronomically important time to flowering (tf), alkaloid synthesis and stem height (Ph). Use of HRM-STS markers also allowed us to make direct comparisons between our map and that of the related crop, Lupinus angustifolius, based on the conversion of RFLP, microsatellite and single nucleotide polymorphism (SNP) markers into HRM markers. PMID:18684160

  3. RBPmap: a web server for mapping binding sites of RNA-binding proteins.

    PubMed

    Paz, Inbal; Kosti, Idit; Ares, Manuel; Cline, Melissa; Mandel-Gutfreund, Yael

    2014-07-01

    Regulation of gene expression is executed in many cases by RNA-binding proteins (RBPs) that bind to mRNAs as well as to non-coding RNAs. RBPs recognize their RNA target via specific binding sites on the RNA. Predicting the binding sites of RBPs is known to be a major challenge. We present a new webserver, RBPmap, freely accessible through the website http://rbpmap.technion.ac.il/ for accurate prediction and mapping of RBP binding sites. RBPmap has been developed specifically for mapping RBPs in human, mouse and Drosophila melanogaster genomes, though it supports other organisms too. RBPmap enables the users to select motifs from a large database of experimentally defined motifs. In addition, users can provide any motif of interest, given as either a consensus or a PSSM. The algorithm for mapping the motifs is based on a Weighted-Rank approach, which considers the clustering propensity of the binding sites and the overall tendency of regulatory regions to be conserved. In addition, RBPmap incorporates a position-specific background model, designed uniquely for different genomic regions, such as splice sites, 5' and 3' UTRs, non-coding RNA and intergenic regions. RBPmap was tested on high-throughput RNA-binding experiments and was proved to be highly accurate. PMID:24829458

  4. RBPmap: a web server for mapping binding sites of RNA-binding proteins

    PubMed Central

    Paz, Inbal; Kosti, Idit; Ares, Manuel; Cline, Melissa; Mandel-Gutfreund, Yael

    2014-01-01

    Regulation of gene expression is executed in many cases by RNA-binding proteins (RBPs) that bind to mRNAs as well as to non-coding RNAs. RBPs recognize their RNA target via specific binding sites on the RNA. Predicting the binding sites of RBPs is known to be a major challenge. We present a new webserver, RBPmap, freely accessible through the website http://rbpmap.technion.ac.il/ for accurate prediction and mapping of RBP binding sites. RBPmap has been developed specifically for mapping RBPs in human, mouse and Drosophila melanogaster genomes, though it supports other organisms too. RBPmap enables the users to select motifs from a large database of experimentally defined motifs. In addition, users can provide any motif of interest, given as either a consensus or a PSSM. The algorithm for mapping the motifs is based on a Weighted-Rank approach, which considers the clustering propensity of the binding sites and the overall tendency of regulatory regions to be conserved. In addition, RBPmap incorporates a position-specific background model, designed uniquely for different genomic regions, such as splice sites, 5’ and 3’ UTRs, non-coding RNA and intergenic regions. RBPmap was tested on high-throughput RNA-binding experiments and was proved to be highly accurate. PMID:24829458

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

    SciTech Connect

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

    1995-05-01

    New techniques for mapping mammalian DNA replication origins are needed. We have modified the existing nascent-strand size analysis technique 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. 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. 51 refs., 5 figs.

  6. Combining Natural Sequence Variation with High Throughput Mutational Data to Reveal Protein Interaction Sites

    PubMed Central

    Melamed, Daniel; Young, David L.; Miller, Christina R.; Fields, Stanley

    2015-01-01

    Many protein interactions are conserved among organisms despite changes in the amino acid sequences that comprise their contact sites, a property that has been used to infer the location of these sites from protein homology. In an inter-species complementation experiment, a sequence present in a homologue is substituted into a protein and tested for its ability to support function. Therefore, substitutions that inhibit function can identify interaction sites that changed over evolution. However, most of the sequence differences within a protein family remain unexplored because of the small-scale nature of these complementation approaches. Here we use existing high throughput mutational data on the in vivo function of the RRM2 domain of the Saccharomyces cerevisiae poly(A)-binding protein, Pab1, to analyze its sites of interaction. Of 197 single amino acid differences in 52 Pab1 homologues, 17 reduce the function of Pab1 when substituted into the yeast protein. The majority of these deleterious mutations interfere with the binding of the RRM2 domain to eIF4G1 and eIF4G2, isoforms of a translation initiation factor. A large-scale mutational analysis of the RRM2 domain in a two-hybrid assay for eIF4G1 binding supports these findings and identifies peripheral residues that make a smaller contribution to eIF4G1 binding. Three single amino acid substitutions in yeast Pab1 corresponding to residues from the human orthologue are deleterious and eliminate binding to the yeast eIF4G isoforms. We create a triple mutant that carries these substitutions and other humanizing substitutions that collectively support a switch in binding specificity of RRM2 from the yeast eIF4G1 to its human orthologue. Finally, we map other deleterious substitutions in Pab1 to inter-domain (RRM2–RRM1) or protein-RNA (RRM2–poly(A)) interaction sites. Thus, the combined approach of large-scale mutational data and evolutionary conservation can be used to characterize interaction sites at single amino acid resolution. PMID:25671604

  7. Hsp90·Cdc37 Complexes with Protein Kinases Form Cooperatively with Multiple Distinct Interaction Sites.

    PubMed

    Eckl, Julia M; Scherr, Matthias J; Freiburger, Lee; Daake, Marina A; Sattler, Michael; Richter, Klaus

    2015-12-25

    Protein kinases are the most prominent group of heat shock protein 90 (Hsp90) clients and are recruited to the molecular chaperone by the kinase-specific cochaperone cell division cycle 37 (Cdc37). The interaction between Hsp90 and nematode Cdc37 is mediated by binding of the Hsp90 middle domain to an N-terminal region of Caenorhabditis elegans Cdc37 (CeCdc37). Here we map the binding site by NMR spectroscopy and define amino acids relevant for the interaction between CeCdc37 and the middle domain of Hsp90. Apart from these distinct Cdc37/Hsp90 interfaces, binding of the B-Raf protein kinase to the cochaperone is conserved between mammals and nematodes. In both cases, the C-terminal part of Cdc37 is relevant for kinase binding, whereas the N-terminal domain displaces the nucleotide from the kinase. This interaction leads to a cooperative formation of the ternary complex of Cdc37 and kinase with Hsp90. For the mitogen-activated protein kinase extracellular signal-regulated kinase 2 (Erk2), we observe that certain features of the interaction with Cdc37·Hsp90 are conserved, but the contribution of Cdc37 domains varies slightly, implying that different kinases may utilize distinct variations of this binding mode to interact with the Hsp90 chaperone machinery. PMID:26511315

  8. Shear wave velocity mapping of Hat Yai district, southern Thailand: implication for seismic site classification

    NASA Astrophysics Data System (ADS)

    Yordkayhun, Sawasdee; Sujitapan, Chedtaporn; Chalermyanont, Tanit

    2015-02-01

    Soil characteristics play an important role in the degree of ground shaking due to local site amplification during an earthquake. The objectives of this work are to study shear wave velocity (Vs) distribution in the near surface, and to develop a seismic site classification map for soil effect characterization and seismic hazard assessment in Hat Yai district, southern Thailand. The Vs determination based on the multichannel analysis of surface waves technique, has been carried out and analyzed at 70 measuring sites throughout the district. On the basis of the weighted-average Vs in the upper 30?m depth (Vs30), a seismic site classification map, based on the National Earthquake Hazards Reduction Program (NEHRP) standard has been developed. It is found that the NEHRP site class in Hat Yai can be classified into four groups in accordance with the value of Vs30 within the range of about 150 to 1160?m?s-1. Most parts of the study area are typically classified as site class C and D. Site class C is mostly found within the colluvial and terrace deposits in the western and eastern part of the area, whereas site class D is concentrated in the alluvial sediment of the middle and northern flood plain areas. A small portion of site class B is observed in the western mountain ranges, where there is a thin overburden on the firm rock. There is a remarkably low Vs30 value at only one site, located near the main stream in the northern part of the study area. The results imply that the soil characteristics in the central and northern Hat Yai district pose a medium to high amplification rate with respect to the other regions. Although Vs data alone are insufficient to verify the potential of the amplification of ground shaking, this study provides an initial attempt to understand seismic hazards in the study area.

  9. About the DNR DNR News Contact Us Site Map A-Z Topic Index

    E-print Network

    Stanier, Charlie

    Construction Bid Lettings Commissions and Boards Camps and Workshops DNR Grants DNR Kids' Pages DNR Online Databases DNR Rules Education Employment Mapping (GIS Interactive) Operator Certification Publications DNR Posted: December 22, 2008 Urbandale ­ The Iowa Department of Natural Resources (DNR) learned today

  10. Matrix model maps and reconstruction of AdS supergravity interactions

    SciTech Connect

    Cremonini, Sera; Mello Koch, Robert de; Jevicki, Antal

    2008-05-15

    We consider the question of reconstructing (cubic) SUGRA interactions in AdS/CFT. The method we introduce is based on the matrix model maps (MMP) which were previously successfully employed at the linearized level. The strategy is to start with the map for 1/2 BPS configurations, which is exactly known (to all orders) in the Hamiltonian framework. We then use the extension of the matrix model map with the corresponding Ward identities to completely specify the interaction. A central point in this construction is the nonvanishing of off-shell interactions (even for highest-weight states)

  11. Mapping Control and Affiliation in Teacher-Student Interaction with State Space Grids

    ERIC Educational Resources Information Center

    Mainhard, M. Tim; Pennings, Helena J. M.; Wubbels, Theo; Brekelmans, Mieke

    2012-01-01

    This paper explores how State Space Grids (SSG), a dynamic systems research method, can be used to map teacher-student interactions from moment-to-moment and thereby to incorporate temporal aspects of interaction. Interactions in two secondary school classrooms are described in terms of level of interpersonal control and affiliation, and of…

  12. 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 meters, as determined from the peak frequency and an estimate of the local shear wave velocity. We will present two preliminary site response parameter maps: one for fundamental frequency and one for minimum site amplification factor.

  13. 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.

  14. Competition between heavy fermion and Kondo interaction in isoelectronic A-site-ordered perovskites.

    PubMed

    Meyers, D; Middey, S; Cheng, J-G; Mukherjee, Swarnakamal; Gray, B A; Cao, Yanwei; Zhou, J-S; Goodenough, J B; Choi, Yongseong; Haskel, D; Freeland, J W; Saha-Dasgupta, T; Chakhalian, J

    2014-01-01

    With current research efforts shifting towards the 4d and 5d transition metal oxides, understanding the evolution of the electronic and magnetic structure as one moves away from 3d materials is of critical importance. Here we perform X-ray spectroscopy and electronic structure calculations on A-site-ordered perovskites with Cu in the A-site and the B-sites descending along the ninth group of the periodic table to elucidate the emerging properties as d-orbitals change from partially filled 3d to 4d to 5d. The results show that when descending from Co to Ir, the charge transfers from the cuprate-like Zhang-Rice state on Cu to the t(2g) orbital of the B site. As the Cu d-orbital occupation approaches the Cu(2+) limit, a mixed valence state in CaCu(3)Rh(4)O(12) and heavy fermion state in CaCu(3)Ir(4)O(12) are obtained. The investigated d-electron compounds are mapped onto the Doniach phase diagram of the competing RKKY and Kondo interactions developed for the f-electron systems. PMID:25517129

  15. Molecular Mapping of Restriction-Site Associated DNA Markers in Allotetraploid Upland Cotton

    PubMed Central

    Wang, Yangkun; Ning, Zhiyuan; Hu, Yan; Chen, Jiedan; Zhao, Rui; Chen, Hong; Ai, Nijiang; Guo, Wangzhen; Zhang, Tianzhen

    2015-01-01

    Upland cotton (Gossypium hirsutum L., 2n = 52, AADD) is an allotetraploid, therefore the discovery of single nucleotide polymorphism (SNP) markers is difficult. The recent emergence of genome complexity reduction technologies based on the next-generation sequencing (NGS) platform has greatly expedited SNP discovery in crops with highly repetitive and complex genomes. Here we applied restriction-site associated DNA (RAD) sequencing technology for de novo SNP discovery in allotetraploid cotton. We identified 21,109 SNPs between the two parents and used these for genotyping of 161 recombinant inbred lines (RILs). Finally, a high dense linkage map comprising 4,153 loci over 3500-cM was developed based on the previous result. Using this map quantitative trait locus (QTLs) conferring fiber strength and Verticillium Wilt (VW) resistance were mapped to a more accurate region in comparison to the 1576-cM interval determined using the simple sequence repeat (SSR) genetic map. This suggests that the newly constructed map has more power and resolution than the previous SSR map. It will pave the way for the rapid identification of the marker-assisted selection in cotton breeding and cloning of QTL of interest traits. PMID:25894395

  16. Shared-Screen Interaction: Engaging Groups in Map-Mediated Nonverbal Communication

    NASA Astrophysics Data System (ADS)

    Chorianopoulos, Konstantinos; Rieniets, Tim

    This chapter describes the design and development of an interactive video installation that allows participants to explore a map narrative, and engage in group interactions through a shared screen. For this purpose, several layers of cartographic information were employed in a computer application, which was programmed with motion-tracking libraries in the open source tool processing. The interactive video installation has been chosen as a medium to achieve the following aims: (1) The visualization of urban-conflict as an interactive map narrative, and (2) the encouragement of social encounters through a shared screen. The development process begins with the design of interaction between the system and the participants, as well as between the participants themselves. Then we map the interaction design concepts into multimedia and architectural design. Finally, we provide a discussion on the creative process and the collaboration between different disciplines, such as architecture, urban planning, cartography, computer engineering, and media studies.

  17. Tetragonal Lysozyme Interactions Studied by Site Directed Mutagenesis

    NASA Technical Reports Server (NTRS)

    Crawford, Lisa; Karr, Laurel; Pusey, Marc

    1998-01-01

    A number of recent experimental and theoretical studies have indicated that tetragonal lysozyme crystal growth proceeds by the addition of aggregates, formed by reversible self association of the solute molecules in the bulk'solution. Periodic bond chain and atomic force microscopy studies have indicated that the probable growth unit is at minimum a 43 tetramer, and most likely an octamer composed of two complete turns about the 4(sub 3) axis. If these results are correct, then there are intermolecular interactions which are only formed in the solution and others only formed at the joining of the growth unit to the crystal surface. We have set out to study these interactions, and the correctness of this hypothesis, using site directed mutagenesis of specific amino acid residues involved in the different bonds. We had initially expressed wild type lysozyme in S. cervasiae with yields of approximately 5 mg/L, which were eventually raised to approximately 40 mg/L. We are now moving the expression to the Pichia system, with anticipated yields of 300 to greater than 500 mg/L, comparable to what can be obtained from egg whites. An additional advantage of using recombinant protein is the greater genetic homogeneity of the material obtained and the absence of any other contaminating egg proteins. The first mutation experiments are TYR 23 yields PHE or ALA and ASN 113 yields ALA or ASP. Both TYR 23 and ASN 113 form part of the postulated dimerization intermolecular binding site which lead to the formation of the 4(sub 3) helix. Tyrosine also participates in an intermolecular hydrogen bond with ARG 114. The results of these and subsequent experiments will be discussed.

  18. Tetragonal Lysozyme Interactions Studied by Site Directed Mutagenesis

    NASA Technical Reports Server (NTRS)

    Crawford, Lisa; Karr, Laurel J.; Nadarajah, Arunan; Pusey, Marc

    1999-01-01

    A number of recent experimental and theoretical studies have indicated that tetragonal lysozyme crystal growth proceeds by the addition of aggregates, formed by reversible self association of the solute molecules in the bulk solution. Periodic bond chain and atomic force microscopy studies have indicated that the probable growth unit is at minimum a 43 tetramer, and most likely an octamer composed of two complete turns about the 43 axis. If these results are correct, then there are intermolecular interactions which are only formed in the solution and others only formed at the joining of the growth unit to the crystal surface. We have set out to study these interactions, and the correctness of this hypothesis, using site directed mutagenesis of specific amino acid residues involved in the different bonds. We had initially expressed wild type lysozyme in S. cervasiae with yields of approximately 5 mg/L, which were eventually raised to approximately 40 mg/L. We are now moving the expression to the Pichia system, with anticipated yields of 300 to (3)500 mg/L, comparable to what can be obtained from egg whites. An additional advantage of using recombinant protein is the greater genetic homogeneity of the material obtained and the absence of any other contaminating egg proteins. The first mutation experiments are TYR 23 (Registered) PHE or ALA and ASN 113 (Registered) ALA or ASP. Both TYR 23 and ASN 113 form part of the postulated dimerization intermolecular binding site which lead to the formation of the 43 helix. Tyrosine also participates in an intermolecular hydrogen bond with ARG 114. The results of these and subsequent experiments will be discussed.

  19. CapsidMaps: protein-protein interaction pattern discovery platform for the structural analysis of virus capsids using Google Maps.

    PubMed

    Carrillo-Tripp, Mauricio; Montiel-García, Daniel Jorge; Brooks, Charles L; Reddy, Vijay S

    2015-04-01

    Structural analysis and visualization of protein-protein interactions is a challenging task since it is difficult to appreciate easily the extent of all contacts made by the residues forming the interfaces. In the case of viruses, structural analysis becomes even more demanding because several interfaces coexist and, in most cases, these are formed by hundreds of contacting residues that belong to multiple interacting coat proteins. CapsidMaps is an interactive analysis and visualization tool that is designed to benefit the structural virology community. Developed as an improved extension of the ?-? Explorer, here we describe the details of its design and implementation. We present results of analysis of a spherical virus to showcase the features and utility of the new tool. CapsidMaps also facilitates the comparison of quaternary interactions between two spherical virus particles by computing a similarity (S)-score. The tool can also be used to identify residues that are solvent exposed and in the process of locating antigenic epitope regions as well as residues forming the inside surface of the capsid that interact with the nucleic acid genome. CapsidMaps is part of the VIPERdb Science Gateway, and is freely available as a web-based and cross-browser compliant application at http://viperdb.scripps.edu. PMID:25697908

  20. Narrative Maps An interactive visualisation interface for the geographic and temporal display of historical data 

    E-print Network

    Johnson, Michael J

    2010-11-24

    Maps is intended to facilitate learning by creating a useful interactive visualisation of a narrative. The current version is available on the University of Edinburgh servers at http://xweb.geos.ed.ac.uk/~s0968681/cgi_bin/NarrativeMaps.pl....

  1. Constraint-based simulation of biological systems described by Molecular Interaction Maps

    E-print Network

    Bortolussi, Luca

    Constraint-based simulation of biological systems described by Molecular Interaction Maps Luca networks described by the graphical notation of Molecular Inter- action Maps within stochastic Concurrent of this work is the simulation of biological regulatory networks described by the graphical notation

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

    SciTech Connect

    Davis, F.W.; Schimel, D.S.; Friedl, M.A.; Michaelsen, J.C.; Kittel, T.G.F.; Dubayah, R.; Dozier, J. Colorado State Univ., Fort Collins Cooperative Inst. for Research in the Atmosphere, Fort Collins, CO Maryland Univ., College Park NASA, Goddard Space Flight Center, Greenbelt, MD )

    1992-11-01

    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. 30 refs.

  3. NATCARB Interactive Maps and the National Carbon Explorer: a National Look at Carbon Sequestration

    DOE Data Explorer

    NATCARB is a national look at carbon sequestration. The NATCARB home page, National Carbon Explorer (http://www.natcarb.org/) provides access to information and interactive maps on a national scale about climate change, DOE's carbon sequestration program and its partnerships, CO2 emissions, and sinks. This portal provides access to interactive maps based on the Carbon Sequestration Atlas of the United States and Canada.

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

    SciTech Connect

    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.

  5. Statewide Repository and Interactive Map of Coastal Elevation Profiles for Alaska

    NASA Astrophysics Data System (ADS)

    Gould, A.; Kinsman, N.; Southerland, L.

    2014-12-01

    Beach elevation profiles are a type of temporal coastal data that can be used to better understand coastal environments, document change and assess hazard vulnerability. The value of these measurements increases when sites are revisited seasonally and/or interannually to capture the dynamic range of coastal landforms. Static measurements of the shoreface have been collected by a number of stakeholders in Alaska since the 1960s, but, have not historically been published or made readily accessible. In cooperation with the Alaska Ocean Observing System, the Alaska Division of Geological & Geophysical Surveys (DGGS) has designed a universal data repository to house these coastal measurements. This new database has an interactive map interface that enables easy access to existing profile locations to encourage repeat observations. Users can explore profile measurements collected by DGGS and others as time-series plots and location-based images of the shoreface environment. The database has been designed to accommodate datasets collected with differing techniques, including differential leveling, survey-grade GPS or extraction from lidar-derived digital elevation models. Non-DGGS profile measurements, including community-led efforts, University of Alaska project datasets, and archived United States Geological Survey coastal profiles have also been incorporated into the database and contributions from other entities are welcomed. In addition to exhibiting the new interactive map capabilities, we also provide a case study example from Yakutat, Alaska illustrating how this tool can be incorporated into broader investigations of coastal dynamics and how these measurements can augment shoreline change assessments. The readily accessible nature of this database also promotes local involvement in community-based coastal monitoring, also demonstrated in the Yakutat example.

  6. Protein-binding RNA aptamers affect molecular interactions distantly from their binding sites.

    PubMed

    Dupont, Daniel M; Thuesen, Cathrine K; Břtkjćr, Kenneth A; Behrens, Manja A; Dam, Karen; Sřrensen, Hans P; Pedersen, Jan S; Ploug, Michael; Jensen, Jan K; Andreasen, Peter A

    2015-01-01

    Nucleic acid aptamer selection is a powerful strategy for the development of regulatory agents for molecular intervention. Accordingly, aptamers have proven their diligence in the intervention with serine protease activities, which play important roles in physiology and pathophysiology. Nonetheless, there are only a few studies on the molecular basis underlying aptamer-protease interactions and the associated mechanisms of inhibition. In the present study, we use site-directed mutagenesis to delineate the binding sites of two 2´-fluoropyrimidine RNA aptamers (upanap-12 and upanap-126) with therapeutic potential, both binding to the serine protease urokinase-type plasminogen activator (uPA). We determine the subsequent impact of aptamer binding on the well-established molecular interactions (plasmin, PAI-1, uPAR, and LRP-1A) controlling uPA activities. One of the aptamers (upanap-126) binds to the area around the C-terminal ?-helix in pro-uPA, while the other aptamer (upanap-12) binds to both the ?-hairpin of the growth factor domain and the kringle domain of uPA. Based on the mapping studies, combined with data from small-angle X-ray scattering analysis, we construct a model for the upanap-12:pro-uPA complex. The results suggest and highlight that the size and shape of an aptamer as well as the domain organization of a multi-domain protein such as uPA, may provide the basis for extensive sterical interference with protein ligand interactions considered distant from the aptamer binding site. PMID:25793507

  7. Protein-Binding RNA Aptamers Affect Molecular Interactions Distantly from Their Binding Sites

    PubMed Central

    Dupont, Daniel M.; Thuesen, Cathrine K.; Břtkjćr, Kenneth A.; Behrens, Manja A.; Dam, Karen; Sřrensen, Hans P.; Pedersen, Jan S.; Ploug, Michael; Jensen, Jan K.; Andreasen, Peter A.

    2015-01-01

    Nucleic acid aptamer selection is a powerful strategy for the development of regulatory agents for molecular intervention. Accordingly, aptamers have proven their diligence in the intervention with serine protease activities, which play important roles in physiology and pathophysiology. Nonetheless, there are only a few studies on the molecular basis underlying aptamer-protease interactions and the associated mechanisms of inhibition. In the present study, we use site-directed mutagenesis to delineate the binding sites of two 2´-fluoropyrimidine RNA aptamers (upanap-12 and upanap-126) with therapeutic potential, both binding to the serine protease urokinase-type plasminogen activator (uPA). We determine the subsequent impact of aptamer binding on the well-established molecular interactions (plasmin, PAI-1, uPAR, and LRP-1A) controlling uPA activities. One of the aptamers (upanap-126) binds to the area around the C-terminal ?-helix in pro-uPA, while the other aptamer (upanap-12) binds to both the ?-hairpin of the growth factor domain and the kringle domain of uPA. Based on the mapping studies, combined with data from small-angle X-ray scattering analysis, we construct a model for the upanap-12:pro-uPA complex. The results suggest and highlight that the size and shape of an aptamer as well as the domain organization of a multi-domain protein such as uPA, may provide the basis for extensive sterical interference with protein ligand interactions considered distant from the aptamer binding site. PMID:25793507

  8. Interactive photogrammetric system for mapping 3D objects

    NASA Astrophysics Data System (ADS)

    Knopp, Dave E.

    1990-08-01

    A new system, FOTO-G, has been developed for 3D photogrammetric applications. It is a production-oriented software system designed to work with highly unconventional photogrammetric image configurations which result when photographing 3D objects. A demonstration with imagery from an actual 3D-mapping project is reported.

  9. Genetic interaction analysis of point mutations enables interrogation of gene function at a residue-level resolution: exploring the applications of high-resolution genetic interaction mapping of point mutations.

    PubMed

    Braberg, Hannes; Moehle, Erica A; Shales, Michael; Guthrie, Christine; Krogan, Nevan J

    2014-07-01

    We have achieved a residue-level resolution of genetic interaction mapping - a technique that measures how the function of one gene is affected by the alteration of a second gene - by analyzing point mutations. Here, we describe how to interpret point mutant genetic interactions, and outline key applications for the approach, including interrogation of protein interaction interfaces and active sites, and examination of post-translational modifications. Genetic interaction analysis has proven effective for characterizing cellular processes; however, to date, systematic high-throughput genetic interaction screens have relied on gene deletions or knockdowns, which limits the resolution of gene function analysis and poses problems for multifunctional genes. Our point mutant approach addresses these issues, and further provides a tool for in vivo structure-function analysis that complements traditional biophysical methods. We also discuss the potential for genetic interaction mapping of point mutations in human cells and its application to personalized medicine. PMID:24842270

  10. Mapping the Interactions between the Alzheimer’s A?-Peptide and Human Serum Albumin beyond Domain Resolution

    PubMed Central

    Algamal, Moustafa; Milojevic, Julijana; Jafari, Naeimeh; Zhang, William; Melacini, Giuseppe

    2013-01-01

    Human serum albumin (HSA) is a potent inhibitor of A? self-association and this novel, to our knowledge, function of HSA is of potential therapeutic interest for the treatment of Alzheimer’s disease. It is known that HSA interacts with A? oligomers through binding sites evenly partitioned across the three albumin domains and with comparable affinities. However, as of this writing, no information is available on the HSA-A? interactions beyond domain resolution. Here, we map the HSA-A? interactions at subdomain and peptide resolution. We show that each separate subdomain of HSA domain 3 inhibits A? self-association. We also show that fatty acids (FAs) compete with A? oligomers for binding to domain 3, but the determinant of the HSA/A? oligomer interactions are markedly distinct from those of FAs. Although salt bridges with the FA carboxylate determine the FA binding affinities, hydrophobic contacts are pivotal for A? oligomer recognition. Specifically, we identified a site of A? oligomer recognition that spans the HSA (494–515) region and aligns with the central hydrophobic core of A?. The HSA (495–515) segment includes residues affected by FA binding and this segment is prone to self-associate into ?-amyloids, suggesting that sites involved in fibrilization may provide a lead to develop inhibitors of A? self-association. PMID:24094411

  11. Mapping Out Atom-Wall Interaction with Atomic Clocks

    SciTech Connect

    Derevianko, A.; Obreshkov, B.; Dzuba, V. A.

    2009-09-25

    We explore the feasibility of probing atom-wall interaction with atomic clocks based on atoms trapped in engineered optical lattices. Optical lattice is normal to the wall. By monitoring the wall-induced clock shift at individual wells of the lattice, one would measure the dependence of the atom-wall interaction on the atom-wall separation. We find that the induced clock shifts are large and observable at already experimentally demonstrated levels of accuracy. We show that this scheme may uniquely probe the long-range atom-wall interaction in all three qualitatively distinct regimes of the interaction: van der Waals (image-charge interaction), Casimir-Polder (QED vacuum fluctuations), and Lifshitz (thermal-bath fluctuations) regimes.

  12. 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.

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

    SciTech Connect

    Omitaomu, Olufemi A; Liu, Cheng; Cetiner, Mustafa Sacit; 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. Identification of the sites in MAP kinase kinase-1 phosphorylated by p74raf-1.

    PubMed

    Alessi, D R; Saito, Y; Campbell, D G; Cohen, P; Sithanandam, G; Rapp, U; Ashworth, A; Marshall, C J; Cowley, S

    1994-04-01

    Many growth factors whose receptors are protein tyrosine kinases stimulate the MAP kinase pathway by activating first the GTP-binding protein Ras and then the protein kinase p74raf-1. p74raf-1 phosphorylates and activates MAP kinase kinase (MAPKK). To understand the mechanism of activation of MAPKK, we have identified Ser217 and Ser221 of MAPKK1 as the sites phosphorylated by p74raf-1. This represents the first characterization of sites phosphorylated by this proto-oncogene product. Ser217 and Ser221 lie in a region of the catalytic domain where the activating phosphorylation sites of several other protein kinases are located. Among MAPKK family members, this region is the most conserved, suggesting that all members of the family are activated by the phosphorylation of these sites. A 'kinase-dead' MAPKK1 mutant was phosphorylated at the same residues as the wild-type enzyme, establishing that both sites are phosphorylated directly by p74raf-1, and not by autophosphorylation. Only the diphosphorylated form of MAPKK1 (phosphorylated at both Ser217 and Ser221) was detected, even when the stoichiometry of phosphorylation by p74raf-1 was low, indicating that phosphorylation of one of these sites is rate limiting, phosphorylation of the second then occurring extremely rapidly. Ser217 and Ser221 were both phosphorylated in vivo within minutes when PC12 cells were stimulated with nerve growth factor. Analysis of MAPKK1 mutants in which either Ser217 or Ser221 were changed to glutamic acid, and the finding that inactivation of maximally activated MAPKK1 required the dephosphorylation of both serines, shows that phosphorylation of either residue is sufficient for maximal activation. PMID:8157000

  15. Global mapping of the regulatory interactions of histone residues.

    PubMed

    Jung, Inkyung; Seo, Jungmin; Lee, Heun-Sik; Stanton, Lawrence W; Kim, Dongsup; Choi, Jung Kyoon

    2015-12-21

    Histone residues can serve as platforms for specific regulatory function. Here we constructed a map of regulatory associations between histone residues and a wide spectrum of chromatin regulation factors based on gene expression changes by histone point mutations in Saccharomyces cerevisiae. Detailed analyses of this map revealed novel associations. Regarding the modulation of H3K4 and K36 methylation by Set1, Set2, or Jhd2, we proposed a role for H4K91 acetylation in early Pol II elongation, and for H4K16 deacetylation in late elongation and crosstalk with H3K4 demethylation for gene silencing. The association of H3K56 with nucleosome positioning suggested that this lysine residue and its acetylation might contribute to nucleosome mobility for transcription activation. Further insights into chromatin regulation are expected from this approach. PMID:26602082

  16. A Strategy for Constructing Large Protein Interaction Maps Using the Yeast Two-Hybrid

    E-print Network

    Finley Jr., Russell L.

    A Strategy for Constructing Large Protein Interaction Maps Using the Yeast Two-Hybrid System how proteins work together to mediate biological processes. One of the most effective methods for detecting biologically important protein interactions has been the yeast two-hybrid system. Here we present

  17. 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. PMID:26627376

  18. 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.

  19. Functional Mapping of Protein-Protein Interactions in an Enzyme Complex by Directed Evolution

    PubMed Central

    Roderer, Kathrin; Neuenschwander, Martin; Codoni, Giosiana; Sasso, Severin; Gamper, Marianne; Kast, Peter

    2014-01-01

    The shikimate pathway enzyme chorismate mutase converts chorismate into prephenate, a precursor of Tyr and Phe. The intracellular chorismate mutase (MtCM) of Mycobacterium tuberculosis is poorly active on its own, but becomes >100-fold more efficient upon formation of a complex with the first enzyme of the shikimate pathway, 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase (MtDS). The crystal structure of the enzyme complex revealed involvement of C-terminal MtCM residues with the MtDS interface. Here we employed evolutionary strategies to probe the tolerance to substitution of the C-terminal MtCM residues from positions 84–90. Variants with randomized positions were subjected to stringent selection in vivo requiring productive interactions with MtDS for survival. Sequence patterns identified in active library members coincide with residue conservation in natural chorismate mutases of the AroQ? subclass to which MtCM belongs. An Arg-Gly dyad at positions 85 and 86, invariant in AroQ? sequences, was intolerant to mutation, whereas Leu88 and Gly89 exhibited a preference for small and hydrophobic residues in functional MtCM-MtDS complexes. In the absence of MtDS, selection under relaxed conditions identifies positions 84–86 as MtCM integrity determinants, suggesting that the more C-terminal residues function in the activation by MtDS. Several MtCM variants, purified using a novel plasmid-based T7 RNA polymerase gene expression system, showed that a diminished ability to physically interact with MtDS correlates with reduced activatability and feedback regulatory control by Tyr and Phe. Mapping critical protein-protein interaction sites by evolutionary strategies may pinpoint promising targets for drugs that interfere with the activity of protein complexes. PMID:25551646

  20. 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 or miles wide. The information from the Thermal Emission Imaging System allows more than 100-fold higher resolution in mapping variations in the depth to ice.

    The Thermal Emission Imaging System observed the site in infrared wavelengths during night time, providing surface-temperature information, once on March 13, 2005, during summer in Mars' northern hemisphere, and again on April 8, 2005, during autumn there. The colors on this map signify relative differences in how much the surface temperature changed between those two observations. Blue indicates the locations with the least change. Red indicates areas with most change. Modeling provides estimates that the range of temperature changes shown in this map corresponds to a range in depth-to-ice of 5 centimeters (2 inches) to more than 18 centimeters (more than 7 inches). The sensitivity of this method for estimating the depth is not good for depths greater than about 20 centimeters (8 inches).

    The temperature-change data are overlaid on a mosaic of black-and-white, daytime images taken in visible-light wavelengths by the same camera, providing information about shapes in the landscape. The 10-kilometer scale bar is 6.2 miles long.

    NASA's Jet Propulsion Laboratory manages the Mars Odyssey mission for NASA's Science Mission Directorate, Washington, D.C. The Thermal Emission Imaging System was developed by Arizona State University in collaboration with Raytheon Santa Barbara Remote Sensing. Lockheed Martin Space Systems, Denver, is the prime contractor for the Odyssey project, and developed and built the orbiter. Mission operations are conducted jointly from Lockheed Martin and from JPL, a division of the California Institute of Technology in Pasadena.

  1. Histon-histone interactions within chromatin. Preliminary location of multiple contact sites between histones 2A, 2B, and 4.

    PubMed

    Martinson, H G; True, R; Lau, C K; Mehrabian, M

    1979-03-20

    The contact-site cross-linkers tetranitromethane, UV light, formaldehyde, and a monofunctional imido ester have been used to generate a collection of histone-histone dimers and trimers from nuclei and chromatin. Four different H2B-H4 dimers have been isolated. Preliminary CNBr peptide mapping has shown that all are cross-linked at different positions that are apparently clustered within the C-terminal regions of these histones. Similarily, two different H2A-H2B dimers and two different H2A-H2B-H4 trimers have been partially characterized. The data suggest a functional map for H2B in which the N-terminal third interacts with DNA, the middle third interacts with H2A, and the C-terminal third interacts with H4. We hope, by pursuing this type of analysis, to develop a detailed understanding of each histone-histone binding interaction through saturation cross-linking of the binding sites. PMID:427096

  2. Development of Historical Water Table Maps of the 200 West Area of the Hanford Site (1950-1970)

    SciTech Connect

    Kinney, Teena M.; McDonald, John P.

    2006-09-15

    A series of detailed historical water-table maps for the 200-West Area of the Hanford Site was made to aid interpretation of contaminant distribution in the upper aquifer. The contaminants are the result of disposal of large volumes of waste to the ground during Hanford Site operations, which began in 1944 and continued into the mid-1990s. Examination of the contaminant plumes that currently exist on site shows that the groundwater beneath the 200-West Area has deviated from its pre-Hanford west-to-east flow direction during the past 50 years. By using historical water-level measurements from wells around the 200-West Area, it was possible to create water-table contour maps that show probable historic flow directions. These maps are more detailed than previously published water-table maps that encompass the entire Hanford Site.

  3. Meetings Publications Membership Career Central Advertise / Exhibit About MRS Advocacy Store My MRS Media Contact Site Map FAQs View Cart

    E-print Network

    Lin, Zhiqun

    Media Contact Site Map FAQs View Cart Childcare Options at the Fall Meeting The Materials Research, Elizabeth A. Nickels, Peter P. Edwards From MRS Proceedings Volume 1098E Abstract: We review here work

  4. Mapping actin surfaces required for functional interactions in vivo

    PubMed Central

    1994-01-01

    An in vivo strategy to identify amino acids of actin required for functional interactions with actin-binding proteins was developed. This approach is based on the assumption that an actin mutation that specifically impairs the interaction with an actin-binding protein will cause a phenotype similar to a null mutation in the gene that encodes the actin-binding protein. 21 actin mutations were analyzed in budding yeast, and specific regions of actin subdomain 1 were implicated in the interaction with fimbrin, an actin filament-bundling protein. Mutations in this actin subdomain were shown to be, like a null allele of the yeast fimbrin gene (SAC6), lethal in combination with null mutations in the ABP1 and SLA2 genes, and viable in combination with a null mutation in the SLA1 gene. Biochemical experiments with act1-120 actin (E99A, E100A) verified a defect in the fimbrin-actin interaction. Genetic interactions between mutant alleles of the yeast actin gene and null alleles of the SAC6, ABP1, SLA1, and SLA2 genes also demonstrated that the effects of the 21 actin mutations are diverse and allowed four out of seven pseudo-wild-type actin alleles to be distinguished from the wild-type gene for the first time, providing evidence for functional redundancy between different surfaces of actin. PMID:8034743

  5. New predictive equations and site amplification estimates for the next-generation Swiss ShakeMaps

    NASA Astrophysics Data System (ADS)

    Cauzzi, Carlo; Edwards, Benjamin; Fäh, Donat; Clinton, John; Wiemer, Stefan; Kästli, Philipp; Cua, Georgia; Giardini, Domenico

    2014-01-01

    We present a comprehensive scientific and technical update of the Swiss customization of United States Geological Survey ShakeMap, in use at the Swiss Seismological Service since 2007. The new Swiss ShakeMaps are based on predictive equations for peak ground-motions and response spectra derived from stochastic simulations tailored to Swiss seismicity. Using synthetics allows overcoming the difficulties posed by: (i) the paucity of strong-motion data recordings in Switzerland; (ii) the regional dependence of shear wave energy attenuation and focal depth distribution in the Swiss Alps and foreland; (iii) the depth dependence of stress parameters suggested by macroseismic and instrumental observations. In the new Swiss ShakeMaps, VS,30 is no longer used as proxy for site amplification at regional scale, and is replaced by macroseismic intensity increments for different soil classes, based on the recently revised earthquake catalogue of Switzerland (ECOS-09). The new implementation converts ground-motion levels into macroseismic intensity by means of ground-motion to intensity conversion equations based on the Italian strong-motion and intensity databanks and is therefore well constrained for intensities larger than VII. The new Swiss ShakeMaps show a satisfactory agreement with the macroseimic fields of both large historical events and recent well-recorded earthquakes of moderate magnitude. The new implementation is now fully consistent with the state-of-the-art in engineering seismology in Switzerland.

  6. Understanding Urban Watersheds through Digital Interactive Maps, San Francisco Bay Area, California

    NASA Astrophysics Data System (ADS)

    Sowers, J. M.; Ticci, M. G.; Mulvey, P.

    2014-12-01

    Dense urbanization has resulted in the "disappearance" of many local creeks in urbanized areas surrounding the San Francisco Bay. Long reaches of creeks now flow in underground pipes. Municipalities and water agencies trying to reduce non-point-source pollution are faced with a public that cannot see and therefore does not understand the interconnected nature of the drainage system or its ultimate discharge to the bay. Since 1993, we have collaborated with the Oakland Museum, the San Francisco Estuary Institute, public agencies, and municipalities to create creek and watershed maps to address the need for public understanding of watershed concepts. Fifteen paper maps are now published (www.museumca.org/creeks), which have become a standard reference for educators and anyone working on local creek-related issues. We now present digital interactive creek and watershed maps in Google Earth. Four maps are completed covering urbanized areas of Santa Clara and Alameda Counties. The maps provide a 3D visualization of the watersheds, with cartography draped over the landscape in transparent colors. Each mapped area includes both Present and Past (circa 1800s) layers which can be clicked on or off by the user. The Present layers include the modern drainage network, watershed boundaries, and reservoirs. The Past layers include the 1800s-era creek systems, tidal marshes, lagoons, and other habitats. All data are developed in ArcGIS software and converted to Google Earth format. To ensure the maps are interesting and engaging, clickable icons pop-up provide information on places to visit, restoration projects, history, plants, and animals. Maps of Santa Clara Valley are available at http://www.valleywater.org/WOW.aspx. Maps of western Alameda County will soon be available at http://acfloodcontrol.org/. Digital interactive maps provide several advantages over paper maps. They are seamless within each map area, and the user can zoom in or out, and tilt, and fly over to explore any area of interest. They can be easily customized, for example, adding placemarks or notes. Enrichment information can be added, using clickable icons, without cluttering the map. Best, the maps are fun to use. Digital interactive maps will be another effective tool for enhancing public understanding of urban creeks & watersheds.

  7. 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 averaged over patches of ground hundreds of kilometers or miles wide. The information from the Thermal Emission Imaging System allows more than 100-fold higher resolution in mapping variations in the depth to ice.

    The Thermal Emission Imaging System observed the site in infrared wavelengths during night time, providing surface-temperature information. It did so once on Dec. 27, 2005, during late summer in Mars' southern hemisphere, and again on Jan. 22, 2006, the first day of autumn there. The colors on this map signify relative differences in how much the surface temperature changed between those two observations. Blue indicates the locations with the least change. Red indicates areas with most change. Modeling provides estimates that the range of temperature changes shown in this map corresponds to a range in depth-to-ice of less than 1 centimeter (0.4 inch) to more than 19 centimeters (more than 7.5 inches). The sensitivity of this method for estimating the depth is not good for depths greater than about 20 centimeters (8 inches).

    The temperature-change data are overlaid on a mosaic of black-and-white, daytime images taken in infrared wavelengths by the same camera, providing information about shapes in the landscape. The 20-kilometer scale bar is 12.4 miles long.

    NASA's Jet Propulsion Laboratory manages the Mars Odyssey mission for NASA's Science Mission Directorate, Washington, D.C. The Thermal Emission Imaging System (THEMIS) was developed by Arizona State University in collaboration with Raytheon Santa Barbara Remote Sensing. Lockheed Martin Space Systems, Denver, is the prime contractor for the Odyssey project, and developed and built the orbiter. Mission operations are conducted jointly from Lockheed Martin and from JPL, a division of the California Institute of Technology in Pasadena.

  8. Mapping of multiple phosphorylation sites within the structural and catalytic domains of the Fujinami avian sarcoma virus transforming protein.

    PubMed Central

    Weinmaster, G; Hinze, E; Pawson, T

    1983-01-01

    The phosphorylation sites of the P140gag-fps gene product of Fujinami avian sarcoma virus have been identified and localized to different regions of this transforming protein. FSV P140gag-fps isolated from transformed cells is phosphorylated on at least three distinct tyrosine residues and one serine residue, in addition to minor phosphorylation sites shared with Pr76gag. Partial proteolysis with virion protease p15 or with Staphylococcus aureus V8 protease has been used to generate defined peptide fragments of P140gag-fps and thus to map its phosphorylation sites. The amino-terminal gag-encoded region of P140gag-fps contains a phosphotyrosine residue in addition to normal gag phosphorylation sites. The two major phosphotyrosine residues and the major phosphorserine residue are located in the carboxy-terminal portion of the fps-encoded region of P140gag-fps. P140gag-fps radiolabeled in vitro in an immune complex kinase reaction is phosphorylated at only one of the two C-terminal tyrosine residues phosphorylated in vivo and weakly phosphorylated at the gag-encoded tyrosine and at a tyrosine site not detectably phosphorylated in vivo. Thus, the in vitro tyrosine phosphorylation of P140gag-fps is distinct from that seen in the transformed cell. A comparative tryptic phosphopeptide analysis of the gag-fps proteins of three Fujinami avian sarcoma virus variants showed that the phosphotyrosine-containing peptides are invariant, and this high degree of sequence conservation suggests that these sites are functionally important or lie within important regions. The P105gag-fps transforming protein of PRCII avian sarcoma virus lacks one of the C-terminal phosphotyrosine sites found in Fujinami avian sarcoma virus P140gag-fps. Partial trypsin cleavage of FSV P140gag-fps immunoprecipitated with anti-gag serum releases C-terminal fragments of 45K and 29K from the immune complex that retain an associated tyrosine-specific protein kinase activity. This observation, and the localization of the major P140gag-fps phosphorylation sites to the C-terminal fps region, indicate that the kinase domain of P140gag-fps is located at its C terminus. The phosphorylation of P140gag-fps itself is complex, suggesting that it may itself interact with several protein kinases in the transformed cell. Images PMID:6298463

  9. Regional geology of the Venera landing sites: Tentative results of photogeologic mapping

    NASA Technical Reports Server (NTRS)

    Basilevsky, A. T.; Weitz, C. M.

    1993-01-01

    The regional geology of the five Venera landing sites, where geochemical measurements and TV observations on the Venusian surface were made, was studied based on the photogeologic analysis of the Magellan C1-MIDRP imagery for the large area that we will call the Venera region (38 deg. N to 22.6 deg. S and 268 to 344 deg. E). The results of the analysis were compiled in the form of a synoptical geologic map at about 1:10 M scale. MIT-processed Magellan altimetry was also used for the analysis.

  10. Carbon Sequestration Atlas and Interactive Maps from the Southwest Regional Partnership on Carbon Sequestration

    DOE Data Explorer

    McPherson, Brian

    In November of 2002, DOE announced a global climate change initiative involving joint government-industry partnerships working together to find sensible, low cost solutions for reducing GHG emissions. As a result, seven regional partnerships were formed; the Southwest Regional Partnership on Carbon Sequestration (SWP) is one of those. These groups are utilizing their expertise to assess sequestration technologies to capture carbon emissions, identify and evaluate appropriate storage locations, and engage a variety of stakeholders in order to increase awareness of carbon sequestration. Stakeholders in this project are made up of private industry, NGOs, the general public, and government entities. There are a total of 44 current organizations represented in the partnership including electric utilities, oil and gas companies, state governments, universities, NGOs, and tribal nations. The SWP is coordinated by New Mexico Tech and encompasses New Mexico, Arizona, Colorado, Oklahoma, Utah, and portions of Kansas, Nevada, Texas, and Wyoming. Field test sites for the region are located in New Mexico (San Juan Basin), Utah (Paradox Basin), and Texas (Permian Basin).[Taken from the SWP C02 Sequestration Atlas] The SWP makes available at this website their CO2 Sequestration Atlas and an interactive data map.

  11. Genome Wide Mapping of Foxo1 Binding-sites in Murine T Lymphocytes.

    PubMed

    Liao, Will; Ouyang, Weiming; Zhang, Michael Q; Li, Ming O

    2014-12-01

    The Forkhead box O (Foxo) family of transcription factors has a critical role in controlling the development, differentiation, and function of T cells. However, the direct target genes of Foxo transcription factors in T cells have not been well characterized. In this study, we focused on mapping the genome wide Foxo1-binding sites in naďve CD4(+) T cells, CD8(+) T cells, and Foxp3(+) regulatory T (Treg) cells. By using chromatin immunoprecipitation coupled with deep sequencing (ChIP-Seq), we identified Foxo1 binding sites that were shared among or specific to the three T cell populations. Here we describe the experiments, quality controls, as well as the deep sequencing data. Part of the data analysis has been published by Ouyang W et al. in Nature 2012[1] and Kim MV et al. in Immunity 2013[2], and the associated data set were uploaded to NCBI Gene Expression Omnibus. PMID:25302145

  12. Mapping of SUMO sites and analysis of SUMOylation changes induced by external stimuli

    PubMed Central

    Impens, Francis; Radoshevich, Lilliana; Cossart, Pascale; Ribet, David

    2014-01-01

    SUMOylation is an essential ubiquitin-like modification involved in important biological processes in eukaryotic cells. Identification of small ubiquitin-related modifier (SUMO)-conjugated residues in proteins is critical for understanding the role of SUMOylation but remains experimentally challenging. We have set up a powerful and high-throughput method combining quantitative proteomics and peptide immunocapture to map SUMOylation sites and have analyzed changes in SUMOylation in response to stimuli. With this technique we identified 295 SUMO1 and 167 SUMO2 sites on endogenous substrates of human cells. We further used this strategy to characterize changes in SUMOylation induced by listeriolysin O, a bacterial toxin that impairs the host cell SUMOylation machinery, and identified several classes of host proteins specifically deSUMOylated in response to this toxin. Our approach constitutes an unprecedented tool, broadly applicable to various SUMO-regulated cellular processes in health and disease. PMID:25114211

  13. Mapping of SUMO sites and analysis of SUMOylation changes induced by external stimuli.

    PubMed

    Impens, Francis; Radoshevich, Lilliana; Cossart, Pascale; Ribet, David

    2014-08-26

    SUMOylation is an essential ubiquitin-like modification involved in important biological processes in eukaryotic cells. Identification of small ubiquitin-related modifier (SUMO)-conjugated residues in proteins is critical for understanding the role of SUMOylation but remains experimentally challenging. We have set up a powerful and high-throughput method combining quantitative proteomics and peptide immunocapture to map SUMOylation sites and have analyzed changes in SUMOylation in response to stimuli. With this technique we identified 295 SUMO1 and 167 SUMO2 sites on endogenous substrates of human cells. We further used this strategy to characterize changes in SUMOylation induced by listeriolysin O, a bacterial toxin that impairs the host cell SUMOylation machinery, and identified several classes of host proteins specifically deSUMOylated in response to this toxin. Our approach constitutes an unprecedented tool, broadly applicable to various SUMO-regulated cellular processes in health and disease. PMID:25114211

  14. 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.

  15. High resolution dynamical mapping of social interactions with active RFID

    E-print Network

    Barrat, Alain; Colizza, Vittoria; Pinton, Jean-Francois; Broeck, Wouter Van den; Vespignani, Alessandro

    2008-01-01

    In this paper we present an experimental framework to gather data on face-to-face social interactions between individuals, with a high spatial and temporal resolution. We use active Radio Frequency Identification (RFID) devices that assess contacts with one another by exchanging low-power radio packets. When individuals wear the beacons as a badge, a persistent radio contact between the RFID devices can be used as a proxy for a social interaction between individuals. We present the results of a pilot study %recently performed during a conference, and a subsequent preliminary data analysis, that provides an assessment of our method and highlights its versatility and applicability in many areas concerned with human dynamics.

  16. Interacting damage models mapped onto ising and percolation models

    SciTech Connect

    Toussaint, Renaud; Pride, Steven R.

    2004-03-23

    The authors introduce a class of damage models on regular lattices with isotropic interactions between the broken cells of the lattice. Quasistatic fiber bundles are an example. The interactions are assumed to be weak, in the sense that the stress perturbation from a broken cell is much smaller than the mean stress in the system. The system starts intact with a surface-energy threshold required to break any cell sampled from an uncorrelated quenched-disorder distribution. The evolution of this heterogeneous system is ruled by Griffith's principle which states that a cell breaks when the release in potential (elastic) energy in the system exceeds the surface-energy barrier necessary to break the cell. By direct integration over all possible realizations of the quenched disorder, they obtain the probability distribution of each damage configuration at any level of the imposed external deformation. They demonstrate an isomorphism between the distributions so obtained and standard generalized Ising models, in which the coupling constants and effective temperature in the Ising model are functions of the nature of the quenched-disorder distribution and the extent of accumulated damage. In particular, they show that damage models with global load sharing are isomorphic to standard percolation theory, that damage models with local load sharing rule are isomorphic to the standard ising model, and draw consequences thereof for the universality class and behavior of the autocorrelation length of the breakdown transitions corresponding to these models. they also treat damage models having more general power-law interactions, and classify the breakdown process as a function of the power-law interaction exponent. Last, they also show that the probability distribution over configurations is a maximum of Shannon's entropy under some specific constraints related to the energetic balance of the fracture process, which firmly relates this type of quenched-disorder based damage model to standard statistical mechanics.

  17. 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 similar fashion to Jnk-1 siRNA and to rosiglitazone treatment. Together, the data suggest that these new ligand series bind to a novel, allosteric, and physiologically relevant site and therefore represent a unique approach to identify kinase inhibitors.

  18. User-Centric Secure Cross-Site Interaction Framework for Online Social Networking Services

    ERIC Educational Resources Information Center

    Ko, Moo Nam

    2011-01-01

    Social networking service is one of major technological phenomena on Web 2.0. Hundreds of millions of users are posting message, photos, and videos on their profiles and interacting with other users, but the sharing and interaction are limited within the same social networking site. Although users can share some content on a social networking site

  19. Interactive Marine Spatial Planning: Siting Tidal Energy Arrays around the Mull of Kintyre

    PubMed Central

    Alexander, Karen A.; Janssen, Ron; Arciniegas, Gustavo; O'Higgins, Timothy G.; Eikelboom, Tessa; Wilding, Thomas A.

    2012-01-01

    The rapid development of the offshore renewable energy sector has led to an increased requirement for Marine Spatial Planning (MSP) and, increasingly, this is carried out in the context of the ‘ecosystem approach’ (EA) to management. We demonstrate a novel method to facilitate implementation of the EA. Using a real-time interactive mapping device (touch-table) and stakeholder workshops we gathered data and facilitated negotiation of spatial trade-offs at a potential site for tidal renewable energy off the Mull of Kintyre (Scotland). Conflicts between the interests of tidal energy developers and commercial and recreational users of the area were identified, and use preferences and concerns of stakeholders were highlighted. Social, cultural and spatial issues associated with conversion of common pool to private resource were also revealed. The method identified important gaps in existing spatial data and helped to fill these through interactive user inputs. The workshops developed a degree of consensus between conflicting users on the best areas for potential development suggesting that this approach should be adopted during MSP. PMID:22253865

  20. Home Site Map Make Your Home Page Suggestions Enquiry Sunday, March 16, M pays tributes to Potti Sriramulu

    E-print Network

    Lummaa, Virpi

    of the Royal Society B. (ANI) Single Parent Family Fun Fun for you Fun for the kids Free Community site for single parents www.singleparentfun.com UK Single Parent Dating Search 1000s of current profiles JoinHome Site Map Make Your Home Page Suggestions Enquiry Sunday, March 16, M pays tributes to Potti

  1. Functional genomics platform for pooled screening and generation of mammalian genetic interaction maps

    Cancer.gov

    Systematic genetic interaction maps in microorganisms are powerful tools for identifying functional relationships between genes and for defining the function of uncharacterized genes. We have recently implemented this strategy in mammalian cells as a two-stage approach. First, genes of interest are robustly identified in a pooled genome-wide screen using complex shRNA libraries. Second, phenotypes for all pairwise combinations of 'hit' genes are measured in a double-shRNA screen and used to construct a genetic interaction map.

  2. Implications for the domain arrangement of axonin-1 derived from the mapping of its NgCAM binding site.

    PubMed Central

    Rader, C; Kunz, B; Lierheimer, R; Giger, R J; Berger, P; Tittmann, P; Gross, H; Sonderegger, P

    1996-01-01

    The neuronal cell adhesion molecule axonin-1 is composed of six immunoglobulin and four fibronectin type III domains. Axonin-1 promotes neurite outgrowth, when presented as a substratum for neurons in vitro, via a neuronal receptor that has been identified as the neuron-glia cell adhesion molecule, NgCAM, based on the blocking effect of polyclonal antibodies directed to NgCAM. Here we report the identification of axonin-1 domains involved in NgCAM binding. NgCAM-conjugated microspheres were tested for binding to COS cells expressing domain deletion mutants of axonin-1. In addition, monoclonal antibodies directed to axonin-1 were assessed for their ability to block the axonin-1-NgCAM interaction, and their epitopes were mapped using the domain deletion mutants. The results suggest that the four amino-terminal immunoglobulin domains of axonin-1 form a domain conglomerate which is necessary and sufficient for NgCAM binding. Surprisingly, NgCAM binding to membrane-bound axonin-1 was increased strongly by deletion of the fifth or sixth immunoglobulin domains of axonin-1. Based on these results and on negative staining electron microscopy, we propose a horseshoe-shaped domain arrangement of axonin-1 that obscures the NgCAM binding site. Neurite outgrowth studies with truncated forms of axonin-1 show that axonin-1 is a neurite outgrowth-promoting substratum in the absence of the NgCAM binding site. Images PMID:8641271

  3. Mapping of transcription start sites in Saccharomyces cerevisiae using 5? SAGE

    PubMed Central

    Zhang, Zhihong; Dietrich, Fred S.

    2005-01-01

    A minimally addressed area in Saccharomyces cerevisiae research is the mapping of transcription start sites (TSS). Mapping of TSS in S.cerevisiae has the potential to contribute to our understanding of gene regulation, transcription, mRNA stability and aspects of RNA biology. Here, we use 5? SAGE to map 5? TSS in S.cerevisiae. Tags identifying the first 15–17 bases of the transcripts are created, ligated to form ditags, amplified, concatemerized and ligated into a vector to create a library. Each clone sequenced from this library identifies 10–20 TSS. We have identified 13 746 unique, unambiguous sequence tags from 2231 S.cerevisiae genes. TSS identified in this study are consistent with published results, with primer extension results described here, and are consistent with expectations based on previous work on transcription initiation. We have aligned the sequence flanking 4637 TSS to identify the consensus sequence A(Arich)5NPyA(A/T)NN(Arich)6, which confirms and expands the previous reported PyA(A/T)Pu consensus pattern. The TSS data allowed the identification of a previously unrecognized gene, uncovered errors in previous annotation, and identified potential regulatory RNAs and upstream open reading frames in 5?-untranslated region. PMID:15905473

  4. 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).

  5. 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 several morphometric parameters used for template matching, as compared to a mapping based on elevation values only. In comparison to manual digitization, a combination of the described detection routine and a manual removal of falsely detected sites can considerably facilitate the mapping and distribution analysis of kiln sites or other small-scale relief features.

  6. Jules Verne Voyager, Jr: An Interactive Map Tool for Teaching Plate Tectonics

    NASA Astrophysics Data System (ADS)

    Hamburger, M. W.; Meertens, C. M.

    2010-12-01

    We present an interactive, web-based map utility that can make new geological and geophysical results accessible to a large number and variety of users. The tool provides a user-friendly interface that allows users to access a variety of maps, satellite images, and geophysical data at a range of spatial scales. The map tool, dubbed 'Jules Verne Voyager, Jr.', allows users to interactively create maps of a variety of study areas around the world. The utility was developed in collaboration with the UNAVCO Consortium for study of global-scale tectonic processes. Users can choose from a variety of base maps (including "Face of the Earth" and "Earth at Night" satellite imagery mosaics, global topography, geoid, sea-floor age, strain rate and seismic hazard maps, and others), add a number of geographic and geophysical overlays (coastlines, political boundaries, rivers and lakes, earthquake and volcano locations, stress axes, etc.), and then superimpose both observed and model velocity vectors representing a compilation of 2933 GPS geodetic measurements from around the world. A remarkable characteristic of the geodetic compilation is that users can select from some 21 plates' frames of reference, allowing a visual representation of both 'absolute' plate motion (in a no-net rotation reference frame) and relative motion along all of the world's plate boundaries. The tool allows users to zoom among at least three map scales. The map tool can be viewed at http://jules.unavco.org/VoyagerJr/Earth. A more detailed version of the map utility, developed in conjunction with the EarthScope initiative, focuses on North America geodynamics, and provides more detailed geophysical and geographic information for the United States, Canada, and Mexico. The ‘EarthScope Voyager’ can be accessed at http://jules.unavco.org/VoyagerJr/EarthScope. Because the system uses pre-constructed gif images and overlays, the system can rapidly create and display maps to a large number of users simultaneously and does not require any special software installation on users' systems. In addition, a javascript-based educational interface, dubbed "Exploring our Dynamic Planet", incorporates the map tool, explanatory material, background scientific material, and curricular activities that encourage users to explore Earth processes using the Jules Verne Voyager, Jr. tool. Exploring our Dynamic Planet can be viewed at http://www.dpc.ucar.edu/VoyagerJr/. Because of its flexibility, the map utilities can be used for hands-on exercises exploring plate interaction in a range of academic settings, from high school science classes to entry-level undergraduate to graduate-level tectonics courses.

  7. Reactivity at the substrate activation site of yeast pyruvate decarboxylase: inhibition by distortion of domain interactions.

    PubMed

    Baburina, I; Dikdan, G; Guo, F; Tous, G I; Root, B; Jordan, F

    1998-02-01

    The residue C221 on pyruvate decarboxylase (EC. 4.1.1.1) from Saccharomyces cerevisiae has been shown to be the site where the substrate activation cascade is triggered [Baburina et al. (1994) Biochemistry 33, 5630-5635] and is located on the beta domain [Arjunan et al. (1996) J. Mol. Biol. 256, 590], while the active-center thiamin diphosphate is located > 20 A away, at the interface of the alpha and gamma domains. The reactivity of all three exposed cysteines (152, 221, and 222) was examined under the influence of known activators and inhibitors. Protein chemical methods, in conjunction with [1-14C] and [3-3H] analogues of the mechanism-based inhibitor p-ClC6H4CH=CHCOCOOH, demonstrated that the holoenzyme bound approximately 2-3 atoms of tritium/atom of C-14. However, when the labeled enzyme was subjected to trypsinization, followed by sequencing of the labeled peptide, only the tritium label was in evidence at C221, with a stoichiometry of 2 atoms of tritium/tetrameric holoenzyme. Apparently, the product of decarboxylation bonded to the enzyme survived the limited proteolysis and sequencing, but the bound 2-oxoacid was released during the protocol. Surprisingly, the C221S or C222A variants, although they still possess 20-30% specific activity compared to the wild-type enzyme, could still be inhibited by the XC6H4CH=CHCOCOOH class of inhibitors/substrate analogues, as well as by the product of decarboxylation from such compounds, cinnamaldehydes. Other potential nucleophilic sites for the inhibitor [C152 (the third exposed cysteine), residues D28, H114, H115, and E477 at the active center and H92 at the regulatory site] were also substituted by a nonnucleophilic side chain. All variants were still subject to inhibition by p-ClC6H4CH=CHCOCOOH, the active-center variants being inactivated even faster than the wild-type enzyme, suggesting that the active center is involved in the inactivation process. It appears that C221 is one of only two sites of interaction with such compounds (perhaps the result of a Michael addition across the C=C bond), yet the bound [1-14C]-labeled inhibitor could no longer be detected after peptide mapping at this site or at the catalytic site. Upon combining the tritiated inhibitor with [2-14C]-thiamin diphosphate, no evidence could be found for a thiamin-inhibitor-protein ternary complex, suggesting that the thiamin-bound enamine intermediate did not react further with the protein. It is likely that the second form of inhibition is at the active center, with the inhibitor cofactor-bound, which would have been released during the proteolytic protocol. Among other known activators, ketomalonate was found to react at C221 only. Glyoxalic acid, a mechanism-based inhibitor, on the other hand, could react at both the regulatory and the catalytic center. The high reactivity of C221 is consistent with it being in the thiolate form at the optimal pH of the enzyme [forming a Cys221S(-) + HHis92 ion pair; see Baburina et al. (1996) Biochemistry 35, 10249-10255, and Baburina et al. (1998) Biochemistry 37, 1235-1244]. Several additional compounds were tested as potential regulatory site-directed reagents: iodoacetate, 1,3-dibromoacetone, and 1-bromo-2-butanone. All three compounds reduced the Hill coefficient and hence appear to react at C221. It was concluded that either substitution of C221 by a nonnucleophilic residue or large groups attached to C221 in the wild-type enzyme lead to a distortion of domain interactions, interactions which are required for both optimal activity and substrate activation. PMID:9477950

  8. Towards second-generation STS (sequence-tagged sites) linkage maps in conifers: a genetic map of Norway spruce (Picea abies K.).

    PubMed

    Paglia, G P; Olivieri, A M; Morgante, M

    1998-06-01

    Genetic linkage maps have been produced for a wide range of organisms during the last decade, thanks to the increasing availability of molecular markers. The use of microsatellites (or Simple Sequence Repeats, SSRs) as genetic markers has led to the construction of "second-generation" genetic maps for humans, mouse and other organisms of major importance. We constructed a second-generation single-tree genetic linkage map of Norway spruce (Picea abies K.) using a panel of 72 haploid megagametophytes with a total of 447 segregating bands [366 Amplified Fragment Length Polymorphisms (AFLPs), 20 Selective Amplification of Microsatellite Polymorphic Loci (SAMPLs) and 61 SSRs, each single band being treated initially as a dominant marker]. Four hundred and thirteen markers were mapped in 29 linkage groups (including triplets and doublets) covering a genetic length of 2198.3 cM, which represents 77.4% of the estimated genome length of Picea abies (approximately 2839 cM). The map is still far from coalescing into the expected 12 chromosomal linkage groups of Norway spruce (2n = 2x = 24). A possible explanation for this comes from the observed non-random distribution of markers in the framework map. Thirty-eight SSR marker loci could be mapped onto 19 linkage groups. This set of highly informative Sequence Tagged Sites (STSs) can be used in many aspects of genetic analysis of forest trees, such as marker-assisted selection, QTL mapping, positional cloning, gene flow analysis, mating system analysis and genetic diversity studies. PMID:9669328

  9. Linking tumor mutations to drug responses via a quantitative chemical-genetic interaction map*

    Cancer.gov

    There is an urgent need in oncology to link molecular aberrations in tumors with therapeutics that can be administered in a personalized fashion. One approach identifies synthetic-lethal genetic interactions or emergent dependencies that cancer cells acquire in the presence of specific mutations. Using engineered isogenic cells, we generated a systematic and quantitative chemical-genetic interaction map that measures the influence of 51 aberrant cancer genes on 90 drug responses.

  10. An Interactive Immersive Serious Game Application for Kunyu Quantu World Map

    NASA Astrophysics Data System (ADS)

    Peng, S.-T.; Hsu, S.-Y.; Hsieh, K.-C.

    2015-08-01

    In recent years, more and more digital technologies and innovative concepts are applied on museum education. One of the concepts applied is "Serious game." Serious game is not designed for entertainment purpose but allows users to learn real world's cultural and educational knowledge in the virtual world through game-experiencing. Technologies applied on serious game are identical to those applied on entertainment game. Nowadays, the interactive technology applications considering users' movement and gestures in physical spaces are developing rapidly, which are extensively used in entertainment games, such as Kinect-based games. The ability to explore space via Kinect-based games can be incorporated into the design of serious game. The ancient world map, Kunyu Quantu, from the collection of the National Palace Museum is therefore applied in serious game development. In general, the ancient world map does not only provide geological information, but also contains museum knowledge. This particular ancient world map is an excellent content applied in games as teaching material. In the 17th century, it was first used by a missionary as a medium to teach the Kangxi Emperor of the latest geologic and scientific spirits from the West. On this map, it also includes written biological knowledge and climate knowledge. Therefore, this research aims to present the design of the interactive and immersive serious game based installation that developed from the rich content of the Kunyu Quantu World Map, and to analyse visitor's experience in terms of real world's cultural knowledge learning and interactive responses.

  11. INTERACTIONS BETWEEN PASSERINES AND WOODY PLANTS AT A MIGRATORY STOP-OVER SITE

    E-print Network

    Lawrence, Deborah

    spp .suggest a semi-specific mutualism. Other migrant-plant interactions follow models of diffuseINTERACTIONS BETWEEN PASSERINES AND WOODY PLANTS AT A MIGRATORY STOP-OVER SITE: FRUIT CONSUMPTION of Virginia August, 1993 #12;ABSTRACT Interactions between migratory passerines and woody plant fruiting

  12. 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.

  13. Projector Phone: A Study of Using Mobile Phones with Integrated Projector for Interaction with Maps

    E-print Network

    Projector Phone: A Study of Using Mobile Phones with Integrated Projector for Interaction with Maps}@comp.lancs.ac.uk ABSTRACT First working prototypes of mobile phones with integrated pico projectors have already been demonstrated and it is expected that such projector phones will be sold within the next three years

  14. Teacher Use of the Interactive Whiteboards in Flemish Secondary Education--Mapping against a Transition Framework

    ERIC Educational Resources Information Center

    Van Laer, Stijn; Beauchamp, Gary; Colpaert, Jozef

    2014-01-01

    Interactive Whiteboards (IWBs) are a relatively new, but increasingly more common, tool in the classrooms of Flemish Secondary schools. This paper reports on research which attempted to map not only the amount of IWB use in Flemish secondary schools but, perhaps more importantly, to assess how they are used and the progress of teachers in…

  15. RE Atlas: The U.S. Atlas of Renewable Resources (Interactive Map, GIS Data)

    DOE Data Explorer

    This interactive data map allows a user to explore the locations across the U.S. of many different basic, renewable energy resources. The many layers can be activated one at a time or in multiple combinations and the GIS display draws from a rich combination of data collections.

  16. CARTOGRAPHIC ANIMATION AND LEGENDS FOR TEMPORAL MAPS: EXPLORATION AND OR INTERACTION

    E-print Network

    Klippel, Alexander

    CARTOGRAPHIC ANIMATION AND LEGENDS FOR TEMPORAL MAPS: EXPLORATION AND OR INTERACTION Menno@geog.psu.edu & alan@essc.psu.edu Abstract Temporal cartographic animations are increasingly common. For users to understand a temporal animation, they must not only apply an appropriate spatial knowledge schema that allows

  17. Big Data Storytelling through Interactive Maps Jayant Madhavan, Sreeram Balakrishnan, Kathryn Brisbin, Hector Gonzalez, Nitin Gupta,

    E-print Network

    Cortes, Corinna

    Big Data Storytelling through Interactive Maps Jayant Madhavan, Sreeram Balakrishnan, Kathryn) brings big data collaboration and visualization to data-experts who possess neither large data high-profile stories. 1 Introduction Much of the current excitement about Big Data refers to performing

  18. Inclusive Composite Interval Mapping of QTL by Environment Interactions in Biparental Populations

    PubMed Central

    Li, Shanshan; Wang, Jiankang; Zhang, Luyan

    2015-01-01

    Identification of environment-specific QTL and stable QTL having consistent genetic effects across a wide range of environments is of great importance in plant breeding. Inclusive Composite Interval Mapping (ICIM) has been proposed for additive, dominant and epistatic QTL mapping in biparental populations for single environment. In this study, ICIM was extended to QTL by environment interaction (QEI) mapping for multi-environmental trials, where the QTL average effect and QEI effects could be properly estimated. Stepwise regression was firstly applied in each environment to identify the most significant marker variables which were then used to adjust the phenotypic values. One-dimensional scanning was then conducted on the adjusted phenotypic values across the environments in order to detect QTL with either average effect or QEI effects, or both average effect and QEI effects. In this way, the genetic background could be well controlled while the conventional interval mapping was applied. An empirical method to determine the threshold of logarithm of odds was developed, and the efficiency of the ICIM QEI mapping was demonstrated in simulated populations under different genetic models. One actual recombinant inbred line population was used to compare mapping results between QEI mapping and single-environment analysis. PMID:26161656

  19. 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).

  20. Prediction of Carbohydrate Binding Sites on Protein Surfaces with 3-Dimensional Probability Density Distributions of Interacting Atoms

    PubMed Central

    Tsai, Keng-Chang; Jian, Jhih-Wei; Yang, Ei-Wen; Hsu, Po-Chiang; Peng, Hung-Pin; Chen, Ching-Tai; Chen, Jun-Bo; Chang, Jeng-Yih; Hsu, Wen-Lian; Yang, An-Suei

    2012-01-01

    Non-covalent protein-carbohydrate interactions mediate molecular targeting in many biological processes. Prediction of non-covalent carbohydrate binding sites on protein surfaces not only provides insights into the functions of the query proteins; information on key carbohydrate-binding residues could suggest site-directed mutagenesis experiments, design therapeutics targeting carbohydrate-binding proteins, and provide guidance in engineering protein-carbohydrate interactions. In this work, we show that non-covalent carbohydrate binding sites on protein surfaces can be predicted with relatively high accuracy when the query protein structures are known. The prediction capabilities were based on a novel encoding scheme of the three-dimensional probability density maps describing the distributions of 36 non-covalent interacting atom types around protein surfaces. One machine learning model was trained for each of the 30 protein atom types. The machine learning algorithms predicted tentative carbohydrate binding sites on query proteins by recognizing the characteristic interacting atom distribution patterns specific for carbohydrate binding sites from known protein structures. The prediction results for all protein atom types were integrated into surface patches as tentative carbohydrate binding sites based on normalized prediction confidence level. The prediction capabilities of the predictors were benchmarked by a 10-fold cross validation on 497 non-redundant proteins with known carbohydrate binding sites. The predictors were further tested on an independent test set with 108 proteins. The residue-based Matthews correlation coefficient (MCC) for the independent test was 0.45, with prediction precision and sensitivity (or recall) of 0.45 and 0.49 respectively. In addition, 111 unbound carbohydrate-binding protein structures for which the structures were determined in the absence of the carbohydrate ligands were predicted with the trained predictors. The overall prediction MCC was 0.49. Independent tests on anti-carbohydrate antibodies showed that the carbohydrate antigen binding sites were predicted with comparable accuracy. These results demonstrate that the predictors are among the best in carbohydrate binding site predictions to date. PMID:22848404

  1. Genetic Mapping of Specific Interactions between Aedes aegypti Mosquitoes and Dengue Viruses

    PubMed Central

    Diancourt, Laure; Caro, Valérie; Thaisomboonsuk, Butsaya; Richardson, Jason H.; Jarman, Richard G.; Ponlawat, Alongkot; Lambrechts, Louis

    2013-01-01

    Specific interactions between host genotypes and pathogen genotypes (G×G interactions) are commonly observed in invertebrate systems. Such specificity challenges our current understanding of invertebrate defenses against pathogens because it contrasts the limited discriminatory power of known invertebrate immune responses. Lack of a mechanistic explanation, however, has questioned the nature of host factors underlying G×G interactions. In this study, we aimed to determine whether G×G interactions observed between dengue viruses and their Aedes aegypti vectors in nature can be mapped to discrete loci in the mosquito genome and to document their genetic architecture. We developed an innovative genetic mapping strategy to survey G×G interactions using outbred mosquito families that were experimentally exposed to genetically distinct isolates of two dengue virus serotypes derived from human patients. Genetic loci associated with vector competence indices were detected in multiple regions of the mosquito genome. Importantly, correlation between genotype and phenotype was virus isolate-specific at several of these loci, indicating G×G interactions. The relatively high percentage of phenotypic variation explained by the markers associated with G×G interactions (ranging from 7.8% to 16.5%) is consistent with large-effect host genetic factors. Our data demonstrate that G×G interactions between dengue viruses and mosquito vectors can be assigned to physical regions of the mosquito genome, some of which have a large effect on the phenotype. This finding establishes the existence of tangible host genetic factors underlying specific interactions between invertebrates and their pathogens in a natural system. Fine mapping of the uncovered genetic loci will elucidate the molecular mechanisms of mosquito-virus specificity. PMID:23935524

  2. MAPPING OF GENE-ASSOCIATED SEQUENCE TAGGED SITES (STSS) TO THE BOVINE LINKAGE AND RADIATION HYBRID MAPS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study describes the mapping of 42 bovine gene-associated markers to the cattle genome using expressed sequence tag (EST) data derived from the mammary gland. A total of 21 gene loci were placed on the USDA reference linkage map, and 36 were positioned on the Roslin 3000-rad radiation hybrid (RH...

  3. Research Networks Map | Division of Cancer Prevention

    Cancer.gov

    Click the check boxes to show or hide sites by category. Zoom in to view sites that are in close proximity to each other; zoom out to view sites in Hawaii and Puerto Rico. A text equivalent of the interactive map is below the map.

  4. 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.

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

    NASA Astrophysics Data System (ADS)

    Riahi, H.; Donvito, G.; Fanň, 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.

  6. On the Mapping of Epistatic Genetic Interactions in Natural Isolates: Combining Classical Genetics and Genomics.

    PubMed

    Hou, Jing; Schacherer, Joseph

    2016-01-01

    Genetic variation within species is the substrate of evolution. Epistasis, which designates the non-additive interaction between loci affecting a specific phenotype, could be one of the possible outcomes of genetic diversity. Dissecting the basis of such interactions is of current interest in different fields of biology, from exploring the gene regulatory network, to complex disease genetics, to the onset of reproductive isolation and speciation. We present here a general workflow to identify epistatic interactions between independently evolving loci in natural populations of the yeast Saccharomyces cerevisiae. The idea is to exploit the genetic diversity present in the species by evaluating a large number of crosses and analyzing the phenotypic distribution in the offspring. For a cross of interest, both parental strains would have a similar phenotypic value, whereas the resulting offspring would have a bimodal distribution of the phenotype, possibly indicating the presence of epistasis. Classical segregation analysis of the tetrads uncovers the penetrance and complexity of the interaction. In addition, this segregation could serve as the guidelines for choosing appropriate mapping strategies to narrow down the genomic regions involved. Depending on the segregation patterns observed, we propose different mapping strategies based on bulk segregant analysis or consecutive backcrosses followed by high-throughput genome sequencing. Our method is generally applicable to all systems with a haplodiplobiontic life cycle and allows high resolution mapping of interacting loci that govern various DNA polymorphisms from single nucleotide mutations to large-scale structural variations. PMID:26483031

  7. Pigment epithelium-derived factor binds to hyaluronan. Mapping of a hyaluronan binding site.

    PubMed

    Becerra, S Patricia; Perez-Mediavilla, L Alberto; Weldon, John E; Locatelli-Hoops, Silvia; Senanayake, Preenie; Notari, Luigi; Notario, Vicente; Hollyfield, Joe G

    2008-11-28

    Pigment epithelium-derived factor (PEDF) is a multifunctional serpin with antitumorigenic, antimetastatic, and differentiating activities. PEDF is found within tissues rich in the glycosaminoglycan hyaluronan (HA), and its amino acid sequence contains putative HA-binding motifs. We show that PEDF coprecipitation with glycosaminoglycans in media conditioned by human retinoblastoma Y-79 cells decreased after pretreatments with hyaluronidase, implying an association between HA and PEDF. Direct binding of human recombinant PEDF to highly purified HA was demonstrated by coprecipitation in the presence of cetylpyridinium chloride. Binding of PEDF to HA was concentration-dependent and saturable. The PEDF-HA interactions were sensitive to increasing NaCl concentrations, indicating an ionic nature of these interactions and having affinity higher than PEDF-heparin. Competition assays showed that PEDF can bind heparin and HA simultaneously. PEDF chemically modified with fluorescein retained the capacity for interacting with HA but lacked heparin affinity, suggesting one or more distinct HA-binding regions on PEDF. The HA-binding region was examined by site-directed mutagenesis. Single-point and cumulative alterations at basic residues within the putative HA-binding motif K189A/K191A/R194A/K197A drastically reduced the HA-binding activity without affecting heparin- or collagen I binding of PEDF. Cumulative alterations at sites critical for heparin binding (K146A/K147A/R149A) decreased HA affinity but not collagen I binding. Thus these clusters of basic residues (BXBXXBXXB and BX3AB2XB motifs) in PEDF are functional regions for binding HA. In the spatial PEDF structure they are located in distinct areas away from the collagen-binding site. The HA-binding activity of PEDF may contribute to deposition in the extracellular matrix and to its reported antitumor/antimetastatic effects. PMID:18805795

  8. Global mapping of transcription start sites and promoter motifs in the symbiotic ?-proteobacterium Sinorhizobium meliloti 1021

    PubMed Central

    2013-01-01

    Background Sinorhizobium meliloti is a soil-dwelling ?-proteobacterium that possesses a large, tripartite genome and engages in a nitrogen fixing symbiosis with its plant hosts. Although much is known about this important model organism, global characterization of genetic regulatory circuits has been hampered by a lack of information about transcription and promoters. Results Using an RNAseq approach and RNA populations representing 16 different growth and stress conditions, we comprehensively mapped S. meliloti transcription start sites (TSS). Our work identified 17,001 TSS that we grouped into six categories based on the genomic context of their transcripts: mRNA (4,430 TSS assigned to 2,657 protein-coding genes), leaderless mRNAs (171), putative mRNAs (425), internal sense transcripts (7,650), antisense RNA (3,720), and trans-encoded sRNAs (605). We used this TSS information to identify transcription factor binding sites and putative promoter sequences recognized by seven of the 15 known S. meliloti ? factors ?70, ?54, ?H1, ?H2, ?E1, ?E2, and ?E9). Altogether, we predicted 2,770 new promoter sequences, including 1,302 located upstream of protein coding genes and 722 located upstream of antisense RNA or trans-encoded sRNA genes. To validate promoter predictions for targets of the general stress response ? factor, RpoE2 (?E2), we identified rpoE2-dependent genes using microarrays and confirmed TSS for a subset of these by 5? RACE mapping. Conclusions By identifying TSS and promoters on a global scale, our work provides a firm foundation for the continued study of S. meliloti gene expression with relation to gene organization, ? factors and other transcription factors, and regulatory RNAs. PMID:23497287

  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 Hřrlřkke, 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. Exploring 3D Interaction in Alternate Control-Display Space Mappings Jeroen Keijser Sheelagh Carpendale* Mark Hancock* Tobias Isenberg*

    E-print Network

    Exploring 3D Interaction in Alternate Control-Display Space Mappings Jeroen Keijser Sheelagh As a culture, we have had fantastical ideas about exploring alter- nate 3D spaces for at least a century ­ take to the display space. To explore alter- nate experiences in 3D interaction, we consider the 3D to 3D map- ping

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

    PubMed

    de Araújo, Adolpho Guido; Gusmăo, 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

  12. Web Mapping for Promoting Interaction and Collaboration in Community Land Planning

    NASA Astrophysics Data System (ADS)

    Veenendaal, B.; Dhliwayo, M.

    2013-10-01

    There is an inherent advantage of geographic information Systems (GIS) and mapping in facilitating dialogue between experts and non-experts during land use plan development. Combining visual mapping information and effective user interaction can result in considerable benefits for developing countries like Botswana. Although the adoption of information and communication technologies has lagged behind that for developed countries, initiatives by the Botswana government in providing suitable information infrastructures, including internet and web based communications, are enabling multiple users to interact and collaborate in community land planning. A web mapping application was developed for the Maun Development Plan (MDP) in the Okavango Delta region in Botswana. It was designed according to requirements of land planners and managers and implemented using ArcGIS Viewer for Flex. Land planners and managers from two organisations in Maun involved in the development of the MDP were asked to evaluate the web mapping tools. This paper describes the results of implementation and some preliminary results of the web mapping evaluation.

  13. Effective on-site interaction for dynamical mean-field theory

    NASA Astrophysics Data System (ADS)

    Nomura, Yusuke; Kaltak, Merzuk; Nakamura, Kazuma; Taranto, Ciro; Sakai, Shiro; Toschi, Alessandro; Arita, Ryotaro; Held, Karsten; Kresse, Georg; Imada, Masatoshi

    2012-08-01

    A scheme to incorporate nonlocal polarizations into the dynamical mean-field theory (DMFT) and a tailor-made way to determine the effective interaction for DMFT are systematically investigated. Applying it to the two-dimensional Hubbard model, we find that nonlocal polarizations induce a nontrivial filling-dependent antiscreening effect for the effective interaction. The present scheme combined with density functional theory offers an ab initio way to derive effective on-site interactions for the impurity problem in DMFT. We apply it to SrVO3 and find that the antiscreening competes with the screening caused by the off-site interaction.

  14. GIS-based interactive tool to map the advent of world conquerors

    NASA Astrophysics Data System (ADS)

    Lakkaraju, Mahesh

    The objective of this thesis is to show the scale and extent of some of the greatest empires the world has ever seen. This is a hybrid project between the GIS based interactive tool and the web-based JavaScript tool. This approach lets the students learn effectively about the emperors themselves while understanding how long and far their empires spread. In the GIS based tool, a map is displayed with various points on it, and when a user clicks on one point, the relevant information of what happened at that particular place is displayed. Apart from this information, users can also select the interactive animation button and can walk through a set of battles in chronological order. As mentioned, this uses Java as the main programming language, and MOJO (Map Objects Java Objects) provided by ESRI. MOJO is very effective as its GIS related features can be included in the application itself. This app. is a simple tool and has been developed for university or high school level students. D3.js is an interactive animation and visualization platform built on the Javascript framework. Though HTML5, CSS3, Javascript and SVG animations can be used to derive custom animations, this tool can help bring out results with less effort and more ease of use. Hence, it has become the most sought after visualization tool for multiple applications. D3.js has provided a map-based visualization feature so that we can easily display text-based data in a map-based interface. To draw the map and the points on it, D3.js uses data rendered in TOPO JSON format. The latitudes and longitudes can be provided, which are interpolated into the Map svg. One of the main advantages of doing it this way is that more information is retained when we use a visual medium.

  15. 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 thicknesses in Oceanus Procellarum and Mare Serenitatis determined from Clementine multi-spectral data," Icarus, 209, 323-336, (2010). Wilcox, B.B., Lucey, P.G., Gillis, J.J., 2005. Mapping iron in the lunar mare: An improved approach. J. Geophys. Res. 110(E11):2156-2202.

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

    PubMed Central

    Klingler, J; Friedrich, T

    1997-01-01

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

  17. An interactive, online Geographic Information System (GIS) for stakeholder participation in environmental site selection

    E-print Network

    Adams, Christiaan Scott, 1973-

    2004-01-01

    An interactive, online geographic information system (GIS) was developed to enhance the involvement of stakeholders in the public participation processes of site selection issues in the marine environment. Displaying ...

  18. 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.

  19. Genetic mapping of a major site of phosphorylation in adenovirus type 2 E1A proteins.

    PubMed Central

    Tsukamoto, A S; Ponticelli, A; Berk, A J; Gaynor, R B

    1986-01-01

    Adenovirus early region 1A (E1A) encodes two acidic phosphoproteins which are required for transactivation of viral transcription, efficient viral DNA replication in phase G0-arrested human cells, and oncogenic transformation of rodent cells. Biochemical analysis of in vivo 32P-labeled adenovirus type 2 E1A proteins purified with monoclonal antibodies demonstrated that these proteins were phosphorylated at multiple serine residues. Two-dimensional phosphotryptic peptide maps of wild-type and mutant E1A proteins were used to locate a major site of E1A protein phosphorylation at serine-219 of the large E1A protein. Although this serine fell within a consensus sequence for phosphorylation by the cyclic AMP-dependent protein kinases, experiments with mutant CHO cells defective in these enzymes indicated that it was not. Oligonucleotide-directed mutagenesis was used to substitute an alanine for serine-219. This mutation prevented phosphorylation at this site. Nonetheless, the mutant was indistinguishable from the wild type for early gene transactivation, replication on G0-arrested WI-38 cells, and transformation of cloned rat embryo fibroblast cells. Images PMID:2940374

  20. Interactive Mapping of the Planets: An Online Activity Using the Google Earth Platform

    NASA Astrophysics Data System (ADS)

    Osinski, G. R.; Gilbert, A.; Harrison, T. N.; Mader, M. M.; Shankar, B.; Tornabene, L. L.

    2013-12-01

    With funding from the Natural Sciences and Engineering Research Council of Canada's PromoScience program and support from the Department of Earth Sciences at The University of Western Ontario, the Centre for Planetary Science and Exploration (CPSX) has developed a new web-based initiative called Interactive Mapping of the Planets (IMAPS). Additional components include in person school visits to deliver inquiry-based workshops, week-long summer camps, and pre-prepared impact rock lending kits, all framed around the IMAPS activity. IMAPS will is now in beta testing mode and will be demonstrated in this session. The general objective of the online activity is for participants to plan and design a rover mission to Mars based on a given mission goal - e.g., to find evidence for past water flow. The activity begins with participants receiving image-analysis training to learn about the different landforms on Mars and which ones are potentially caused by water flow. They then need to pass a short test to show they can consistently identify Martian landforms. From there, the participants choose a landing site and plan a traverse - utilizing the free Google Earth plug-in - and taking into account factors such as hazards and their sites of interest. A mission control blog will provide updates on the status of their mission and a 'choose your rover' option provides the opportunity to unlock more advanced rovers by collaborating with other scientists and rating their missions. Indeed, evaluation of missions will be done using a crowd-sourcing method. In addition to being fully accessible online, CPSX will also target primary- and secondary-school grades in which astronomy and space science is taught. Teachers in K-12 classrooms will be able to sign-up for the activity ahead of time in order to receive a workshop package, which will guide them on how to use the IMAPS online activity with their class. Teachers will be able to set up groups for their classroom so that they can evaluate their students based on pre-determined criteria. The IMAPS activities are developed in partnerships with the Department of Earth Sciences at Western University, Sports Western, the Thames Valley District School Board, and Dimentians Web Marketing and Design. We are continually looking for new collaborators to help design or test our inquiry- and web-based activities, provide feedback on our programs, or volunteer with us. Please contact cpsxoutreach@uwo.ca if you are interested.

  1. Prediction of Protein-Protein Interaction Sites Based on Naive Bayes Classifier

    PubMed Central

    Geng, Haijiang; Lu, Tao; Lin, Xiao; Liu, Yu; Yan, Fangrong

    2015-01-01

    Protein functions through interactions with other proteins and biomolecules and these interactions occur on the so-called interface residues of the protein sequences. Identifying interface residues makes us better understand the biological mechanism of protein interaction. Meanwhile, information about the interface residues contributes to the understanding of metabolic, signal transduction networks and indicates directions in drug designing. In recent years, researchers have focused on developing new computational methods for predicting protein interface residues. Here we creatively used a 181-dimension protein sequence feature vector as input to the Naive Bayes Classifier- (NBC-) based method to predict interaction sites in protein-protein complexes interaction. The prediction of interaction sites in protein interactions is regarded as an amino acid residue binary classification problem by applying NBC with protein sequence features. Independent test results suggested that Naive Bayes Classifier-based method with the protein sequence features as input vectors performed well. PMID:26697220

  2. Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells.

    PubMed

    Kind, Jop; Pagie, Ludo; de Vries, Sandra S; Nahidiazar, Leila; Dey, Siddharth S; Bienko, Magda; Zhan, Ye; Lajoie, Bryan; de Graaf, Carolyn A; Amendola, Mario; Fudenberg, Geoffrey; Imakaev, Maxim; Mirny, Leonid A; Jalink, Kees; Dekker, Job; van Oudenaarden, Alexander; van Steensel, Bas

    2015-09-24

    Mammalian interphase chromosomes interact with the nuclear lamina (NL) through hundreds of large lamina-associated domains (LADs). We report a method to map NL contacts genome-wide in single human cells. Analysis of nearly 400 maps reveals a core architecture consisting of gene-poor LADs that contact the NL with high cell-to-cell consistency, interspersed by LADs with more variable NL interactions. The variable contacts tend to be cell-type specific and are more sensitive to changes in genome ploidy than the consistent contacts. Single-cell maps indicate that NL contacts involve multivalent interactions over hundreds of kilobases. Moreover, we observe extensive intra-chromosomal coordination of NL contacts, even over tens of megabases. Such coordinated loci exhibit preferential interactions as detected by Hi-C. Finally, the consistency of NL contacts is inversely linked to gene activity in single cells and correlates positively with the heterochromatic histone modification H3K9me3. These results highlight fundamental principles of single-cell chromatin organization. VIDEO ABSTRACT. PMID:26365489

  3. 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.

  4. Mapping the Complex Morphology of Cell Interactions with Nanowire Substrates Using FIB-SEM

    PubMed Central

    Jensen, Mikkel R. B.; ?opaci?ska, Joanna; Schmidt, Michael S.; Skolimowski, Maciej; Abeille, Fabien; Qvortrup, Klaus; Mřlhave, Kristian

    2013-01-01

    Using high resolution focused ion beam scanning electron microscopy (FIB-SEM) we study the details of cell-nanostructure interactions using serial block face imaging. 3T3 Fibroblast cellular monolayers are cultured on flat glass as a control surface and on two types of nanostructured scaffold substrates made from silicon black (Nanograss) with low- and high nanowire density. After culturing for 72 hours the cells were fixed, heavy metal stained, embedded in resin, and processed with FIB-SEM block face imaging without removing the substrate. The sample preparation procedure, image acquisition and image post-processing were specifically optimised for cellular monolayers cultured on nanostructured substrates. Cells display a wide range of interactions with the nanostructures depending on the surface morphology, but also greatly varying from one cell to another on the same substrate, illustrating a wide phenotypic variability. Depending on the substrate and cell, we observe that cells could for instance: break the nanowires and engulf them, flatten the nanowires or simply reside on top of them. Given the complexity of interactions, we have categorised our observations and created an overview map. The results demonstrate that detailed nanoscale resolution images are required to begin understanding the wide variety of individual cells’ interactions with a structured substrate. The map will provide a framework for light microscopy studies of such interactions indicating what modes of interactions must be considered. PMID:23326412

  5. Understanding Patterns of User Visits to Web Sites: Interactive Starfield Visualizations of WWW Log Data.

    ERIC Educational Resources Information Center

    Hochheiser, Harry; Shneiderman, Ben

    1999-01-01

    Describes the use of Spotfire, a starfield visualization tool, to generate interactive visualizations of log data, ranging from aggregate views of all Web site hits in a time interval to close-ups that approximate the path of a user through a site. Highlights current efforts and provides examples of the visualizations created in Spotfire.…

  6. Building a Better Web Site: A Practical Guide to Interactivity for Libraries.

    ERIC Educational Resources Information Center

    Braun, Linda W.

    1998-01-01

    Describes selected commercial and academic Web sites providing interactive services (Amazon; Jones Library, Amherst, MA; Pine Crest Lower School, Ft. Lauderdale, FL; Barnes & Noble; Cal State's Information Literacy Tutorials; PBS's techknow site; K.I.D.S. Report), and argues that libraries that stop at links and policy statements miss…

  7. Friedman Web Site Student Cheat Sheet This document explains the different ways you can interact, while logged in, to the Friedman web site.

    E-print Network

    Dennett, Daniel

    1 Friedman Web Site Student Cheat Sheet This document explains the different ways you can interact, while logged in, to the Friedman web site. Contents Friedman Web Site Student Cheat Sheet page on the Friedman web site and click on the white text Login in the red footer. In the next screen

  8. Web GIS in practice VIII: HTML5 and the canvas element for interactive online mapping

    PubMed Central

    2010-01-01

    HTML5 is being developed as the next major revision of HTML (Hypertext Markup Language), the core markup language of the World Wide Web. It aims at reducing the need for proprietary, plug-in-based rich Internet application (RIA) technologies such as Adobe Flash. The canvas element is part of HTML5 and is used to draw graphics using scripting (e.g., JavaScript). This paper introduces Cartagen, an open-source, vector-based, client-side framework for rendering plug-in-free, offline-capable, interactive maps in native HTML5 on a wide range of Web browsers and mobile phones. Cartagen was developed at MIT Media Lab's Design Ecology group. Potential applications of the technology as an enabler for participatory online mapping include mapping real-time air pollution, citizen reporting, and disaster response, among many other possibilities. PMID:20199681

  9. Web GIS in practice VIII: HTML5 and the canvas element for interactive online mapping.

    PubMed

    Boulos, Maged N Kamel; Warren, Jeffrey; Gong, Jianya; Yue, Peng

    2010-01-01

    HTML5 is being developed as the next major revision of HTML (Hypertext Markup Language), the core markup language of the World Wide Web. It aims at reducing the need for proprietary, plug-in-based rich Internet application (RIA) technologies such as Adobe Flash. The canvas element is part of HTML5 and is used to draw graphics using scripting (e.g., JavaScript). This paper introduces Cartagen, an open-source, vector-based, client-side framework for rendering plug-in-free, offline-capable, interactive maps in native HTML5 on a wide range of Web browsers and mobile phones. Cartagen was developed at MIT Media Lab's Design Ecology group. Potential applications of the technology as an enabler for participatory online mapping include mapping real-time air pollution, citizen reporting, and disaster response, among many other possibilities. PMID:20199681

  10. Functional Site Prediction by Exploiting Correlations between Labels of Interacting Residues

    E-print Network

    Ravindran, Balaraman

    Functional Site Prediction by Exploiting Correlations between Labels of Interacting Residues propose a method for prediction of functional residues in a given protein from its three-dimensional (3D) structure. Our method exploits cor- relation between labels of interacting residues to obtain sig- nificant

  11. Determination of Electrostatic Interaction Energies and Protonation State Populations in Enzyme Active Sites

    E-print Network

    McIntosh, Lawrence P.

    Determination of Electrostatic Interaction Energies and Protonation State Populations in Enzyme Active Sites Chresten R. Sřndergaard1,2 , Lawrence P. McIntosh3 Gianluca Pollastri2 and Jens Erik Nielsen interaction energies between protein residues. Furthermore, by performing simultaneous fits of NMR titration

  12. Method of predicting Splice Sites based on signal interactions

    PubMed Central

    Churbanov, Alexander; Rogozin, Igor B; Deogun, Jitender S; Ali, Hesham

    2006-01-01

    Background Predicting and proper ranking of canonical splice sites (SSs) is a challenging problem in bioinformatics and machine learning communities. Any progress in SSs recognition will lead to better understanding of splicing mechanism. We introduce several new approaches of combining a priori knowledge for improved SS detection. First, we design our new Bayesian SS sensor based on oligonucleotide counting. To further enhance prediction quality, we applied our new de novo motif detection tool MHMMotif to intronic ends and exons. We combine elements found with sensor information using Naive Bayesian Network, as implemented in our new tool SpliceScan. Results According to our tests, the Bayesian sensor outperforms the contemporary Maximum Entropy sensor for 5' SS detection. We report a number of putative Exonic (ESE) and Intronic (ISE) Splicing Enhancers found by MHMMotif tool. T-test statistics on mouse/rat intronic alignments indicates, that detected elements are on average more conserved as compared to other oligos, which supports our assumption of their functional importance. The tool has been shown to outperform the SpliceView, GeneSplicer, NNSplice, Genio and NetUTR tools for the test set of human genes. SpliceScan outperforms all contemporary ab initio gene structural prediction tools on the set of 5' UTR gene fragments. Conclusion Designed methods have many attractive properties, compared to existing approaches. Bayesian sensor, MHMMotif program and SpliceScan tools are freely available on our web site. Reviewers This article was reviewed by Manyuan Long, Arcady Mushegian and Mikhail Gelfand. PMID:16584568

  13. Quantitative Chemical-Genetic Interaction Map Connects Gene Alterations to Drug Responses | Office of Cancer Genomics

    Cancer.gov

    In a recent Cancer Discovery report, CTD2 researchers at the University of California in San Francisco developed a new quantitative chemical-genetic interaction mapping approach to evaluate drug sensitivity or resistance in isogenic cell lines. Performing a high-throughput screen with isogenic cell lines allowed the researchers to explore the impact of a panel of emerging and established drugs on cells overexpressing a single cancer-associated gene in isolation.

  14. Lettuce necrotic yellows cytorhabdovirus protein localization and interaction map, and comparison with nucleorhabdoviruses.

    PubMed

    Martin, Kathleen M; Dietzgen, Ralf G; Wang, Renyuan; Goodin, Michael M

    2012-04-01

    Lettuce necrotic yellows virus (LNYV), Sonchus yellow net virus (SYNV) and Potato yellow dwarf virus (PYDV) are members of the family Rhabdoviridae that infect plants. LNYV is a cytorhabdovirus that replicates in the cytoplasm, while SYNV and PYDV are nucleorhabdoviruses that replicate in the nuclei of infected cells. LNYV and SYNV share a similar genome organization with a gene order of nucleoprotein (N), phosphoprotein (P), putative movement protein (Mv), matrix protein (M), glycoprotein (G) and polymerase (L). PYDV contains an additional predicted gene of unknown function located between N and P. In order to gain insight into the associations of viral structural and non-structural proteins and the mechanisms by which they may function, we constructed protein localization and interaction maps. Subcellular localization was determined by transiently expressing the viral proteins fused to green or red fluorescent protein in leaf epidermal cells of Nicotiana benthamiana. Protein interactions were tested in planta by using bimolecular fluorescence complementation. All three viruses showed Mv to be localized at the cell periphery and the G protein to be membrane associated. Comparing the interaction maps revealed that only the N-P and M-M interactions are common to all three viruses. Associations unique to only one virus include P-M for LNYV, G-Mv for SYNV and M-Mv, M-G and N-M for PYDV. The cognate N-P proteins of all three viruses interacted and exhibited characteristic changes in localization when co-expressed. PMID:22190014

  15. English home Forum Photo Gallery Features Newsletter Archive About US Help Site Map languages Culture/Life

    E-print Network

    Help Site Map languages China World Opinion Business Sci-Edu Culture/Life Sports Photos Services - - - - - - - - - China Business World Sci-Edu Culture/Life Sports Photos Most Popular FM Briefings Search About China Program is aimed at combining scientists' pioneering spirit with the nation's strategic scientific

  16. English home Forum Photo Gallery Features Newsletter Archive About US Help Site Map languages Culture/Life

    E-print Network

    Newsletter Weather Community English home Forum Photo Gallery Features Newsletter Archive About US Help Site Map languages China World Opinion Business Sci-Edu Culture/Life Sports Photos Services Ethnic minorities Selected Works of Deng Xiaoping >>Home Sci-Edu UPDATED: 10:52, January 21, 2006 China

  17. English home Forum Photo Gallery Features Newsletter Archive About US Help Site Map languages Culture/Life

    E-print Network

    Newsletter Weather Community English home Forum Photo Gallery Features Newsletter Archive About US Help Site Map languages China World Opinion Business Sci-Edu Culture/Life Sports Photos Services Ethnic minorities Selected Works of Deng Xiaoping >>Home Sci-Edu UPDATED: 20:06, July 01, 2005 China

  18. Functional genomics platform for pooled screening and mammalian genetic interaction maps

    PubMed Central

    Kampmann, Martin; Bassik, Michael C.; Weissman, Jonathan S.

    2014-01-01

    Systematic genetic interaction maps in microorganisms are powerful tools for identifying functional relationships between genes and defining the function of uncharacterized genes. We have recently implemented this strategy in mammalian cells as a two-stage approach. First, genes of interest are robustly identified in a pooled genome-wide screen using complex shRNA libraries. Second, phenotypes for all pairwise combinations of hit genes are measured in a double-shRNA screen and used to construct a genetic interaction map. Our protocol allows for rapid pooled screening under various conditions without a requirement for robotics, in contrast to arrayed approaches. Each stage of the protocol can be implemented in ~2 weeks, with additional time for analysis and generation of reagents. We discuss considerations for screen design, and present complete experimental procedures as well as a full computational analysis suite for identification of hits in pooled screens and generation of genetic interaction maps. While the protocols outlined here were developed for our original shRNA-based approach, they can be applied more generally, including to CRISPR-based approaches. PMID:24992097

  19. Spa2p functions as a scaffold-like protein to recruit the Mpk1p MAP kinase module to sites of polarized growth.

    PubMed

    van Drogen, Frank; Peter, Matthias

    2002-10-01

    Scaffold proteins play a major role in regulating MAP kinase pathways. In yeast, the Mpk1p-MAP kinase pathway functions to maintain the integrity of the cytoskeleton and the cell wall. In this module, the MEKK Bck1p functions upstream of the MEKs Mkk1p and Mkk2p, which in turn activate the MAP kinase Mpk1p. Mpk1p regulates several nuclear targets, including the transcription factors Rlm1p and SBF, and the two HMG1-like proteins NHP6A and NHP6B. Here we show that Mpk1p constitutively shuttles between the nucleus and the cytoplasm, and both Mpk1p and Mkk1p localize to sites of polarized growth in a Spa2p-dependent manner. Spa2p belongs to a group of proteins that includes Bni1p, Bud6p, and Pea2p, which are involved in the dynamic organization of the actin cytoskeleton during polarized growth. FRAP analysis shows that Spa2p-GFP is stably anchored at bud tips, whereas Mpk1p binds transiently. Spa2p interacts with Mkk1p and Mpk1p, and membrane bound Spa2p is sufficient to recruit Mkk1p and Mpk1p but not other MAP kinases to the cell cortex. Taken together, these results suggest that Spa2p functions as a scaffold-like protein for the cell wall integrity pathway during polarized growth. PMID:12361575

  20. Mapping of the alpha-bungarotoxin binding site within the alpha subunit of the acetylcholine receptor.

    PubMed Central

    Neumann, D; Barchan, D; Safran, A; Gershoni, J M; Fuchs, S

    1986-01-01

    Synthetic peptides and their respective antibodies have been used in order to map the alpha-bungarotoxin binding site within the alpha subunit of the acetylcholine receptor. By using antibodies to a synthetic peptide corresponding to residues 169-181 of the alpha subunit, we demonstrate that this sequence is included within the 18-kDa toxin binding fragment previously reported. Furthermore, the 18-kDa fragment was also found to bind a monoclonal antibody (5.5) directed against the cholinergic binding site. Sequential proteolysis of the acetylcholine receptor with trypsin, prior to Staphylococcus aureus V8 protease digestion, resulted in a 15-kDa toxin binding fragment that is included within the 18-kDa fragment but is shorter than it only at its carboxyl terminus. This 15-kDa fragment therefore initiates beyond Asp-152 and terminates in the region of Arg-313/Lys-314. In addition, experiments are reported that indicate that in the intact acetylcholine receptor, Cys-128 and/or Cys-142 are not crosslinked by disulfide bridges with any of the cysteines (at positions 192, 193, and 222) that reside in the 15-kDa toxin binding fragment. Finally, the synthetic dodecapeptide Lys-His-Trp-Val-Tyr-Tyr-Thr-Cys-Cys-Pro-Asp-Thr, which is present in the 15-kDa fragment (corresponding to residues 185-196 of the alpha subunit) was shown to bind alpha-bungarotoxin directly. This binding was completely inhibited by competition with d-tubocurarine. Images PMID:3458258

  1. Mapping of the alpha-bungarotoxin binding site within the alpha subunit of the acetylcholine receptor.

    PubMed

    Neumann, D; Barchan, D; Safran, A; Gershoni, J M; Fuchs, S

    1986-05-01

    Synthetic peptides and their respective antibodies have been used in order to map the alpha-bungarotoxin binding site within the alpha subunit of the acetylcholine receptor. By using antibodies to a synthetic peptide corresponding to residues 169-181 of the alpha subunit, we demonstrate that this sequence is included within the 18-kDa toxin binding fragment previously reported. Furthermore, the 18-kDa fragment was also found to bind a monoclonal antibody (5.5) directed against the cholinergic binding site. Sequential proteolysis of the acetylcholine receptor with trypsin, prior to Staphylococcus aureus V8 protease digestion, resulted in a 15-kDa toxin binding fragment that is included within the 18-kDa fragment but is shorter than it only at its carboxyl terminus. This 15-kDa fragment therefore initiates beyond Asp-152 and terminates in the region of Arg-313/Lys-314. In addition, experiments are reported that indicate that in the intact acetylcholine receptor, Cys-128 and/or Cys-142 are not crosslinked by disulfide bridges with any of the cysteines (at positions 192, 193, and 222) that reside in the 15-kDa toxin binding fragment. Finally, the synthetic dodecapeptide Lys-His-Trp-Val-Tyr-Tyr-Thr-Cys-Cys-Pro-Asp-Thr, which is present in the 15-kDa fragment (corresponding to residues 185-196 of the alpha subunit) was shown to bind alpha-bungarotoxin directly. This binding was completely inhibited by competition with d-tubocurarine. PMID:3458258

  2. Comprehensive human transcription factor binding site map for combinatory binding motifs discovery.

    PubMed

    Müller-Molina, Arnoldo J; Schöler, Hans R; Araúzo-Bravo, Marcos J

    2012-01-01

    To know the map between transcription factors (TFs) and their binding sites is essential to reverse engineer the regulation process. Only about 10%-20% of the transcription factor binding motifs (TFBMs) have been reported. This lack of data hinders understanding gene regulation. To address this drawback, we propose a computational method that exploits never used TF properties to discover the missing TFBMs and their sites in all human gene promoters. The method starts by predicting a dictionary of regulatory "DNA words." From this dictionary, it distills 4098 novel predictions. To disclose the crosstalk between motifs, an additional algorithm extracts TF combinatorial binding patterns creating a collection of TF regulatory syntactic rules. Using these rules, we narrowed down a list of 504 novel motifs that appear frequently in syntax patterns. We tested the predictions against 509 known motifs confirming that our system can reliably predict ab initio motifs with an accuracy of 81%-far higher than previous approaches. We found that on average, 90% of the discovered combinatorial binding patterns target at least 10 genes, suggesting that to control in an independent manner smaller gene sets, supplementary regulatory mechanisms are required. Additionally, we discovered that the new TFBMs and their combinatorial patterns convey biological meaning, targeting TFs and genes related to developmental functions. Thus, among all the possible available targets in the genome, the TFs tend to regulate other TFs and genes involved in developmental functions. We provide a comprehensive resource for regulation analysis that includes a dictionary of "DNA words," newly predicted motifs and their corresponding combinatorial patterns. Combinatorial patterns are a useful filter to discover TFBMs that play a major role in orchestrating other factors and thus, are likely to lock/unlock cellular functional clusters. PMID:23209563

  3. 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. PMID:15876215

  4. 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.

  5. Processing Map and Essential Cleavage Sites of the Nonstructural Polyprotein Encoded by ORF1 of the Feline Calicivirus Genome

    PubMed Central

    Sosnovtsev, Stanislav V.; Garfield, Mark; Green, Kim Y.

    2002-01-01

    Feline calicivirus (FCV) nonstructural proteins are translated as part of a large polyprotein that undergoes autocatalytic processing by the virus-encoded 3C-like proteinase. In this study, we mapped three new cleavage sites (E46/A47, E331/D332, and E685/N686) recognized by the virus proteinase in the N-terminal part of the open reading frame 1 (ORF1) polyprotein to complete the processing map. Taken together with two sites we identified previously (E960/A961 and E1071/S1072), the FCV ORF1 polyprotein contains five cleavage sites that define the borders of six proteins with calculated molecular masses of 5.6, 32, 38.9, 30.1, 12.7, and 75.7 kDa, which we designated p5.6, p32, p39 (NTPase), p30, p13 (VPg), and p76 (Pro-Pol), respectively. Mutagenesis of the E to A in each of these cleavage sites in an infectious FCV cDNA clone was lethal for the virus, indicating that these cleavages are essential in a productive virus infection. Mutagenesis of two cleavage sites (E1345/T1346 and E1419/G1420) within the 75.7-kDa Pro-Pol protein previously mapped in bacterial expression studies was not lethal. PMID:12072506

  6. 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.

  7. Active Site Mapping of Human Cathepsin?F with Dipeptide Nitrile Inhibitors.

    PubMed

    Schmitz, Janina; Furtmann, Norbert; Ponert, Moritz; Frizler, Maxim; Löser, Reik; Bartz, Ulrike; Bajorath, Jürgen; Gütschow, Michael

    2015-08-01

    Cleavage of the invariant chain is the key event in the trafficking pathway of major histocompatibility complex class?II. Cathepsin?S is the major processing enzyme of the invariant chain, but cathepsin?F acts in macrophages as its functional synergist which is as potent as cathepsin?S in invariant chain cleavage. Dedicated low-molecular-weight inhibitors for cathepsin?F have not yet been developed. An active site mapping with 52 dipeptide nitriles, reacting as covalent-reversible inhibitors, was performed to draw structure-activity relationships for the non-primed binding region of human cathepsin?F. In a stepwise process, new compounds with optimized fragment combinations were designed and synthesized. These dipeptide nitriles were evaluated on human cysteine cathepsins?F, B, L, K and S. Compounds 10 (N-(4-phenylbenzoyl)-leucylglycine nitrile) and 12 (N-(4-phenylbenzoyl)leucylmethionine nitrile) were found to be potent inhibitors of human cathepsin?F, with Ki values <10?nM. With all dipeptide nitriles from our study, a 3D activity landscape was generated to visualize structure-activity relationships for this series of cathepsin?F inhibitors. PMID:26119278

  8. 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.

  9. 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.

  10. 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 ?-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

  11. 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

  12. 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 preliminary results of crater morphology show that highest H/D for studied craters of the Lunokhod 1 area is ~0.14, that is noticeably smaller than that for very fresh well studied small craters, for example, in the Apollo 14 [6]. At present more detailed geomorphology analyses using orthoimages with different illumination is in progress and will be shown at the conference. Conclusions and future works. While new missions to the Lunar surface are being planned, it is of utmost importance to identify and make available for access all Lunar surface data. We show that these data can be used for large-scale mapping and surface studies of landing sites for future lunar missions, for example LUNA-GLOB and LUNA-RESOURCE. Acknowledgments: This research was partly funded by the Ministry of Education and Science of the Russian Federation (MEGA-GRANT, Project name: "Geodesy, cartography and the study of planets and satellites", contract No. 11.G34.31.0021).

  13. Network structure beyond food webs: mapping non-trophic and trophic interactions on Chilean rocky shores.

    PubMed

    Sonia Kéfi; Berlow, Eric L; Wieters, Evie A; Joppa, Lucas N; Wood, Spencer A; Brose, Ulrich; Navarrete, Sergio A

    2015-01-01

    How multiple types of non-trophic interactions map onto trophic networks in real communities remains largely unknown. We present the first effort, to our knowledge, describing a comprehensive ecological network that includes all known trophic and diverse non-trophic links among >100 coexisting species for the marine rocky intertidal community of the central Chilean coast. Our results suggest that non-trophic interactions exhibit highly nonrandom structures both alone and with respect to food web structure. The occurrence of different types of interactions, relative to all possible links, was well predicted by trophic structure and simple traits of the source and target species. In this community, competition for space and positive interactions related to habitat/refuge provisioning by sessile and/or basal species were by far the most abundant non-trophic interactions. If these patterns are orroborated in other ecosystems, they may suggest potentially important dynamic constraints on the combined architecture of trophic and non-trophic interactions. The nonrandom patterning of non-trophic interactions suggests a path forward for developing a more comprehensive ecological network theory to predict the functioning and resilience of ecological communities. PMID:26236914

  14. iMAR: An Interactive Web-Based Application for Mapping Herbicide Resistant Weeds.

    PubMed

    Panozzo, Silvia; Colauzzi, Michele; Scarabel, Laura; Collavo, Alberto; Rosan, Valentina; Sattin, Maurizio

    2015-01-01

    Herbicides are the major weed control tool in most cropping systems worldwide. However, the high reliance on herbicides has led to environmental issues as well as to the evolution of herbicide-resistant biotypes. Resistance is a major concern in modern agriculture and early detection of resistant biotypes is therefore crucial for its management and prevention. In this context, a timely update of resistance biotypes distribution is fundamental to devise and implement efficient resistance management strategies. Here we present an innovative web-based application called iMAR (interactive MApping of Resistance) for the mapping of herbicide resistant biotypes. It is based on open source software tools and translates into maps the data reported in the GIRE (Italian herbicide resistance working group) database of herbicide resistance at national level. iMAR allows an automatic, easy and cost-effective updating of the maps a nd provides two different systems, "static" and "dynamic". In the first one, the user choices are guided by a hierarchical tree menu, whereas the latter is more flexible and includes a multiple choice criteria (type of resistance, weed species, region, cropping systems) that permits customized maps to be created. The generated information can be useful to various stakeholders who are involved in weed resistance management: farmers, advisors, national and local decision makers as well as the agrochemical industry. iMAR is freely available, and the system has the potential to handle large datasets and to be used for other purposes with geographical implications, such as the mapping of invasive plants or pests. PMID:26266545

  15. iMAR: An Interactive Web-Based Application for Mapping Herbicide Resistant Weeds

    PubMed Central

    Panozzo, Silvia; Colauzzi, Michele; Scarabel, Laura; Collavo, Alberto; Rosan, Valentina; Sattin, Maurizio

    2015-01-01

    Herbicides are the major weed control tool in most cropping systems worldwide. However, the high reliance on herbicides has led to environmental issues as well as to the evolution of herbicide-resistant biotypes. Resistance is a major concern in modern agriculture and early detection of resistant biotypes is therefore crucial for its management and prevention. In this context, a timely update of resistance biotypes distribution is fundamental to devise and implement efficient resistance management strategies. Here we present an innovative web-based application called iMAR (interactive MApping of Resistance) for the mapping of herbicide resistant biotypes. It is based on open source software tools and translates into maps the data reported in the GIRE (Italian herbicide resistance working group) database of herbicide resistance at national level. iMAR allows an automatic, easy and cost-effective updating of the maps a nd provides two different systems, “static” and “dynamic”. In the first one, the user choices are guided by a hierarchical tree menu, whereas the latter is more flexible and includes a multiple choice criteria (type of resistance, weed species, region, cropping systems) that permits customized maps to be created. The generated information can be useful to various stakeholders who are involved in weed resistance management: farmers, advisors, national and local decision makers as well as the agrochemical industry. iMAR is freely available, and the system has the potential to handle large datasets and to be used for other purposes with geographical implications, such as the mapping of invasive plants or pests. PMID:26266545

  16. Interactive Maps on War and Peace: A WebGIS Application for Civic Education

    NASA Astrophysics Data System (ADS)

    Wirkus, Lars; Strunck, Alexander

    2013-04-01

    War and violent conflict are omnipresent-be it war in the Middle East, violent conflicts in failed states or increasing military expenditures and exports/ imports of military goods. To understand certain conflicts or peace processes and their possible interrelation, to conduct a well-founded political discussion and to support or influence decision-making, one matter is of special importance: easily accessible and, in particular, reliable data and information. Against this background, the Bonn International Center for Conversion (BICC) in close cooperation with the German Federal Agency for Civic Education (bpb) has been developing a map-based information portal on war and peace with various thematic modules for the latter's online service (http://sicherheitspolitik.bpb.de). The portal will eventually offer nine of such modules that are intended to give various target groups, such as interested members of the public, teachers and learners, policymakers and representatives of the media access to the required information in form of an interactive and country-based global overview or a comparison of different issues. Five thematic modules have been completed so far: War and conflict, peace and demobilization, military capacities, resources and conflict, conventional weapons. The portal offers a broad spectrum of different data processing and visualization tools. Its central feature is an interactive mapping component based on WebGIS and a relational database. Content and data provided through thematic maps in the form of WebGIS layers are generally supplemented by info graphics, data tables and short articles providing deeper knowledge on the respective issue. All modules and their sub-chapters are introduced by background texts. They put all interactive maps of a module into an appropriate context and help the users to also understand the interrelation between various layers. If a layer is selected, all corresponding texts and graphics are shown automatically below the map. Data tables are offered if the copyright of datasets allows such use. All data of all thematic modules is presented in country profiles in a consolidated manner. The portal has been created with Open Source Software. PostgreSQL and PostGIS, MapServer, OpenLayers, MapProxy and cmsmadesimple are combined to manipulate and transform global data sets into interactive thematic maps. A purpose-programmed layer selection menu enables users to select single layers or to combine up to three matching layers from all possible pre-set layer combinations. This applies both to fields of topics within a module and across various modules. Due to the complexity of the structure and visualization constraints, no more than three layers can be combined. The WebGIS-based information portal on war and peace is an excellent example of how GIS technologies can be used for education and outreach. Not only can they play a crucial role in supporting the educational mandate and mission of certain institutions. They can also directly support various target groups in obtaining the knowledge needed by providing a collection of straight forward designed, ready-to-use data, info graphics and maps.

  17. Tentative Mapping of Transcription-Induced Interchromosomal Interaction using Chimeric EST and mRNA Data

    PubMed Central

    Unneberg, Per; Claverie, Jean-Michel

    2007-01-01

    Recent studies on chromosome conformation show that chromosomes colocalize in the nucleus, bringing together active genes in transcription factories. This spatial proximity of actively transcribing genes could provide a means for RNA interaction at the transcript level. We have screened public databases for chimeric EST and mRNA sequences with the intent of mapping transcription-induced interchromosomal interactions. We suggest that chimeric transcripts may be the result of close encounters of active genes, either as functional products or “noise” in the transcription process, and that they could be used as probes for chromosome interactions. We have found a total of 5,614 chimeric ESTs and 587 chimeric mRNAs that meet our selection criteria. Due to their higher quality, the mRNA findings are of particular interest and we hope that they may serve as food for thought for specialists in diverse areas of molecular biology. PMID:17330142

  18. Interactive web-based mapping: bridging technology and data for health

    PubMed Central

    2011-01-01

    Background The Community Health Information System (CHIS) online mapping system was first launched in 1998. Its overarching goal was to provide researchers, residents and organizations access to health related data reflecting the overall health and well-being of their communities within the Greater Houston area. In September 2009, initial planning and development began for the next generation of CHIS. The overarching goal for the new version remained to make health data easily accessible for a wide variety of research audiences. However, in the new version we specifically sought to make the CHIS truly interactive and give the user more control over data selection and reporting. Results In July 2011, a beta version of the next-generation of the application was launched. This next-generation is also a web based interactive mapping tool comprised of two distinct portals: the Breast Health Portal and Project Safety Net. Both are accessed via a Google mapping interface. Geographic coverage for the portals is currently an 8 county region centered on Harris County, Texas. Data accessed by the application include Census 2000, Census 2010 (underway), cancer incidence from the Texas Cancer Registry (TX Dept. of State Health Services), death data from Texas Vital Statistics, clinic locations for free and low-cost health services, along with service lists, hours of operation, payment options and languages spoken, uninsured and poverty data. Conclusions The system features query on the fly technology, which means the data is not generated until the query is provided to the system. This allows users to interact in real-time with the databases and generate customized reports and maps. To the author's knowledge, the Breast Health Portal and Project Safety Net are the first local-scale interactive online mapping interfaces for public health data which allow users to control the data generated. For example, users may generate breast cancer incidence rates by Census tract, in real time, for women aged 40-64. Conversely, they could then generate the same rates for women aged 35-55. The queries are user controlled. PMID:22195603

  19. A novel combined RNA-protein interaction analysis distinguishes HIV-1 Gag protein binding sites from structural change in the viral RNA leader

    PubMed Central

    Kenyon, Julia C.; Prestwood, Liam J.; Lever, Andrew M. L.

    2015-01-01

    RNA-protein interactions govern many viral and host cell processes. Conventional ‘footprinting’ to examine RNA-protein complex formation often cannot distinguish between sites of RNA-protein interaction and sites of RNA structural remodelling. We have developed a novel technique combining photo crosslinking with RNA 2? hydroxyl reactivity (‘SHAPE’) that achieves rapid and hitherto unachievable resolution of both RNA structural changes and the sites of protein interaction within an RNA-protein complex. ‘XL-SHAPE’ was validated using well-characterized viral RNA-protein interactions: HIV-1 Tat/TAR and bacteriophage MS2 RNA/Coat Binding Protein. It was then used to map HIV-1 Gag protein interactions on 2D and 3D models of the viral RNA leader. Distinct Gag binding sites were identified on exposed RNA surfaces corresponding to regions identified by mutagenesis as important for genome packaging. This widely applicable technique has revealed a first view of the stoichiometry and structure of the initial complex formed when HIV captures its genome. PMID:26449409

  20. A novel combined RNA-protein interaction analysis distinguishes HIV-1 Gag protein binding sites from structural change in the viral RNA leader.

    PubMed

    Kenyon, Julia C; Prestwood, Liam J; Lever, Andrew M L

    2015-01-01

    RNA-protein interactions govern many viral and host cell processes. Conventional 'footprinting' to examine RNA-protein complex formation often cannot distinguish between sites of RNA-protein interaction and sites of RNA structural remodelling. We have developed a novel technique combining photo crosslinking with RNA 2' hydroxyl reactivity ('SHAPE') that achieves rapid and hitherto unachievable resolution of both RNA structural changes and the sites of protein interaction within an RNA-protein complex. 'XL-SHAPE' was validated using well-characterized viral RNA-protein interactions: HIV-1 Tat/TAR and bacteriophage MS2 RNA/Coat Binding Protein. It was then used to map HIV-1 Gag protein interactions on 2D and 3D models of the viral RNA leader. Distinct Gag binding sites were identified on exposed RNA surfaces corresponding to regions identified by mutagenesis as important for genome packaging. This widely applicable technique has revealed a first view of the stoichiometry and structure of the initial complex formed when HIV captures its genome. PMID:26449409

  1. A systematic mammalian genetic interaction map reveals pathways underlying ricin susceptibility.

    PubMed

    Bassik, Michael C; Kampmann, Martin; Lebbink, Robert Jan; Wang, Shuyi; Hein, Marco Y; Poser, Ina; Weibezahn, Jimena; Horlbeck, Max A; Chen, Siyuan; Mann, Matthias; Hyman, Anthony A; Leproust, Emily M; McManus, Michael T; Weissman, Jonathan S

    2013-02-14

    Genetic interaction (GI) maps, comprising pairwise measures of how strongly the function of one gene depends on the presence of a second, have enabled the systematic exploration of gene function in microorganisms. Here, we present a two-stage strategy to construct high-density GI maps in mammalian cells. First, we use ultracomplex pooled shRNA libraries (25 shRNAs/gene) to identify high-confidence hit genes for a given phenotype and effective shRNAs. We then construct double-shRNA libraries from these to systematically measure GIs between hits. A GI map focused on ricin susceptibility broadly recapitulates known pathways and provides many unexpected insights. These include a noncanonical role for COPI, a previously uncharacterized protein complex affecting toxin clearance, a specialized role for the ribosomal protein RPS25, and functionally distinct mammalian TRAPP complexes. The ability to rapidly generate mammalian GI maps provides a potentially transformative tool for defining gene function and designing combination therapies based on synergistic pairs. PMID:23394947

  2. A Systematic Mammalian Genetic Interaction Map Reveals Pathways Underlying Ricin Susceptibility

    PubMed Central

    Bassik, Michael C.; Kampmann, Martin; Lebbink, Robert Jan; Wang, Shuyi; Hein, Marco Y.; Poser, Ina; Weibezahn, Jimena; Horlbeck, Max A.; Chen, Siyuan; Mann, Matthias; Hyman, Anthony A.; LeProust, Emily M.; McManus, Michael T.; Weissman, Jonathan S.

    2013-01-01

    SUMMARY Genetic interaction (GI) maps, comprising pairwise measures of how strongly the function of one gene depends on the presence of a second, have enabled the systematic exploration of gene function in microorganisms. Here, we present a two-stage strategy to construct high-density GI maps in mammalian cells. First, we use ultra-complex pooled shRNA libraries (25 shRNAs/gene) to identify high-confidence hit genes for a given phenotype and effective shRNAs. We then construct double-shRNA libraries from these to systematically measure GIs between hits. A GI map focused on ricin susceptibility broadly recapitulates known pathways and provides many unexpected insights. These include a non-canonical role for COPI, a novel protein complex (SRIC) affecting toxin clearance, a specialized role for the ribosomal protein RPS25, and functionally distinct mammalian TRAPP complexes. The ability to rapidly generate mammalian GI maps provides a potentially transformative tool for defining gene function and designing combination therapies based on synergistic pairs. PMID:23394947

  3. Mapping texts through dimensionality reduction and visualization techniques for interactive exploration of document collections

    NASA Astrophysics Data System (ADS)

    de Andrade Lopes, Alneu; Minghim, Rosane; Melo, Vinícius; Paulovich, Fernando V.

    2006-01-01

    The current availability of information many times impair the tasks of searching, browsing and analyzing information pertinent to a topic of interest. This paper presents a methodology to create a meaningful graphical representation of documents corpora targeted at supporting exploration of correlated documents. The purpose of such an approach is to produce a map from a document body on a research topic or field based on the analysis of their contents, and similarities amongst articles. The document map is generated, after text pre-processing, by projecting the data in two dimensions using Latent Semantic Indexing. The projection is followed by hierarchical clustering to support sub-area identification. The map can be interactively explored, helping to narrow down the search for relevant articles. Tests were performed using a collection of documents pre-classified into three research subject classes: Case-Based Reasoning, Information Retrieval, and Inductive Logic Programming. The map produced was capable of separating the main areas and approaching documents by their similarity, revealing possible topics, and identifying boundaries between them. The tool can deal with the exploration of inter-topics and intra-topic relationship and is useful in many contexts that need deciding on relevant articles to read, such as scientific research, education, and training.

  4. 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 assemblages consisting of diverse taxa at neutral pH background sites. Terrestrial serpentinite-hosted microbial ecosystems with their accessibility, their low phylogenetic diversity, and limited range of energetic resources provide an excellent opportunity to explore the interplay between geochemical energy and life and to elucidate the native serpentinite subsurface biosphere. From the perspective of Mars exploration, studies of serpentinite ecosystems provide the opportunity to pinpoint the organisms and physiological adaptations specifically associated with serpentinization and to directly measure their geochemical impacts. Both of these results will inform modeling and life detection efforts of the Martian subsurface environment.

  5. Genome-wide Mapping of Cellular Protein–RNA Interactions Enabled by Chemical Crosslinking

    PubMed Central

    Li, Xiaoyu; Song, Jinghui; Yi, Chengqi

    2014-01-01

    RNA–protein interactions influence many biological processes. Identifying the binding sites of RNA-binding proteins (RBPs) remains one of the most fundamental and important challenges to the studies of such interactions. Capturing RNA and RBPs via chemical crosslinking allows stringent purification procedures that significantly remove the non-specific RNA and protein interactions. Two major types of chemical crosslinking strategies have been developed to date, i.e., UV-enabled crosslinking and enzymatic mechanism-based covalent capture. In this review, we compare such strategies and their current applications, with an emphasis on the technologies themselves rather than the biology that has been revealed. We hope such methods could benefit broader audience and also urge for the development of new methods to study RNA?RBP interactions. PMID:24747191

  6. Analyzing Interactions by an IIS-Map-Based Method in Face-to-Face Collaborative Learning: An Empirical Study

    ERIC Educational Resources Information Center

    Zheng, Lanqin; Yang, Kaicheng; Huang, Ronghuai

    2012-01-01

    This study proposes a new method named the IIS-map-based method for analyzing interactions in face-to-face collaborative learning settings. This analysis method is conducted in three steps: firstly, drawing an initial IIS-map according to collaborative tasks; secondly, coding and segmenting information flows into information items of IIS; thirdly,…

  7. Systematic analysis of the Hmga2 3' UTR identifies many independent regulatory sequences and a novel interaction between distal sites.

    PubMed

    Kristjánsdóttir, Katla; Fogarty, Elizabeth A; Grimson, Andrew

    2015-07-01

    The 3' untranslated regions (3' UTRs) of mRNAs regulate transcripts by serving as binding sites for regulatory factors, including microRNAs and RNA binding proteins. Binding of such trans-acting factors can control the rates of mRNA translation, decay, and other aspects of mRNA biology. To better understand the role of 3' UTRs in gene regulation, we performed a detailed analysis of a model mammalian 3' UTR, that of Hmga2, with the principal goals of identifying the complete set of regulatory elements within a single 3' UTR, and determining the extent to which elements interact with and affect one another. Hmga2 is an oncogene whose overexpression in cancers often stems from mutations that remove 3'-UTR regulatory sequences. We used reporter assays in cultured cells to generate maps of cis-regulatory information across the Hmga2 3' UTR at different resolutions, ranging from 50 to 400 nt. We found many previously unidentified regulatory sites, a large number of which were up-regulating. Importantly, the overall location and impact of regulatory sites was conserved between different species (mouse, human, and chicken). By systematically comparing the regulatory impact of 3'-UTR segments of different sizes we were able to determine that the majority of regulatory sequences function independently; only a very small number of segments showed evidence of any interactions. However, we discovered a novel interaction whereby terminal 3'-UTR sequences induced internal up-regulating elements to convert to repressive elements. By fully characterizing one 3' UTR, we hope to better understand the principles of 3'-UTR-mediated gene regulation. PMID:25999317

  8. An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions.

    PubMed

    Sengupta, Raghuvir N; Van Schie, Sabine N S; Giamba?u, George; Dai, Qing; Yesselman, Joseph D; York, Darrin; Piccirilli, Joseph A; Herschlag, Daniel

    2016-01-01

    Biological catalysis hinges on the precise structural integrity of an active site that binds and transforms its substrates and meeting this requirement presents a unique challenge for RNA enzymes. Functional RNAs, including ribozymes, fold into their active conformations within rugged energy landscapes that often contain misfolded conformers. Here we uncover and characterize one such "off-pathway" species within an active site after overall folding of the ribozyme is complete. The Tetrahymena group I ribozyme (E) catalyzes cleavage of an oligonucleotide substrate (S) by an exogenous guanosine (G) cofactor. We tested whether specific catalytic interactions with G are present in the preceding E•S•G and E•G ground-state complexes. We monitored interactions with G via the effects of 2'- and 3'-deoxy (-H) and -amino (-NH2) substitutions on G binding. These and prior results reveal that G is bound in an inactive configuration within E•G, with the nucleophilic 3'-OH making a nonproductive interaction with an active site metal ion termed MA and with the adjacent 2'-OH making no interaction. Upon S binding, a rearrangement occurs that allows both -OH groups to contact a different active site metal ion, termed MC, to make what are likely to be their catalytic interactions. The reactive phosphoryl group on S promotes this change, presumably by repositioning the metal ions with respect to G. This conformational transition demonstrates local rearrangements within an otherwise folded RNA, underscoring RNA's difficulty in specifying a unique conformation and highlighting Nature's potential to use local transitions of RNA in complex function. PMID:26567314

  9. On-site screened Coulomb interactions for localized electrons in transition metal oxides and defect systems

    NASA Astrophysics Data System (ADS)

    Shih, Bi-Ching; Zhang, Peihong; Department of Physics Team

    2011-03-01

    Electronic and structural properties of strongly correlated material systems are largely determined by the strength of the on-site Coulomb interaction. Theoretical models devised to capture the physics of strongly correlated materials usually involve screened Coulomb interactions as adjustable parameters. We present first-principles results for the screened on-site Coulomb and exchange energy for transition metal oxides. The dielectric screening is calculated within the random phase approximation and the localized electrons are represented by maximally localized Wannier functions. We further extend our study to calculate on-site Coulomb interactions for localized defect states in semiconductors. We acknowledge the computational support provided by the Center for Computational Research at the University at Buffalo, SUNY. This work is supported by the National Science Foundation under Grant No. DMR-0946404 and by the Department of Energy under Grant No. DE-SC0002623.

  10. Mapping the Interactions between the NS4B and NS3 Proteins of Dengue Virus

    PubMed Central

    Zou, Jing; Lee, Le Tian; Wang, Qing Yin; Xie, Xuping; Lu, Siyan; Yau, Yin Hoe; Yuan, Zhiming; Geifman Shochat, Susana; Kang, Congbao

    2015-01-01

    ABSTRACT Flavivirus RNA synthesis is mediated by a multiprotein complex associated with the endoplasmic reticulum membrane, named the replication complex (RC). Within the flavivirus RC, NS4B, an integral membrane protein with a role in virulence and regulation of the innate immune response, binds to the NS3 protease-helicase. NS4B modulates the RNA helicase activity of NS3, but the molecular details of their interaction remain elusive. Here, we used dengue virus (DENV) to map the determinants for the NS3-NS4B interaction. Coimmunoprecipitation and an in situ proximity ligation assay confirmed that NS3 colocalizes with NS4B in both DENV-infected cells and cells coexpressing both proteins. Surface plasmon resonance demonstrated that subdomains 2 and 3 of the NS3 helicase region and the cytoplasmic loop of NS4B are required for binding. Using nuclear magnetic resonance (NMR), we found that the isolated cytoplasmic loop of NS4B is flexible, with a tendency to form a three-turn ?-helix and two short ?-strands. Upon binding to the NS3 helicase, 12 amino acids within the cytoplasmic loop of NS4B exhibited line broadening, suggesting a participation in the interaction. Sequence alignment showed that 4 of these 12 residues are strictly conserved across different flaviviruses. Mutagenesis analysis showed that three (Q134, G140, and N144) of the four evolutionarily conserved NS4B residues are essential for DENV replication. The mapping of the NS3/NS4B-interacting regions described here can assist the design of inhibitors that disrupt their interface for antiviral therapy. IMPORTANCE NS3 and NS4B are essential components of the flavivirus RC. Using DENV as a model, we mapped the interaction between the viral NS3 and NS4B proteins. The subdomains 2 and 3 of NS3 helicase as well as the cytoplasmic loop of NS4B are critical for the interaction. Functional analysis delineated residues within the NS4B cytoplasmic loop that are crucial for DENV replication. Our findings reveal molecular details of how flavivirus NS3 protein cooperates with NS4B within the RC. In addition, this study has established the rationale and assays to search for inhibitors disrupting the NS3-NS4B interaction for antiviral drug discovery. PMID:25589636

  11. Metallicity at the explosion sites of interacting transients

    NASA Astrophysics Data System (ADS)

    Taddia, F.; Sollerman, J.; Fremling, C.; Pastorello, A.; Leloudas, G.; Fransson, C.; Nyholm, A.; Stritzinger, M. D.; Ergon, M.; Roy, R.; Migotto, K.

    2015-08-01

    Context. Some circumstellar-interacting (CSI) supernovae (SNe) are produced by the explosions of massive stars that have lost mass shortly before the SN explosion. There is evidence that the precursors of some SNe IIn were luminous blue variable (LBV) stars. For a small number of CSI SNe, outbursts have been observed before the SN explosion. Eruptive events of massive stars are named SN impostors (SN IMs) and whether they herald a forthcoming SN or not is still unclear. The large variety of observational properties of CSI SNe suggests the existence of other progenitors, such as red supergiant (RSG) stars with superwinds. Furthermore, the role of metallicity in the mass loss of CSI SN progenitors is still largely unexplored. Aims: Our goal is to gain insight into the nature of the progenitor stars of CSI SNe by studying their environments, in particular the metallicity at their locations. Methods: We obtain metallicity measurements at the location of 60 transients (including SNe IIn, SNe Ibn, and SN IMs) via emission-line diagnostic on optical spectra obtained at the Nordic Optical Telescope and through public archives. Metallicity values from the literature complement our sample. We compare the metallicity distributions among the different CSI SN subtypes, and to those of other core-collapse SN types. We also search for possible correlations between metallicity and CSI SN observational properties. Results: We find that SN IMs tend to occur in environments with lower metallicity than those of SNe IIn. Among SNe IIn, SN IIn-L(1998S-like) SNe show higher metallicities, similar to those of SNe IIL/P, whereas long-lasting SNe IIn (1988Z-like) show lower metallicities, similar to those of SN IMs. The metallicity distribution of SNe IIn can be reproduced by combining the metallicity distributions of SN IMs (which may be produced by major outbursts of massive stars like LBVs) and SNe IIP (produced by RSGs). The same applies to the distributions of the normalized cumulative rank (NCR) values, which quantifies the SN association to H ii regions. For SNe IIn, we find larger mass-loss rates and higher CSM velocities at higher metallicities. The luminosity increment in the optical bands during SN IM outbursts tend to be larger at higher metallicity, whereas the SN IM quiescent optical luminosities tend to be lower. Conclusions: The difference in metallicity between SNe IIn and SN IMs indicates that LBVs are only one of the progenitor channels for SNe IIn, with 1988Z-like and 1998S-like SNe possibly arising from LBVs and RSGs, respectively. Finally, even though line-driven winds likely do not primarily drive the late mass-loss of CSI SN progenitors, metallicity has some impact on the observational properties of these transients. Based on observations performed at the Nordic Optical Telescope (Proposal numbers: P45-004, P49-016; PI: F. Taddia), La Palma, Spain.Tables 1-3, 5-7 and Figs. 4-7, 11-14 are available in electronic form at http://www.aanda.org

  12. Membrane Yeast Two-Hybrid (MYTH) Mapping of Full-Length Membrane Protein Interactions.

    PubMed

    Snider, Jamie; Stagljar, Igor

    2016-01-01

    Mapping of protein interaction networks is a major strategy for obtaining a global understanding of protein function in cells and represents one of the primary goals of proteomics research. Membrane proteins, which play key roles in human disease and as drug targets, are of considerable interest; however, because of their hydrophobic nature, mapping their interactions presents significant technical challenges and requires the use of special methodological approaches. One powerful approach is the membrane yeast two-hybrid (MYTH) assay, a split-ubiquitin-based system specifically suited to the study of full-length membrane protein interactions in vivo using the yeast Saccharomyces cerevisiae as a host. The system can be used in both low- and high-throughput formats to study proteins from a wide range of different organisms. There are two primary variants of MYTH: integrated (iMYTH), which involves endogenous expression and tagging of baits and is suitable for studying native yeast membrane proteins, and traditional (tMYTH), which involves ectopic plasmid-based expression of tagged baits and is suitable for studying membrane proteins from other organisms. Here we provide an introduction to the MYTH assay, including both the iMYTH and tMYTH variants. MYTH can be set up in almost any laboratory environment, with results typically obtainable within 4 to 6 wk. PMID:26729912

  13. Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis

    PubMed Central

    Moore, Michael; Zhang, Chaolin; Gantman, Emily Conn; Mele, Aldo; Darnell, Jennifer C.; Darnell, Robert B.

    2014-01-01

    Summary Identifying sites where RNA binding proteins (RNABPs) interact with target RNAs opens the door to understanding the vast complexity of RNA regulation. UV-crosslinking and immunoprecipitation (CLIP) is a transformative technology in which RNAs purified from in vivo cross-linked RNA-protein complexes are sequenced to reveal footprints of RNABP:RNA contacts. CLIP combined with high throughput sequencing (HITS-CLIP) is a generalizable strategy to produce transcriptome-wide RNA binding maps with higher accuracy and resolution than standard RNA immunoprecipitation (RIP) profiling or purely computational approaches. Applying CLIP to Argonaute proteins has expanded the utility of this approach to mapping binding sites for microRNAs and other small regulatory RNAs. Finally, recent advances in data analysis take advantage of crosslinked-induced mutation sites (CIMS) to refine RNA-binding maps to single-nucleotide resolution. Once IP conditions are established, HITS-CLIP takes approximately eight days to prepare RNA for sequencing. Established pipelines for data analysis, including for CIMS, take 3-4 days. PMID:24407355

  14. Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis.

    PubMed

    Moore, Michael J; Zhang, Chaolin; Gantman, Emily Conn; Mele, Aldo; Darnell, Jennifer C; Darnell, Robert B

    2014-02-01

    The identification of sites where RNA-binding proteins (RNABPs) interact with target RNAs opens the door to understanding the vast complexity of RNA regulation. UV cross-linking and immunoprecipitation (CLIP) is a transformative technology in which RNAs purified from in vivo cross-linked RNA-protein complexes are sequenced to reveal footprints of RNABP:RNA contacts. CLIP combined with high-throughput sequencing (HITS-CLIP) is a generalizable strategy to produce transcriptome-wide maps of RNA binding with higher accuracy and resolution than standard RNA immunoprecipitation (RIP) profiling or purely computational approaches. The application of CLIP to Argonaute proteins has expanded the utility of this approach to mapping binding sites for microRNAs and other small regulatory RNAs. Finally, recent advances in data analysis take advantage of cross-link-induced mutation sites (CIMS) to refine RNA-binding maps to single-nucleotide resolution. Once IP conditions are established, HITS-CLIP takes ?8 d to prepare RNA for sequencing. Established pipelines for data analysis, including those for CIMS, take 3-4 d. PMID:24407355

  15. Mapping the cofilin binding site on yeast G-actin by chemical cross-linking

    PubMed Central

    Grintsevich, Elena E.; Benchaar, Sabrina A.; Warshaviak, Dora; Boontheung, Pinmanee; Halgand, Frédéric; Whitelegge, Julian P.; Faull, Kym F.; Ogorzalek Loo, Rachel R.; Sept, David; Loo, Joseph A.

    2009-01-01

    Cofilin is a major cytoskeletal protein that binds to both monomeric (G-) and polymeric (F-) actin and is involved in microfilament dynamics. Although an atomic structure of the G-actin-cofilin complex does not exist, models of the complex have been built using molecular dynamics simulations, structural homology considerations, and synchrotron radiolytic footprinting data. The hydrophobic cleft between actin subdomains 1 and 3 and, alternatively, the cleft between actin subdomains 1 and 2 have been proposed as possible high affinity cofilin binding sites. In this study, the proposed binding of cofilin to the subdomain 1/3 region on G-actin has been probed using site-directed mutagenesis, fluorescence labeling, and chemical cross-linking with yeast actin mutants containing single reactive cysteines in the actin hydrophobic cleft and cofilin mutants carrying reactive cysteines in the regions predicted to bind to G-actin. Mass spectrometric analysis of the cross-linked complex revealed that cysteine 345 in subdomain 1 of mutant G-actin was cross-linked to native cysteine 62 on cofilin. A cofilin mutant that carried a cysteine substitution in the ?3 helix (residue 95) formed a cross-link with residue 144 in actin subdomain 3. Distance constraints imposed by these cross-links provide experimental evidence for cofilin binding between actin subdomains 1 and 3 and fit a corresponding, docking-based structure of the complex. The cross-linking of the N-terminal region of recombinant yeast cofilin to actin residues 346 and 374 with dithio-bis-maleimidoethane (DTME, 12.4 Ĺ) and via disulfide bond formation was also documented. This set of cross-linking data confirms the important role the N-terminal segment of cofilin in the interactions with G-actin. PMID:18258262

  16. Isostatic gravity map of the Nevada Test Site and vicinity, Nevada

    SciTech Connect

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

    1988-12-31

    The isostatic gravity map of the Nevada Test Site (NTS) and vicinity is based on about 16,000 gravity stations. Principal facts of the gravity data were listed by Harris and others (1989) and their report included descriptions of base stations, high-precision and absolute gravity stations, and data accuracy. Observed gravity values were referenced to the International Gravity Standardization Net 1971 gravity datum described by Morelli (1974) and reduced using the Geodetic Reference System 1967 formula for the normal gravity on the ellipsoid (International Union of Geodesy and Geophysics, 1971). Free-air, Bouguer, curvature, and terrain corrections for a standard reduction density of 2.67 g/cm{sup 3} were made to compute complete Bouguer anomalies. Terrain corrections were made to a radial distance of 166.7 km from each station using a digital elevation model and a computer procedure by Plouff (1977) and, in general, include manually estimated inner-zone terrain corrections. Finally, isostatic corrections were made using a procedure by Simpson and others (1983) based on an Airy-Heiskanen model with local compensation (Heiskanen and Moritz, 1967) with an upper-crustal density of 2.67 g/cm{sup 3}, a crustal thickness of 25 km, and a density contrast between the lower-crust and upper-mantle of 0.4 g/cm{sup 3}. Isostatic corrections help remove the effects of long-wavelength anomalies related to topography and their compensating masses and, thus, enhance short- to moderate-wavelength anomalies caused by near surface geologic features. 6 refs.

  17. Multi-Modal, Multi-Touch Interaction with Maps in Disaster Management Applications

    NASA Astrophysics Data System (ADS)

    Paelke, V.; Nebe, K.; Geiger, C.; Klompmaker, F.; Fischer, H.

    2012-07-01

    Multi-touch interaction has become popular in recent years and impressive advances in technology have been demonstrated, with the presentation of digital maps as a common presentation scenario. However, most existing systems are really technology demonstrators and have not been designed with real applications in mind. A critical factor in the management of disaster situations is the access to current and reliable data. New sensors and data acquisition platforms (e.g. satellites, UAVs, mobile sensor networks) have improved the supply of spatial data tremendously. However, in many cases this data is not well integrated into current crisis management systems and the capabilities to analyze and use it lag behind sensor capabilities. Therefore, it is essential to develop techniques that allow the effective organization, use and management of heterogeneous data from a wide variety of data sources. Standard user interfaces are not well suited to provide this information to crisis managers. Especially in dynamic situations conventional cartographic displays and mouse based interaction techniques fail to address the need to review a situation rapidly and act on it as a team. The development of novel interaction techniques like multi-touch and tangible interaction in combination with large displays provides a promising base technology to provide crisis managers with an adequate overview of the situation and to share relevant information with other stakeholders in a collaborative setting. However, design expertise on the use of such techniques in interfaces for real-world applications is still very sparse. In this paper we report on interdisciplinary research with a user and application centric focus to establish real-world requirements, to design new multi-modal mapping interfaces, and to validate them in disaster management applications. Initial results show that tangible and pen-based interaction are well suited to provide an intuitive and visible way to control who is changing data in a multi-user command and control interface.

  18. The interaction of high-resolution electrophoresis and computational analysis in genome mapping

    SciTech Connect

    Carrano, A.V.; Branscomb, E.W.; de Jong, P.J.; Mohrenweiser, H.; Olsen, A.; Slezak, T.

    1990-07-26

    The construction of physical maps and the determination of the DNA sequence of chromosome-size segments of the human genome is a complex, multidisciplinary undertaking. The approach we have taken to construct a physical map and sequence of human chromosome 19 typifies these interactions. We exploit the power of both acrylamide and agarose gel electrophoresis to provide a simple and versatile method for DNA fingerprinting and the creation of contigs or sets of overlapping genomic clones. Cosmid libraries are constructed from Yeast Artificial Chromosomes (YAC) clones or from flow-sorted chromosomes. Cosmid DNA isolated from the screened library array is cut with a combination of five restriction enzymes and the fragment ends labeled with one of four different fluorochromes. Our approach to contig construction uses a robotic system to label restriction fragments from cosmids with fluorochromes, use of an automated DNA sequencer to capture fragment mobility data in a high resolution multiplex mode processes the mobility data to determine fragment length and provide a statistical measure of overlap among cosmids; and display the contigs and underlying cosmids for operator interaction and access to a database. Data analyses and interactions are conducted over a network of SUN workstations using a set of software tools that we developed and coupled to a commercially available database. Applying these methods, we have analyzed 5154 cosmid clones and assembled 515 contigs for chromosome 19. Some of these contigs have been identified with known genes and many have been mapped to the chromosome by fluorescence in situ hybridization. Existing contigs are being extended by a combination of walking and fingerprinting. 21 refs., 2 figs.

  19. 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

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

    PubMed Central

    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

  1. Quantitative Chemical-Genetic Interaction Map Connects Gene Alterations to Drug Responses | Office of Cancer Genomics

    Cancer.gov

    In a recent Cancer Discovery report, CTD2 researchers at the University of California in San Francisco developed a new quantitative chemical-genetic interaction mapping approach to evaluate drug sensitivity or resistance in isogenic cell lines. Performing a high-throughput screen with isogenic cell lines allowed the researchers to explore the impact of a panel of emerging and established drugs on cells overexpressing a single cancer-associated gene in isolation. The use of isogenic cell lines also helped identify synthetic lethal relationships, or tumor gene dependencies.

  2. Simple Protein Complex Purification and Identification Method Suitable for High- throughput Mapping of Protein Interaction Networks

    SciTech Connect

    Markillie, Lye Meng; Lin, Chiann Tso; Adkins, Joshua N.; Auberry, Deanna L.; Hill, Eric A.; Hooker, Brian S.; Moore, Priscilla A.; Moore, Ronald J.; Shi, Liang; Wiley, H. S.; Kery, Vladimir

    2005-04-11

    Most of the current methods for purification and identification of protein complexes use endogenous expression of affinity tagged bait, tandem affinity tag purification of protein complexes followed by specific elution of complexes from beads, gel separation, in-gel digestion and mass spectrometric analysis of protein interactors. We propose a single affinity tag in vitro pulldown assay with denaturing elution, trypsin digestion in organic solvent and LC ESI MS/MS protein identification using SEQUEST analysis. Our method is simple, easy to scale up and automate thus suitable for high throughput mapping of protein interaction networks and functional proteomics.

  3. Quantitative Chemical-Genetic Interaction Map Connects Gene Alterations to Drug Responses

    Cancer.gov

    In a recent Cancer Discovery report, CTD2 researchers at the University of California in San Francisco developed a new quantitative chemical-genetic interaction mapping approach to evaluate drug sensitivity or resistance in isogenic cell lines. Performing a high-throughput screen with isogenic cell lines allowed the researchers to explore the impact of a panel of emerging and established drugs on cells overexpressing a single cancer-associated gene in isolation. The use of isogenic cell lines also helped identify synthetic lethal relationships, or tumor gene dependencies.

  4. AFSM sequencing approach: a simple and rapid method for genome-wide SNP and methylation site discovery and genetic mapping

    PubMed Central

    Xia, Zhiqiang; Zou, Meiling; Zhang, Shengkui; Feng, Binxiao; Wang, Wenquan

    2014-01-01

    We describe methods for the assessment of amplified-fragment single nucleotide polymorphism and methylation (AFSM) sites using a quick and simple molecular marker-assisted breeding strategy based on the use of two restriction enzyme pairs (EcoRI-MspI and EcoRI-HpaII) and a next-generation sequencing platform. Two sets of 85 adapter pairs were developed to concurrently identify SNPs, indels and methylation sites for 85 lines of cassava population in this study. In addition to SNPs and indels, the simplicity of the AFSM protocol makes it particularly suitable for high-throughput full methylation and hemi-methylation analyses. To further demonstrate the ease of this approach, a cassava genetic linkage map was constructed. This approach should be widely applicable for genetic mapping in a variety of organisms and will improve the application of crop genomics in assisted breeding. PMID:25466435

  5. 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.

  6. PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes.

    PubMed

    Sheu, Shu-Hsien; Lancia, David R; Clodfelter, Karl H; Landon, Melissa R; Vajda, Sandor

    2005-01-01

    PRECISE (Predicted and Consensus Interaction Sites in Enzymes) is a database of interactions between the amino acid residues of an enzyme and its ligands (substrate and transition state analogs, cofactors, inhibitors and products). It is available online at http://precise.bu.edu/. In the current version, all information on interactions is extracted from the enzyme-ligand complexes in the Protein Data Bank (PDB) by performing the following steps: (i) clustering homologous enzyme chains such that, in each cluster, the proteins have the same EC number and all sequences are similar; (ii) selecting a representative chain for each cluster; (iii) selecting ligand types; (iv) finding non-bonded interactions and hydrogen bonds; and (v) summing the interactions for all chains within the cluster. The output of the search is the color-coded sequence of the representative. The colors indicate the total number of interactions found at each amino acid position in all chains of the cluster. Clicking on a residue displays a detailed list of interactions for that residue. Optional filters allow restricting the output to selected chains in the cluster, to non-bonded or hydrogen bonding interactions, and to selected ligand types. The binding site information is essential for understanding and altering substrate specificity and for the design of enzyme inhibitors. PMID:15608178

  7. Individual-site binding data and the energetics of protein-DNA interactions.

    PubMed

    Saroff, H A

    1993-09-01

    Individual-site isotherms for the binding of bacteriophage lambda repressor to the left and right lambda operators have been determined [D. F. Senear, M. Brenowitz, M. A. Shea, and G. K. Ackers (1986) Biochemistry, Vol. 25, pp. 7344-7354.] using the DNAse protection technique [footprinting; D. J. Galas and A. Schmitz (1978) Nucleic Acids Research, Vol. 5, pp. 3157-3170]. These extensive data have been interpreted with a quantitative model that emphasized cooperative interactions between adjacently bound ligands [occupied <==> occupied interactions; G. K. Ackers, A. D. Johnson, and M. A. Shea (1982) Proceedings of the National Academy of Science, USA, Vol. 79, pp. 1129-1133]. Overlooked in this model are the effects of cooperative interactions between a site containing a bound ligand and its neighboring unoccupied site (occupied <==> unoccupied interactions). This paper reinterprets the existing data with a model that considers occupied <==> unoccupied as well as occupied <==> occupied interactions. The results yield parameters that differ substantially from those already reported. A discussion on the advisability of ignoring occupied <==> unoccupied interactions is included. PMID:8400030

  8. Analysis of the Interaction of the Eg5 Loop5 with the Nucleotide Site

    SciTech Connect

    Harrington, Timothy D.; Naber, Nariman; Larson, Adam G.; Cooke, Roger; Rice, Sarah E.; Pate, Edward F.

    2011-11-21

    Loop 5 (L5) is a conserved loop that projects from the ?2-helix adjacent to the nucleotide site of all kinesin-family motors. L5 is critical to the function of the mito tickinesin-5 family motors and is the binding site for several kinesin-5 inhibitors that are currently in clinical trials. Its conformational dynamics and its role in motor function are not fully understood. Our previous work using EPR spectroscopy suggested that L5 alters the nucleotide pocket conformation of the kinesin-5 motor Eg5 (Larsonetal.,2010). EPR spectra of a spin-labeled nucleotide analog bound at the nucleotide site of Eg5 display a highly immobilized component that is absent if L5 is shortened or if the inhibitor STLC is added (Larson etal.,2010), which X-ray structures suggest stabilizes an L5 conformation pointing away from the nucleotide site. These data, coupled with the proximity of L5 to the nucleotide site suggest L5 could interact with a bound nucleotide, modulating function. Here we use molecular dynamics (MD) simulations of Eg5 to explore the interaction of L5 with the nucleotide site in greater detail. We performed MD simulations in which the L5-domain of the Eg5•ADP X-ray structure was manually deformed via backbone bond rotations. The L5-domain of Eg5 was sufficiently lengthy that portions of L5 could belocated in proximity to bound ADP. The MD simulations evolved to thermodynamically stable structures at 300K showing that L5 can interact directly with bound nucleotide with significant impingement on the ribosehydroxyls, consistent with the EPR spectroscopy results. Taken together, these data provide support for the hypothes is that L5 modulates Eg5 function via interaction with the nucleotide-binding site.

  9. Robust co-regulation of tyrosine phosphorylation sites on proteins reveals novel protein interactions

    PubMed Central

    Naegle, Kristen M.; White, Forest M.; Lauffenburger, Douglas A.; Yaffe, Michael B.

    2012-01-01

    Cell signaling networks propagate information from extracellular cues via dynamic modulation of protein–protein interactions in a context-dependent manner. Networks based on receptor tyrosine kinases (RTKs), for example, phosphorylate intracellular proteins in response to extracellular ligands, resulting in dynamic protein–protein interactions that drive phenotypic changes. Most commonly used methods for discovering these protein–protein interactions, however, are optimized for detecting stable, longer-lived complexes, rather than the type of transient interactions that are essential components of dynamic signaling networks such as those mediated by RTKs. Substrate phosphorylation downstream of RTK activation modifies substrate activity and induces phospho-specific binding interactions, resulting in the formation of large transient macromolecular signaling complexes. Since protein complex formation should follow the trajectory of events that drive it, we reasoned that mining phosphoproteomic datasets for highly similar dynamic behavior of measured phosphorylation sites on different proteins could be used to predict novel, transient protein–protein interactions that had not been previously identified. We applied this method to explore signaling events downstream of EGFR stimulation. Our computational analysis of robustly co-regulated phosphorylation sites, based on multiple clustering analysis of quantitative time-resolved mass-spectrometry phosphoproteomic data, not only identified known sitewise-specific recruitment of proteins to EGFR, but also predicted novel, a priori interactions. A particularly intriguing prediction of EGFR interaction with the cytoskeleton-associated protein PDLIM1 was verified within cells using co-immunoprecipitation and in situ proximity ligation assays. Our approach thus offers a new way to discover protein–protein interactions in a dynamic context- and phosphorylation site-specific manner. PMID:22851037

  10. Ground-water maps of the Hanford Site Separations Area, December 1987

    SciTech Connect

    Schatz, A.L.; Ammerman, J.J.

    1988-03-01

    The ground-water maps of the Separations Area are prepared by the Environmental Technology Section of the Defense Waste Management Division of Westinghouse Hanford Company. The Separations Area consists of the 200 East and 200 West Areas, where chemical processing activities are carried out. This set of ground-water maps consists of a water-table map of the unconfined aquifer, a depth-to-water map of the unconfined aquifer, and a potentiometric map of the uppermost confined aquifer (the Rattlesnake Ridge sedimentary interbed) in the area where West Lake, the deactivated Gable Mountain Pond, and the B Pond system are located. The Separations Area water-table map is prepared from water-level measurements made in June and December. For the December 1987 map approximately 200 wells were used for contouring the water table. The water-table mound beneath the deactivated U Pond has decreased in size since the June 1987 measurements were taken, reflecting the impact of shutting off flow to the pond in the fall of 1984. This mound has declined approximately 8 ft. since 1984. The water-table map also shows the locations of wells where the December 1987 measurements were made, and the data for these measurements are listed.

  11. 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.

  12. CANCER MORTALITY MAPS AND GRAPHS

    EPA Science Inventory

    The Cancer Mortality Maps & Graph Web Site provides interactive maps, graphs (which are accessible to the blind and visually-impaired), text, tables and figures showing geographic patterns and time trends of cancer death rates for the time period 1950-1994 for more than 40 cancer...

  13. Entanglement and quantum teleportation in a three-qubit Heisenberg chain with three-site interactions

    NASA Astrophysics Data System (ADS)

    Xi, Yu-Xing; Cheng, Wei-Wen; Huang, Yan-Xia

    2015-07-01

    The thermal entanglement of a three-qubit XXZ Heisenberg model with three-site interactions in an external magnetic field, and the quantum teleportation via this model in thermal equilibrium state are investigated. It is found that entanglement and average fidelity depend on temperature, magnetic field, and anisotropy parameter . Only ferromagnetic system is suitable for quantum teleportation. interaction is in favor of entanglement, average fidelity, and critical temperatures, while interaction against all of them. Moreover, we also find entanglement does not fully reflect average fidelity in virtue of study the relation between entanglement and average fidelity.

  14. Web GIS in practice V: 3-D interactive and real-time mapping in Second Life

    PubMed Central

    Boulos, Maged N Kamel; Burden, David

    2007-01-01

    This paper describes technologies from Daden Limited for geographically mapping and accessing live news stories/feeds, as well as other real-time, real-world data feeds (e.g., Google Earth KML feeds and GeoRSS feeds) in the 3-D virtual world of Second Life, by plotting and updating the corresponding Earth location points on a globe or some other suitable form (in-world), and further linking those points to relevant information and resources. This approach enables users to visualise, interact with, and even walk or fly through, the plotted data in 3-D. Users can also do the reverse: put pins on a map in the virtual world, and then view the data points on the Web in Google Maps or Google Earth. The technologies presented thus serve as a bridge between mirror worlds like Google Earth and virtual worlds like Second Life. We explore the geo-data display potential of virtual worlds and their likely convergence with mirror worlds in the context of the future 3-D Internet or Metaverse, and reflect on the potential of such technologies and their future possibilities, e.g. their use to develop emergency/public health virtual situation rooms to effectively manage emergencies and disasters in real time. The paper also covers some of the issues associated with these technologies, namely user interface accessibility and individual privacy. PMID:18042275

  15. Evolutionary, structural and biochemical evidence for a new interaction site of the leptin obesity protein

    NASA Technical Reports Server (NTRS)

    Gaucher, Eric A.; Miyamoto, Michael M.; Benner, Steven A.

    2003-01-01

    The Leptin protein is central to the regulation of energy metabolism in mammals. By integrating evolutionary, structural, and biochemical information, a surface segment, outside of its known receptor contacts, is predicted as a second interaction site that may help to further define its roles in energy balance and its functional differences between humans and other mammals.

  16. Understanding and Designing for Interactional Privacy Needs within Social Networking Sites

    ERIC Educational Resources Information Center

    Wisniewski, Pamela J.

    2012-01-01

    "Interpersonal boundary regulation" is a way to optimize social interactions when sharing and connecting through Social Networking Sites (SNSs). The theoretical foundation of much of my research comes from Altman's work on privacy management in the physical world. Altman believed that "we should attempt to design responsive…

  17. WebFEATURE: An interactive web tool for identifying and visualizing functional sites on macromolecular structures

    E-print Network

    Brutlag, Doug

    1 WebFEATURE: An interactive web tool for identifying and visualizing functional sites University, Stanford CA 94305 USA Abstract WebFEATURE (http://feature.stanford.edu/webfeature/) is a web and nucleic acids. WebFEATURE is the public interface to the scanning algorithm of the FEATURE package

  18. Identifying protein-protein interaction sites on a genome-wide scale

    E-print Network

    Anderson, Charles W.

    Identifying protein-protein interaction sites on a genome-wide scale Haidong Wang Eran Segal Asa}@cs.stanford.edu Dept. of Biochemistry {asa.benhur, brutlag}@stanford.edu Stanford University, CA 94305 Abstract Protein on proteins, with red denoting active and gray denoting inactive motifs. (b) A fragment of our probabilistic

  19. An experimental investigation on the characteristics of fluidstructure interactions of a wind turbine model sited

    E-print Network

    Hu, Hui

    turbine model sited in microburst-like winds Yan Zhang, Partha P. Sarkar, Hui Hu n Department of Aerospace: Received 6 December 2014 Accepted 23 June 2015 Keywords: Wind turbine aeromechanics Microburst-like wind the characteristics of the fluid­ structure interactions and microburst-induced wind loads acting on a wind turbine

  20. Lunar Mapping and Modeling On-the-Go: A mobile framework for viewing and interacting with large geospatial datasets

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

    The Lunar Mapping and Modeling Portal (LMMP, https://www.lmmp.nasa.gov/) is a collaboration between four NASA centers, JPL, Marshall, Goddard, and Ames, along with the USGS and US Army to provide a centralized geospatial repository for storing processed lunar data collected from the Apollo missions to the latest data acquired by the Lunar Reconnaissance Orbiter (LRO). We offer various scientific and visualization tools to analyze rock and crater densities, lighting maps, thermal measurements, mineral concentrations, slope hazards, and digital elevation maps with the intention of serving not only scientists and lunar mission planners, but also the general public. The project has pioneered in leveraging new technologies and embracing new computing paradigms to create a system that is sophisticated, secure, robust, and scalable all the while being easy to use, streamlined, and modular. We have led innovations through the use of a hybrid cloud infrastructure, authentication through various sources, and utilizing an in-house GIS framework, TWMS (TiledWMS) as well as the commercial ArcGIS product from ESRI. On the client end, we also provide a Flash GUI framework as well as REST web services to interact with the portal. We have also developed a visualization framework on mobile devices, specifically Apple's iOS, which allows anyone from anywhere to interact with LMMP. At the most basic level, the framework allows users to browse LMMP's entire catalog of over 600 data imagery products ranging from global basemaps to LRO's Narrow Angle Camera (NAC) images that provide details of up to .5 meters/pixel. Users are able to view map metadata and can zoom in and out as well as pan around the entire lunar surface with the appropriate basemap. They can arbitrarily stack the maps and images on top of each other to show a layered view of the surface with layer transparency adjusted to suit the user's desired look. Once the user has selected a combination of layers, he can also bookmark those layers for quick access in subsequent sessions. A search tool is also provided to allow users to quickly find points of interests on the moon and to view the auxiliary data associated with that feature. More advanced features include the ability to interact with the data. Using the services provided by the portal, users will be able to log in and access the same scientific analysis tools provided on the web site including measuring between two points, generating subsets, and running other analysis tools, all by using a customized touch interface that are immediately familiar to users of these smart mobile devices. Users can also access their own storage on the portal and view or send the data to other users. Finally, there are features that will utilize functionality that can only be enabled by mobile devices. This includes the use of the gyroscopes and motion sensors to provide a haptic interface visualize lunar data in 3D, on the device as well as potentially on a large screen. The mobile framework that we have developed for LMMP provides a glimpse of what is possible in visualizing and manipulating large geospatial data on small portable devices. While the framework is currently tuned to our portal, we hope that we can generalize the tool to use data sources from any type of GIS services.

  1. Multiphase Micro-Drop Interaction in Inkjet Printing of 3d Structures for Tactile Maps

    NASA Astrophysics Data System (ADS)

    Ahmed, Kafeel; McCallum, Don; Sheldon, Derek F.

    Ink-jet technology is a novel method for rapid deposition of accurately measured material with high precision. Consequently it has been used for applications such as, deposition of light emitting polymers and more recently for fabricating 3D objects and micro-mechanical structures. Ink-jet technology is also being applied to produce tactile maps for the visually impaired. The efficiency of the tactile maps, as outlined by psychophysical and cartographic studies of haptics, depends on its 3D features. To comprehend and control these features, detailed understanding of interaction amongst micro-drops, which are typically 50?m in diameter, is imperative. Multiphase interaction takes place between each liquid drop at impact with liquid or solid cured drops (deposited previously) and the solid substrate in an envelop of air. The behavior of micro-drops with regards to surface tension, drop coalescence among liquid and solid drops, drop impact kinetics, wettability, surface energy and drop spread has been analyzed using a computational model.

  2. ?-Lactoglobulin nanofibrils can be assembled into nanotapes via site-specific interactions with pectin.

    PubMed

    Hettiarachchi, Charith A; Melton, Laurence D; McGillivray, Duncan J; Loveday, Simon M; Gerrard, Juliet A; Williams, Martin A K

    2016-01-21

    Controlling the self-assembly of individual supramolecular entities, such as amyloid fibrils, into hierarchical architectures enables the 'bottom-up' fabrication of useful bionanomaterials. Here, we present the hierarchical assembly of ?-lactoglobulin nanofibrils into the form of 'nanotapes' in the presence of a specific pectin with a high degree of methylesterification. The nanotapes produced were highly ordered, and had an average width of 180 nm at pH 3. Increasing the ionic strength or the pH of the medium led to the disassembly of nanotapes, indicating that electrostatic interactions stabilised the nanotape architecture. Small-angle X-ray scattering experiments conducted on the nanotapes showed that adequate space is available between adjacent nanofibrils to accommodate pectin molecules. To locate the interaction sites on the pectin molecule, it was subjected to endopolygalacturonase digestion, and the resulting products were analysed using capillary electrophoresis and size-exclusion chromatography for their charge and molecular weight, respectively. Results suggested that the functional pectin molecules carry short (<10 residues) enzyme-susceptible blocks of negatively charged, non-methylesterified galacturonic acid residues in the middle of their homogalacturonan backbones (and possibly near their ends), that specifically bind to sites on the nanofibrils. Blocking the interaction sites on the nanofibril surface using small oligomers of non-methylesterified galacturonic acid residues similar in size to the interaction sites of the pectin molecule decreased the nanotape formation, indicating that site-specific electrostatic interactions are vital for the cross-linking of nanofibrils. We propose a structural model for the pectin-cross-linked ?-lactoglobulin nanotapes, the elements of which will inform the future design of bionanomaterials. PMID:26517088

  3. An Overview of Plume Tracker: Mapping Volcanic Emissions with Interactive Radiative Transfer Modeling

    NASA Astrophysics Data System (ADS)

    Realmuto, V. J.; Berk, A.; Guiang, C.

    2014-12-01

    Infrared remote sensing is a vital tool for the study of volcanic plumes, and radiative transfer (RT) modeling is required to derive quantitative estimation of the sulfur dioxide (SO2), sulfate aerosol (SO4), and silicate ash (pulverized rock) content of these plumes. In the thermal infrared, we must account for the temperature, emissivity, and elevation of the surface beneath the plume, plume altitude and thickness, and local atmospheric temperature and humidity. Our knowledge of these parameters is never perfect, and interactive mapping allows us to evaluate the impact of these uncertainties on our estimates of plume composition. To enable interactive mapping, the Jet Propulsion Laboratory is collaborating with Spectral Sciences, Inc., (SSI) to develop the Plume Tracker toolkit. This project is funded by a NASA AIST Program Grant (AIST-11-0053) to SSI. Plume Tracker integrates (1) retrieval procedures for surface temperature and emissivity, SO2, NH3, or CH4 column abundance, and scaling factors for H2O vapor and O3 profiles, (2) a RT modeling engine based on MODTRAN, and (3) interactive visualization and analysis utilities under a single graphics user interface. The principal obstacle to interactive mapping is the computational overhead of the RT modeling engine. Under AIST-11-0053 we have achieved a 300-fold increase in the performance of the retrieval procedures through the use of indexed caches of model spectra, optimization of the minimization procedures, and scaling of the effects of surface temperature and emissivity on model radiance spectra. In the final year of AIST-11-0053 we will implement parallel processing to exploit multi-core CPUs and cluster computing, and optimize the RT engine to eliminate redundant calculations when iterating over a range of gas concentrations. These enhancements will result in an additional 8 - 12X increase in performance. In addition to the improvements in performance, we have improved the accuracy of the Plume Tracker retrievals through refinements in the description of surface emissivity and use of vector projection to define the misfit between model and observed spectra. Portions of this research were conducted at the Jet Propulsion Laboratory, California Institute of Technology, under contract to the National Aeronautics and Space Administration.

  4. 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.

  5. WHERE MULTIFUNCTIONAL DNA REPAIR PROTEINS MEET: MAPPING THE INTERACTION DOMAINS BETWEEN XPG AND WRN

    SciTech Connect

    Rangaraj, K.; Cooper, P.K.; Trego, K.S.

    2009-01-01

    The rapid recognition and repair of DNA damage is essential for the maintenance of genomic integrity and cellular survival. Multiple complex and interconnected DNA damage responses exist within cells to preserve the human genome, and these repair pathways are carried out by a specifi c interplay of protein-protein interactions. Thus a failure in the coordination of these processes, perhaps brought about by a breakdown in any one multifunctional repair protein, can lead to genomic instability, developmental and immunological abnormalities, cancer and premature aging. This study demonstrates a novel interaction between two such repair proteins, Xeroderma pigmentosum group G protein (XPG) and Werner syndrome helicase (WRN), that are both highly pleiotropic and associated with inherited genetic disorders when mutated. XPG is a structure-specifi c endonuclease required for the repair of UV-damaged DNA by nucleotide excision repair (NER), and mutations in XPG result in the diseases Xeroderma pigmentosum (XP) and Cockayne syndrome (CS). A loss of XPG incision activity results in XP, whereas a loss of non-enzymatic function(s) of XPG causes CS. WRN is a multifunctional protein involved in double-strand break repair (DSBR), and consists of 3’–5’ DNA-dependent helicase, 3’–5’ exonuclease, and single-strand DNA annealing activities. Nonfunctional WRN protein leads to Werner syndrome, a premature aging disorder with increased cancer incidence. Far Western analysis was used to map the interacting domains between XPG and WRN by denaturing gel electrophoresis, which separated purifi ed full length and recombinant XPG and WRN deletion constructs, based primarily upon the length of each polypeptide. Specifi c interacting domains were visualized when probed with the secondary protein of interest which was then detected by traditional Western analysis using the antibody of the secondary protein. The interaction between XPG and WRN was mapped to the C-terminal region of XPG as well as the C-terminal region of WRN. The physical interaction between XPG and WRN links NER, (made evident by the disease XP) with DSBR, which imparts additional knowledge of the overlapping nature of these two proteins and the previously distinct DNA repair pathways they are associated with. Since genomic integrity is constantly threatened by both endogenous and exogenous (internal and external) damage, understanding the roles of these proteins in coordinating DNA repair processes with replication will signifi cantly further understanding how defects instigate physiological consequences in response to various DNA damaging sources. This ultimately contributes to our understanding of cancer and premature aging.

  6. Mapping the interaction between factor VIII and von Willebrand factor by electron microscopy and mass spectrometry

    PubMed Central

    Chiu, Po-Lin; Bou-Assaf, George M.; Chhabra, Ekta Seth; Chambers, Melissa G.; Peters, Robert T.; Kulman, John D.

    2015-01-01

    Association with the D?D3 domain of von Willebrand factor (VWF) stabilizes factor VIII (FVIII) in the circulation and maintains it at a level sufficient to prevent spontaneous bleeding. We used negative-stain electron microscopy (EM) to visualize complexes of FVIII with dimeric and monomeric forms of the D?D3 domain. The EM averages show that FVIII interacts with the D?D3 domain primarily through its C1 domain, with the C2 domain providing a secondary attachment site. Hydrogen-deuterium exchange mass spectrometry corroborated the importance of the C1 domain in D?D3 binding and implicates additional surface regions on FVIII in the interaction. Together, our results establish that the C1 domain is the major binding site on FVIII for VWF, reiterate the importance of the a3 acidic peptide in VWF binding, and suggest that the A3 and C2 domains play ancillary roles in this interaction. PMID:26065652

  7. Large-Scale Mapping of Transposable Element Insertion Sites Using Digital Encoding of Sample Identity

    PubMed Central

    Gohl, Daryl M.; Freifeld, Limor; Silies, Marion; Hwa, Jennifer J.; Horowitz, Mark; Clandinin, Thomas R.

    2014-01-01

    Determining the genomic locations of transposable elements is a common experimental goal. When mapping large collections of transposon insertions, individualized amplification and sequencing is both time consuming and costly. We describe an approach in which large numbers of insertion lines can be simultaneously mapped in a single DNA sequencing reaction by using digital error-correcting codes to encode line identity in a unique set of barcoded pools. PMID:24374352

  8. Quantum mechanics study of the hydroxyethylamines-BACE-1 active site interaction energies.

    PubMed

    Gueto-Tettay, Carlos; Drosos, Juan Carlos; Vivas-Reyes, Ricardo

    2011-06-01

    The identification of BACE-1, a key enzyme in the production of Amyloid-? (A?) peptides, generated by the proteolytic processing of amyloid precursor protein, was a major advance in the field of Alzheimer's disease as this pathology is characterized by the presence of extracellular senile plaques, mainly comprised of A? peptides. Hydroxyethylamines have demonstrated a remarkable potential, like candidate drugs, for this disease using BACE-1 as target. Density Functional Theory calculations were employed to estimate interaction energies for the complexes formed between the hydroxyethylamine derivated inhibitors and 24 residues in the BACE-1 active site. The collected data offered not only a general but a particular quantitative description that gives a deep insight of the interactions in the active site, showing at the same time how ligand structural variations affect them. Polar interactions are the major energetic contributors for complex stabilization and those ones with charged aspartate residues are highlighted, as they contribute over 90% of the total attractive interaction energy. Ligand-ARG296 residue interaction reports the most repulsive value and decreasing of the magnitude of this repulsion can be a key feature for the design of novel and more potent BACE-1 inhibitors. Also it was explained why sultam derivated BACE-1 inhibitors are better ones than lactam based. Hydrophobic interactions concentrated at S1 zone and other relevant repulsions and attractions were also evaluated. The comparison of two different theory levels (X3LYP and M062X) allowed to confirm the relevance of the detected interactions as each theory level has its own strength to depict the forces involved, as is the case of M062X which is better describing the hydrophobic interactions. Those facts were also evaluated and confirmed by comparing the quantitative trend, of selected ligand-residue interactions, with MP2 theory level as reference standard method for electrostatic plus dispersion energies. PMID:21691813

  9. 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. PMID:24070451

  10. Combining Solvent Thermodynamic Profiles with Functionality Maps of the Hsp90 Binding Site to Predict the Displacement of Water Molecules

    PubMed Central

    2013-01-01

    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. PMID:24070451

  11. In vivo interaction of the Escherichia coli integration host factor with its specific binding sites.

    PubMed Central

    Engelhorn, M; Boccard, F; Murtin, C; Prentki, P; Geiselmann, J

    1995-01-01

    The histone-like protein integration host factor (IHF) of Escherichia coli binds to specific binding sites on the chromosome or on mobile genetic elements, and is involved in many cellular processes. We have analyzed the interaction of IHF with five different binding sites in vitro and in vivo using UV laser footprinting, a technique that probes the immediate environment and conformation of a segment of DNA. Using this generally applicable technique we can directly compare the binding modes and interaction strengths of a DNA binding protein in its physiological environment within the cell to measurements performed in vitro. We conclude that the interactions between IHF and its specific binding sites are identical in vitro and in vivo. The footprinting signal is consistent with the model of IHF-binding to DNA proposed by Yang and Nash (1989). The occupancy of binding sites varies with the concentration of IHF in the cell and allows to estimate the concentration of free IHF protein in the cell. Images PMID:7659518

  12. BAID: The Barrow Area Information Database - an interactive web mapping portal and cyberinfrastructure for scientific activities in the vicinity of Barrow, Alaska

    NASA Astrophysics Data System (ADS)

    Cody, R. P.; Kassin, A.; Gaylord, A. G.; Tweedie, C. E.

    2013-12-01

    In 2013, the Barrow Area Information Database (BAID, www.baid.utep.edu) project resumed field operations in Barrow, AK. The Barrow area of northern Alaska is one of the most intensely researched locations in the Arctic. BAID is a cyberinfrastructure (CI) that details much of the historic and extant research undertaken within in the Barrow region in a suite of interactive web-based mapping and information portals (geobrowsers). The BAID user community and target audience for BAID is diverse and includes research scientists, science logisticians, land managers, educators, students, and the general public. BAID contains information on more than 11,000 Barrow area research sites that extend back to the 1940's and more than 640 remote sensing images and geospatial datasets. In a web-based setting, users can zoom, pan, query, measure distance, and save or print maps and query results. Data are described with metadata that meet Federal Geographic Data Committee standards and are archived at the University Corporation for Atmospheric Research Earth Observing Laboratory (EOL) where non-proprietary BAID data can be freely downloaded. Highlights for the 2013 season include the addition of more than 2000 additional research sites, providing differential global position system (dGPS) support to visiting scientists, surveying over 80 miles of coastline to document rates of erosion, training of local GIS personal, deployment of a wireless sensor network, and substantial upgrades to the BAID website and web mapping applications.

  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. PMID:26507855

  14. Mapping DNA cleavage by the Type ISP restriction-modification enzymes following long-range communication between DNA sites in different orientations

    PubMed Central

    van Aelst, Kara; Saikrishnan, Kayarat; Szczelkun, Mark D.

    2015-01-01

    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. PMID:26507855

  15. Association mapping and gene-gene interaction for stem rust resistance in CIMMYT spring wheat germplasm.

    PubMed

    Yu, Long-Xi; Lorenz, Aaron; Rutkoski, Jessica; Singh, Ravi P; Bhavani, Sridhar; Huerta-Espino, Julio; Sorrells, Mark E

    2011-12-01

    The recent emergence of wheat stem rust Ug99 and evolution of new races within the lineage threatens global wheat production because they overcome widely deployed stem rust resistance (Sr) genes that had been effective for many years. To identify loci conferring adult plant resistance to races of Ug99 in wheat, we employed an association mapping approach for 276 current spring wheat breeding lines from the International Maize and Wheat Improvement Center (CIMMYT). Breeding lines were genotyped with Diversity Array Technology (DArT) and microsatellite markers. Phenotypic data was collected on these lines for stem rust race Ug99 resistance at the adult plant stage in the stem rust resistance screening nursery in Njoro, Kenya in seasons 2008, 2009 and 2010. Fifteen marker loci were found to be significantly associated with stem rust resistance. Several markers appeared to be linked to known Sr genes, while other significant markers were located in chromosome regions where no Sr genes have been previously reported. Most of these new loci colocalized with QTLs identified recently in different biparental populations. Using the same data and Q + K covariate matrices, we investigated the interactions among marker loci using linear regression models to calculate P values for pairwise marker interactions. Resistance marker loci including the Sr2 locus on 3BS and the wPt1859 locus on 7DL had significant interaction effects with other loci in the same chromosome arm and with markers on chromosome 6B. Other resistance marker loci had significant pairwise interactions with markers on different chromosomes. Based on these results, we propose that a complex network of gene-gene interactions is, in part, responsible for resistance to Ug99. Further investigation may provide insight for understanding mechanisms that contribute to this resistance gene network. PMID:21811818

  16. A Structure-Based Classification and Analysis of Protein Domain Family Binding Sites and Their Interactions

    PubMed Central

    Ghoorah, Anisah W.; Devignes, Marie-Dominique; Alborzi, Seyed Ziaeddin; Smaďl-Tabbone, Malika; Ritchie, David W.

    2015-01-01

    While the number of solved 3D protein structures continues to grow rapidly, the structural rules that distinguish protein-protein interactions between different structural families are still not clear. Here, we classify and analyse the secondary structural features and promiscuity of a comprehensive non-redundant set of domain family binding sites (DFBSs) and hetero domain-domain interactions (DDIs) extracted from our updated KBDOCK resource. We have partitioned 4001 DFBSs into five classes using their propensities for three types of secondary structural elements (“?” for helices, “?” for strands, and “?” for irregular structure) and we have analysed how frequently these classes occur in DDIs. Our results show that ? elements are not highly represented in DFBSs compared to ? and ? elements. At the DDI level, all classes of binding sites tend to preferentially bind to the same class of binding sites and ?/? contacts are significantly disfavored. Very few DFBSs are promiscuous: 80% of them interact with just one Pfam domain. About 50% of our Pfam domains bear only one single-partner DFBS and are therefore monogamous in their interactions with other domains. Conversely, promiscuous Pfam domains bear several DFBSs among which one or two are promiscuous, thereby multiplying the promiscuity of the concerned protein. PMID:25860777

  17. Doxorubicin inhibits E. coli division by interacting at a novel site in FtsZ.

    PubMed

    Panda, Pragnya; Taviti, Ashoka Chary; Satpati, Suresh; Kar, Mitali Madhusmita; Dixit, Anshuman; Beuria, Tushar Kant

    2015-11-01

    The increase in antibiotic resistance has become a major health concern in recent times. It is therefore essential to identify novel antibacterial targets as well as discover and develop new antibacterial agents. FtsZ, a highly conserved bacterial protein, is responsible for the initiation of cell division in bacteria. The functions of FtsZ inside cells are tightly regulated and any perturbation in its functions leads to inhibition of bacterial division. Recent reports indicate that small molecules targeting the functions of FtsZ may be used as leads to develop new antibacterial agents. To identify small molecules targeting FtsZ and inhibiting bacterial division, we screened a U.S. FDA (Food and Drug Administration)-approved drug library of 800 molecules using an independent computational, biochemical and microbial approach. From this screen, we identified doxorubicin, an anthracycline molecule that inhibits Escherichia coli division and forms filamentous cells. A fluorescence-binding assay shows that doxorubicin interacts strongly with FtsZ. A detailed biochemical analysis demonstrated that doxorubicin inhibits FtsZ assembly and its GTPase activity through binding to a site other than the GTP-binding site. Furthermore, using molecular docking, we identified a probable doxorubicin-binding site in FtsZ. A number of single amino acid mutations at the identified binding site in FtsZ resulted in a severalfold decrease in the affinity of FtsZ for doxorubicin, indicating the importance of this site for doxorubicin interaction. The present study suggests the presence of a novel binding site in FtsZ that interacts with the small molecules and can be targeted for the screening and development of new antibacterial agents. PMID:26285656

  18. DARC 2.0: Improved Docking and Virtual Screening at Protein Interaction Sites

    PubMed Central

    Gowthaman, Ragul; Lyskov, Sergey; Karanicolas, John

    2015-01-01

    Over the past decade, protein-protein interactions have emerged as attractive but challenging targets for therapeutic intervention using small molecules. Due to the relatively flat surfaces that typify protein interaction sites, modern virtual screening tools developed for optimal performance against “traditional” protein targets perform less well when applied instead at protein interaction sites. Previously, we described a docking method specifically catered to the shallow binding modes characteristic of small-molecule inhibitors of protein interaction sites. This method, called DARC (Docking Approach using Ray Casting), operates by comparing the topography of the protein surface when “viewed” from a vantage point inside the protein against the topography of a bound ligand when “viewed” from the same vantage point. Here, we present five key enhancements to DARC. First, we use multiple vantage points to more accurately determine protein-ligand surface complementarity. Second, we describe a new scheme for rapidly determining optimal weights in the DARC scoring function. Third, we incorporate sampling of ligand conformers “on-the-fly” during docking. Fourth, we move beyond simple shape complementarity and introduce a term in the scoring function to capture electrostatic complementarity. Finally, we adjust the control flow in our GPU implementation of DARC to achieve greater speedup of these calculations. At each step of this study, we evaluate the performance of DARC in a “pose recapitulation” experiment: predicting the binding mode of 25 inhibitors each solved in complex with its distinct target protein (a protein interaction site). Whereas the previous version of DARC docked only one of these inhibitors to within 2 Ĺ RMSD of its position in the crystal structure, the newer version achieves this level of accuracy for 12 of the 25 complexes, corresponding to a statistically significant performance improvement (p < 0.001). Collectively then, we find that the five enhancements described here – which together make up DARC 2.0 – lead to dramatically improved speed and performance relative to the original DARC method. PMID:26181386

  19. Interactive segmentation of tongue contours in ultrasound video sequences using quality maps

    NASA Astrophysics Data System (ADS)

    Ghrenassia, Sarah; Ménard, Lucie; Laporte, Catherine

    2014-03-01

    Ultrasound (US) imaging is an effective and non invasive way of studying the tongue motions involved in normal and pathological speech, and the results of US studies are of interest for the development of new strategies in speech therapy. State-of-the-art tongue shape analysis techniques based on US images depend on semi-automated tongue segmentation and tracking techniques. Recent work has mostly focused on improving the accuracy of the tracking techniques themselves. However, occasional errors remain inevitable, regardless of the technique used, and the tongue tracking process must thus be supervised by a speech scientist who will correct these errors manually or semi-automatically. This paper proposes an interactive framework to facilitate this process. In this framework, the user is guided towards potentially problematic portions of the US image sequence by a segmentation quality map that is based on the normalized energy of an active contour model and automatically produced during tracking. When a problematic segmentation is identified, corrections to the segmented contour can be made on one image and propagated both forward and backward in the problematic subsequence, thereby improving the user experience. The interactive tools were tested in combination with two different tracking algorithms. Preliminary results illustrate the potential of the proposed framework, suggesting that the proposed framework generally improves user interaction time, with little change in segmentation repeatability.

  20. Mapping Features of HIV-1 Integrase Near Selected Sites on Viral and Target DNA Molecules in an Active Enzyme-DNA Complex by Photo-Cross-Linking

    E-print Network

    Mapping Features of HIV-1 Integrase Near Selected Sites on Viral and Target DNA Molecules-cross-linking approach to address these issues. Our findings suggest that HIV-1 integrase contacts with conserved

  1. Theoretical investigation on nevirapine and HIV-1 reverse transcriptase binding site interaction, based on ONIOM method

    NASA Astrophysics Data System (ADS)

    Kuno, Mayuso; Hannongbua, Supa; Morokuma, Keiji

    2003-10-01

    The ONIOM method was applied to the interaction of nevirapine with the HIV-1 reverse transcriptase binding site. The isolated complex of pyridine (part of nevirapine) and methyl phenol (part of Tyr181) was found at the MP2/6-31+G(d) level to have stacking interaction with 8.8 kcal/mol binding energy. Optimization of nevirapine and Tyr181 geometry in the pocket of 16 amino acid residues at the ONIOM3(MP2/6-31G(d):HF/3-21G:PM3) level gave the complex structure with weak hydrogen bonding but without stacking interaction. The binding energy of 8.9 kcal/mol comes almost entirely from the interaction of nevirapine with amino acid residues other than Tyr181.

  2. POLYSITE - An interactive package for the selection and refinement of Landsat image training sites

    NASA Technical Reports Server (NTRS)

    Mack, Marilyn J. P.

    1986-01-01

    A versatile multifunction package, POLYSITE, developed for Goddard's Land Analysis System, is described which simplifies the process of interactively selecting and correcting the sites used to study Landsat TM and MSS images. Image switching between the zoomed and nonzoomed image, color and shape cursor change and location display, and bit plane erase or color change, are global functions which are active at all times. Local functions possibly include manipulation of intensive study areas, new site definition, mensuration, and new image copying. The program is illustrated with the example of a full TM maser scene of metropolitan Washington, DC.

  3. Genetic Interaction Mapping Reveals a Role for the SWI/SNF Nucleosome Remodeler in Spliceosome Activation in Fission Yeast

    PubMed Central

    Patrick, Kristin L.; Ryan, Colm J.; Xu, Jiewei; Lipp, Jesse J.; Nissen, Kelly E.; Roguev, Assen; Shales, Michael; Krogan, Nevan J.; Guthrie, Christine

    2015-01-01

    Although numerous regulatory connections between pre-mRNA splicing and chromatin have been demonstrated, the precise mechanisms by which chromatin factors influence spliceosome assembly and/or catalysis remain unclear. To probe the genetic network of pre-mRNA splicing in the fission yeast Schizosaccharomyces pombe, we constructed an epistatic mini-array profile (E-MAP) and discovered many new connections between chromatin and splicing. Notably, the nucleosome remodeler SWI/SNF had strong genetic interactions with components of the U2 snRNP SF3 complex. Overexpression of SF3 components in ?SWI/SNF cells led to inefficient splicing of many fission yeast introns, predominantly those with non-consensus splice sites. Deletion of SWI/SNF decreased recruitment of the splicing ATPase Prp2, suggesting that SWI/SNF promotes co-transcriptional spliceosome assembly prior to first step catalysis. Importantly, defects in SWI/SNF as well as SF3 overexpression each altered nucleosome occupancy along intron-containing genes, illustrating that the chromatin landscape both affects—and is affected by—co-transcriptional splicing. PMID:25825871

  4. Genetic interaction mapping reveals a role for the SWI/SNF nucleosome remodeler in spliceosome activation in fission yeast.

    PubMed

    Patrick, Kristin L; Ryan, Colm J; Xu, Jiewei; Lipp, Jesse J; Nissen, Kelly E; Roguev, Assen; Shales, Michael; Krogan, Nevan J; Guthrie, Christine

    2015-03-01

    Although numerous regulatory connections between pre-mRNA splicing and chromatin have been demonstrated, the precise mechanisms by which chromatin factors influence spliceosome assembly and/or catalysis remain unclear. To probe the genetic network of pre-mRNA splicing in the fission yeast Schizosaccharomyces pombe, we constructed an epistatic mini-array profile (E-MAP) and discovered many new connections between chromatin and splicing. Notably, the nucleosome remodeler SWI/SNF had strong genetic interactions with components of the U2 snRNP SF3 complex. Overexpression of SF3 components in ?SWI/SNF cells led to inefficient splicing of many fission yeast introns, predominantly those with non-consensus splice sites. Deletion of SWI/SNF decreased recruitment of the splicing ATPase Prp2, suggesting that SWI/SNF promotes co-transcriptional spliceosome assembly prior to first step catalysis. Importantly, defects in SWI/SNF as well as SF3 overexpression each altered nucleosome occupancy along intron-containing genes, illustrating that the chromatin landscape both affects--and is affected by--co-transcriptional splicing. PMID:25825871

  5. [Cloning-idependent mapping technology for genomic fidelity, contig linking, C-DNA site analysis, and gene detection]. Final report

    SciTech Connect

    Lerman, L.S.

    1994-12-25

    The project was designed to develop and apply a novel unconventional approach to genome mapping based on physical properties of DNA that are a sensitive function of the base sequence, and so does not depend on the clonability of the sequences to be mapped nor on the presence of particular restriction sites. We have shown that a broad array of DNA fragments are retarded at nearly the same level in denaturing gradient gel electrophoresis (DGGE) if the segment with the lowest thermal stability has the same melting temperature, regardless of the length of the fragment. The retarded pattern remain steady in the gel, changing little with continued field exposure. Mapping proceeds by the analysis of two-dimensional patterns produced by random fragmentation of genomic DNA and denaturing gradient gel electrophoresis. Random fragments are first separated according to length by conventional agarose electrophoresis. The result is a two- dimensional pattern which can be idealized as an array of nearly parallel, mostly separated lines of DNA. The pattern is blotted onto a membrane and probed sequentially with oligos or relevant DNA or RNA fragments. The endpoints on the fragment length scale of each line hybridizing with each probe, the distribution along each line, and the depth in the gradient constitute specific map information.

  6. Systematic discovery of linear binding motifs targeting an ancient protein interaction surface on MAP kinases.

    PubMed

    Zeke, András; Bastys, Tomas; Alexa, Anita; Garai, Ágnes; Mészáros, Bálint; Kirsch, Klára; Dosztányi, Zsuzsanna; Kalinina, Olga V; Reményi, Attila

    2015-01-01

    Mitogen-activated protein kinases (MAPK) are broadly used regulators of cellular signaling. However, how these enzymes can be involved in such a broad spectrum of physiological functions is not understood. Systematic discovery of MAPK networks both experimentally and in silico has been hindered because MAPKs bind to other proteins with low affinity and mostly in less-characterized disordered regions. We used a structurally consistent model on kinase-docking motif interactions to facilitate the discovery of short functional sites in the structurally flexible and functionally under-explored part of the human proteome and applied experimental tools specifically tailored to detect low-affinity protein-protein interactions for their validation in vitro and in cell-based assays. The combined computational and experimental approach enabled the identification of many novel MAPK-docking motifs that were elusive for other large-scale protein-protein interaction screens. The analysis produced an extensive list of independently evolved linear binding motifs from a functionally diverse set of proteins. These all target, with characteristic binding specificity, an ancient protein interaction surface on evolutionarily related but physiologically clearly distinct three MAPKs (JNK, ERK, and p38). This inventory of human protein kinase binding sites was compared with that of other organisms to examine how kinase-mediated partnerships evolved over time. The analysis suggests that most human MAPK-binding motifs are surprisingly new evolutionarily inventions and newly found links highlight (previously hidden) roles of MAPKs. We propose that short MAPK-binding stretches are created in disordered protein segments through a variety of ways and they represent a major resource for ancient signaling enzymes to acquire new regulatory roles. PMID:26538579

  7. Systematic discovery of linear binding motifs targeting an ancient protein interaction surface on MAP kinases

    PubMed Central

    Zeke, András; Bastys, Tomas; Alexa, Anita; Garai, Ágnes; Mészáros, Bálint; Kirsch, Klára; Dosztányi, Zsuzsanna; Kalinina, Olga V; Reményi, Attila

    2015-01-01

    Mitogen-activated protein kinases (MAPK) are broadly used regulators of cellular signaling. However, how these enzymes can be involved in such a broad spectrum of physiological functions is not understood. Systematic discovery of MAPK networks both experimentally and in silico has been hindered because MAPKs bind to other proteins with low affinity and mostly in less-characterized disordered regions. We used a structurally consistent model on kinase-docking motif interactions to facilitate the discovery of short functional sites in the structurally flexible and functionally under-explored part of the human proteome and applied experimental tools specifically tailored to detect low-affinity protein–protein interactions for their validation in vitro and in cell-based assays. The combined computational and experimental approach enabled the identification of many novel MAPK-docking motifs that were elusive for other large-scale protein–protein interaction screens. The analysis produced an extensive list of independently evolved linear binding motifs from a functionally diverse set of proteins. These all target, with characteristic binding specificity, an ancient protein interaction surface on evolutionarily related but physiologically clearly distinct three MAPKs (JNK, ERK, and p38). This inventory of human protein kinase binding sites was compared with that of other organisms to examine how kinase-mediated partnerships evolved over time. The analysis suggests that most human MAPK-binding motifs are surprisingly new evolutionarily inventions and newly found links highlight (previously hidden) roles of MAPKs. We propose that short MAPK-binding stretches are created in disordered protein segments through a variety of ways and they represent a major resource for ancient signaling enzymes to acquire new regulatory roles. PMID:26538579

  8. 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.

  9. Thermodynamic mapping of the inhibitor site of the aspartic protease endothiapepsin.

    PubMed

    Gómez, J; Freire, E

    1995-09-22

    The discovery that the protease from the human immunodeficiency virus (HIV) belongs to the aspartic protease family has generated renewed interest in this class of proteins. In this paper, the interactions of endothiapepsin, an aspartic proteinase from the fungus Endothia parasitica, with the inhibitor pepstatin A have been studied by high-sensitivity calorimetric techniques. These experiments have permitted a complete characterization of the temperature and pH-dependence of the binding energetics. The binding reaction is characterized by negative intrinsic binding enthalpy and negative heat capacity changes. The association constant is maximal at low pH (2 x 10(9) M-1 at pH 3) but decreases upon increasing pH (8.1 x 10(6) M-1 at pH 7). The binding of the inhibitor is coupled to the protonation of one of the aspartic moieties in the Asp dyad of the catalytic site of the protein. This phenomenon is responsible for the decrease in the apparent affinity of the inhibitor for the enzyme upon increasing pH. The experimental results presented here indicate that the binding of the inhibitor is favored both enthalpically and entropically. While the favorable enthalpic contribution is intuitively expected, the favorable entropic contribution is due to the large gain in solvent-related entropy associated with the burial of a large hydrophobic surface, that overcompensates the loss in conformational and translational/rotational degrees of freedom upon complex formation. The characteristics of the molecular recognition process have been evaluated by means of structure-based thermodynamic analysis. Three regions in the protein contribute significantly to the free energy of binding: the residues surrounding the Asp dyad (Asp32 in the N-terminal lobe and Asp215 in the C-terminal domain) and the flap region (Ile73 to Asp77). In addition, the rearrangement of residues that are not in immediate contact with the inhibitor provides close to 40% of the protease contribution to the binding free energy. On the other hand, the two statine residues provide more than half of the inhibitor contributions to the total free energy of binding. It is demonstrated that a previously developed empirical structural parametrization of the thermodynamic parameters that define the Gibbs energy, accurately accounts for the binding energetics and its temperature and pH-dependence. PMID:7563055

  10. 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.

  11. BrainMaps.org - Interactive High-Resolution Digital Brain Atlases and Virtual Microscopy.

    PubMed

    Mikula, Shawn; Stone, James M; Jones, Edward G

    2008-01-01

    BrainMaps.org is an interactive high-resolution digital brain atlas and virtual microscope that is based on over 20 million megapixels of scanned images of serial sections of both primate and non-primate brains and that is integrated with a high-speed database for querying and retrieving data about brain structure and function over the internet. Complete brain datasets for various species, including Homo sapiens, Macaca mulatta, Chlorocebus aethiops, Felis catus, Mus musculus, Rattus norvegicus, and Tyto alba, are accessible online. The methods and tools we describe are useful for both research and teaching, and can be replicated by labs seeking to increase accessibility and sharing of neuroanatomical data. These tools offer the possibility of visualizing and exploring completely digitized sections of brains at a sub-neuronal level, and can facilitate large-scale connectional tracing, histochemical and stereological analyses. PMID:19129928

  12. An interactive Barnes objective map analysis scheme for use with satellite and conventional data

    NASA Technical Reports Server (NTRS)

    Koch, S. E.; Desjardins, M.; Kocin, P. J.

    1983-01-01

    The Barnes (1973) objective map analysis scheme is employed to develop an interactive analysis package for assessing the impact of satellite-derived data on analyses of conventional meteorological data sets. The method permits modification of the values of input parameters in the objective analysis within objectively determined, internally set limits. The effects of the manipulations are rapidly displayed, and methods are included for assimilating the spatially clustered characteristics of satellite data and the various horizontal resolutions of the data types. Data sets from the SESAME rawinsonde wind data with uniform spatial distribution, with the same data set plus satellite cloud motion data, and a data set from the atmospheric sounder radiometer on the GOES satellite were analyzed as examples. The scheme is demonstrated to recover details after two iterations through the data.

  13. An interactive program for computer-aided map design, display, and query: EMAPKGS2

    USGS Publications Warehouse

    Pouch, G.W.

    1997-01-01

    EMAPKGS2 is a user-friendly, PC-based electronic mapping tool for use in hydrogeologic exploration and appraisal. EMAPKGS2 allows the analyst to construct maps interactively from data stored in a relational database, perform point-oriented spatial queries such as locating all wells within a specified radius, perform geographic overlays, and export the data to other programs for further analysis. EMAPKGS2 runs under Microsoft?? Windows??? 3.1 and compatible operating systems. EMAPKGS2 is a public domain program available from the Kansas Geological Survey. EMAPKGS2 is the centerpiece of WHEAT, the Windows-based Hydrogeologic Exploration and Appraisal Toolkit, a suite of user-friendly Microsoft?? Windows??? programs for natural resource exploration and management. The principal goals in development of WHEAT have been ease of use, hardware independence, low cost, and end-user extensibility. WHEAT'S native data format is a Microsoft?? Access?? database. WHEAT stores a feature's geographic coordinates as attributes so they can be accessed easily by the user. The WHEAT programs are designed to be used in conjunction with other Microsoft?? Windows??? software to allow the natural resource scientist to perform work easily and effectively. WHEAT and EMAPKGS have been used at several of Kansas' Groundwater Management Districts and the Kansas Geological Survey on groundwater management operations, groundwater modeling projects, and geologic exploration projects. ?? 1997 Elsevier Science Ltd.

  14. Analysis of genotype × environment interactions for polyphenols and antioxidant capacity of rice by association mapping.

    PubMed

    Shao, Yafang; Tang, Fufu; Huang, Yan; Xu, Feifei; Chen, Yaling; Tong, Chuan; Chen, Hao; Bao, Jinsong

    2014-06-11

    Uncovering the genetic basis of polyphenol content and antioxidant activity traits in rice accessions is important to improve the nutritional quality of whole grain rice and to ameliorate the increasing nutrition problem of the rice-eating population. In this study, 20 diverse rice accessions were planted in Hainan province, China, for 2 years to investigate the effects of genotype, environment, and their interactions on total phenolic (TPC), flavonoid (TFC), proanthocyanidins content (TPAC), ABTS, and DPPH radical scavenging activity by association mapping. Analyses of variance (ANOVA) showed that TPC, TFC, TPAC, ABTS, and DPPH were mainly affected by genetic variance, accounting for >94% of the total variance. The interaction between genotype × environment (G × E) was also highly significant (P < 0.001). Red-pericarp rice accumulates proanthocyanidins, which had significantly higher TPC, TFC, ABTS, and DPPH than white-pericarp rice. The correlation coefficient among these parameters were highly significant (r > 0.96; P < 0.001). Twenty-three putative unique loci were identified by association mapping. Five loci were close to previously identified genes or quantitative trait loci (QTLs). Among them, qPAC7-3 identified for TPAC in 2011 was near to the brown pericarp and seed coat (Rc) gene, and the locus at the qPC4/qFC4/qPAC4/qACA4/qACD4 cluster on chromosome 4 detected in two environments was near to a transcriptional activator A (Ra) gene. Some loci were identified in only one environment, indicating that these QTLs were sensitive to environment. This study provides a primary SNP-resource for further identification of genes responsible for polyhenol contents and antioxidant activity in rice whole grains. PMID:24833475

  15. Interacted QTL Mapping in Partial NCII Design Provides Evidences for Breeding by Design

    PubMed Central

    Yi, Can; Wen, Jia; Jinxing, Tu; Zhang, Yuan Ming

    2015-01-01

    The utilization of heterosis in rice, maize and rapeseed has revolutionized crop production. Although elite hybrid cultivars are mainly derived from the F1 crosses between two groups of parents, named NCII mating design, little has been known about the methodology of how interacted effects influence quantitative trait performance in the population. To bridge genetic analysis with hybrid breeding, here we integrated an interacted QTL mapping approach with breeding by design in partial NCII mating design. All the potential main and interacted effects were included in one full model. If the number of the effects is huge, bulked segregant analysis were used to test which effects were associated with the trait. All the selected effects were further shrunk by empirical Bayesian, so significant effects could be identified. A series of Monte Carlo simulations was performed to validate the new method. Furthermore, all the significant effects were used to calculate genotypic values of all the missing F1 hybrids, and all these F1 phenotypic or genotypic values were used to predict elite parents and parental combinations. Finally, the new method was adopted to dissect the genetic foundation of oil content in 441 rapeseed parents and 284 F1 hybrids. As a result, 8 main-effect QTL and 37 interacted QTL were found and used to predict 10 elite restorer lines, 10 elite sterile lines and 10 elite parental crosses. Similar results across various methods and in previous studies and a high correlation coefficient (0.76) between the predicted and observed phenotypes validated the proposed method in this study. PMID:25822501

  16. Mapping of glycolytic enzyme-binding sites on human erythrocyte band 3

    PubMed Central

    Chu, Haiyan; Low, Philip S.

    2006-01-01

    Previous work has shown that GAPDH (glyceraldehyde-3-phosphate dehydrogenase), aldolase, PFK (phosphofructokinase), PK (pyruvate kinase) and LDH (lactate dehydrogenase) assemble into a GE (glycolytic enzyme) complex on the inner surface of the human erythrocyte membrane. In an effort to define the molecular architecture of this complex, we have undertaken to localize the binding sites of these enzymes more accurately. We report that: (i) a major aldolase-binding site on the erythrocyte membrane is located within N-terminal residues 1–23 of band 3 and that both consensus sequences D6DYED10 and E19EYED23 are necessary to form a single enzyme-binding site; (ii) GAPDH has two tandem binding sites on band 3, located in residues 1–11 and residues 12–23 respectively; (iii) a PFK-binding site resides between residues 12 and 23 of band 3; (iv) no GEs bind to the third consensus sequence (residues D902EYDE906) at the C-terminus of band 3; and (v) the LDH- and PK-binding sites on the erythrocyte membrane do not reside on band 3. Taken together, these results argue that band 3 provides a nucleation site for the GE complex on the human erythrocyte membrane and that other components near band 3 must also participate in organizing the enzyme complex. PMID:16836485

  17. Mapping precursor-binding site on TatC subunit of twin arginine-specific protein translocase by site-specific photo cross-linking.

    PubMed

    Zoufaly, Stefan; Fröbel, Julia; Rose, Patrick; Flecken, Tobias; Maurer, Carlo; Moser, Michael; Müller, Matthias

    2012-04-13

    A number of secreted precursor proteins of bacteria, archaea, and plant chloroplasts stand out by a conserved twin arginine-containing sequence motif in their signal peptides. Many of these precursor proteins are secreted in a completely folded conformation by specific twin arginine translocation (Tat) machineries. Tat machineries are high molecular mass complexes consisting of two types of membrane proteins, a hexahelical TatC protein, and usually one or two single-spanning membrane proteins, called TatA and TatB. TatC has previously been shown to be involved in the recognition of twin arginine signal peptides. We have performed an extensive site-specific cross-linking analysis of the Escherichia coli TatC protein under resting and translocating conditions. This strategy allowed us to map the recognition site for twin arginine signal peptides to the cytosolic N-terminal region and first cytosolic loop of TatC. In addition, discrete contact sites between TatC, TatB, and TatA were revealed. We discuss a tentative model of how a twin arginine signal sequence might be accommodated in the Tat translocase. PMID:22362773

  18. Functional genomics platform for pooled screening and generation of mammalian genetic interaction maps | Office of Cancer Genomics

    Cancer.gov

    Systematic genetic interaction maps in microorganisms are powerful tools for identifying functional relationships between genes and for defining the function of uncharacterized genes. We have recently implemented this strategy in mammalian cells as a two-stage approach. First, genes of interest are robustly identified in a pooled genome-wide screen using complex shRNA libraries. Second, phenotypes for all pairwise combinations of 'hit' genes are measured in a double-shRNA screen and used to construct a genetic interaction map.

  19. 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...

  20. 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...

  1. 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...

  2. 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...

  3. 24 CFR 3285.103 - Site suitability with design zone maps.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... § 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...

  4. A New Tool to Quantify Receptor Recruitment to Cell Contact Sites during Host-Pathogen Interaction

    PubMed Central

    Wester, Michael J.; Davidson, Lisa B.; Steinberg, Stanly L.; Neumann, Aaron K.

    2014-01-01

    To understand the process of innate immune fungal recognition, we developed computational tools for the rigorous quantification and comparison of receptor recruitment and distribution at cell-cell contact sites. We used these tools to quantify pattern recognition receptor spatiotemporal distributions in contacts between primary human dendritic cells and the fungal pathogens C. albicans, C. parapsilosis and the environmental yeast S. cerevisiae, imaged using 3D multichannel laser scanning confocal microscopy. The detailed quantitative analysis of contact sites shows that, despite considerable biochemical similarity in the composition and structure of these species' cell walls, the receptor spatiotemporal distribution in host-microbe contact sites varies significantly between these yeasts. Our findings suggest a model where innate immune cells discriminate fungal microorganisms based on differential mobilization and coordination of receptor networks. Our analysis methods are also broadly applicable to a range of cell-cell interactions central to many biological problems. PMID:24874253

  5. Calculating the habitable zones of multiple star systems with a new interactive Web site

    SciTech Connect

    Müller, Tobias W. A.; Haghighipour, Nader

    2014-02-10

    We have developed a comprehensive methodology and an interactive Web site for calculating the habitable zone (HZ) of multiple star systems. Using the concept of spectral weight factor, as introduced in our previous studies of the calculations of HZ in and around binary star systems, we calculate the contribution of each star (based on its spectral energy distribution) to the total flux received at the top of the atmosphere of an Earth-like planet, and use the models of the HZ of the Sun to determine the boundaries of the HZ in multiple star systems. Our interactive Web site for carrying out these calculations is publicly available at http://astro.twam.info/hz. We discuss the details of our methodology and present its application to some of the multiple star systems detected by the Kepler space telescope. We also present the instructions for using our interactive Web site, and demonstrate its capabilities by calculating the HZ for two interesting analytical solutions of the three-body problem.

  6. Identification and Characterization of the Interaction Site between cFLIPL and Calmodulin

    PubMed Central

    Guo, Bingqian; Pellegrini, Maria; Mierke, Dale F.

    2015-01-01

    Overexpression of the cellular FLICE-like inhibitory protein (cFLIP) has been reported in a number of tumor types. As an inactive procaspase-8 homologue, cFLIP is recruited to the intracellular assembly known as the Death Inducing Signaling Complex (DISC) where it inhibits apoptosis, leading to cancer cell proliferation. Here we characterize the molecular details of the interaction between cFLIPL and calmodulin, a ubiquitous calcium sensing protein. By expressing the individual domains of cFLIPL, we demonstrate that the interaction with calmodulin is mediated by the N-terminal death effector domain (DED1) of cFLIPL. Additionally, we mapped the interaction to a specific region of the C-terminus of DED1, referred to as DED1 R4. By designing DED1/DED2 chimeric constructs in which the homologous R4 regions of the two domains were swapped, calmodulin binding properties were transferred to DED2 and removed from DED1. Furthermore, we show that the isolated DED1 R4 peptide binds to calmodulin and solve the structure of the peptide-protein complex using NMR and computational refinement. Finally, we demonstrate an interaction between cFLIPL and calmodulin in cancer cell lysates. In summary, our data implicate calmodulin as a potential player in DISC-mediated apoptosis and provide evidence for a specific interaction with the DED1 of cFLIPL. PMID:26529318

  7. The Methodology of Interactive Parametric Modelling of Construction Site Facilities in BIM Environment

    NASA Astrophysics Data System (ADS)

    Kozlovská, Mária; ?abala, Jozef; Struková, Zuzana

    2014-11-01

    Information technology is becoming a strong tool in different industries, including construction. The recent trend of buildings designing is leading up to creation of the most comprehensive virtual building model (Building Information Model) in order to solve all the problems relating to the project as early as in the designing phase. Building information modelling is a new way of approaching to the design of building projects documentation. Currently, the building site layout as a part of the building design documents has a very little support in the BIM environment. Recently, the research of designing the construction process conditions has centred on improvement of general practice in planning and on new approaches to construction site layout planning. The state of art in field of designing the construction process conditions indicated an unexplored problem related to connection of knowledge system with construction site facilities (CSF) layout through interactive modelling. The goal of the paper is to present the methodology for execution of 3D construction site facility allocation model (3D CSF-IAM), based on principles of parametric and interactive modelling.

  8. Effect of Surface Site Interactions on Potentiometric Titration of Hematite (?-Fe2O3) Crystal Faces

    SciTech Connect

    Chatman, Shawn ME; Zarzycki, Piotr P.; Preocanin, Tajana; Rosso, Kevin M.

    2013-02-01

    Time dependent potentiometric pH titrations were used to study the effect of atomic scale surface structure on the protonation behavior of the structurally well defined hematite/aqueous electrolyte interfaces. Our recently proposed thermodynamic model [1,23] was applied to measured acidimetric and alkalimetric titration hysteresis loops, collected from highly organized (001), (012), and (113) crystal face terminations using pH equilibration times ranging from 15 to 30 mins. Hysteresis loop areas indicate that (001) faces equilibrate faster than the (012) and (113) faces, consistent with the different expected ensembles of singly, doubly, and triply coordinated surface sites on each face. Strongly non-linear hysteretic pH-potential relationships were found, with slopes exceeding Nernstian, collectively indicating that protonation and deprotonation is much more complex than embodied in present day surface complexation models. The asymmetrical shape of the acidimetric and alkalimetric titration branches were used to illustrate a proposed steric "leaky screen" repulsion/trapping interaction mechanism that stems from high affinity singly-coordinated sites electrostatically and sterically screening lower affinity doubly and triply coordinated sites. Our data indicate that site interaction is the dominant phenomenon defining surface potential accumulation behavior on single crystal faces of metal oxide minerals.

  9. Multivariate PLS Modeling of Apicomplexan FabD-Ligand Interaction Space for Mapping Target-Specific Chemical Space and Pharmacophore Fingerprints

    PubMed Central

    Surolia, Avadhesha

    2015-01-01

    Biomolecular recognition underlying drug-target interactions is determined by both binding affinity and specificity. Whilst, quantification of binding efficacy is possible, determining specificity remains a challenge, as it requires affinity data for multiple targets with the same ligand dataset. Thus, understanding the interaction space by mapping the target space to model its complementary chemical space through computational techniques are desirable. In this study, active site architecture of FabD drug target in two apicomplexan parasites viz. Plasmodium falciparum (PfFabD) and Toxoplasma gondii (TgFabD) is explored, followed by consensus docking calculations and identification of fifteen best hit compounds, most of which are found to be derivatives of natural products. Subsequently, machine learning techniques were applied on molecular descriptors of six FabD homologs and sixty ligands to induce distinct multivariate partial-least square models. The biological space of FabD mapped by the various chemical entities explain their interaction space in general. It also highlights the selective variations in FabD of apicomplexan parasites with that of the host. Furthermore, chemometric models revealed the principal chemical scaffolds in PfFabD and TgFabD as pyrrolidines and imidazoles, respectively, which render target specificity and improve binding affinity in combination with other functional descriptors conducive for the design and optimization of the leads. PMID:26535573

  10. Mapping the interactions of the single-stranded DNA binding protein of bacteriophage T4 (gp32) with DNA lattices at single nucleotide resolution: gp32 monomer binding

    PubMed Central

    Jose, Davis; Weitzel, Steven E.; Baase, Walter A.; von Hippel, Peter H.

    2015-01-01

    Combining biophysical measurements on T4 bacteriophage replication complexes with detailed structural information can illuminate the molecular mechanisms of these ‘macromolecular machines’. Here we use the low energy circular dichroism (CD) and fluorescent properties of site-specifically introduced base analogues to map and quantify the equilibrium binding interactions of short (8 nts) ssDNA oligomers with gp32 monomers at single nucleotide resolution. We show that single gp32 molecules interact most directly and specifically near the 3?-end of these ssDNA oligomers, thus defining the polarity of gp32 binding with respect to the ssDNA lattice, and that only 2–3 nts are directly involved in this tight binding interaction. The loss of exciton coupling in the CD spectra of dimer 2-AP (2-aminopurine) probes at various positions in the ssDNA constructs, together with increases in fluorescence intensity, suggest that gp32 binding directly extends the sugar-phosphate backbone of this ssDNA oligomer, particularly at the 3?-end and facilitates base unstacking along the entire 8-mer lattice. These results provide a model (and ‘DNA map’) for the isolated gp32 binding to ssDNA targets, which serves as the nucleation step for the cooperative binding that occurs at transiently exposed ssDNA sequences within the functioning T4 DNA replication complex. PMID:26275775

  11. Disruption of NAD+ binding site in glyceraldehyde 3-phosphate dehydrogenase affects its intranuclear interactions

    PubMed Central

    Phadke, Manali; Krynetskaia, Natalia; Mishra, Anurag; Barrero, Carlos; Merali, Salim; Gothe, Scott A; Krynetskiy, Evgeny

    2015-01-01

    AIM: To characterize phosphorylation of human glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and mobility of GAPDH in cancer cells treated with chemotherapeutic agents. METHODS: We used proteomics analysis to detect and characterize phosphorylation sites within human GAPDH. Site-specific mutagenesis and alanine scanning was then performed to evaluate functional significance of phosphorylation sites in the GAPDH polypeptide chain. Enzymatic properties of mutated GAPDH variants were assessed using kinetic studies. Intranuclear dynamics parameters (diffusion coefficient and the immobile fraction) were estimated using fluorescence recovery after photobleaching (FRAP) experiments and confocal microscopy. Molecular modeling experiments were performed to estimate the effects of mutations on NAD+ cofactor binding. RESULTS: Using MALDI-TOF analysis, we identified novel phosphorylation sites within the NAD+ binding center of GAPDH at Y94, S98, and T99. Using polyclonal antibody specific to phospho-T99-containing peptide within GAPDH, we demonstrated accumulation of phospho-T99-GAPDH in the nuclear fractions of A549, HCT116, and SW48 cancer cells after cytotoxic stress. We performed site-mutagenesis, and estimated enzymatic properties, intranuclear distribution, and intranuclear mobility of GAPDH mutated variants. Site-mutagenesis at positions S98 and T99 in the NAD+ binding center reduced enzymatic activity of GAPDH due to decreased affinity to NAD+ (Km = 741 ± 257 ?mol/L in T99I vs 57 ± 11.1 µmol/L in wild type GAPDH. Molecular modeling experiments revealed the effect of mutations on NAD+ binding with GAPDH. FRAP (fluorescence recovery after photo bleaching) analysis showed that mutations in NAD+ binding center of GAPDH abrogated its intranuclear interactions. CONCLUSION: Our results suggest an important functional role of phosphorylated amino acids in the NAD+ binding center in GAPDH interactions with its intranuclear partners. PMID:26629320

  12. Process maps for plasma spray: Part 1: Plasma-particle interactions

    SciTech Connect

    GILMORE,DELWYN L.; NEISER JR.,RICHARD A.; WAN,YUEPENG; SAMPATH,SANJAY

    2000-01-26

    This is the first paper of a two part series based on an integrated study carried out at Sandia National Laboratories and the State University of New York at Stony Brook. The aim of the study is to develop a more fundamental understanding of plasma-particle interactions, droplet-substrate interactions, deposit formation dynamics and microstructural development as well as final deposit properties. The purpose is to create models that can be used to link processing to performance. Process maps have been developed for air plasma spray of molybdenum. Experimental work was done to investigate the importance of such spray parameters as gun current, auxiliary gas flow, and powder carrier gas flow. In-flight particle diameters, temperatures, and velocities were measured in various areas of the spray plume. Samples were produced for analysis of microstructures and properties. An empirical model was developed, relating the input parameters to the in-flight particle characteristics. Multi-dimensional numerical simulations of the plasma gas flow field and in-flight particles under different operating conditions were also performed. In addition to the parameters which were experimentally investigated, the effect of particle injection velocity was also considered. The simulation results were found to be in good general agreement with the experimental data.

  13. Mapping Strain-rate Dependent Dislocation-Defect Interactions by Atomistic Simulations

    SciTech Connect

    Fan, Yue; Osetskiy, Yury N; Yip, Sidney; Yildiz-Botterud, Bilge

    2013-01-01

    Probing the mechanisms of defect-defect interactions at strain rates lower than 106 s-1 is an unresolved challenge to date to molecular dynamics (MD) techniques. Here we propose a novel atomistic approach based on transition state theory and the concept of a strain-dependent effective activation barrier that is capable of simulating the kinetics of dislocation-defect interactions at virtually any strain rate, exemplified within 10-7 to 107 s-1. We apply this approach to the problem of an edge dislocation colliding with a cluster of self-interstitial atoms (SIA) under shear deformation. Using an activation-relaxation algorithm (1), we uncover a unique strain-rate dependent trigger mechanism that allows the SIA cluster to be absorbed during the process leading to dislocation climb. Guided by this finding, we determine the activation barrier of the trigger mechanism as a function of shear strain, and use that in a coarse-graining rate equation formulation for constructing a mechanism map in the phase space of strain-rate and temperature. Our predictions of a crossover from a defect recovery at the low strain rate regime to defect absorption behavior in the high strain-rate regime are validated against our own independent, direct MD simulations at 105 to 107 s-1. Implications of the present approach for probing molecular-level mechanisms in strain-rate regimes previously considered inaccessible to atomistic simulations are discussed.

  14. Mapping strain rate dependence of dislocation-defect interactions by atomistic simulations

    PubMed Central

    Fan, Yue; Osetskiy, Yuri N.; Yip, Sidney; Yildiz, Bilge

    2013-01-01

    Probing the mechanisms of defect–defect interactions at strain rates lower than 106 s?1 is an unresolved challenge to date to molecular dynamics (MD) techniques. Here we propose an original atomistic approach based on transition state theory and the concept of a strain-dependent effective activation barrier that is capable of simulating the kinetics of dislocation–defect interactions at virtually any strain rate, exemplified within 10?7 to 107 s?1. We apply this approach to the problem of an edge dislocation colliding with a cluster of self-interstitial atoms (SIAs) under shear deformation. Using an activation–relaxation algorithm [Kushima A, et al. (2009) J Chem Phys 130:224504], we uncover a unique strain-rate–dependent trigger mechanism that allows the SIA cluster to be absorbed during the process, leading to dislocation climb. Guided by this finding, we determine the activation barrier of the trigger mechanism as a function of shear strain, and use that in a coarse-graining rate equation formulation for constructing a mechanism map in the phase space of strain rate and temperature. Our predictions of a crossover from a defect recovery at the low strain-rate regime to defect absorption behavior in the high strain-rate regime are validated against our own independent, direct MD simulations at 105 to 107 s?1. Implications of the present approach for probing molecular-level mechanisms in strain-rate regimes previously considered inaccessible to atomistic simulations are discussed. PMID:24114271

  15. Forest Types in the Lower Suwannee River Floodplain, Florida?-A Report and Interactive Map

    USGS Publications Warehouse

    Darst, M.R.; Light, H.M.; Lewis, L.J.; Sepulveda, A.A.

    2003-01-01

    A map of forest types in the lower Suwannee River floodplain, Florida, was created during a study conducted from 1996 to 2000 by the U.S. Geological Survey in cooperation with the Suwannee River Water Management District. The map is presented with this report on a compact disc with interactive viewing software. The forest map can be used by scientists for ecological studies in the floodplain based on land cover types and by landowners and management personnel making land use decisions. The study area is the 10-year floodplain of the lower Suwannee River from its confluence with the Santa Fe River to the lower limit of forests near the Gulf of Mexico. The floodplain is divided into three reaches: riverine (non-tidal), upper tidal, and lower tidal, due to changes in hydrology, vegetation, and soils with proximity to the coast. The 10-year floodplain covers about 21,170 hectares; nearly 88 percent of this area (18,580 hectares) is mapped as 14 major forest types. Approximately 29 percent (5,319 hectares) of these forests have been altered by agriculture or development. About 75 percent of the area of major forest types (13,994 hectares) is wetland forests and about 25 percent (4,586 hectares) is upland forests. Tidal wetland forests (8,955 hectares) cover a much greater area than riverine wetland forests (5,039 hectares). Oak/pine upland forests are present in the riverine and upper tidal reaches of the floodplain on elevations that are inundated only briefly during the highest floods. High bottomland hardwoods are present on the higher levees, ridges, and flats of the riverine reach where soils are usually sandy. Low bottomland hardwood forests are present in the riverine reach on swamp margins and low levees and flats that are flooded continuously for several weeks or longer every 1 to 3 years. Riverine swamps are present in the lowest and wettest areas of the non-tidal floodplain that are either inundated or saturated most of the time. Upper tidal bottomland hardwood forests are present on sandy soils on high flats and in transitional areas between upland forests and swamps. Upper tidal mixed forests are found on low levees or between swamps and higher forest types. Upper tidal swamps are present at elevations below median monthly high stage and usually have surface soils that are permanently saturated mucks. Lower tidal hammocks are found on higher elevations that do not receive regular tidal inundation but have a high water table and are briefly inundated by storm surges several times a decade. Lower tidal mixed forests include swamps with numerous small hummocks or less common larger hummocks. Lower tidal swamps are found on deep muck soils that are below the elevation of the median daily or monthly high stage. Seven additional land cover types (2,590 hectares) are mapped. Water in the main channel of the lower Suwannee River (1,767 hectares) was mapped separately from open water in the floodplain (239 hectares). Other land cover types are: seepage slopes (70 hectares), isolated forested wetlands (19 hectares), marshes upstream of the tree line (505 hectares), beds of emergent aquatic vegetation (21 hectares), and floodplain glades (46 hectares)

  16. Deconstructing the DGAT1 Enzyme: Membrane Interactions at Substrate Binding Sites

    PubMed Central

    Lopes, Jose L. S.; Beltramini, Leila M.; Wallace, Bonnie A.; Araujo, Ana P. U.

    2015-01-01

    Diacylglycerol acyltransferase 1 (DGAT1) is a key enzyme in the triacylglyceride synthesis pathway. Bovine DGAT1 is an endoplasmic reticulum membrane-bound protein associated with the regulation of fat content in milk and meat. The aim of this study was to evaluate the interaction of DGAT1 peptides corresponding to putative substrate binding sites with different types of model membranes. Whilst these peptides are predicted to be located in an extramembranous loop of the membrane-bound protein, their hydrophobic substrates are membrane-bound molecules. In this study, peptides corresponding to the binding sites of the two substrates involved in the reaction were examined in the presence of model membranes in order to probe potential interactions between them that might influence the subsequent binding of the substrates. Whilst the conformation of one of the peptides changed upon binding several types of micelles regardless of their surface charge, suggesting binding to hydrophobic domains, the other peptide bound strongly to negatively-charged model membranes. This binding was accompanied by a change in conformation, and produced leakage of the liposome-entrapped dye calcein. The different hydrophobic and electrostatic interactions observed suggest the peptides may be involved in the interactions of the enzyme with membrane surfaces, facilitating access of the catalytic histidine to the triacylglycerol substrates. PMID:25719207

  17. 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.

  18. Linking tumor mutations to drug responses via a quantitative chemical-genetic interaction map* | Office of Cancer Genomics

    Cancer.gov

    There is an urgent need in oncology to link molecular aberrations in tumors with therapeutics that can be administered in a personalized fashion. One approach identifies synthetic-lethal genetic interactions or emergent dependencies that cancer cells acquire in the presence of specific mutations. Using engineered isogenic cells, we generated a systematic and quantitative chemical-genetic interaction map that measures the influence of 51 aberrant cancer genes on 90 drug responses.

  19. A Novel Interaction between Pyk2 and MAP4K4 Is Integrated with Glioma Cell Migration

    PubMed Central

    Loftus, Joseph C.; Dhruv, Harshil; Tran, Nhan L.; Riggs, Daniel L.

    2013-01-01

    Glioma cell migration correlates with Pyk2 activity, but the intrinsic mechanism that regulates the activity of Pyk2 is not fully understood. Previous studies have supported a role for the N-terminal FERM domain in the regulation of Pyk2 activity as mutations in the FERM domain inhibit Pyk2 phosphorylation. To search for novel protein-protein interactions mediated by the Pyk2 FERM domain, we utilized a yeast two-hybrid genetic selection to identify the mammalian Ste20 homolog MAP4K4 as a binding partner for the Pyk2 FERM domain. MAP4K4 coimmunoprecipitated with Pyk2 and was a substrate for Pyk2 but did not coimmunoprecipitate with the closely related focal adhesion kinase FAK. Knockdown of MAP4K4 expression inhibited glioma cell migration and effectively blocked Pyk2 stimulation of glioma cell. Increased expression of MAP4K4 stimulated glioma cell migration; however, this stimulation was blocked by knockdown of Pyk2 expression. These data support that the interaction of MAP4K4 and Pyk2 is integrated with glioma cell migration and suggest that inhibition of this interaction may represent a potential therapeutic strategy to limit glioblastoma tumor dispersion. PMID:24163766

  20. NMR mapping of RANTES surfaces interacting with CCR5 using linked extracellular domains

    PubMed Central

    Schnur, Einat; Kessler, Naama; Zherdev, Yuri; Noah, Eran; Scherf, Tali; Ding, Fa-Xiang; Rabinovich, Svetlana; Arshava, Boris; Kurbatska, Victoria; Leonciks, Ainars; Tsimanis, Alexander; Rosen, Osnat; Naider, Fred; Anglister, Jacob

    2013-01-01

    Chemokines constitute a large family of small proteins that regulate leukocyte trafficking to the site of inflammation by binding to specific cell-surface receptors belonging to the GPCR superfamily. The interactions between N-terminal (Nt-) peptides of these GPCRs and chemokines have been studied extensively using NMR spectroscopy. However, due to lower affinities of peptides representing the three extracellular loops (ECLs) of chemokine receptors to their respective chemokine ligands, information concerning these interactions is scarce. To overcome the low affinity of ECL peptides to chemokines, we linked two or three CCR5 extracellular domains by either biosynthesis in Escherichia coli or by chemical synthesis. Using such chimeras, CCR5 binding to RANTES was followed using 1H-15N-HSQC spectra to monitor titration of the chemokine with peptides corresponding to the extracellular surface of the receptor. Nt-CCR5 and ECL2 were found to be the major contributors to CCR5 binding to RANTES, creating a nearly closed ring around this protein by interacting with opposing faces of the chemokine. A RANTES positively charged surface involved in Nt-CCR5 binding resembles the positively charged surface in HIV-1 gp120 formed by the C4 and the base of the V3. The opposing surface on RANTES, composed primarily of ?2-?3 hairpin residues, binds ECL2 and was found to be analogous to a surface in the crown of the gp120 V3. The chemical and biosynthetic approaches for linking GPCR surface regions discussed herein should be widely applicable to investigation of interactions of extracellular segments of chemokine receptors with their respective ligands. PMID:23480650

  1. 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

  2. Fine Mapping of a Major Insect Resistance QTL in Soybean and its Interaction with Minor Resistance QTLs

    E-print Network

    Parrott, Wayne

    Fine Mapping of a Major Insect Resistance QTL in Soybean and its Interaction with Minor Resistance insect resistance genes can be an important component for managing insects in soybean [Glycine max (L the effec- tiveness of a Bacillus thuringiensis (Bt) transgene in soybean. The objectives of this study were

  3. Using Student Interactions to Foster Rule-Diagram Mapping during Problem Solving in an Intelligent Tutoring System

    ERIC Educational Resources Information Center

    Butcher, Kirsten R.; Aleven, Vincent

    2013-01-01

    In many domains, problem solving involves the application of general domain principles to specific problem representations. In 3 classroom studies with an intelligent tutoring system, we examined the impact of (learner-generated) interactions and (tutor-provided) visual cues designed to facilitate rule-diagram mapping (where students connect…

  4. Restriction site polymorphism-based candidate gene mapping for seedling drought tolerance in cowpea [Vigna unguiculata (L.) Walp.].

    PubMed

    Muchero, Wellington; Ehlers, Jeffrey D; Roberts, Philip A

    2010-02-01

    Quantitative trait loci (QTL) studies provide insight into the complexity of drought tolerance mechanisms. Molecular markers used in these studies also allow for marker-assisted selection (MAS) in breeding programs, enabling transfer of genetic factors between breeding lines without complete knowledge of their exact nature. However, potential for recombination between markers and target genes limit the utility of MAS-based strategies. Candidate gene mapping offers an alternative solution to identify trait determinants underlying QTL of interest. Here, we used restriction site polymorphisms to investigate co-location of candidate genes with QTL for seedling drought stress-induced premature senescence identified previously in cowpea. Genomic DNA isolated from 113 F(2:8) RILs of drought-tolerant IT93K503-1 and drought susceptible CB46 genotypes was digested with combinations of EcoR1 and HpaII, Mse1, or Msp1 restriction enzymes and amplified with primers designed from 13 drought-responsive cDNAs. JoinMap 3.0 and MapQTL 4.0 software were used to incorporate polymorphic markers onto the AFLP map and to analyze their association with the drought response QTL. Seven markers co-located with peaks of previously identified QTL. Isolation, sequencing, and blast analysis of these markers confirmed their significant homology with drought or other abiotic stress-induced expressed sequence tags (EST) from cowpea and other plant systems. Further, homology with coding sequences for a multidrug resistance protein 3 and a photosystem I assembly protein ycf3 was revealed in two of these candidates. These results provide a platform for the identification and characterization of genetic trait determinants underlying seedling drought tolerance in cowpea. PMID:19834655

  5. 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 ...

  6. 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. PMID:26466659

  7. Exploring the Binding Site Structure of the PPAR Ligand-Binding Domain by Computational Solvent Mapping

    E-print Network

    Vajda, Sandor

    Exploring the Binding Site Structure of the PPAR Ligand-Binding Domain by Computational Solvent receptor (PPAR) ligand-binding domain (LBD), including 2 structures without a ligand, 2 structures with a partial agonist, and 8 structures with a PPAR agonist bound. The analysis revealed 10 binding "hot spots

  8. The multiscale coarse-graining method. XI. Accurate interactions based on the centers of charge of coarse-grained sites

    NASA Astrophysics Data System (ADS)

    Cao, Zhen; Voth, Gregory A.

    2015-12-01

    It is essential to be able to systematically construct coarse-grained (CG) models that can efficiently and accurately reproduce key properties of higher-resolution models such as all-atom. To fulfill this goal, a mapping operator is needed to transform the higher-resolution configuration to a CG configuration. Certain mapping operators, however, may lose information related to the underlying electrostatic properties. In this paper, a new mapping operator based on the centers of charge of CG sites is proposed to address this issue. Four example systems are chosen to demonstrate this concept. Within the multiscale coarse-graining framework, CG models that use this mapping operator are found to better reproduce the structural correlations of atomistic models. The present work also demonstrates the flexibility of the mapping operator and the robustness of the force matching method. For instance, important functional groups can be isolated and emphasized in the CG model.

  9. Road-map to plan and structure the preliminary site investigation program for a geological repository in Japan

    SciTech Connect

    Deguchi, Akira; Tsuchi, Hiroyuki; Kitayama, Kazumi; Chapman, Neil; Andersson, Johan; Tanaka, Tatsuya

    2007-07-01

    Available in abstract form only. Full text of publication follows: A stepwise site selection process has been adopted for geological disposal of HLW in Japan. Literature surveys (LS), followed by preliminary investigations (PI) and, finally, detailed investigations (DI) in underground facilities will be carried out in the successive selection stages. In the PI stage, surface-based investigations such as borehole surveys and geophysical prospecting will be implemented with two main objectives. The first is to obtain information relating to legal requirements on siting, such as the occurrence of igneous or fault activity, and to confirm the extremely low likelihood of adverse impacts on the candidate site resulting from such phenomena. The second is to obtain the information required for the design and performance assessment of the engineered barrier system and the repository. In order to implement these preliminary investigations rigorously and efficiently within the constraints of a limited time period, budget and resources, PI planning before commencing investigations and on-site PI management during the investigation phase are very important issues. The planning and management of PI have to be performed by NUMO staff, but not all staff have sufficient experience in the range of disciplines involved. NUMO therefore decided to compile existing knowledge and experience in the planning and management of investigations in the form of manuals to be used to improve and maintain internal expertise. Experts with experience in overseas investigation programs were requested to prepare these manuals. This paper outlines the structure and scope of the upper level manual (road-map) and discusses NUMO's experience in applying it in 'dry-runs' to model sites. (authors)

  10. Study of Cytochrome c-DNA Interaction - Evaluation of Binding Sites on the Redox Protein

    NASA Astrophysics Data System (ADS)

    Wettstein, Christoph; Kyne, Ciara; M. Doolan, Aishling; Möhwald, Helmuth; Crowley, Peter B.; Lisdat, Fred

    2014-10-01

    Artificial assemblies consisting of the cationic cytochrome c (cyt c) and double-stranded DNA are interesting for the field of biohybrid systems because of the high electro-activity of the incorporated redox protein. However, little is known about the interactions between these two biomolecules. Here, the complex of reduced cyt c and a 41 base pair oligonucleotide was characterized in solution as a function of pH and ionic strength. Persistent cyt c-DNA agglomerates were observed by UV-vis and DLS (dynamic light scattering) at pH 5.0 and low ionic strength. The strength of the interaction was attenuated by raising the pH or the ionic strength. At pH 7.0 agglomerates were not formed, allowing interaction analysis by NMR spectroscopy. Using TROSY (transverse relaxation-optimized spectroscopy)-HSQC (heteronuclear single quantum coherence) experiments it was possible to identify the DNA binding site on the cyt c surface. Numerous residues surrounding the exposed heme edge of cyt c were involved in transient binding to DNA under these conditions. This result was supported by SEC (size exclusion chromatography) experiments at pH 7.0 showing that the interaction is sufficient for co-elution of cyt c and DNA.Artificial assemblies consisting of the cationic cytochrome c (cyt c) and double-stranded DNA are interesting for the field of biohybrid systems because of the high electro-activity of the incorporated redox protein. However, little is known about the interactions between these two biomolecules. Here, the complex of reduced cyt c and a 41 base pair oligonucleotide was characterized in solution as a function of pH and ionic strength. Persistent cyt c-DNA agglomerates were observed by UV-vis and DLS (dynamic light scattering) at pH 5.0 and low ionic strength. The strength of the interaction was attenuated by raising the pH or the ionic strength. At pH 7.0 agglomerates were not formed, allowing interaction analysis by NMR spectroscopy. Using TROSY (transverse relaxation-optimized spectroscopy)-HSQC (heteronuclear single quantum coherence) experiments it was possible to identify the DNA binding site on the cyt c surface. Numerous residues surrounding the exposed heme edge of cyt c were involved in transient binding to DNA under these conditions. This result was supported by SEC (size exclusion chromatography) experiments at pH 7.0 showing that the interaction is sufficient for co-elution of cyt c and DNA. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr05301j

  11. Delineating the Tes Interaction Site in Zyxin and Studying Cellular Effects of Its Disruption

    PubMed Central

    Hadzic, Ermin; Catillon, Marie; Halavatyi, Aliaksandr; Medves, Sandrine; Van Troys, Marleen; Moes, Michčle; Baird, Michelle A.; Davidson, Michael W.; Schaffner-Reckinger, Elisabeth; Ampe, Christophe; Friederich, Evelyne

    2015-01-01

    Focal adhesions are integrin-based structures that link the actin cytoskeleton and the extracellular matrix. They play an important role in various cellular functions such as cell signaling, cell motility and cell shape. To ensure and fine tune these different cellular functions, adhesions are regulated by a large number of proteins. The LIM domain protein zyxin localizes to focal adhesions where it participates in the regulation of the actin cytoskeleton. Because of its interactions with a variety of binding partners, zyxin has been proposed to act as a molecular scaffold. Here, we studied the interaction of zyxin with such a partner: Tes. Similar to zyxin, Tes harbors three highly conserved LIM domains of which the LIM1 domain directly interacts with zyxin. Using different zyxin variants in pull-down assays and ectopic recruitment experiments, we identified the Tes binding site in zyxin and showed that four highly conserved amino acids are crucial for its interaction with Tes. Based upon these findings, we used a zyxin mutant defective in Tes-binding to assess the functional consequences of abrogating the zyxin-Tes interaction in focal adhesions. Performing fluorescence recovery after photobleaching, we showed that zyxin recruits Tes to focal adhesions and modulates its turnover in these structures. However, we also provide evidence for zyxin-independent localization of Tes to focal adhesions. Zyxin increases focal adhesion numbers and reduces focal adhesion lifetimes, but does so independent of Tes. Quantitative analysis showed that the loss of interaction between zyxin and Tes affects the process of cell spreading. We conclude that zyxin influences focal adhesion dynamics, that it recruits Tes and that this interaction is functional in regulating cell spreading. PMID:26509500

  12. Synthetic physical interactions map kinetochore regulators and regions sensitive to constitutive Cdc14 localization.

    PubMed

    Ólafsson, Guđjón; Thorpe, Peter H

    2015-08-18

    The location of proteins within eukaryotic cells is often critical for their function and relocation of proteins forms the mainstay of regulatory pathways. To assess the importance of protein location to cellular homeostasis, we have developed a methodology to systematically create binary physical interactions between a query protein and most other members of the proteome. This method allows us to rapidly assess which of the thousands of possible protein interactions modify a phenotype. As proof of principle we studied the kinetochore, a multiprotein assembly that links centromeres to the microtubules of the spindle during cell division. In budding yeast, the kinetochores from the 16 chromosomes cluster together to a single location within the nucleus. The many proteins that make up the kinetochore are regulated through ubiquitylation and phosphorylation. By systematically associating members of the proteome to the kinetochore, we determine which fusions affect its normal function. We identify a number of candidate kinetochore regulators, including the phosphatase Cdc14. We examine where within the kinetochore Cdc14 can act and show that the effect is limited to regions that correlate with known phosphorylation sites, demonstrating the importance of serine phospho-regulation for normal kinetochore homeostasis. PMID:26240346

  13. 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.

  14. Opportunity rover localization and topographic mapping at the landing site of Meridiani Planum, Mars

    NASA Astrophysics Data System (ADS)

    Li, Rongxing; Arvidson, Raymond E.; Di, Kaichang; Golombek, Matt; Guinn, Joe; Johnson, Andrew; Maimone, Mark; Matthies, Larry H.; Malin, Mike; Parker, Tim; Squyres, Steven W.; Watters, Wesley A.

    2007-02-01

    This paper presents the results of Mars topographic mapping and lander and rover localization for the Opportunity rover at Meridiani Planum during the Mars Exploration Rover (MER) 2003 mission. By Sol 458, the Opportunity rover traversed a distance of 5.20 km. We localized the lander using two-way Doppler radio positioning and cartographic triangulation of craters visible in both orbital and ground images. Additional high-resolution orbital images were taken to verify the determined lander position. Visual odometry and bundle adjustment techniques were applied to overcome wheel slippages, azimuthal angle drift, and other navigation errors (as large as 21% within Eagle crater). In addition, orbit-to-ground image-based adjustment was applied to correct rover location errors where bundle adjustment was not applicable. We generated timely topographic products, including orthoimages, digital terrain models (DTMs), three-dimensional (3-D) crater models, and rover traverse maps. In particular, detailed 3-D terrain models of major features, such as Endurance crater, have been generated using multisite panoramic stereo images based on bundle adjustment and wide baseline stereo technique.

  15. Patient-oriented interactive E-health tools on U.S. hospital Web sites.

    PubMed

    Huang, Edgar; Chang, Chiu-Chi Angela

    2012-01-01

    The purpose of this study is to provide evidence for strategic planning regarding e-health development in U.S. hospitals. A content analysis of a representative sample of the U.S. hospital Web sites has revealed how U.S. hospitals have taken advantage of the 21 patient-oriented interactive tools identified in this study. Significant gaps between various types of hospitals have also been found. It is concluded that although the majority of the U.S. hospitals have adopted traditional functional tools, they need to make significant inroad in implementing the core e-business tools to serve their patients/users, making their Web sites more efficient marketing tools. PMID:23210673

  16. 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.

  17. Mapping the Substrate Binding Site of Phenylacetone Monooxygenase from Thermobifida fusca by Mutational Analysis?†

    PubMed Central

    Dudek, Hanna M.; de Gonzalo, Gonzalo; Torres Pazmińo, Daniel E.; St?pniak, Piotr; Wyrwicz, Lucjan S.; Rychlewski, Leszek; Fraaije, Marco W.

    2011-01-01

    Baeyer-Villiger monooxygenases catalyze oxidations that are of interest for biocatalytic applications. Among these enzymes, phenylacetone monooxygenase (PAMO) from Thermobifida fusca is the only protein showing remarkable stability. While related enzymes often present a broad substrate scope, PAMO accepts only a limited number of substrates. Due to the absence of a substrate in the elucidated crystal structure of PAMO, the substrate binding site of this protein has not yet been defined. In this study, a structural model of cyclopentanone monooxygenase, which acts on a broad range of compounds, has been prepared and compared with the structure of PAMO. This revealed 15 amino acid positions in the active site of PAMO that may account for its relatively narrow substrate specificity. We designed and analyzed 30 single and multiple mutants in order to verify the role of these positions. Extensive substrate screening revealed several mutants that displayed increased activity and altered regio- or enantioselectivity in Baeyer-Villiger reactions and sulfoxidations. Further substrate profiling resulted in the identification of mutants with improved catalytic properties toward synthetically attractive compounds. Moreover, the thermostability of the mutants was not compromised in comparison to that of the wild-type enzyme. Our data demonstrate that the positions identified within the active site of PAMO, namely, V54, I67, Q152, and A435, contribute to the substrate specificity of this enzyme. These findings will aid in more dedicated and effective redesign of PAMO and related monooxygenases toward an expanded substrate scope. PMID:21724896

  18. Mapping the substrate binding site of phenylacetone monooxygenase from Thermobifida fusca by mutational analysis.

    PubMed

    Dudek, Hanna M; de Gonzalo, Gonzalo; Pazmińo, Daniel E Torres; Stepniak, Piotr; Wyrwicz, Lucjan S; Rychlewski, Leszek; Fraaije, Marco W

    2011-08-15

    Baeyer-Villiger monooxygenases catalyze oxidations that are of interest for biocatalytic applications. Among these enzymes, phenylacetone monooxygenase (PAMO) from Thermobifida fusca is the only protein showing remarkable stability. While related enzymes often present a broad substrate scope, PAMO accepts only a limited number of substrates. Due to the absence of a substrate in the elucidated crystal structure of PAMO, the substrate binding site of this protein has not yet been defined. In this study, a structural model of cyclopentanone monooxygenase, which acts on a broad range of compounds, has been prepared and compared with the structure of PAMO. This revealed 15 amino acid positions in the active site of PAMO that may account for its relatively narrow substrate specificity. We designed and analyzed 30 single and multiple mutants in order to verify the role of these positions. Extensive substrate screening revealed several mutants that displayed increased activity and altered regio- or enantioselectivity in Baeyer-Villiger reactions and sulfoxidations. Further substrate profiling resulted in the identification of mutants with improved catalytic properties toward synthetically attractive compounds. Moreover, the thermostability of the mutants was not compromised in comparison to that of the wild-type enzyme. Our data demonstrate that the positions identified within the active site of PAMO, namely, V54, I67, Q152, and A435, contribute to the substrate specificity of this enzyme. These findings will aid in more dedicated and effective redesign of PAMO and related monooxygenases toward an expanded substrate scope. PMID:21724896

  19. Ligand-apomyoglobin interactions. Configurational adaptability of the haem-binding site.

    PubMed Central

    Lind, K E; Moller, J V

    1976-01-01

    1. The interaction of the haem-binding region of apomyoglobin with different ligands was examined by ultrafiltration, equilibrium dialysis and spectrophotometry, to study unspecific features of protein-ligand interactions such as they occur in, for example, serum albumin binding. 2. Apomyoglobin, in contrast with metmyoglobin, binds at pH 7, with a high affinity, one molecule of Bromophenol Blue, bilirubin and protoporphyrin IX, two molecules of n-dodecanoate and n-decyl sulphate and four molecules of n-dodecyl sulphate and n-tetradecyl sulphate. 3. The number of high-affinity sites and/or association constants for the alkyl sulphates are enhanced by an increase of hydrocarbon length, indicating hydrophobic interactions with the protein. 4. Measurements of the temperature-dependence of the association constants of the high-affinity sites imply that the binding processes are largely entropy-driven. 5. Binding studies in the presence of two ligands show that bilirubin plus Bromophenol Blue and dodecanoate plus Bromophenol Blue can be simultaneously bound by apomyoglobin, but with decreased affinities. By contrast, the apomyoglobin-protoporphyrin IX complex does not react with Bromophenol Blue. 6. Optical-rotatory-dispersion measurements show that the laevorotation of apomyoglobin is increased towards that of metmyglobin in the presence of haemin and protoporphyrin IX. Small changes in the optical-rotatory-dispersion spectrum of apomyoglobin are observed in the presence of the other ligands. 7. It is concluded that the binding sites on apomyoglobin probably do not pre-exist but appear to be moulded from predominantly non-polar amino acid residues by reaction with hydrophobic ligands. 8. Comparison with data in the literature indicates that apomyoglobin on a weight basis has a larger hydrophobic area avaialble for binding of ligands than has human serum albumin. On the other hand, the association constants of serum for the ligands used in this study are generally somewhat larger than those of apomyoglobin. PMID:949328

  20. 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 land-use) to the evolution of risk. This communication, realized within the framework of Safeland project, is supported by the European Commission under the 7th Framework Programme for Research and Technological Development, Area "Environment", Activity 1.3.3.1 "Prediction of triggering and risk assessment for landslides" (grant agreement n°226479).

  1. Interaction of Sr-90 with site candidate soil for demonstration disposal facility at Serpong

    NASA Astrophysics Data System (ADS)

    Setiawan, Budi; Mila, Oktri; Safni

    2014-03-01

    Interaction of radiostrontium (Sr-90) with site candidate soil for demonstration disposal facility to be constructed in the near future at Serpong has been done. This activity is to anticipate the interim storage facility at Serpong nuclear area becomes full off condition, and show to the public how radioactive waste can be well managed with the existing technology. To ensure that the location is save, a reliability study of site candidate soil becomes very importance to be conducted through some experiments consisted some affected parameters such as contact time, effect of ionic strength, and effect of Sr+ ion in solution. Radiostrontium was used as a tracer on the experiments and has role as radionuclide reference in low-level radioactive waste due to its long half-live and it's easy to associate with organism in nature. So, interaction of radiostrontium and soil samples from site becomes important to be studied. Experiment was performed in batch method, and soil sample-solution containing radionuclide was mixed in a 20 ml of PE vial. Ratio of solid: liquid was 10-2 g/ml. Objective of the experiment is to collect the specific characteristics data of radionuclide sorption onto soil from site candidate. Distribution coefficient value was used as indicator where the amount of initial and final activities of radiostrontium in solution was compared. Result showed that equilibrium condition was reached after contact time 10 days with Kd values ranged from 1600-2350 ml/g. Increased in ionic strength in solution made decreased of Kd value into soil sample due to competition of background salt and radiostrontium into soil samples, and increased in Sr ion in solution caused decreased of Kd value in soil sample due to limitation of sorption capacity in soil samples. Fast condition in saturated of metal ion into soil samples was reached due to a simple reaction was occurred.

  2. Interaction of Sr-90 with site candidate soil for demonstration disposal facility at Serpong

    SciTech Connect

    Setiawan, Budi; Mila, Oktri; Safni

    2014-03-24

    Interaction of radiostrontium (Sr-90) with site candidate soil for demonstration disposal facility to be constructed in the near future at Serpong has been done. This activity is to anticipate the interim storage facility at Serpong nuclear area becomes full off condition, and show to the public how radioactive waste can be well managed with the existing technology. To ensure that the location is save, a reliability study of site candidate soil becomes very importance to be conducted through some experiments consisted some affected parameters such as contact time, effect of ionic strength, and effect of Sr{sup +} ion in solution. Radiostrontium was used as a tracer on the experiments and has role as radionuclide reference in low-level radioactive waste due to its long half-live and it's easy to associate with organism in nature. So, interaction of radiostrontium and soil samples from site becomes important to be studied. Experiment was performed in batch method, and soil sample-solution containing radionuclide was mixed in a 20 ml of PE vial. Ratio of solid: liquid was 10{sup ?2} g/ml. Objective of the experiment is to collect the specific characteristics data of radionuclide sorption onto soil from site candidate. Distribution coefficient value was used as indicator where the amount of initial and final activities of radiostrontium in solution was compared. Result showed that equilibrium condition was reached after contact time 10 days with Kd values ranged from 1600-2350 ml/g. Increased in ionic strength in solution made decreased of Kd value into soil sample due to competition of background salt and radiostrontium into soil samples, and increased in Sr ion in solution caused decreased of Kd value in soil sample due to limitation of sorption capacity in soil samples. Fast condition in saturated of metal ion into soil samples was reached due to a simple reaction was occurred.

  3. 3d interaction homology: The structurally known rotamers of tyrosine derive from a surprisingly limited set of information-rich hydropathic interaction environments described by maps.

    PubMed

    Ahmed, Mostafa H; Koparde, Vishal N; Safo, Martin K; Neel Scarsdale, J; Kellogg, Glen E

    2015-06-01

    Sidechain rotamer libraries are obtained through exhaustive statistical analysis of existing crystallographic structures of proteins and have been applied in multiple aspects of structural biology, for example, crystallography of relatively low-resolution structures, in homology model building and in biomolecular NMR. Little is known, however, about the driving forces that lead to the preference or suitability of one rotamer over another. Construction of 3D hydropathic interaction maps for nearly 30,000 tyrosines reveals the environment around each, in terms of hydrophobic (?-? stacking, etc.) and polar (hydrogen bonding, etc.) interactions. After partitioning the tyrosines into backbone-dependent (?, ?) bins, a map similarity metric based on the correlation coefficient was applied to each map-map pair to build matrices suitable for clustering with k-means. The first bin (-200° ? ??interactions with many different residue partner types. Polar interactions for tyrosine include surprisingly ubiquitous hydrogen bonding with the phenolic OH and a handful of unique environments surrounding the tyrosine backbone. The memberships of all but one of the 14 environments are dominated (>50%) by a single ?(1)/?(2) rotamer. The last environment has weak or no interactions with the tyrosine ring and its ?(1)/?(2) rotamer is indeterminate, which is consistent with it being composed of mostly surface residues. Each tyrosine residue attempts to fulfill its hydropathic valence and thus, structural water molecules are seen in a variety of roles throughout protein structure. PMID:25900573

  4. Topographical mapping of ?- and ?-keratins on developing chicken skin integuments: Functional interaction and evolutionary perspectives.

    PubMed

    Wu, Ping; Ng, Chen Siang; Yan, Jie; Lai, Yung-Chih; Chen, Chih-Kuan; Lai, Yu-Ting; Wu, Siao-Man; Chen, Jiun-Jie; Luo, Weiqi; Widelitz, Randall B; Li, Wen-Hsiung; Chuong, Cheng-Ming

    2015-12-01

    Avian integumentary organs include feathers, scales, claws, and beaks. They cover the body surface and play various functions to help adapt birds to diverse environments. These keratinized structures are mainly composed of corneous materials made of ?-keratins, which exist in all vertebrates, and ?-keratins, which only exist in birds and reptiles. Here, members of the keratin gene families were used to study how gene family evolution contributes to novelty and adaptation, focusing on tissue morphogenesis. Using chicken as a model, we applied RNA-seq and in situ hybridization to map ?- and ?-keratin genes in various skin appendages at embryonic developmental stages. The data demonstrate that temporal and spatial ?- and ?-keratin expression is involved in establishing the diversity of skin appendage phenotypes. Embryonic feathers express a higher proportion of ?-keratin genes than other skin regions. In feather filament morphogenesis, ?-keratins show intricate complexity in diverse substructures of feather branches. To explore functional interactions, we used a retrovirus transgenic system to ectopically express mutant ?- or antisense ?-keratin forms. ?- and ?-keratins show mutual dependence and mutations in either keratin type results in disrupted keratin networks and failure to form proper feather branches. Our data suggest that combinations of ?- and ?-keratin genes contribute to the morphological and structural diversity of different avian skin appendages, with feather-?-keratins conferring more possible composites in building intrafeather architecture complexity, setting up a platform of morphological evolution of functional forms in feathers. PMID:26598683

  5. HAZPAC; an interactive map of Pacific Rim natural hazards, population, and infrastructure

    USGS Publications Warehouse

    Bemis, B.L.; Goss, H.V.; Yurkovich, E.S.; Perron, T.J.; Howell, D.G.

    2002-01-01

    This is an online version of a CD-ROM publication. The text files that describe using this publication make reference to software provided on the disc. For this online version the software can be downloaded for free from Adobe Systems and Environmental Systems Research Institute, Inc. (ESRI). Welcome to HAZPAC! HAZPAC is an interactive map about natural hazard risk in the Pacific Rim region. It is intended to communicate to a broad audience the ideas of 'Crowding the Rim,' which is an international, public-private partnership that fosters collaborative solutions for regional risks. HAZPAC, which stands for 'HAZards of the PACific,' uses Geographic Information System (GIS) technology to help people visualize the socioeconomic connections and shared hazard vulnerabilities among Pacific Rim countries, as well as to explore the general nature of risk. Please refer to the 'INTRODUCTION TO HAZPAC' section of the readme file below to determine which HAZPAC project will be right for you. Once you have decided which HAZPAC project is suitable for you, please refer to the 'GETTING STARTED' sections in the readme file for some basic information that will help you begin using HAZPAC. Also, we highly recommend that you follow the Tutorial exercises in the project-specific HAZPAC User Guides. The User Guides are PDF (Portable Document Format) files that must be read with Adobe Acrobat Reader (a free copy of Acrobat Reader is available using the link near the bottom of this page).

  6. Identification of Links Between Cellular Pathways by Genetic Interaction Mapping (GIM).

    PubMed

    Malabat, Christophe; Saveanu, Cosmin

    2016-01-01

    The yeast systematic deletion collection offered the basis for a number of different strategies that establish functional links between genes by analyzing the phenotype of cells that combine two different deletions or mutations. A distinguishing feature of the collection is the presence of molecular barcodes at each deleted locus, which can be used to quantify the presence and abundance of cells bearing a given allele in a complex mix. As a result, a large number of mutants can be tested in batch cultures, replacing tedious manipulation of thousands of individual strains with a barcode microarray readout. Barcode-based genetic screens like Genetic Interaction Mapping (GIM) thus require little investment in terms of specific equipment, are fast to perform, and allow precise measurements of double mutant growth rates for both aggravating (synthetic sick) and alleviating (epistatic) effects. We describe here protocols for preparing the pools of haploid double mutant S. cerevisiae cells, testing their composition with barcode microarrays, and analyzing the results to extract useful functional information. PMID:26483030

  7. PAR-CLIP: A Method for Transcriptome-Wide Identification of RNA Binding Protein Interaction Sites.

    PubMed

    Danan, Charles; Manickavel, Sudhir; Hafner, Markus

    2016-01-01

    During post-transcriptional gene regulation (PTGR), RNA binding proteins (RBPs) interact with all classes of RNA to control RNA maturation, stability, transport, and translation. Here, we describe Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP), a transcriptome-scale method for identifying RBP binding sites on target RNAs with nucleotide-level resolution. This method is readily applicable to any protein directly contacting RNA, including RBPs that are predicted to bind in a sequence- or structure-dependent manner at discrete RNA recognition elements (RREs), and those that are thought to bind transiently, such as RNA polymerases or helicases. PMID:26463383

  8. Air-sea interaction at contrasting sites in the Eastern Tropical Pacific : mesoscale variability and atmospheric convection at 10°N

    E-print Network

    Farrar, J. Thomas (John Thomas), 1976-

    2007-01-01

    The role of ocean dynamics in driving air-sea interaction is examined at two contrasting sites on 125°W in the eastern tropical Pacific Ocean using data from the Pan American Climate Study (PACS) field program. Analysis ...

  9. Differential Effects of Methoxy Group on the Interaction of Curcuminoids with Two Major Ligand Binding Sites of Human Serum Albumin

    PubMed Central

    Sato, Hiroki; Chuang, Victor Tuan Giam; Yamasaki, Keishi; Yamaotsu, Noriyuki; Watanabe, Hiroshi; Nagumo, Kohei; Anraku, Makoto; Kadowaki, Daisuke; Ishima, Yu; Hirono, Shuichi; Otagiri, Masaki; Maruyama, Toru

    2014-01-01

    Curcuminoids are a group of compounds with a similar chemical backbone structure but containing different numbers of methoxy groups that have therapeutic potential due to their anti-inflammatory and anti-oxidant properties. They mainly bind to albumin in plasma. These findings influence their body disposition and biological activities. Spectroscopic analysis using site specific probes on human serum albumin (HSA) clearly indicated that curcumin (Cur), demethylcurcumin (Dmc) and bisdemethoxycurcumin (Bdmc) bind to both Site I (sub-site Ia and Ib) and Site II on HSA. At pH 7.4, the binding constants for Site I were relatively comparable between curcuminoids, while the binding constants for Site II at pH 7.4 were increased in order Cur < Dmc < Bdmc. Binding experiments using HSA mutants showed that Trp214 and Arg218 at Site I, and Tyr411 and Arg410 at Site II are involved in the binding of curcuminoids. The molecular docking of all curcuminoids to the Site I pocket showed that curcuminoids stacked with Phe211 and Trp214, and interacted with hydrophobic and aromatic amino acid residues. In contrast, each curcuminoid interacted with Site II in a different manner depending whether a methoxy group was present or absent. A detailed analysis of curcuminoids-albumin interactions would provide valuable information in terms of understanding the pharmacokinetics and the biological activities of this class of compounds. PMID:24498401

  10. Implementing the web map service for the University of Edinburgh 

    E-print Network

    Dai, Songheng

    2007-11-27

    This paper describes for a necessity of new approach to the web based-map service for the University of Edinburgh. An interactive online map is developed to implement the feature of the static map in the web site of the ...

  11. A Robust Protocol to Map Binding Sites of the 14-3-3 Interactome: Cdc25C Requires Phosphorylation of Both S216 and S263 to bind 14-3-3*

    PubMed Central

    Chan, Perry M.; Ng, Yuen-Wai; Manser, Ed

    2011-01-01

    Modern proteomic techniques have identified hundreds of proteins that bind 14-3-3s, the most widespread eukaryotic phosphoserine/threonine sensors, but accurate prediction of the target phospho-sites is difficult. Here we describe a systematic approach using synthetic peptides that tests large numbers of potential binding sites in parallel for human 14-3-3. By profiling the sequence requirements for three diverse 14-3-3 binding sites (from IRS-1, IRSp53 and GIT2), we have generated enhanced bioinformatics tools to score sites and allow more tractable testing by co-immunoprecipitation. This approach has allowed us to identify two additional sites other than Ser216 in the widely studied cell division cycle (Cdc) protein 25C, whose function depends on 14-3-3 binding. These Ser247 and Ser263 sites in human Cdc25C, which were not predicted by the existing Scansite search, are conserved across species and flank the nuclear localization region. Furthermore, we found strong interactions between 14-3-3 and peptides with the sequence Rxx[S/T]xR typical for PKC sites, and which is as abundant as the canonical Rxx[S/T]xP motif in the proteome. Two such sites are required for 14-3-3 binding in the polarity protein Numb. A recent survey of >200 reported sites identified only a handful containing this motif, suggesting that it is currently under-appreciated as a candidate binding site. This approach allows one to rapidly map 14-3-3 binding sites and has revealed alternate motifs. PMID:21189416

  12. 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. J. Cell. Biochem. 116: 2903-2914, 2015. © 2015 Wiley Periodicals, Inc. PMID:26018553

  13. Proteins interacting with mitochondrial ATP-dependent Lon protease (MAP1) in Magnaporthe oryzae are involved in rice blast disease.

    PubMed

    Cui, Xiao; Wei, Yi; Wang, Yu-Han; Li, Jian; Wong, Fuk-Ling; Zheng, Ya-Jie; Yan, Hai; Liu, Shao-Shuai; Liu, Jin-Liang; Jia, Bao-Lei; Zhang, Shi-Hong

    2015-10-01

    The ATP-dependent Lon protease is involved in many physiological processes. In bacteria, Lon regulates pathogenesis and, in yeast, Lon protects mitochondia from oxidative damage. However, little is known about Lon in fungal phytopathogens. MAP1, a homologue of Lon in Magnaporthe oryzae, was recently identified to be important for stress resistance and pathogenesis. Here, we focus on a novel pathogenic pathway mediated by MAP1. Based on an interaction system between rice and a tandem affinity purification (TAP)-tagged MAP1 complementation strain, we identified 23 novel fungal proteins from infected leaves using a TAP approach with mass spectrometry, and confirmed that 14 of these proteins physically interact with MAP1?in?vivo. Among these 14 proteins, 11 candidates, presumably localized to the mitochondria, were biochemically determined to be substrates of MAP1 hydrolysis. Deletion mutants were created and functionally analysed to further confirm the involvement of these proteins in pathogenesis. The results indicated that all mutants showed reduced conidiation and sensitivity to hydrogen peroxide. Appressorial formations were not affected, although conidia from certain mutants were morphologically altered. In addition, virulence was reduced in four mutants, enhanced (with lesions forming earlier) in two mutants and remained unchanged in one mutant. Together with the known virulence-related proteins alternative oxidase and enoyl-CoA hydratase, we propose that most of the Lon-interacting proteins are involved in the pathogenic regulation pathway mediated by MAP1 in M.?oryzae. Perturbation of this pathway may represent an effective approach for the inhibition of rice blast disease. PMID:25605006

  14. Rhodopsin TM6 Can Interact with Two Separate and Distinct Sites on Arrestin: Evidence for Structural Plasticity and Multiple Docking Modes in Arrestin–Rhodopsin Binding

    PubMed Central

    2015-01-01

    Various studies have implicated the concave surface of arrestin in the binding of the cytosolic surface of rhodopsin. However, specific sites of contact between the two proteins have not previously been defined in detail. Here, we report that arrestin shares part of the same binding site on rhodopsin as does the transducin G? subunit C-terminal tail, suggesting binding of both proteins to rhodopsin may share some similar underlying mechanisms. We also identify two areas of contact between the proteins near this region. Both sites lie in the arrestin N-domain, one in the so-called “finger” loop (residues 67–79) and the other in the 160 loop (residues 155–165). We mapped these sites using a novel tryptophan-induced quenching method, in which we introduced Trp residues into arrestin and measured their ability to quench the fluorescence of bimane probes attached to cysteine residues on TM6 of rhodopsin (T242C and T243C). The involvement of finger loop binding to rhodopsin was expected, but the evidence of the arrestin 160 loop contacting rhodopsin was not. Remarkably, our data indicate one site on rhodopsin can interact with multiple structurally separate sites on arrestin that are almost 30 Ĺ apart. Although this observation at first seems paradoxical, in fact, it provides strong support for recent hypotheses that structural plasticity and conformational changes are involved in the arrestin–rhodopsin binding interface and that the two proteins may be able to interact through multiple docking modes, with arrestin binding to both monomeric and dimeric rhodopsin. PMID:24724832

  15. Varenicline Interactions at the 5-HT3 Receptor Ligand Binding Site are Revealed by 5-HTBP

    PubMed Central

    2015-01-01

    Cys-loop receptors are the site of action of many therapeutic drugs. One of these is the smoking cessation agent varenicline, which has its major therapeutic effects at nicotinic acetylcholine (nACh) receptors but also acts at 5-HT3 receptors. Here, we report the X-ray crystal structure of the 5-HT binding protein (5-HTBP) in complex with varenicline, and test the predicted interactions by probing the potency of varenicline in a range of mutant 5-HT3 receptors expressed in HEK293 cells and Xenopus oocytes. The structure reveals a range of interactions between varenicline and 5-HTBP. We identified residues within 5 Ĺ of varenicline and substituted the equivalent residues in the 5-HT3 receptor with Ala or a residue with similar chemical properties. Functional characterization of these mutant 5-HT3 receptors, using a fluorescent membrane potential dye in HEK cells and voltage clamp in oocytes, supports interactions between varenicline and the receptor that are similar to those in 5-HTBP. The structure also revealed C-loop closure that was less than in the 5-HT-bound 5-HTBP, and hydrogen bonding between varenicline and the complementary face of the binding pocket via a water molecule, which are characteristics consistent with partial agonist behavior of varenicline in the 5-HT3 receptor. Together, these data reveal detailed insights into the molecular interaction of varenicline in the 5-HT3 receptor. PMID:25648658

  16. GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs.

    PubMed

    Zhao, Qi; Xie, Yubin; Zheng, Yueyuan; Jiang, Shuai; Liu, Wenzhong; Mu, Weiping; Liu, Zexian; Zhao, Yong; Xue, Yu; Ren, Jian

    2014-07-01

    Small ubiquitin-like modifiers (SUMOs) regulate a variety of cellular processes through two distinct mechanisms, including covalent sumoylation and non-covalent SUMO interaction. The complexity of SUMO regulations has greatly hampered the large-scale identification of SUMO substrates or interaction partners on a proteome-wide level. In this work, we developed a new tool called GPS-SUMO for the prediction of both sumoylation sites and SUMO-interaction motifs (SIMs) in proteins. To obtain an accurate performance, a new generation group-based prediction system (GPS) algorithm integrated with Particle Swarm Optimization approach was applied. By critical evaluation and comparison, GPS-SUMO was demonstrated to be substantially superior against other existing tools and methods. With the help of GPS-SUMO, it is now possible to further investigate the relationship between sumoylation and SUMO interaction processes. A web service of GPS-SUMO was implemented in PHP+JavaScript and freely available at http://sumosp.biocuckoo.org. PMID:24880689

  17. RICH MAPS

    EPA Science Inventory

    Michael Goodchild recently gave eight reasons why traditional maps are limited as communication devices, and how interactive internet mapping can overcome these limitations. In the past, many authorities in cartography, from Jenks to Bertin, have emphasized the importance of sim...

  18. Framing medical tourism: an examination of appeal, risk, convalescence, accreditation, and interactivity in medical tourism web sites.

    PubMed

    Mason, Alicia; Wright, Kevin B

    2011-02-01

    This exploratory study analyzed the content of medical tourism Web sites in an attempt to examine how they convey information about benefits and risks of medical procedures, how they frame credibility, and the degree to which these Web sites include interactive features for consumers. Drawing upon framing theory, the researchers content analyzed a sample of 66 medical tourism Web sites throughout the world. The results indicated that medical tourism Web sites largely promote the benefits of medical procedures while downplaying the risks, and relatively little information regarding the credibility of these services appears. In addition, the presentation of benefits/risks, credibility, and Web site interactivity were found to differ by region and type of facility. The authors discuss the implications of these findings concerning the framing of medical tourism Web site content, future directions for research, and limitations. PMID:21161812

  19. MARs Tools for Interactive ANalysis (MARTIAN): Google Maps Tools for Visual Exploration of Geophysical Modeling on Mars

    NASA Astrophysics Data System (ADS)

    Dimitrova, L. L.; Haines, M.; Holt, W. E.; Schultz, R. A.; Richard, G.; Haines, A. J.

    2006-12-01

    Interactive maps of surface-breaking faults and stress models on Mars provide important tools to engage undergraduate students, educators, and scientists with current geological and geophysical research. We have developed a map based on the Google Maps API -- an Internet based tool combining DHTML and AJAX, -- which allows very large maps to be viewed over the World Wide Web. Typically, small portions of the maps are downloaded as needed, rather than the entire image at once. This set-up enables relatively fast access for users with low bandwidth. Furthermore, Google Maps provides an extensible interactive interface making it ideal for visualizing multiple data sets at the user's choice. The Google Maps API works primarily with data referenced to latitudes and longitudes, which is then mapped in Mercator projection only. We have developed utilities for general cylindrical coordinate systems by converting these coordinates into equivalent Mercator projection before including them on the map. The MARTIAN project is available at http://rock.geo.sunysb.edu/~holt/Mars/MARTIAN/. We begin with an introduction to the Martian surface using a topography model. Faults from several datasets are classified by type (extension vs. compression) and by time epoch. Deviatoric stresses due to gravitational potential energy differences, calculated from the topography and crustal thickness, can be overlain. Several quantitative measures for the fit of the stress field to the faults are also included. We provide introductory text and exercises spanning a range of topics: how are faults identified, what stress is and how it relates to faults, what gravitational potential energy is and how variations in it produce stress, how the models are created, and how these models can be evaluated and interpreted. The MARTIAN tool is used at Stony Brook University in GEO 310: Introduction to Geophysics, a class geared towards junior and senior geosciences majors. Although this project is in its early stages, high school and college teachers, as well as researchers have expressed interest in using and extending these tools for visualizing and interacting with data on Earth and other planetary bodies.

  20. 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

    Geologic hazards on US Forest Service lands have a long history of producing catastrophic events. In 1890 (prior to the establishment of the Forest Service), the China Mine landslide buried a miner’s camp along the Trinity River in NW California, killing a number of miners. An earthquake in southwestern Montana triggered a massive landslide which killed 28 people in a US Forest Service campground in 1959. In 1980, Mount St. Helens erupted in Oregon, killing 57 people. Debris flows from a winter storm in 2003 on the burned hillslopes of the San Bernardino National Forest in California killed 14 people at the St. Sophia youth Camp. A rockfall in the summer of 2009 in Lassen National Park killed a 9 year old boy. The most recent catastrophe occurred on June 11, 2010 when 20 people died in a flash flood at the Albert Pike Campground on the Ouachita National Forest. These and other disasters point out the need for geologic hazard mapping and assessments on the National Forests. The US Forest Service (USFS) is currently assessing geologic hazards in the Northern Province of USFS Region 5 (Pacific Southwest Region), which includes the Klamath, Mendocino, Shasta-Trinity, and Six Rivers National Forests. The most common geologic hazards (relatively short return intervals) in this area include landslides, rock falls, debris flows, flooding, temporary dam failures (landslide or woody debris), naturally occurring hazardous materials, (asbestos radon, etc), and rarely, karst subsidence. Seismic and volcanic hazards are also important at longer return intervals. This assessment will be conducted in three phases, and is patterned after a process developed by Region 8 of the US Forest Service. The first phase is a reconnaissance level assessment based on existing information such as spatial databases, aerial photos, Digital Elevation Models, State of California Alquist-Priolo Earthquake Fault Zone maps, previous investigations and anecdotal accounts of past events. The bedrock 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.

  1. Progesterone receptor gene maps to human chromosome band 11q13, the site of the mammary oncogene int-2

    SciTech Connect

    Law, M.L.; Kao, F.T.; Wei, Q.; Hartz, J.A.; Greene, G.L.; Zarucki-Schulz, T.; Conneely, O.M.; Jones, C.; Puck, T.T.; O'Malley, B.W.; Horwitz, K.B.

    1987-05-01

    Progesterone is involved in the development and progression of breast cancers, and progesterone receptors (PR) are important markers of hormone dependence and disease prognosis. The authors have used a human PR cDNA probe, genomic DNA blotting of a series of Chinese hamster-human cell hybrids, and in situ hybridization to map the human PR gene to chromosome 11, band q13. This band also contains the human homolog of the mouse mammary tumor virus integration site, int-2, which surrounds a protooncogene thought to be involved in the development of murine mammary cancers. That these two genes share the same chromosomal location raises important questions about their possible linkage and about the relationship between the mammary-specific oncogene and the steroid hormone in the development, growth, and hormone dependence of human breast cancers.

  2. An Application of Comparative Corpora of Interactional Data toward the Sound Profiles of Sites of Initiation in French and

    E-print Network

    An Application of Comparative Corpora of Interactional Data ­ toward the Sound Profiles of Sites of Initiation in French and Mandarin Recycling Repair Helen Kai-yun Chen Phonetics Lab, Institute of Linguistics of sites of initiation in French and Mandarin recycling repair (also disfluent repetitions). 150 examples

  3. Physical mapping of a commonly deleted region, the site of a candidate tumor suppressor gene, at 12q22 in human male germ cell tumors

    SciTech Connect

    Murty, V.V.V.S.; Bosl, G.J.; Chaganti, R.S.K.

    1996-08-01

    A candidate tumor suppressor gene (TSG) site at 12q22 characterized by a high frequency of loss of heterozygosity (LOH) and a homozygous deletion has previously (LOH) and a homozygous deletion has previously been reported in human male germ cell tumors (GCTs). In a detailed deletion mapping analysis of 67 normal-tumor DNAs utilizing 20 polymorphic markers mapped to 12q22-q24, we identified the limits of the minimal region of deletion at 12q22 between D12S377 (priximal) and D12S296 (distal). We have constructed a YAC contig map of a 3-cM region of this band between the proximal marker D12S101 and the distal marker D12S346, which contained the minimal region of deletion in GCTs. The map is composed of 53 overlapping YACs and 3 cosmids onto which 25 polymorphic and nonpolymorphic sequence-tagged sites (STSs) were placed in a unique order. The size of the minimal region of deletion was approximately 2 Mb from overlapping, nonchimeric YACs that spanned the region. We also developed a radiation hybrid (RH) map of the region between D12S101 and D12S346 containing 17 loci. The consensus order developed by RH mapping is in good agreement with the YAC STS-content map order. The RH map estimated the distance between D12S101 and D12S346 to be 246 cR{sub 8000} and the minimal region of deletion to be 141 cR{sub 8000}. In addition, four genes that were previously mapped to 12q22 have been excluded as candidate genes. The leads gained from the deletion mapping and physical maps should expedite the isolation and characterization of the TSG at 12q22. 35 refs., 4 figs., 2 tabs.

  4. Chromatin Immunoprecipitation-Sequencing (ChIP-seq) for Mapping of Estrogen Receptor-Chromatin Interactions in Breast Cancer.

    PubMed

    Holmes, Kelly A; Brown, Gordon D; Carroll, Jason S

    2016-01-01

    Chromatin immunoprecipitation-sequencing (ChIP-Seq) is a powerful tool which combines the established method of ChIP with next-generation sequencing (NGS) to determine DNA-binding sites of a protein of interest on a genome-wide level, importantly, allowing for de novo discovery of binding events. Here we describe ChIP-seq using the well-established example of estrogen receptor-? mapping in the MCF7 breast cancer cell line. PMID:26585129

  5. Mapping the aspartic acid binding site of Escherichia coli asparagine synthetase B using substrate analogs.

    PubMed

    Parr, I B; Boehlein, S K; Dribben, A B; Schuster, S M; Richards, N G

    1996-06-01

    Novel inhibitors of asparagine synthetase, that will lower circulating levels of blood asparagine, have considerable potential in developing new protocols for the treatment of acute lymphoblastic leukemia. We now report the indirect characterization of the aspartate binding site of Escherichia coli asparagine synthetase B (AS-B) using a number of stereochemically, and conformationally, defined aspartic acid analogs. Two compounds, prepared using novel reaction conditions for the stereospecific beta-functionalization of aspartic acid diesters, have been found to be competitive inhibitors with respect to aspartate in kinetic studies on AS-B. Chemical modification experiments employing [(fluorosulfonyl)benzoyl]adenosine (FSBA), an ATP analog, demonstrate that both inhibitors bind to the aspartate binding site of AS-B. Our results reveal that large steric alterations in the substrate are not tolerated by the enzyme, consistent with the failure of previous efforts to develop AS inhibitors using random screening approaches, and that all of the ionizable groups are placed in close proximity in the bound conformation of aspartate. PMID:8691431

  6. 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 provide good quality clumping index estimates at pertinent scales for modeling local carbon and energy fluxes.

  7. Mapping Functional Group Free Energy Patterns at Protein Occluded Sites: Nuclear Receptors and G-Protein Coupled Receptors

    PubMed Central

    2015-01-01

    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-? (PPAR?) NRs and the metabotropic glutamate (mGluR) and ?2-adreneric (?2AR) 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 ?2AR LBP were used in virtual screening to identify high efficacy agonists targeting ?2AR 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. PMID:25692383

  8. BAID: The Barrow Area Information Database - an interactive web mapping portal and cyberinfrastructure for scientific activities in the vicinity of Barrow, Alaska.

    NASA Astrophysics Data System (ADS)

    Cody, R. P.; Kassin, A.; Kofoed, K. B.; Copenhaver, W.; Laney, C. M.; Gaylord, A. G.; Collins, J. A.; Tweedie, C. E.

    2014-12-01

    The Barrow area of northern Alaska is one of the most intensely researched locations in the Arctic and the Barrow Area Information Database (BAID, www.barrowmapped.org) tracks and facilitates a gamut of research, management, and educational activities in the area. BAID is a cyberinfrastructure (CI) that details much of the historic and extant research undertaken within in the Barrow region in a suite of interactive web-based mapping and information portals (geobrowsers). The BAID user community and target audience for BAID is diverse and includes research scientists, science logisticians, land managers, educators, students, and the general public. BAID contains information on more than 12,000 Barrow area research sites that extend back to the 1940's and more than 640 remote sensing images and geospatial datasets. In a web-based setting, users can zoom, pan, query, measure distance, save or print maps and query results, and filter or view information by space, time, and/or other tags. Data are described with metadata that meet Federal Geographic Data Committee standards and are archived at the University Corporation for Atmospheric Research Earth Observing Laboratory (EOL) where non-proprietary BAID data can be freely downloaded. Recent advances include the addition of more than 2000 new research sites, provision of differential global position system (dGPS) and Unmanned Aerial Vehicle (UAV) support to visiting scientists, surveying over 80 miles of coastline to document rates of erosion, training of local GIS personal to better make use of science in local decision making, deployment and near real time connectivity to a wireless micrometeorological sensor network, links to Barrow area datasets housed at national data archives and substantial upgrades to the BAID website and web mapping applications.

  9. 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.

  10. 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 ?mol/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 the substantial possibility of a gross error in the labeling of charts. Our results show that simple, rapid, and cost effective surveys of these sites can be made, that the found debris field of rusted barrels and other objects appears to have contained more mundane waste material that long ago dissipated or hydrolyzed. It is likely that the majority of disposed material is far from the center of the charted area and thus a re-drawing of the warning zone following additional surveying of the actual extent of the dump site to reflect this would be a significant improvement.

  11. 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 dčcollement. If the dčcollement is an important aquifer, apparently the fluids are passed either to the strike-slip faults which intersect the dčcollement or to the incipient faults in Cascadia Basin for expulsion. Diagenetic deposits seaward of the prism toe probably consist dominantly of gas hydrates

  12. Proteins and Their Interacting Partners: An Introduction to Protein–Ligand Binding Site Prediction Methods

    PubMed Central

    Roche, Daniel Barry; Brackenridge, Danielle Allison; McGuffin, Liam James

    2015-01-01

    Elucidating the biological and biochemical roles of proteins, and subsequently determining their interacting partners, can be difficult and time consuming using in vitro and/or in vivo methods, and consequently the majority of newly sequenced proteins will have unknown structures and functions. However, in silico methods for predicting protein–ligand binding sites and protein biochemical functions offer an alternative practical solution. The characterisation of protein–ligand binding sites is essential for investigating new functional roles, which can impact the major biological research spheres of health, food, and energy security. In this review we discuss the role in silico methods play in 3D modelling of protein–ligand binding sites, along with their role in predicting biochemical functionality. In addition, we describe in detail some of the key alternative in silico prediction approaches that are available, as well as discussing the Critical Assessment of Techniques for Protein Structure Prediction (CASP) and the Continuous Automated Model EvaluatiOn (CAMEO) projects, and their impact on developments in the field. Furthermore, we discuss the importance of protein function prediction methods for tackling 21st century problems. PMID:26694353

  13. Multiple Interacting Sites of Ectopic Spike Electrogenesis in Primary Sensory Neurons

    PubMed Central

    Amir, Ron; Kocsis, Jeffery D.; Devor, Marshall

    2008-01-01

    Ectopic discharge generated in injured afferent axons and cell somata in vivo contributes significantly to chronic neuropathic dysesthesia and pain after nerve trauma. Progress has been made toward understanding the processes responsible for this discharge using a preparation consisting of whole excised dorsal root ganglia (DRGs) with the cut nerve attached. In the in vitro preparation, however, spike activity originates in the DRG cell soma but rarely in the axon. We have now overcome this impediment to understanding the overall electrogenic processes in soma and axon, including the resulting discharge patterns, by modifying the bath medium in which recordings are made. At both sites, bursts can be triggered by subthreshold oscillations, a phasic stimulus, or spikes arising elsewhere in the neuron. In the soma, once triggered, bursts are maintained by depolarizing afterpotentials, whereas in the axon, an additional process also plays a role, delayed depolarizing potentials. This alternative process appears to be involved in “clock-like” bursting, a discharge pattern much more common in axons than somata. Ectopic spikes arise alternatively in the soma, the injured axon end (neuroma), and the region of the axonal T-junction. Discharge sequences, and even individual multiplet bursts, may be a mosaic of action potentials that originate at these alternative electrogenic sites within the neuron. Correspondingly, discharge generated at these alternative sites may interact, explaining the sometimes-complex firing patterns observed in vivo. PMID:15758167

  14. Proteins and Their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction Methods.

    PubMed

    Roche, Daniel Barry; Brackenridge, Danielle Allison; McGuffin, Liam James

    2015-01-01

    Elucidating the biological and biochemical roles of proteins, and subsequently determining their interacting partners, can be difficult and time consuming using in vitro and/or in vivo methods, and consequently the majority of newly sequenced proteins will have unknown structures and functions. However, in silico methods for predicting protein-ligand binding sites and protein biochemical functions offer an alternative practical solution. The characterisation of protein-ligand binding sites is essential for investigating new functional roles, which can impact the major biological research spheres of health, food, and energy security. In this review we discuss the role in silico methods play in 3D modelling of protein-ligand binding sites, along with their role in predicting biochemical functionality. In addition, we describe in detail some of the key alternative in silico prediction approaches that are available, as well as discussing the Critical Assessment of Techniques for Protein Structure Prediction (CASP) and the Continuous Automated Model EvaluatiOn (CAMEO) projects, and their impact on developments in the field. Furthermore, we discuss the importance of protein function prediction methods for tackling 21st century problems. PMID:26694353

  15. Aerosol-Cloud Interaction at the Land Site of VOCALS-REx

    NASA Astrophysics Data System (ADS)

    Fochesatto, Javier; Shaw, Glenn; Krejci, Radovan; Chand, Duli; Gallarado, Laura; Cordova, Ana

    2010-05-01

    Aerosol-Cloud-Ocean interactions in the South-East Pacific represent one of the best natural laboratories to study aerosol-cloud-climate processes thanks to stable large scale atmospheric and oceanic circulation and large anthropogenic sources associated mainly with copper industry. This article discuss the microphysical and optical characteristics of aerosols in the marine boundary layer (MBL) and the free troposphere(FT) related to the coastal MBL dynamics, stratocumulus cloud formation and dissipation in an environment influenced by air pollution sources in the FT and MBL. The analysis is based on observations from the Land Sites of VOCALS-REx at Paposo (25 S, 70 W, 700 masl) on the Pacific ocean coast, about 150 km south of Antofagasta in Chile and from free tropospheric site at ESO Paranal Observatory located inland at 2435 masl some 40 km NE from Paposo site. Combination of the in situ measurements from both, free troposphere and MBL together with lidar observations provides comprehensive insight into MBL-free troposphere interactions. The aerosol properties in FT are to a large degree controlled by sulfate-dominated aerosol from copper industry in northern Chile. The free tropospheric aerosol close to the coast has very stable accumulation mode dominated size distribution with mode diameter ~0.1 µm, but the aerosol number density for particles > 0.01 µm as well as for particles > 0.26 µm show large variability between 300 and 1600 cm-3 and 5 and 50 cm-3, respectively. The large variability can be attributed to changing influence from individual emission sources due to changing intensity of the coastal jet flow and diurnal ventilation of the shallow boundary layer in hilly region of the Atacama Desert mountain plateau. Polluted aerosols from FT are transported to the MBL along the Andes western slope through katabatic flows and downward mixed into the MBL most intensively in a narrow band along the coast.

  16. 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.

  17. Genome-wide mapping in a house mouse hybrid zone reveals hybrid sterility loci and Dobzhansky-Muller interactions.

    PubMed

    Turner, Leslie M; Harr, Bettina

    2014-01-01

    Mapping hybrid defects in contact zones between incipient species can identify genomic regions contributing to reproductive isolation and reveal genetic mechanisms of speciation. The house mouse features a rare combination of sophisticated genetic tools and natural hybrid zones between subspecies. Male hybrids often show reduced fertility, a common reproductive barrier between incipient species. Laboratory crosses have identified sterility loci, but each encompasses hundreds of genes. We map genetic determinants of testis weight and testis gene expression using offspring of mice captured in a hybrid zone between M. musculus musculus and M. m. domesticus. Many generations of admixture enables high-resolution mapping of loci contributing to these sterility-related phenotypes. We identify complex interactions among sterility loci, suggesting multiple, non-independent genetic incompatibilities contribute to barriers to gene flow in the hybrid zone. PMID:25487987

  18. Site-Specific Secretome Map Evidences VSMC-Related Markers of Coronary Atherosclerosis Grade and Extent in the Hypercholesterolemic Swine

    PubMed Central

    Rocchiccioli, Silvia; Cecchettini, Antonella; Ucciferri, Nadia; Terreni, Marianna; Viglione, Federica; Trivella, Maria Giovanna; Citti, Lorenzo; Parodi, Oberdan; Pelosi, Gualtiero

    2015-01-01

    A major drawback in coronary atherosclerosis (ATS) research is the difficulty of investigating early phase of plaque growth and related features in the clinical context. In this study, secreted proteins from atherosclerotic coronary arteries in a hypercholesterolemic swine model were characterized by a proteomics approach and their expression was correlated to site-specific ATS stage and extent. A wide coronary artery map of secreted proteins has been obtained in high fat (HF) diet induced ATS swine model and a significantly different expression of many proteins related to vascular smooth muscle cell (VSMC) activation/migration has been identified. Significant associations with ATS stage of HF coronary lesions were found for several VSMC-derived proteins and validated for chitinase 3 like protein 1 (CHI3L1) by tissue immunoexpression. A direct correlation (R2 = 0.85) was evidenced with intima to media thickness ratio values and ELISA confirmed the higher blood concentrations of CHI3L1 in HF cases. These findings confirmed the pivotal role of VSMCs in coronary plaque development and demonstrated a strong site-specific relation between VSMC-secreted CHI3L1 and lesion grade, suggesting that this protein could be proposed as a useful biomarker for diagnosing and staging of atherosclerotic lesions in coronary artery disease. PMID:26379359

  19. Alaska Geothermal Sites Map and Database: Bringing together legacy and new geothermal data for research, exploration and development

    NASA Astrophysics Data System (ADS)

    Clough, J. G.; Harun, N. T.; Hughes, C. A.; Weakland, J. R.; Cameron, C. E.

    2013-12-01

    Geothermal exploration activities in Alaska from the late 1970s into the 1980s generated vast quantities of scientific data that currently is in unpublished, forgotten and obscure, as well as published formats. Alaska has 61 hot springs (hotter than 50°C) and 34 'warm to cool springs' (cooler than 50°C). Thirty-seven thermal springs are located within the Aleutian and Alaska Peninsula volcanic arc into and are related to elevated heat flows in areas of arc volcanism as well as crustal scale faults associated with accretionary tectonism. The central interior belt that extends from the Seward Peninsula to Circle Hot Springs contains 37 thermal springs that formed due to mostly extensional tectonic forces. An additional 17 thermal springs are in southeast Alaska and 4 are in the Wrangell Mountains. A new cycle of geothermal exploration is underway in Alaska and is producing a wealth of new geothermal data. The Alaska Division of Geological and Geophysical Surveys (ADGGS), funded by the National Geothermal Data System, is compiling both new and legacy geothermal data into a comprehensive database accessible on the ADGGS website. ADGGS has created a new ';Geothermal Sites of Alaska Map' and associated database that includes data on geothermal hot springs, direct use of geothermal resources, volcanic vents, aqueous geochemistry, borehole temperatures, core descriptions, rock chemistry, earthquakes in proximity to hot springs, and active faults. Geothermal hot springs includes locality, temperature, flow rate, sources and related resources. Direct use of geothermal resources contains facilities, capacity, energy use, temperature, flow rate and contact information from geothermal hot springs that are or have recently been used for recreational use, space heating, agricultural or energy use. Volcanic vents records 395 volcanic vents and fumaroles throughout the state that are Holocene or younger. It includes their age, location, elevation, geologic history, composition, and information source. Aqueous geochemistry, a compilation of aqueous chemistry, free gas and isotopes analyses. Aqueous geochemical analyses consist of 407 aqueous geochemical analyses from 85 geothermal sites throughout Alaska. This template also includes 106 free gas analyses from 31 geothermal sites. Isotopic analyses (285) of waters from 42 geothermal sites are also contained in this geochemical data. Borehole temperature data from geothermal, and oil and gas wells are presented along with thermal depth profiles where available. Earthquakes in proximity to hot springs consists of 1,975 earthquakes that are within 5 km of thermal hot springs and may be used to detect underground movement of thermal waters. Active faults comprises active faults across Alaska (1,527) including fault type, location, orientation and slip rate. Additionally, a new comprehensive and searchable Alaska geothermal bibliography, with links to downloadable reference sources was created during this study. The completed Alaska geothermal sites map and database will be accessible to the public and industry and will enable research and development of geothermal sites in Alaska.

  20. Reference interaction site model and optimized perturbation theories of colloidal dumbbells with increasing anisotropy

    NASA Astrophysics Data System (ADS)

    Munaň, Gianmarco; Gámez, Francisco; Costa, Dino; Caccamo, Carlo; Sciortino, Francesco; Giacometti, Achille

    2015-06-01

    We investigate thermodynamic properties of anisotropic colloidal dumbbells in the frameworks provided by the Reference Interaction Site Model (RISM) theory and an Optimized Perturbation Theory (OPT), this latter based on a fourth-order high-temperature perturbative expansion of the free energy, recently generalized to molecular fluids. Our model is constituted by two identical tangent hard spheres surrounded by square-well attractions with same widths and progressively different depths. Gas-liquid coexistence curves are obtained by predicting pressures, free energies, and chemical potentials. In comparison with previous simulation results, RISM and OPT agree in reproducing the progressive reduction of the gas-liquid phase separation as the anisotropy of the interaction potential becomes more pronounced; in particular, the RISM theory provides reasonable predictions for all coexistence curves, bar the strong anisotropy regime, whereas OPT performs generally less well. Both theories predict a linear dependence of the critical temperature on the interaction strength, reproducing in this way the mean-field behavior observed in simulations; the critical density—that drastically drops as the anisotropy increases—turns to be less accurate. Our results appear as a robust benchmark for further theoretical studies, in support to the simulation approach, of self-assembly in model colloidal systems.

  1. Large, motile epifauna interact strongly with harpacticoid copepods and polychaetes at a bathyal site

    NASA Astrophysics Data System (ADS)

    Thistle, David; Eckman, James E.; Paterson, Gordon L. J.

    2008-03-01

    Strengths of interactions among groups of animals in deep-sea-sediment communities are poorly known. Large, motile epifauna (LME) such as sea cucumbers, star fishes, and demersal fishes occur in the deep sea and are sources of predation, disturbance, and habitat alteration and thus have the potential to interact strongly with infauna. At a site off the southwestern coast of the United States (32°57.3'N, 117°32.2'W, 780 m depth), we excluded the LME from five 75- ×75-cm plots with cages. After 143 d, we sampled these plots and five plots of the same size paired with them as controls. Abundances of harpacticoid copepods and polychaetes were significantly lower in cages than in controls. In several cages, nematodes and kinorhynchs were also dramatically less abundant than in paired controls. Results suggest that LME ordinarily affect the infaunal assemblage in such a way that harpacticoids and polychaetes (and perhaps nematodes and kinorhynchs) can maintain higher abundances than they can in the absence of LME, indicating that strong interactions can influence the organization of deep-sea-sediment communities. In a multivariate analysis of environmental parameters, cage and control samples were intermixed, so if the effect is transmitted by alterations of the environment by the LME, the nature of the alterations must be relatively local and remains to be discovered.

  2. Reference interaction site model and optimized perturbation theories of colloidal dumbbells with increasing anisotropy

    SciTech Connect

    Munaň, Gianmarco Costa, Dino; Caccamo, Carlo; Gámez, Francisco; Giacometti, Achille

    2015-06-14

    We investigate thermodynamic properties of anisotropic colloidal dumbbells in the frameworks provided by the Reference Interaction Site Model (RISM) theory and an Optimized Perturbation Theory (OPT), this latter based on a fourth-order high-temperature perturbative expansion of the free energy, recently generalized to molecular fluids. Our model is constituted by two identical tangent hard spheres surrounded by square-well attractions with same widths and progressively different depths. Gas-liquid coexistence curves are obtained by predicting pressures, free energies, and chemical potentials. In comparison with previous simulation results, RISM and OPT agree in reproducing the progressive reduction of the gas-liquid phase separation as the anisotropy of the interaction potential becomes more pronounced; in particular, the RISM theory provides reasonable predictions for all coexistence curves, bar the strong anisotropy regime, whereas OPT performs generally less well. Both theories predict a linear dependence of the critical temperature on the interaction strength, reproducing in this way the mean-field behavior observed in simulations; the critical density—that drastically drops as the anisotropy increases—turns to be less accurate. Our results appear as a robust benchmark for further theoretical studies, in support to the simulation approach, of self-assembly in model colloidal systems.

  3. A maize map standard with sequenced core markers, grass genome reference points and 932 expressed sequence tagged sites (ESTs) in a 1736-locus map.

    PubMed Central

    Davis, G L; McMullen, M D; Baysdorfer, C; Musket, T; Grant, D; Staebell, M; Xu, G; Polacco, M; Koster, L; Melia-Hancock, S; Houchins, K; Chao, S; Coe, E H

    1999-01-01

    We have constructed a 1736-locus maize genome map containing1156 loci probed by cDNAs, 545 probed by random genomic clones, 16 by simple sequence repeats (SSRs), 14 by isozymes, and 5 by anonymous clones. Sequence information is available for 56% of the loci with 66% of the sequenced loci assigned functions. A total of 596 new ESTs were mapped from a B73 library of 5-wk-old shoots. The map contains 237 loci probed by barley, oat, wheat, rice, or tripsacum clones, which serve as grass genome reference points in comparisons between maize and other grass maps. Ninety core markers selected for low copy number, high polymorphism, and even spacing along the chromosome delineate the 100 bins on the map. The average bin size is 17 cM. Use of bin assignments enables comparison among different maize mapping populations and experiments including those involving cytogenetic stocks, mutants, or quantitative trait loci. Integration of nonmaize markers in the map extends the resources available for gene discovery beyond the boundaries of maize mapping information into the expanse of map, sequence, and phenotype information from other grass species. This map provides a foundation for numerous basic and applied investigations including studies of gene organization, gene and genome evolution, targeted cloning, and dissection of complex traits. PMID:10388831

  4. Association mapping of disease resistance traits in rainbow trout using restriction site associated DNA sequencing.

    PubMed

    Campbell, Nathan R; LaPatra, Scott E; Overturf, Ken; Towner, Richard; Narum, Shawn R

    2014-12-01

    Recent advances in genotyping-by-sequencing have enabled genome-wide association studies in nonmodel species including those in aquaculture programs. As with other aquaculture species, rainbow trout and steelhead (Oncorhynchus mykiss) are susceptible to disease and outbreaks can lead to significant losses. Fish culturists have therefore been pursuing strategies to prevent losses to common pathogens such as Flavobacterium psychrophilum (the etiological agent for bacterial cold water disease [CWD]) and infectious hematopoietic necrosis virus (IHNV) by adjusting feed formulations, vaccine development, and selective breeding. However, discovery of genetic markers linked to disease resistance offers the potential to use marker-assisted selection to increase resistance and reduce outbreaks. For this study we sampled juvenile fish from 40 families from 2-yr classes that either survived or died after controlled exposure to either CWD or IHNV. Restriction site-associated DNA sequencing produced 4661 polymorphic single-nucleotide polymorphism loci after strict filtering. Genotypes from individual survivors and mortalities were then used to test for association between disease resistance and genotype at each locus using the program TASSEL. After we accounted for kinship and stratification of the samples, tests revealed 12 single-nucleotide polymorphism markers that were highly associated with resistance to CWD and 19 markers associated with resistance to IHNV. These markers are candidates for further investigation and are expected to be useful for marker assisted selection in future broodstock selection for various aquaculture programs. PMID:25354781

  5. Single-cell polyadenylation site mapping reveals 3? isoform choice variability

    PubMed Central

    Velten, Lars; Anders, Simon; Pekowska, Aleksandra; Järvelin, Aino I; Huber, Wolfgang; Pelechano, Vicent; Steinmetz, Lars M

    2015-01-01

    Cell-to-cell variability in gene expression is important for many processes in biology, including embryonic development and stem cell homeostasis. While heterogeneity of gene expression levels has been extensively studied, less attention has been paid to mRNA polyadenylation isoform choice. 3? untranslated regions regulate mRNA fate, and their choice is tightly controlled during development, but how 3? isoform usage varies within genetically and developmentally homogeneous cell populations has not been explored. Here, we perform genome-wide quantification of polyadenylation site usage in single mouse embryonic and neural stem cells using a novel single-cell transcriptomic method, BATSeq. By applying BATBayes, a statistical framework for analyzing single-cell isoform data, we find that while the developmental state of the cell globally determines isoform usage, single cells from the same state differ in the choice of isoforms. Notably this variation exceeds random selection with equal preference in all cells, a finding that was confirmed by RNA FISH data. Variability in 3? isoform choice has potential implications on functional cell-to-cell heterogeneity as well as utility in resolving cell populations. PMID:26040288

  6. [Interaction of single-stranded DNA with the second DNA-binding site of RecA nucleoprotein filament].

    PubMed

    Bugreeva, I P; Bugreev, D V; Nevinski?, G A

    2007-01-01

    RecA protein first forms filament on single-stranded (ss) DNA forming the first DNA-binding site for interaction with this ssDNA a formation of the second site for interaction with double-stranded DNA occurs in parallel. Then the formed nucleoprotein filament interacts with molecules of double-stranded (ds) DNA but can also recognize ssDNA. The formed complex realizes a search of homology and exchange of homologous strands. We have studied recently the mechanism of RecA filamentation on ssDNA. Here a study of interaction of different DNAs with the second site of RecA filament using a method of stepwise increase of the ligand complicity was performed. The second site under recognition interacts with every nucleotide units of DNA-ligand forming contact with both internucleotide phosphate groups and bases of DNA. Pyrimidinic d(pC)n [Russian character: see text d(pT)n oligonucleotides interact with the second site of the RecA filament more effectively than with d(pA)n oligonucleotides. This occurs due to a more effective interaction of the RecA filament with 5'-terminal unit of pyrimidinic DNAs and to a difference in specific conformational changes of nucleoprotein filaments in the complex with purinic and pyrimidinic DNAs. A comparison of thermodynamic characteristics of DNA recognition by the first and the second sites of DNA recognition is carried out. It was shown that at n >10 d(pC)n d(pN)n interact with the second site weaker, that with the first site. The complexation of the second site with d(pA)n at n >20 is more effective than with the first site. The difference in the affinity of d(pA)n to the fist and second sites is increased monotonically with the enhancement of their length. Possible mechanisms of RecA-dependent search of homology and strand exchange are discussed. PMID:17685230

  7. Mapping the Transcriptome-Wide Landscape of RBP Binding Sites Using gPAR-CLIP-seq: Experimental Procedures.

    PubMed

    Han, Ting; Kim, John K

    2016-01-01

    An estimated 5-10 % of protein-coding genes in eukaryotic genomes encode RNA-binding proteins (RBPs). Through dynamic changes in RNA recognition, RBPs posttranscriptionally regulate the biogenesis, transport, inheritance, storage, and degradation of RNAs. Understanding such widespread RBP-mediated posttranscriptional regulatory mechanisms requires comprehensive discovery of the in vivo binding sites of RBPs. Here, we describe the experimental procedures of the gPAR-CLIP-seq (global photoactivatable-ribonucleoside-enhanced cross-linking and precipitation followed by deep sequencing) approach we recently developed for capturing and sequencing regions of the transcriptome bound by RBPs in budding yeast. Unlike the standard PAR-CLIP method, which identifies the bound RNA substrates for a single RBP, the gPAR-CLIP-seq method was developed to isolate and sequence all mRNA sites bound by the cellular "RBPome." The gPAR-CLIP-seq approach is readily applicable to a variety of organisms and cell lines to profile global RNA-protein interactions underlying posttranscriptional gene regulation. The complete landscape of RBP binding sites provides insights to the function of all RNA cis-regulatory elements in an organism and reveals fundamental mechanisms of posttranscriptional gene regulation. PMID:26483017

  8. Fine Mapping of the Interaction between C4b-Binding Protein and Outer Membrane Proteins LigA and LigB of Pathogenic Leptospira interrogans.

    PubMed

    Breda, Leandro C D; Hsieh, Ching-Lin; Castiblanco Valencia, Mónica M; da Silva, Ludmila B; Barbosa, Angela S; Blom, Anna M; Yung-Fu, Chang; Isaac, Lourdes

    2015-10-01

    The complement system consists of more than 40 proteins that participate in the inflammatory response and in pathogen killing. Complement inhibitors are necessary to avoid the excessive consumption and activation of this system on host cells. Leptospirosis is a worldwide zoonosis caused by spirochetes from the genus Leptospira. Pathogenic leptospires are able to escape from complement activation by binding to host complement inhibitors Factor H [FH] and C4b-binding protein (C4BP) while non-pathogenic leptospires are rapidly killed in the presence of fresh serum. In this study, we demonstrate that complement control protein domains (CCP) 7 and 8 of C4BP ?-chain interact with the outer membrane proteins LcpA, LigA and LigB from the pathogenic leptospire L. interrogans. The interaction between C4BP and LcpA, LigA and LigB is sensitive to ionic strength and inhibited by heparin. We fine mapped the LigA and LigB domains involved in its binding to C4BP and heparin and found that both interactions are mediated through the bacterial immunoglobulin-like (Big) domains 7 and 8 (LigA7-8 and LigB7-8) of both LigA and LigB and also through LigB9-10. Therefore, C4BP and heparin may share the same binding sites on Lig proteins. PMID:26517116

  9. Fine Mapping of the Interaction between C4b-Binding Protein and Outer Membrane Proteins LigA and LigB of Pathogenic Leptospira interrogans

    PubMed Central

    Breda, Leandro C. D.; Hsieh, Ching-Lin; Castiblanco Valencia, Mónica M.; da Silva, Ludmila B.; Barbosa, Angela S.; Blom, Anna M.; Yung-Fu, Chang; Isaac, Lourdes

    2015-01-01

    The complement system consists of more than 40 proteins that participate in the inflammatory response and in pathogen killing. Complement inhibitors are necessary to avoid the excessive consumption and activation of this system on host cells. Leptospirosis is a worldwide zoonosis caused by spirochetes from the genus Leptospira. Pathogenic leptospires are able to escape from complement activation by binding to host complement inhibitors Factor H [FH] and C4b-binding protein (C4BP) while non-pathogenic leptospires are rapidly killed in the presence of fresh serum. In this study, we demonstrate that complement control protein domains (CCP) 7 and 8 of C4BP ?-chain interact with the outer membrane proteins LcpA, LigA and LigB from the pathogenic leptospire L. interrogans. The interaction between C4BP and LcpA, LigA and LigB is sensitive to ionic strength and inhibited by heparin. We fine mapped the LigA and LigB domains involved in its binding to C4BP and heparin and found that both interactions are mediated through the bacterial immunoglobulin-like (Big) domains 7 and 8 (LigA7-8 and LigB7-8) of both LigA and LigB and also through LigB9-10. Therefore, C4BP and heparin may share the same binding sites on Lig proteins. PMID:26517116

  10. Mapping the interactions of the single-stranded DNA binding protein of bacteriophage T4 (gp32) with DNA lattices at single nucleotide resolution: polynucleotide binding and cooperativity

    PubMed Central

    Jose, Davis; Weitzel, Steven E.; Baase, Walter A.; Michael, Miya M.; von Hippel, Peter H.

    2015-01-01

    We here use our site-specific base analog mapping approach to study the interactions and binding equilibria of cooperatively-bound clusters of the single-stranded DNA binding protein (gp32) of the T4 DNA replication complex with longer ssDNA (and dsDNA) lattices. We show that in cooperatively bound clusters the binding free energy appears to be equi-partitioned between the gp32 monomers of the cluster, so that all bind to the ssDNA lattice with comparable affinity, but also that the outer domains of the gp32 monomers at the ends of the cluster can fluctuate on and off the lattice and that the clusters of gp32 monomers can slide along the ssDNA. We also show that at very low binding densities gp32 monomers bind to the ssDNA lattice at random, but that cooperatively bound gp32 clusters bind preferentially at the 5?-end of the ssDNA lattice. We use these results and the gp32 monomer-binding results of the companion paper to propose a detailed model for how gp32 might bind to and interact with ssDNA lattices in its various binding modes, and also consider how these clusters might interact with other components of the T4 DNA replication complex. PMID:26275774

  11. Mapping the CD4 binding site for human immunodeficiency virus by alanine-scanning mutagenesis.

    PubMed Central

    Ashkenazi, A; Presta, L G; Marsters, S A; Camerato, T R; Rosenthal, K A; Fendly, B M; Capon, D J

    1990-01-01

    Infection of mononuclear cells by human immunodeficiency virus (HIV) begins with binding of the viral envelope glycoprotein, gp120, to its receptor, CD4. CD4 contains four extracellular immunoglobulin-like domains, the first of which (V1) is sufficient for HIV binding. V1 contains three sequences homologous to the antigen-complementarity-determining regions (CDR1 to -3) of immunoglobulin variable domains. While all three immunoglobulin CDRs are involved in antigen binding, only amino acids within and flanking the CDR2-like region of CD4 have been shown previously to be involved in gp120 binding. To investigate whether other regions in V1 take part in gp120 binding, we substituted alanine for each of 64 amino acids, including all of the hydrophilic residues in this domain. Mutations at four locations outside the CDR2-like sequence (amino acids 29, 59-64, 77-81, and 85) markedly affected gp120 binding, but not the overall structure of V1 as probed with eight conformationally sensitive monoclonal antibodies. Thus, the gp120-binding site of CD4 is not limited to the CDR2-like sequence and consists of several discontinuous segments. Several amino acids were identified that are critical for the conformation of V1; the importance of these residues suggests some differences in the folding of this domain compared to immunoglobulin variable domains. Three amino acid substitutions were found that increase the affinity for gp120 significantly (1.7- to 2-fold individually and 4.2-fold when combined), suggesting that it may be possible to improve the HIV-blocking ability of CD4-based molecules by increasing their gp120 binding affinity. Images PMID:2402498

  12. Mapping the Binding Site of the Inhibitor Tariquidar That Stabilizes the First Transmembrane Domain of P-glycoprotein.

    PubMed

    Loo, Tip W; Clarke, David M

    2015-12-01

    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

  13. Interactions of aniline with soil and groundwater at an industrial spill site.

    PubMed Central

    Kosson, D S; Byrne, S V

    1995-01-01

    The interactions of aniline with soil at an industrial spill site were investigated. Sorption of aniline to the soil was observed to occur through a two-step mechanism. The first step was an ion exchange process with the protonated amine serving as an organic cation. This step was influenced by solution pH and ionic composition. The second step was covalent bonding most likely with quinone moieties and oxidation with polymerization of aniline. The extent of covalent bonding was influenced by the presence of oxygen and redox potential. The majority of aniline that was bound to the soil did not readily desorb under a variety of abiotic conditions. However, aniline was released to a significant extent in the presence of denitrifying and methanogenic microbial activity. Aniline in aqueous solution was readily biodegradable under aerobic and denitrifying conditions. Soil-bound aniline was observed not to be biodegradable. This paper provides an overview of results. PMID:8565915

  14. Accurate calculations of the hydration free energies of druglike molecules using the reference interaction site model

    NASA Astrophysics Data System (ADS)

    Palmer, David S.; Sergiievskyi, Volodymyr P.; Jensen, Frank; Fedorov, Maxim V.

    2010-07-01

    We report on the results of testing the reference interaction site model (RISM) for the estimation of the hydration free energy of druglike molecules. The optimum model was selected after testing of different RISM free energy expressions combined with different quantum mechanics and empirical force-field methods of structure optimization and atomic partial charge calculation. The final model gave a systematic error with a standard deviation of 2.6 kcal/mol for a test set of 31 molecules selected from the SAMPL1 blind challenge set [J. P. Guthrie, J. Phys. Chem. B 113, 4501 (2009)]. After parametrization of this model to include terms for the excluded volume and the number of atoms of different types in the molecule, the root mean squared error for a test set of 19 molecules was less than 1.2 kcal/mol.

  15. Identifying and Mapping Factors Affecting the Siting of Offshore This work is supported in part by the National Science Foundation under NSF award number 1460461. Any opinions, findings,

    E-print Network

    Mountziaris, T. J.

    . (2010). Large- Scale Offshore Wind Power in the United States Assessment of Opportunities and barriers., & Kempton, W. (2012). Calculating the offshore wind power resource: Robust assessment methods appliedIdentifying and Mapping Factors Affecting the Siting of Offshore Wind Farms This work is supported

  16. Science-Policy Interactions in MPA Site Selection in the Dutch Part of the North Sea

    NASA Astrophysics Data System (ADS)

    van Haastrecht, Eline K.; Toonen, Hilde M.

    2011-04-01

    At the 7th conference of the parties to the Convention on Biological Diversity (CBD-COP7, Kuala Lumpur, 2004) it was agreed to establish a global network of marine and coastal protected areas by 2012. The defined objectives of this MPA-network are based on the ecosystem approach: to protect biodiversity and other ecological values, and to ensure sustainable use. The (inter)national policy guidelines state that the selection of MPAs should be based on scientific information and ecological criteria only. As a signatory to the Convention, the Netherlands is now faced with meeting this obligation, and the process of designating the first Marine Protected Areas (MPAs) in the Dutch part of the North Sea is currently in progress. We focus on the science-policy interactions that are part of this Dutch MPA selection process. By taking a closer look at the contemporary site selection process as well as its historical background, we show that ecological, socio-economic and political considerations cannot always be easily separated. Uncertainty is high and the ultimate selection and delimitation of candidate sites rather seems to be the result of a balancing act between ecological, socio-economic and political interests, in which scientific and policy guiding procedures blend with ad-hoc political decision making, and with expert judgment in cases where data is lacking. As such, this paper presents an example of present-day environmental policy making in action.

  17. Development of a Model Protein Interaction Pair as a Benchmarking Tool for the Quantitative Analysis of 2-Site Protein-Protein Interactions.

    PubMed

    Yamniuk, Aaron P; Newitt, John A; Doyle, Michael L; Arisaka, Fumio; Giannetti, Anthony M; Hensley, Preston; Myszka, David G; Schwarz, Fred P; Thomson, James A; Eisenstein, Edward

    2015-12-01

    A significant challenge in the molecular interaction field is to accurately determine the stoichiometry and stepwise binding affinity constants for macromolecules having >1 binding site. The mission of the Molecular Interactions Research Group (MIRG) of the Association of Biomolecular Resource Facilities (ABRF) is to show how biophysical technologies are used to quantitatively characterize molecular interactions, and to educate the ABRF members and scientific community on the utility and limitations of core technologies [such as biosensor, microcalorimetry, or analytic ultracentrifugation (AUC)]. In the present work, the MIRG has developed a robust model protein interaction pair consisting of a bivalent variant of the Bacillus amyloliquefaciens extracellular RNase barnase and a variant of its natural monovalent intracellular inhibitor protein barstar. It is demonstrated that this system can serve as a benchmarking tool for the quantitative analysis of 2-site protein-protein interactions. The protein interaction pair enables determination of precise binding constants for the barstar protein binding to 2 distinct sites on the bivalent barnase binding partner (termed binase), where the 2 binding sites were engineered to possess affinities that differed by 2 orders of magnitude. Multiple MIRG laboratories characterized the interaction using isothermal titration calorimetry (ITC), AUC, and surface plasmon resonance (SPR) methods to evaluate the feasibility of the system as a benchmarking model. Although general agreement was seen for the binding constants measured using solution-based ITC and AUC approaches, weaker affinity was seen for surface-based method SPR, with protein immobilization likely affecting affinity. An analysis of the results from multiple MIRG laboratories suggests that the bivalent barnase-barstar system is a suitable model for benchmarking new approaches for the quantitative characterization of complex biomolecular interactions. PMID:26543437

  18. Development of a Model Protein Interaction Pair as a Benchmarking Tool for the Quantitative Analysis of 2-Site Protein-Protein Interactions

    PubMed Central

    Newitt, John A.; Doyle, Michael L.; Arisaka, Fumio; Giannetti, Anthony M.; Hensley, Preston; Myszka, David G.; Schwarz, Fred P.; Thomson, James A.; Eisenstein, Edward

    2015-01-01

    A significant challenge in the molecular interaction field is to accurately determine the stoichiometry and stepwise binding affinity constants for macromolecules having >1 binding site. The mission of the Molecular Interactions Research Group (MIRG) of the Association of Biomolecular Resource Facilities (ABRF) is to show how biophysical technologies are used to quantitatively characterize molecular interactions, and to educate the ABRF members and scientific community on the utility and limitations of core technologies [such as biosensor, microcalorimetry, or analytic ultracentrifugation (AUC)]. In the present work, the MIRG has developed a robust model protein interaction pair consisting of a bivalent variant of the Bacillus amyloliquefaciens extracellular RNase barnase and a variant of its natural monovalent intracellular inhibitor protein barstar. It is demonstrated that this system can serve as a benchmarking tool for the quantitative analysis of 2-site protein-protein interactions. The protein interaction pair enables determination of precise binding constants for the barstar protein binding to 2 distinct sites on the bivalent barnase binding partner (termed binase), where the 2 binding sites were engineered to possess affinities that differed by 2 orders of magnitude. Multiple MIRG laboratories characterized the interaction using isothermal titration calorimetry (ITC), AUC, and surface plasmon resonance (SPR) methods to evaluate the feasibility of the system as a benchmarking model. Although general agreement was seen for the binding constants measured using solution-based ITC and AUC approaches, weaker affinity was seen for surface-based method SPR, with protein immobilization likely affecting affinity. An analysis of the results from multiple MIRG laboratories suggests that the bivalent barnase-barstar system is a suitable model for benchmarking new approaches for the quantitative characterization of complex biomolecular interactions. PMID:26543437

  19. Genotype to Phenotype Maps: Multiple Input Abiotic Signals Combine to Produce Growth Effects via Attenuating Signaling Interactions in Maize

    PubMed Central

    Makumburage, G. Buddhika; Richbourg, H. Lee; LaTorre, Kalindi D.; Capps, Andrew; Chen, Cuixen; Stapleton, Ann E.

    2013-01-01

    The complexity of allele interactions constrains crop improvement and the prediction of disease susceptibility. Additive allele effects are the foundation for selection in animal and plant breeding, and complex genetic and environmental interactions contribute to inefficient detection of desirable loci. Manipulation and modeling of other sources of variation, such as environmental variables, have the potential to improve our prediction of phenotype from genotype. As an example of our approach to analysis of the network linking environmental input to alleles, we mapped the genetic architecture of single and combined abiotic stress responses in two maize mapping populations and compared the observed genetic architecture patterns to simple theoretical predictions. Comparisons of single and combined stress effects on growth and biomass traits exhibit patterns of allele effects that suggest attenuating interactions among physiological signaling steps in drought and ultraviolet radiation stress responses. The presence of attenuating interactions implies that shared QTL found in sets of environments could be used to group environment types and identify underlying environmental similarities, and that patterns of stress-dependent genetic architecture should be studied as a way to prioritize prebreeding populations. A better understanding of whole-plant interactor pathways and genetic architecture of multiple-input environmental signaling has the potential to improve the prediction of genomic value in plant breeding and crop modeling. PMID:24142926

  20. Intermolecular versus intramolecular interactions of the vinculin binding site 33 of talin

    SciTech Connect

    Yogesha, S.D.; SHarff, A.; Bricogne, G.; Izard, .T.

    2012-03-13

    The cytoskeletal proteins talin and vinculin are localized at cell-matrix junctions and are key regulators of cell signaling, adhesion, and migration. Talin couples integrins via its FERM domain to F-actin and is an important regulator of integrin activation and clustering. The 220 kDa talin rod domain comprises several four- and five-helix bundles that harbor amphipathic {alpha}-helical vinculin binding sites (VBSs). In its inactive state, the hydrophobic VBS residues involved in binding to vinculin are buried within these helix bundles, and the mechanical force emanating from bound integrin receptors is thought necessary for their release and binding to vinculin. The crystal structure of a four-helix bundle of talin that harbors one of these VBSs, coined VBS33, was recently determined. Here we report the crystal structure of VBS33 in complex with vinculin at 2 {angstrom} resolution. Notably, comparison of the apo and vinculin bound structures shows that intermolecular interactions of the VBS33 {alpha}-helix with vinculin are more extensive than the intramolecular interactions of the VBS33 within the talin four-helix bundle.

  1. PDZ interaction site in ephrinB2 is required for the remodeling of lymphatic vasculature

    PubMed Central

    Mäkinen, Taija; Adams, Ralf H.; Bailey, John; Lu, Qiang; Ziemiecki, Andrew; Alitalo, Kari; Klein, Rüdiger; Wilkinson, George A.

    2005-01-01

    The transmembrane ligand ephrinB2 and its cognate Eph receptor tyrosine kinases are important regulators of embryonic blood vascular morphogenesis. However, the molecular mechanisms required for ephrinB2 transduced cellular signaling in vivo have not been characterized. To address this question, we generated two sets of knock-in mice: ephrinB2?V mice expressed ephrinB2 lacking the C-terminal PDZ interaction site, and ephrinB25F mice expressed ephrinB2 in which the five conserved tyrosine residues were replaced by phenylalanine to disrupt phosphotyrosine-dependent signaling events. Our analysis revealed that the homozygous mutant mice survived the requirement of ephrinB2 in embryonic blood vascular remodeling. However, ephrinB2?V/?V mice exhibited major lymphatic defects, including a failure to remodel their primary lymphatic capillary plexus into a hierarchical vessel network, hyperplasia, and lack of luminal valve formation. Unexpectedly, ephrinB25F/5F mice displayed only a mild lymphatic phenotype. Our studies define ephrinB2 as an essential regulator of lymphatic development and indicate that interactions with PDZ domain effectors are required to mediate its functions. PMID:15687262

  2. Modeling Groundwater-Surface Water Interaction and Contaminant Transport of Chlorinated Solvent Contaminated Site

    NASA Astrophysics Data System (ADS)

    Yimer Ebrahim, Girma; Jonoski, Andreja; van Griensven, Ann; Dujardin, Juliette; Baetelaan, Okke; Bronders, Jan

    2010-05-01

    Chlorinated-solvent form one of the largest groups of environmental chemicals. Their use and misuse in industry have lead to a large entry of these chemicals into the environment, resulting in widespread dissemination and oftentimes environmental contamination. Chlorinated solvent contamination of groundwater resources has been widely reported. For instance, there has been much interest in the assessment of these contaminant levels and their evolutions with time in the groundwater body below the Vilvoorde-Machelen industrial area (Belgium). The long industrial history of the area has lead to complex patterns of pollution from multiple sources and the site has been polluted to the extent that individual plumes are not definable any more. Understanding of groundwater/surface water interaction is a critical component for determining the fate of contaminant both in streams and ground water due to the fact that groundwater and surface water are in continuous dynamic interaction in the hydrologic cycle. The interaction has practical consequences in the quantity and quality of water in either system in the sense that depletion and/or contamination of one of the system will eventually affect the other one. The transition zone between a stream and its adjacent aquifer referred to as the hyporheic zone plays a critical role in governing contaminant exchange and transformation during water exchange between the two water bodies. The hyporheic zone of Zenne River ( the main receptor ) is further complicated due to the fact that the river banks are artificially trained with sheet piles along its reach extending some 12 m below the surface. This study demonstrates the use of MODFLOW, a widely used modular three-dimensional block-centred finite difference, saturated flow model for simulating the flow and direction of movement of groundwater through aquifer and stream-aquifer interaction and the use of transport model RT3D, a three-dimensional multi-species reactive transport model capable of incorporating multiple chemical and biological reactions to model the movement and chemical alteration of chlorinated solvents as they move with groundwater through the subsurface and reach to the surface water of the Zenne River . Keywords: MODFLOW, RT3D, Chlorinated-solvent; groundwater/surface water interaction ACKNOWLEDGEMENT The authors would like to thank the EU/FP7 AQUAREHAB Project for the financial support.

  3. 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.

  4. Geomorphic Mapping and Paleoterrain Generation for use in Modeling Holocene (8,000 1,500 yr) Agropastoral Landuse and Landscape Interactions in Southeast Spain

    NASA Astrophysics Data System (ADS)

    Arrowsmith, J. R.; Dimaggio, E. N.; Barton, C. M.; Sarjoughian, H. S.; Fall, P.; Falconer, S. E.; Ullah, I. I.

    2006-12-01

    Dramatic changes in land use were associated with the rise of agriculture in the mid Holocene. Both the surface properties and the drainage networks were changed. Along with the direct modifications to surface properties (vegetation change, sediment liberation, and compaction) and drainage network alteration (terracing, canals), up and downstream responses in the watersheds communicated these changes throughout the landscape. The magnitude, rate, and feedbacks with the growing human populations are critical questions in our effort to assess human-landscape interactions. Our interdisciplinary team has focused on two field sites around the Mediterranean for model development and testing. We are combining high resolution process- based models of landscape change implemented within the GRASS GIS with agent based models of agropastoral behavior and driven by high resolution climate and vegetation models. In the Spanish field area (Penaguila Valley, 38.41 N 0.23 W), we have produced detailed (1:10,000) geomorphic maps which we combine with high resolution Digital Elevation Models (DEMs) on which we can run the surface process models to assess the portions of the landscape that are most sensitive to the postulated agropastoral landuse changes. To support this modeling we have produced the 1 m DEMs from softcopy photogrammetry. This DEM has greatly improved our overall spatial resolution to permit more accurate terrace correlations and improved quantitative assessment of morphologic processes (e.g. channel erosion, slope stability). In stereo, we have mapped overall landscape morphology that emphasizes areas of active erosion and alluvial terrace surfaces. Alluvial terraces are crucial to this research because they record periods of past stable topography and those of mid Holocene age were settled and farmed. We have correlated mapped terraces across the landscape using elevation and morphological distinctions. Using ArcGIS, we interpolated surfaces across equivalent terraces using triangulated irregular networks (TINs) allowing reconstruction of multiple regional landscapes to establish a chronosequence of absolute landscape change. This mapping and reconstruction will be field checked and numerical age constraints applied. Interestingly, our tentative age assessment of the lowest broad surface indicates that it was occupied about 5 ka, and now has been incised by 20 m. Archeological sites have been cut by the incision. This change from a broad low relief alluvial surface to one cut by narrow channels may have been an important change for the local populations and caused them to change their behaviors, even though it may have been initially triggered by distributed landscape change in the watershed, due to agropastoral activities.

  5. A General Pairwise Interaction Model Provides an Accurate Description of In Vivo Transcription Factor Binding Sites

    PubMed Central

    Santolini, Marc; Mora, Thierry; Hakim, Vincent

    2014-01-01

    The identification of transcription factor binding sites (TFBSs) on genomic DNA is of crucial importance for understanding and predicting regulatory elements in gene networks. TFBS motifs are commonly described by Position Weight Matrices (PWMs), in which each DNA base pair contributes independently to the transcription factor (TF) binding. However, this description ignores correlations between nucleotides at different positions, and is generally inaccurate: analysing fly and mouse in vivo ChIPseq data, we show that in most cases the PWM model fails to reproduce the observed statistics of TFBSs. To overcome this issue, we introduce the pairwise interaction model (PIM), a generalization of the PWM model. The model is based on the principle of maximum entropy and explicitly describes pairwise correlations between nucleotides at different positions, while being otherwise as unconstrained as possible. It is mathematically equivalent to considering a TF-DNA binding energy that depends additively on each nucleotide identity at all positions in the TFBS, like the PWM model, but also additively on pairs of nucleotides. We find that the PIM significantly improves over the PWM model, and even provides an optimal description of TFBS statistics within statistical noise. The PIM generalizes previous approaches to interdependent positions: it accounts for co-variation of two or more base pairs, and predicts secondary motifs, while outperforming multiple-motif models consisting of mixtures of PWMs. We analyse the structure of pairwise interactions between nucleotides, and find that they are sparse and dominantly located between consecutive base pairs in the flanking region of TFBS. Nonetheless, interactions between pairs of non-consecutive nucleotides are found to play a significant role in the obtained accurate description of TFBS statistics. The PIM is computationally tractable, and provides a general framework that should be useful for describing and predicting TFBSs beyond PWMs. PMID:24926895

  6. 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 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.

  7. Functional mapping of the neural circuitry of rat maternal motivation: effects of site-specific transient neural inactivation

    PubMed Central

    Pereira, Mariana; Morrell, Joan I.

    2011-01-01

    The present review focuses on recent studies from our laboratory examining the neural circuitry subserving rat maternal motivation across postpartum. We employed a site-specific neural inactivation method by infusion of bupivacaine to map the maternal motivation circuitry using two complementary behavioral approaches: unconditioned maternal responsiveness and choice of pup- over cocaine-conditioned incentives in a concurrent pup/cocaine choice conditioned place preference task. Our findings revealed that during the early postpartum period, distinct brain structures, including the medial preoptic area, ventral tegmental area and medial prefrontal cortex infralimbic and anterior cingulate subregions, contribute a pup-specific bias to the motivational circuitry. As the postpartum period progresses and the pups grow older, our findings further revealed that maternal responsiveness becomes progressively less dependent on medial preoptic area and medial prefrontal cortex infralimbic activity, and more distributed in the maternal circuitry, such that additional network components, including the medial prefrontal cortex prelimbic subregion, are recruited with maternal experience, and contribute to the expression of late postpartum maternal behavior. Collectively, our findings provide strong evidence that the remarkable ability of postpartum females to successfully care for their developing infants is subserved by a distributed neural network that carries out efficient and dynamic processing of complex, constantly changing incoming environmental and pup-related stimuli, ultimately allowing the progression of appropriate expression and waning of maternal responsiveness across the postpartum period. PMID:21815954

  8. Genome-Wide Mapping of Collier In Vivo Binding Sites Highlights Its Hierarchical Position in Different Transcription Regulatory Networks.

    PubMed

    de Taffin, Mathilde; Carrier, Yannick; Dubois, Laurence; Bataillé, Laetitia; Painset, Anaďs; Le Gras, Stéphanie; Jost, Bernard; Crozatier, Michčle; 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

  9. 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, Anaďs; Le Gras, Stéphanie; Jost, Bernard; Crozatier, Michčle; 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

  10. Human Alzheimer's disease synaptic O-GlcNAc site mapping and iTRAQ expression proteomics with ion trap mass spectrometry.

    PubMed

    Skorobogatko, Yuliya V; Deuso, John; Adolf-Bryfogle, Jared; Adolf-Bergfoyle, Jared; Nowak, Matthew G; Gong, Yuesong; Lippa, Carol Frances; Vosseller, Keith

    2011-03-01

    Neuronal synaptic functional deficits are linked to impaired learning and memory in Alzheimer's disease (AD). We recently demonstrated that O-GlcNAc, a novel cytosolic and nuclear carbohydrate post-translational modification, is enriched at neuronal synapses and positively regulates synaptic plasticity linked to learning and memory in mice. Reduced levels of O-GlcNAc have been observed in AD, suggesting a possible link to deficits in synaptic plasticity. Using lectin enrichment and mass spectrometry, we mapped several human cortical synaptic O-GlcNAc modification sites. Overlap in patterns of O-GlcNAcation between mouse and human appears to be high, as previously mapped mouse synaptic O-GlcNAc sites in Bassoon, Piccolo, and tubulin polymerization promoting protein p25 were identified in human. Novel O-GlcNAc modification sites were identified on Mek2 and RPN13/ADRM1. Mek2 is a signaling component of the Erk 1/2 pathway involved in synaptic plasticity. RPN13 is a component of the proteasomal degradation pathway. The potential interplay of phosphorylation with mapped O-GlcNAc sites, and possible implication of those sites in synaptic plasticity in normal versus AD states is discussed. iTRAQ is a powerful differential isotopic quantitative approach in proteomics. Pulsed Q dissociation (PQD) is a recently introduced fragmentation strategy that enables detection of low mass iTRAQ reporter ions in ion trap mass spectrometry. We optimized LTQ ion trap settings for PQD-based iTRAQ quantitation and demonstrated its utility in O-GlcNAc site mapping. Using iTRAQ, abnormal synaptic expression levels of several proteins previously implicated in AD pathology were observed in addition to novel changes in synaptic specific protein expression including Synapsin II. PMID:20563614

  11. HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms

    PubMed Central

    Persico, Maria; Ceol, Arnaud; Gavrila, Caius; Hoffmann, Robert; Florio, Arnaldo; Cesareni, Gianni

    2005-01-01

    Background The application of high throughput approaches to the identification of protein interactions has offered for the first time a glimpse of the global interactome of some model organisms. Until now, however, such genome-wide approaches have not been applied to the human proteome. Results In order to fill this gap we have assembled an inferred human protein interaction network where interactions discovered in model organisms are mapped onto the corresponding human orthologs. In addition to a stringent assignment to orthology classes based on the InParanoid algorithm, we have implemented a string matching algorithm to filter out orthology assignments of proteins whose global domain organization is not conserved. Finally, we have assessed the accuracy of our own, and related, inferred networks by benchmarking them against i) an assembled experimental interactome, ii) a network derived by mining of the scientific literature and iii) by measuring the enrichment of interacting protein pairs sharing common Gene Ontology annotation. Conclusion The resulting networks are named HomoMINT and HomoMINT_filtered, the latter being based on the orthology table filtered by the domain architecture matching algorithm. They contains 9749 and 5203 interactions respectively and can be analyzed and viewed in the context of the experimentally verified interactions between human proteins stored in the MINT database. HomoMINT is constantly updated to take into account the growing information in the MINT database. PMID:16351748

  12. Mapping DNA-Lac repressor interaction with ultra-fast optical tweezers

    NASA Astrophysics Data System (ADS)

    Monico, Carina; Tempestini, Alessia; Vanzi, Francesco; Pavone, Francesco S.; Capitanio, Marco

    2015-03-01

    The lac operon is a well-known example of gene expression regulation, based on the specific interaction of Lac repressor protein (LacI) with its target DNA sequence (operator). We recently developed an ultrafast force-clamp laser trap technique capable of probing molecular interactions with sub-ms temporal resolution, under controlled pN-range forces. With this technique, we tested the interaction of LacI with different DNA constructs. Based on position along the DNA sequence, the observed interactions can be interpreted as specific binding to operator sequences and transient interactions with nonspecific sequences.

  13. Mapping and Quantitation of the Interaction between the Recombination Activating Gene Proteins RAG1 and RAG2.

    PubMed

    Zhang, Yu-Hang; Shetty, Keerthi; Surleac, Marius D; Petrescu, Andrei J; Schatz, David G

    2015-05-01

    The RAG endonuclease consists of RAG1, which contains the active site for DNA cleavage, and RAG2, an accessory factor whose interaction with RAG1 is critical for catalytic function. How RAG2 activates RAG1 is not understood. Here, we used biolayer interferometry and pulldown assays to identify regions of RAG1 necessary for interaction with RAG2 and to measure the RAG1-RAG2 binding affinity (KD ?0.4 ?M) (where RAG1 and RAG2 are recombination activating genes 1 or 2). Using the Hermes transposase as a guide, we constructed a 36-kDa "mini" RAG1 capable of interacting robustly with RAG2. Mini-RAG1 consists primarily of the catalytic center and the residues N-terminal to it, but it lacks a zinc finger region in RAG1 previously implicated in binding RAG2. The ability of Mini-RAG1 to interact with RAG2 depends on a predicted ?-helix (amino acids 997-1008) near the RAG1 C terminus and a region of RAG1 from amino acids 479 to 559. Two adjacent acidic amino acids in this region (Asp-546 and Glu-547) are important for both the RAG1-RAG2 interaction and recombination activity, with Asp-546 of particular importance. Structural modeling of Mini-RAG1 suggests that Asp-546/Glu-547 lie near the predicted 997-1008 ?-helix and components of the active site, raising the possibility that RAG2 binding alters the structure of the RAG1 active site. Quantitative Western blotting allowed us to estimate that mouse thymocytes contain on average ?1,800 monomers of RAG1 and ?15,000 molecules of RAG2, implying that nuclear concentrations of RAG1 and RAG2 are below the KD value for their interaction, which could help limit off-target RAG activity. PMID:25745109

  14. Quantitative trait loci mapping of phenotypic plasticity and genotype–environment interactions in plant and insect performance

    PubMed Central

    Tétard-Jones, C.; Kertesz, M. A.; Preziosi, R. F.

    2011-01-01

    Community genetic studies generally ignore the plasticity of the functional traits through which the effect is passed from individuals to the associated community. However, the ability of organisms to be phenotypically plastic allows them to rapidly adapt to changing environments and plasticity is commonly observed across all taxa. Owing to the fitness benefits of phenotypic plasticity, evolutionary biologists are interested in its genetic basis, which could explain how phenotypic plasticity is involved in the evolution of species interactions. Two current ideas exist: (i) phenotypic plasticity is caused by environmentally sensitive loci associated with a phenotype; (ii) phenotypic plasticity is caused by regulatory genes that simply influence the plasticity of a phenotype. Here, we designed a quantitative trait loci (QTL) mapping experiment to locate QTL on the barley genome associated with barley performance when the environment varies in the presence of aphids, and the composition of the rhizosphere. We simultaneously mapped aphid performance across variable rhizosphere environments. We mapped main effects, QTL × environment interaction (QTL×E), and phenotypic plasticity (measured as the difference in mean trait values) for barley and aphid performance onto the barley genome using an interval mapping procedure. We found that QTL associated with phenotypic plasticity were co-located with main effect QTL and QTL×E. We also located phenotypic plasticity QTL that were located separately from main effect QTL. These results support both of the current ideas of how phenotypic plasticity is genetically based and provide an initial insight into the functional genetic basis of how phenotypically plastic traits may still be important sources of community genetic effects. PMID:21444311

  15. 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 - Sand deposits and clays, terrace deposits of Pleistocene age; and S6 - Alluvium, mud, sands, clay, silt and sand dune of Holocene age. The time-average shear-wave velocity in the upper 30m (Vs30) from the database sites range from 123m/s to 1870m/s. The variance of the distribution of Vs30 values varies significantly with the generalized geological unit, being larger S1 and S2 units. The use of proxies based either on the geological-geographical units developed for California by Wills and Clahan (2006) or on correlations with the topographic slope for stable continental regions (Wald and Allen, 2007) shows relatively unbiased total residual distributions of the logarithm of Vs30, although with a large variance. However, the performance of both methods varies significantly with the generalized geological unit analyzed. Both methods are highly biased towards lower values of Vs30 for unit S1 (hard rock). The topographic-slope method shows inconsistent bias for each generalized unit. These results are not in agreement with those of Lemoine et al. (2012) who concluded that, for stable continental regions, the topographic-slope method performance was best for rock sites (A/B NERPH class). This discrepancy points to the limitations of the database on near-surface site-conditions used in project SHARE in what concerns stable continental regions.

  16. DTP Site Map

    Cancer.gov

    Data from Human Tumor Cell Line Assay Data from AIDS Antiviral Assay Data from Yeast Assay Structures for over 200,000 Compounds Diversity Sets Molecular Targets Data from Microarray Project Data Search by chemical names, NSC numbers, structures, etc.

  17. Site Map - SEER

    Cancer.gov

    SEER is an authoritative source of information on cancer incidence and survival in the United States. SEER currently collects and publishes cancer incidence and survival data from population-based cancer registries covering approximately 28 percent of the U.S. population.

  18. Integrated platform for genome-wide screening and construction of high-density genetic interaction maps in mammalian cells

    PubMed Central

    Kampmann, Martin; Bassik, Michael C.; Weissman, Jonathan S.

    2013-01-01

    A major challenge of the postgenomic era is to understand how human genes function together in normal and disease states. In microorganisms, high-density genetic interaction (GI) maps are a powerful tool to elucidate gene functions and pathways. We have developed an integrated methodology based on pooled shRNA screening in mammalian cells for genome-wide identification of genes with relevant phenotypes and systematic mapping of all GIs among them. We recently demonstrated the potential of this approach in an application to pathways controlling the susceptibility of human cells to the toxin ricin. Here we present the complete quantitative framework underlying our strategy, including experimental design, derivation of quantitative phenotypes from pooled screens, robust identification of hit genes using ultra-complex shRNA libraries, parallel measurement of tens of thousands of GIs from a single double-shRNA experiment, and construction of GI maps. We describe the general applicability of our strategy. Our pooled approach enables rapid screening of the same shRNA library in different cell lines and under different conditions to determine a range of different phenotypes. We illustrate this strategy here for single- and double-shRNA libraries. We compare the roles of genes for susceptibility to ricin and Shiga toxin in different human cell lines and reveal both toxin-specific and cell line-specific pathways. We also present GI maps based on growth and ricin-resistance phenotypes, and we demonstrate how such a comparative GI mapping strategy enables functional dissection of physical complexes and context-dependent pathways. PMID:23739767

  19. Distinct parietal sites mediate the influences of mood, arousal, and their interaction on human recognition memory.

    PubMed

    Greene, Ciara M; Flannery, Oliver; Soto, David

    2014-12-01

    The two dimensions of emotion, mood valence and arousal, have independent effects on recognition memory. At present, however, it is not clear how those effects are reflected in the human brain. Previous research in this area has generally dealt with memory for emotionally valenced or arousing stimuli, but the manner in which interacting mood and arousal states modulate responses in memory substrates remains poorly understood. We investigated memory for emotionally neutral items while independently manipulating mood valence and arousal state by means of music exposure. Four emotional conditions were created: positive mood/high arousal, positive mood/low arousal, negative mood/high arousal, and negative mood/low arousal. We observed distinct effects of mood valence and arousal in parietal substrates of recognition memory. Positive mood increased activity in ventral posterior parietal cortex (PPC) and orbitofrontal cortex, whereas arousal condition modulated activity in dorsal PPC and the posterior cingulate. An interaction between valence and arousal was observed in left ventral PPC, notably in a parietal area distinct from the those identified for the main effects, with a stronger effect of mood on recognition memory responses here under conditions of relative high versus low arousal. We interpreted the PPC activations in terms of the attention-to-memory hypothesis: Increased arousal may lead to increased top-down control of memory, and hence dorsal PPC activation, whereas positive mood valence may result in increased activity in ventral PPC regions associated with bottom-up attention to memory. These findings indicate that distinct parietal sites mediate the influences of mood, arousal, and their interplay during recognition memory. PMID:24604603

  20. Uranyl Solvation by a Three-Dimensional Reference Interaction Site Model.

    PubMed

    Matveev, Alexei; Li, Bo; Rösch, Notker

    2015-08-13

    We report an implementation of the three-dimensional reference interaction site model (3D RISM) that in particular addresses the treatment of the long-range Coulomb field of charged species, represented by point charges and/or a distributed charge density. A comparison of 1D and 3D results for atomic ions demonstrates a reasonable accuracy, even for a moderate size of the unit cell and a moderate grid resolution. In an application to uranyl complexes with 4-6 explicit aqua ligands and an implicit bulk solvent modeled by RISM, we show that the 3D technique is not susceptible to the deficiencies of the 1D technique exposed in our previous work [Li, Matveev, Krüger, Rösch, Comp. Theor. Chem. 2015, 1051, 151]. The 3D method eliminates the artificial superposition of explicit aqua ligands and the RISM medium and predicts essentially the same values for uranyl and uranyl-water bond lengths as a state-of-the-art polarizable continuum model. With the first solvation shell treated explicitly, the observables are nearly independent of the order of the closure relationship used when solving the set of integral equations for the various distribution functions. Furthermore, we calculated the activation barrier of water exchange with a hybrid approach that combines the 3D RISM model for the bulk aqueous solvent and a quantum mechanical description (at the level of electronic density functional theory) of uranyl interacting with explicitly represented water molecules. The calculated result agrees very well with experiment and the best theoretical estimates. PMID:26167741

  1. Mapping QTL main and interaction influences on milling quality in elite U.S. rice germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rice (Oryza sativa L.) head-rice yield (HR) is a key export and domestic quality trait whose genetic control is poorly understood. With the goal of identifying genomic regions influencing HR, quantitative-trait-locus (QTL) mapping was carried out for quality-related traits in recombinant inbred line...

  2. FISH HABITAT MAPPING Results of a short study of interactions of cetaceans

    E-print Network

    Pierce, Graham

    by false killer whales occurred although highGuest editor: V. D. Valavanis Essential Fish Habitat Mapping detected when delphinids were sighted and false killer whales were by-caught. This may indicate that false killer whales are not echolo- cating when feeding on fish hooked on a longline. Keywords Cetaceans Á

  3. Interactive remote data processing using Pixelize Wavelet Filtration (PWF-method) and PeriodMap analysis

    NASA Astrophysics Data System (ADS)

    Sych, Robert; Nakariakov, Valery; Anfinogentov, Sergey

    Wavelet analysis is suitable for investigating waves and oscillating in solar atmosphere, which are limited in both time and frequency. We have developed an algorithms to detect this waves by use the Pixelize Wavelet Filtration (PWF-method). This method allows to obtain information about the presence of propagating and non-propagating waves in the data observation (cube images), and localize them precisely in time as well in space. We tested the algorithm and found that the results of coronal waves detection are consistent with those obtained by visual inspection. For fast exploration of the data cube, in addition, we applied early-developed Period- Map analysis. This method based on the Fast Fourier Transform and allows on initial stage quickly to look for "hot" regions with the peak harmonic oscillations and determine spatial distribution at the significant harmonics. We propose the detection procedure of coronal waves separate on two parts: at the first part, we apply the PeriodMap analysis (fast preparation) and than, at the second part, use information about spatial distribution of oscillation sources to apply the PWF-method (slow preparation). There are two possible algorithms working with the data: in automatic and hands-on operation mode. Firstly we use multiply PWF analysis as a preparation narrowband maps at frequency subbands multiply two and/or harmonic PWF analysis for separate harmonics in a spectrum. Secondly we manually select necessary spectral subband and temporal interval and than construct narrowband maps. For practical implementation of the proposed methods, we have developed the remote data processing system at Institute of Solar-Terrestrial Physics, Irkutsk. The system based on the data processing server - http://pwf.iszf.irk.ru. The main aim of this resource is calculation in remote access through the local and/or global network (Internet) narrowband maps of wave's sources both in whole spectral band and at significant harmonics. In addition, we can obtain temporal dynamics (mpeg- files) of the main oscillation characteristics: amplitude, power and phase as a spatial-temporal coordinates. For periodogram mapping of data cubes as a method for the pre-analysis, we developed preparation of the color maps where the pixel's colour corresponds to the frequency of the power spectrum maximum. The computer system based on applications ION-scripts, algorithmic languages IDL and PHP, and Apache WEB server. The IDL ION-scripts use for preparation and configuration of network requests at the central data server with subsequent connection to IDL run-unit software and graphic output on FTP-server and screen. Web page is constructed using PHP language.

  4. Human Interactive Analysis Using Video: Mapping the Dynamics of Complex Work Environments.

    ERIC Educational Resources Information Center

    Terrell, William R.; And Others

    1992-01-01

    Explains human interactive analysis as an architecture for using computer interactive technologies in the analysis of complex work environments. A project at the Naval Training Systems Center that used video-audio data to develop a multimedia database is described; the analysis and management of data are discussed; and decision processes are…

  5. Solvation free-energy pressure corrections in the Three Dimensional Reference Interaction Site Model

    E-print Network

    Sergiievskyi, Volodymyr; Levesque, Maximilien; Borgis, Daniel

    2015-01-01

    Solvation free energies are efficiently predicted by molecular density functionnal theory (MDFT) if one corrects the overpressure introduced by the usual homogeneous reference fluid approximation. Sergiievskyi et al. [Sergiievskyi et al., JPCL, 2014, 5, 1935-1942] recently derived the rigorous compensation of this excess of pressure (PC) and proposed an empirical "ideal gas" supplementary correction (PC+) that further enhances the calculated solvation free energies. In a recent paper [Misin et al, JCP, 2015, 142, 091105], those corrections were applied to solvation free energy calculations using the three-dimensional reference interaction site model (3D-RISM). As for classical DFT, PC and PC+ corrections improve greatly the predictions of 3D-RISM, but PC+ is described as decreasing the accuracy. In this article, we first derive rigorously the PC and PC+ corrections for 3D-RISM. We show the reported discrepancy is then taken off by introducing the correct expression of the pressure in 3D-RISM. This provides a ...

  6. Problematic use of social network sites: the interactive relationship between gratifications sought and privacy concerns.

    PubMed

    Chen, Hsuan-Ting; Kim, Yonghwan

    2013-11-01

    Problematic Internet use has long been a matter of concern; however, few studies extend this line of research from general Internet use to the use of social network sites (SNSs), or explicate the problematic use of SNSs by understanding what factors may enhance or reduce users' compulsive behaviors and excessive form of use on SNSs. Building on literature that found a positive relationship between gratifications sought from the Internet and problematic Internet use, this study first explores the types of gratifications sought from SNSs and examines their relationship with problematic SNS use. It found that three types of gratifications-diversion, self-presentation, and relationship building-were positively related to problematic SNS use. In addition, with a growing body of research on SNS privacy, a moderating role of privacy concerns on SNSs has been proposed to understand how it can influence the relationship between gratifications sought from SNSs and problematic SNS use. The findings suggest that different subdimensions of privacy concerns interact with gratifications sought in different manners. In other words, privacy concerns, including unauthorized secondary use and improper access, play a more influential role in constraining the positive relationship between gratifications sought and problematic SNS use when individuals seek to build relationships on SNSs. However, if individuals seek to have diversion on SNSs, their privacy concerns will be overridden by their gratifications sought, which in turn leads to problematic SNS use. Implications of these findings for future research are discussed. PMID:24053383

  7. The effects of reading comprehension and launch site on frequency-predictability interactions during paragraph reading.

    PubMed

    Whitford, Veronica; Titone, Debra

    2014-01-01

    We used eye movement measures of paragraph reading to examine whether word frequency and predictability interact during the earliest stages of lexical processing, with a specific focus on whether these effects are modulated by individual differences in reading comprehension or launch site (i.e., saccade length between the prior and currently fixated word--a proxy for the amount of parafoveal word processing). The joint impact of frequency and predictability on reading will elucidate whether these variables additively or multiplicatively affect the earliest stages of lexical access, which, in turn, has implications for computational models of eye movements during reading. Linear mixed effects models revealed additive effects during both early- and late-stage reading, where predictability effects were comparable for low- and high-frequency words. Moreover, less cautious readers (e.g., readers who engaged in skimming, scanning, mindless reading) demonstrated smaller frequency effects than more cautious readers. Taken together, our findings suggest that during extended reading, frequency and predictability exert additive influences on lexical and postlexical processing, and that individual differences in reading comprehension modulate sensitivity to the effects of word frequency. PMID:24205888

  8. Group tele-immersion:enabling natural interactions between groups at distant sites.

    SciTech Connect

    Yang, Christine L. (Sandia National Laboratories, Livermore, CA); Stewart, Corbin (Sandia National Laboratories, Livermore, CA); Nashel, Andrew (University of North Carolina at Chapel Hill, Chapel Hill, NC)

    2005-08-01

    We present techniques and a system for synthesizing views for video teleconferencing between small groups. In place of replicating one-to-one systems for each pair of users, we create a single unified display of the remote group. Instead of performing dense 3D scene computation, we use more cameras and trade-off storage and hardware for computation. While it is expensive to directly capture a scene from all possible viewpoints, we have observed that the participants viewpoints usually remain at a constant height (eye level) during video teleconferencing. Therefore, we can restrict the possible viewpoint to be within a virtual plane without sacrificing much of the realism, and in cloning so we significantly reduce the number of required cameras. Based on this observation, we have developed a technique that uses light-field style rendering to guarantee the quality of the synthesized views, using a linear array of cameras with a life-sized, projected display. Our full-duplex prototype system between Sandia National Laboratories, California and the University of North Carolina at Chapel Hill has been able to synthesize photo-realistic views at interactive rates, and has been used to video conference during regular meetings between the sites.

  9. A novel MeCP2 acetylation site regulates interaction with ATRX and HDAC1.

    PubMed

    Pandey, Somnath; Simmons, Glenn E; Malyarchuk, Svitlana; Calhoun, Tara N; Pruitt, Kevin

    2015-09-01

    Methyl-CpG-binding protein-2 (MeCP2) regulates gene expression by recruiting SWI/SNF DNA helicase/ATPase (ATRX) and Histone Deacetylase-1 (HDAC1) to methylated gene regions and modulates heterochromatin association by interacting with Heterochromatin protein-1. As MeCP2 contributes to tumor suppressor gene silencing and its mutation causes Rett Syndrome, we investigated how novel post-translational-modification contributes to its function. Herein we report that upon pharmacological inhibition of SIRT1 in RKO colon and MCF-7 breast cancer cells, endogenous MeCP2 is acetylated at sites critical for binding to DNA and transcriptional regulators. We created an acetylation mimetic mutation in MeCP2 and found it to possess decreased binding to ATRX and HDAC1. Conditions inducing MeCP2 acetylation do not alter its promoter occupancy at a subset of target genes analyzed, but do cause decreased binding to ATRX and HDAC1. We also report here that a specific inhibitor of SIRT1, IV, can be used to selectively decrease H3K27me3 repressive marks on a subset of repressed target gene promoters analyzed. Lastly, we show that RKO cells over-expressing MeCP2 mutant show reduced proliferation compared to those over-expressing MeCP2-wildtype. Our study demonstrates the importance of acetylated lysine residues and suggests their key role in regulating MeCP2 function and its ability to bind transcriptional regulators. PMID:26622943

  10. Interatomic Coulombic Decay Effects in Theoretical DNA Recombination Systems Involving Protein Interaction Sites

    NASA Astrophysics Data System (ADS)

    Vargas, E. L.; Rivas, D. A.; Duot, A. C.; Hovey, R. T.; Andrianarijaona, V. M.

    2015-03-01

    DNA replication is the basis for all biological reproduction. A strand of DNA will ``unzip'' and bind with a complimentary strand, creating two identical strands. In this study, we are considering how this process is affected by Interatomic Coulombic Decay (ICD), specifically how ICD affects the individual coding proteins' ability to hold together. ICD mainly deals with how the electron returns to its original state after excitation and how this affects its immediate atomic environment, sometimes affecting the connectivity between interaction sites on proteins involved in the DNA coding process. Biological heredity is fundamentally controlled by DNA and its replication therefore it affects every living thing. The small nature of the proteins (within the range of nanometers) makes it a good candidate for research of this scale. Understanding how ICD affects DNA molecules can give us invaluable insight into the human genetic code and the processes behind cell mutations that can lead to cancer. Authors wish to give special thanks to Pacific Union College Student Senate in Angwin, California, for their financial support.

  11. Solvation free-energy pressure corrections in the three dimensional reference interaction site model.

    PubMed

    Sergiievskyi, Volodymyr; Jeanmairet, Guillaume; Levesque, Maximilien; Borgis, Daniel

    2015-11-14

    Solvation free energies are efficiently predicted by molecular density functional theory if one corrects the overpressure introduced by the usual homogeneous reference fluid approximation. Sergiievskyi et al. [J. Phys. Chem. Lett. 5, 1935-1942 (2014)] recently derived the rigorous compensation of this excess of pressure (referred as "pressure correction" or PC) and proposed an empirical "ideal gas" supplementary correction (referred as "advanced pressure correction" or PC+) that further enhances the calculated solvation free energies. In a recent paper [M. Misin, M. V. Fedorov, and D. S. Palmer, J. Chem. Phys. 142, 091105 (2015)], those corrections were applied to solvation free energy calculations using the three-dimensional reference interaction site model (3D-RISM). As for classical DFT, PC and PC+ improve greatly the predictions of 3D-RISM, but PC+ is described as decreasing the accuracy. In this article, we derive rigorously the expression of the pressure in 3D-RISM as well as the associated PC and PC+. This provides a consistent way to correct the solvation free-energies calculated by 3D-RISM method. PMID:26567655

  12. Solvation free-energy pressure corrections in the three dimensional reference interaction site model

    NASA Astrophysics Data System (ADS)

    Sergiievskyi, Volodymyr; Jeanmairet, Guillaume; Levesque, Maximilien; Borgis, Daniel

    2015-11-01

    Solvation free energies are efficiently predicted by molecular density functional theory if one corrects the overpressure introduced by the usual homogeneous reference fluid approximation. Sergiievskyi et al. [J. Phys. Chem. Lett. 5, 1935-1942 (2014)] recently derived the rigorous compensation of this excess of pressure (referred as "pressure correction" or PC) and proposed an empirical "ideal gas" supplementary correction (referred as "advanced pressure correction" or PC+) that further enhances the calculated solvation free energies. In a recent paper [M. Misin, M. V. Fedorov, and D. S. Palmer, J. Chem. Phys. 142, 091105 (2015)], those corrections were applied to solvation free energy calculations using the three-dimensional reference interaction site model (3D-RISM). As for classical DFT, PC and PC+ improve greatly the predictions of 3D-RISM, but PC+ is described as decreasing the accuracy. In this article, we derive rigorously the expression of the pressure in 3D-RISM as well as the associated PC and PC+. This provides a consistent way to correct the solvation free-energies calculated by 3D-RISM method.

  13. Exact solution of Heisenberg model with site-dependent exchange couplings and Dzyloshinsky-Moriya interaction

    NASA Astrophysics Data System (ADS)

    Yang, Li-Jun; Cao, Jun-Peng; Yang, Wen-Li

    2015-10-01

    We propose an integrable spin-1/2 Heisenberg model where the exchange couplings and Dzyloshinky-Moriya interactions are dependent on the sites. By employing the quantum inverse scattering method, we obtain the eigenvalues and the Bethe ansatz equation of the system with the periodic boundary condition. Furthermore, we obtain the exact solution and study the boundary effect of the system with the anti-periodic boundary condition via the off-diagonal Bethe ansatz. The operator identities of the transfer matrix at the inhomogeneous points are proved at the operator level. We construct the T-Q relation based on them. From which, we obtain the energy spectrum of the system. The corresponding eigenstates are also constructed. We find an interesting coherence state that is induced by the topological boundary. Project supported by the National Natural Science Foundation of China (Grant Nos. 11174335, 11375141, 11374334, and 11434013) and the National Program for Basic Research of China and the Fund from the Chinese Academy of Sciences.

  14. A novel MeCP2 acetylation site regulates interaction with ATRX and HDAC1

    PubMed Central

    Pandey, Somnath; Simmons, Glenn E.; Malyarchuk, Svitlana; Calhoun, Tara N.; Pruitt, Kevin

    2015-01-01

    Methyl-CpG-binding protein-2 (MeCP2) regulates gene expression by recruiting SWI/SNF DNA helicase/ATPase (ATRX) and Histone Deacetylase-1 (HDAC1) to methylated gene regions and modulates heterochromatin association by interacting with Heterochromatin protein-1. As MeCP2 contributes to tumor suppressor gene silencing and its mutation causes Rett Syndrome, we investigated how novel post-translational-modification contributes to its function. Herein we report that upon pharmacological inhibition of SIRT1 in RKO colon and MCF-7 breast cancer cells, endogenous MeCP2 is acetylated at sites critical for binding to DNA and transcriptional regulators. We created an acetylation mimetic mutation in MeCP2 and found it to possess decreased binding to ATRX and HDAC1. Conditions inducing MeCP2 acetylation do not alter its promoter occupancy at a subset of target genes analyzed, but do cause decreased binding to ATRX and HDAC1. We also report here that a specific inhibitor of SIRT1, IV, can be used to selectively decrease H3K27me3 repressive marks on a subset of repressed target gene promoters analyzed. Lastly, we show that RKO cells over-expressing MeCP2 mutant show reduced proliferation compared to those over-expressing MeCP2-wildtype. Our study demonstrates the importance of acetylated lysine residues and suggests their key role in regulating MeCP2 function and its ability to bind transcriptional regulators. PMID:26622943

  15. Potential sites of interaction between catecholamines and LHRH in the sheep brain.

    PubMed

    Lehman, M N; Karsch, F J; Silverman, A J

    1988-01-01

    A combined immunoperoxidase/immunofluorescence procedure was used to examine potential sites of overlap between catecholamine and LHRH systems in the brains of ewes sacrificed during either anestrous or the breeding season. Cells and fibers immunoreactive for either tyrosine hydroxylase (TH) or dopamine-beta-hydroxylase (DBH) were visualized in the same sections as immunopositive LHRH perikarya and fibers. TH- and DBH-positive varicosities in the preoptic area and anterior hypothalamus appeared to contact both LHRH cell bodies and their dendrites. Clusters of TH-positive cells and fibers were found in the organum vasculosum of the lamina terminalis, and partially overlapped the location of immunoreactive LHRH fibers in that structure. Immunoreactive TH and LHRH fibers were densely interspersed within the zona externa of the median eminence, particularly within its lateral portion. No obvious qualitative differences were apparent in either the distribution of catecholamine cells and fibers or their overlap with LHRH elements between the brains of anestrous and breeding season ewes. These observations suggest the possibility of catecholaminergic synaptic inputs onto LHRH neurons in the ewe, as well as the potential for interaction between catecholamines and LHRH at the level of the median eminence. PMID:2893658

  16. Interaction of P-aminobenzoic acid with normal and sickel erythrocyte membrane: photoaffinity labelling of the binding sites

    SciTech Connect

    Premachandra, B.R.

    1986-03-05

    Electron microscopic studies revealed that P-Amino benzoic acid (PABA) could prevent eichinocytosis of red cells in vitro. Equilibrium binding studies with right side out membrane vesicles (ROV) revealed a similar number of binding sites (1.2-1.4 ..mu..mol/mg) and Kd (1.4-1.6 mM) values for both normal and sickle cell membranes. /sup 14/C-Azide analogue of PABA was synthesized as a photoaffinity label to probe its sites of interaction on the erythrocyte membranes. Competitive binding studies of PABA with its azide indicated that both the compounds share common binding sites on the membrane surface since a 20 fold excess of azide inhibited PABA binding in a linear fashion. The azide was covalently incorporated into the membrane components only upon irradiation (52-35% of the label found in the proteins and the rest in lipids). Electrophoretic analysis of photolabelled ROV revealed that the azide interacts chiefly with Band 3 protein. PABA inhibited both high and low affinity calcium (Ca) binding sites situated on either surface of the membrane in a non-competitive manner; however, Ca binding stimulated by Mg-ATP was not affected. Ca transport into inside out vesicles was inhibited by PABA; but it did not affect the calcium ATP-ase activity. The authors studies suggest that the mechanism of action of PABA is mediated by its interaction with Band 3 protein (anion channel), calcium channel and calcium binding sites of erythrocyte membrane.

  17. WATER-ROCK INTERACTIONS INFLUENCING MERCURY FATE AND TRANSPORT FROM AN ABANDONED MINE SITE TO AN ADJACENT AQUATIC ECOSYSTEM: ABSTRACT

    EPA Science Inventory

    NRMRL-ADA-01319 Jewett*, D.G., Manges, E., Reller, G.J., Engle, and Bauman. Water-Rock Interactions Influencing Mercury Fate and Transport From An Abandoned Mine Site To An Adjacent Aquatic Ecosystem. Amer. Geophysical Union Conference, San Francisco, CA, 12/10-14/2001. 2001. 0...

  18. Adopting Social Networking Sites (SNSs) as Interactive Communities among English Foreign Language (EFL) Learners in Writing: Opportunities and Challenges

    ERIC Educational Resources Information Center

    Razak, Norizan Abdul; Saeed, Murad; Ahmad, Zulkifli

    2013-01-01

    As most traditional classroom environments in English as Foreign Language (EFL) still restrict learners' collaboration and interaction in college writing classes, today, the majority of EFL learners are accessing Social Networking Sites (SNSs) as online communities of practice (CoPs) for adopting informal collaborative learning as a way of…

  19. Effect of Mutations in the A Site of 16 S rRNA on Aminoglycoside Antibiotic-Ribosome Interaction

    E-print Network

    Dahlquist, Kam D.

    Effect of Mutations in the A Site of 16 S rRNA on Aminoglycoside Antibiotic-Ribosome Interaction. The ribosomal decoding region is associated with highly conserved sequences near the 3H end of 16 S rRNA of rRNA. Mutations of certain nucleotides in rRNA reduce amino- glycoside binding af

  20. Ethanol impairs microtubule formation via interactions at a microtubule associated protein-sensitive site

    PubMed Central

    Smith, Katherine J.; Butler, Tracy R.; Prendergast, Mark A.

    2014-01-01

    Prolonged ethanol abuse has been associated with brain injury caused by impaired synaptogenesis, cellular migration, neurogenesis, and cell signaling, all of which require proper microtubule functioning. However, the means by which ethanol may impair microtubule formation or function and the role that microtubule-associated proteins (MAPs) have in mediating such effects are not clear. In the present studies, purified MAP-deficient (2 mg/mL) and MAP-rich (pre-conjugated; 1 mg/mL) bovine ?/? tubulin dimer were allowed to polymerize at 37 °C, forming microtubules in the presence or absence of ethanol (25–500 mM). Microtubule formation was assessed in a 96-well format using a turbidity assay, with absorption measured at 340 nm for 45 min. Additional studies co-exposed ?/? tubulin dimers to 50 mM ethanol and purified MAPs (0.1 mg/mL) for 45 min. Polymerization of MAP-deficient tubulin was significantly decreased (at 15–45 min of polymerization) during exposure to ethanol (> 25 mM). In contrast, ethanol exposure did not alter polymerization of ?/? tubulin dimers pre-conjugated to MAPs, at any concentration. Concurrent exposure of MAP-deficient tubulin with purified MAPs and ethanol resulted in significant and time-dependent decreases in tubulin polymerization, with recovery from inhibition at later time points. The present results suggest that ethanol disrupts MAP-independent microtubule formation and MAP-dependent microtubule formation via direct actions at a MAP-sensitive microtubule residue, indicating that disruption of neuronal microtubule formation and function may contribute to the neurodegenerative effects of binge-like ethanol intake. PMID:24055335

  1. Mapping Soluble Guanylyl Cyclase and Protein Disulfide Isomerase Regions of Interaction

    PubMed Central

    Jain, Mohit; Liu, Tong; Li, Hong; Beuve, Annie

    2015-01-01

    Soluble guanylyl cyclase (sGC) is a heterodimeric nitric oxide (NO) receptor that produces cyclic GMP. This signaling mechanism is a key component in the cardiovascular system. NO binds to heme in the ? subunit and stimulates the catalytic conversion of GTP to cGMP several hundred fold. Several endogenous factors have been identified that modulate sGC function in vitro and in vivo. In previous work, we determined that protein disulfide isomerase (PDI) interacts with sGC in a redox-dependent manner in vitro and that PDI inhibited NO-stimulated activity in cells. To our knowledge, this was the first report of a physical interaction between sGC and a thiol-redox protein. To characterize this interaction between sGC and PDI, we first identified peptide linkages between sGC and PDI, using a lysine cross-linking reagent and recently developed mass spectrometry analysis. Together with Flag-immunoprecipitation using sGC domain deletions, wild-type (WT) and mutated PDI, regions of sGC involved in this interaction were identified. The observed data were further explored with computational modeling to gain insight into the interaction mechanism between sGC and oxidized PDI. Our results indicate that PDI interacts preferentially with the catalytic domain of sGC, thus providing a mechanism for PDI inhibition of sGC. A model in which PDI interacts with either the ? or the ? catalytic domain is proposed. PMID:26618351

  2. An active site–tail interaction in the structure of hexahistidine-tagged Thermoplasma acidophilum citrate synthase

    PubMed Central

    Murphy, Jesse R.; Donini, Stefano; Kappock, T. Joseph

    2015-01-01

    Citrate synthase (CS) plays a central metabolic role in aerobes and many other organisms. The CS reaction comprises two half-reactions: a Claisen aldol condensation of acetyl-CoA (AcCoA) and oxaloacetate (OAA) that forms citryl-CoA (CitCoA), and CitCoA hydrolysis. Protein conformational changes that ‘close’ the active site play an important role in the assembly of a catalytically competent condensation active site. CS from the thermoacidophile Thermoplasma acidophilum (TpCS) possesses an endogenous Trp fluorophore that can be used to monitor the condensation reaction. The 2.2?Ĺ resolution crystal structure of TpCS fused to a C-terminal hexahistidine tag (TpCSH6) reported here is an ‘open’ structure that, when compared with several liganded TpCS structures, helps to define a complete path for active-site closure. One active site in each dimer binds a neighboring His tag, the first nonsubstrate ligand known to occupy both the AcCoA and OAA binding sites. Solution data collectively suggest that this fortuitous interaction is stabilized by the crystalline lattice. As a polar but almost neutral ligand, the active site–tail interaction provides a new starting point for the design of bisubstrate-analog inhibitors of CS. PMID:26457521

  3. The concept of movable heritage cartographic presentation on the interactive map / Koncepcja kartograficznej prezentacji ruchomego dziedzictwa kulturowego na interaktywnej mapie

    NASA Astrophysics Data System (ADS)

    Mo?cicka, Albina

    2012-11-01

    This paper presents the proposition of cartographic presentation of the movable cultural heritage on interactive map. The original solution on how to link movable monuments with geographical space as well as the different types of spatial reference were described. The text shows both: the way of presentation of single movable monuments and collections of historical objects. The proposed solutions were based on the assumption that the number of heritage resources shown on the map is huge and, what is more, they can keep growing. So, the proposed solution must be able to apply for a resource of indeterminate size. For the presentation of the movable heritage the traditional methods of cartographic presentation, as well as interactive technologies were applied. Artyku? przedstawia propozycj? kartograficznej prezentacji informacji o ruchomym dziedzictwie kulturowym na interaktywnej mapie. Zaprezentowano autorskie spojrzenie na powi?zanie zabytków ruchomych z przestrzeni? geograficzn? oraz wynikaj?ce z niego ró?ne typy odniesie? przestrzennych. W tek?cie przedstawiono sposób prezentacji zarówno pojedynczego zabytku ruchomego, jak i kolekcji obiektów historycznych. Proponowane rozwi?zania bazowa?y na za?o?eniu, i? liczba zasobów dziedzictwa jest ogromna, wi?c zasób prezentowany na mapie mo?e si? stale powi?ksza?, zatem rozwi?zania musz? by? mo?liwe do zastosowania dla zasobu o nieokre?lonej wielko?ci. Do prezentacji ruchomego dziedzictwa wykorzystano tradycyjne metody prezentacji kartograficznej, poszerzone o mo?liwo?ci technologii interaktywnych.

  4. Mapping strain rate dependence of dislocation-defect interactions by atomistic simulations

    E-print Network

    Fan, Yue

    Probing the mechanisms of defect–defect interactions at strain rates lower than 10[superscript 6] s[superscript ?1] is an unresolved challenge to date to molecular dynamics (MD) techniques. Here we propose an original ...

  5. Redrawing the Map of Great Britain from a Network of Human Interactions

    E-print Network

    Ratti, Carlo

    Do regional boundaries defined by governments respect the more natural ways that people interact across space? This paper proposes a novel, fine-grained approach to regional delineation, based on analyzing networks of ...

  6. ARSENIC GEOCHEMICAL BEHAVIOR DURING GROUND WATER-SURFACE WATER INTERACTIONS AT A CONTAMINATED SITE

    EPA Science Inventory

    Research results will be presented that address arsenic mobilization and cycling mechanisms at a Superfund site in eastern Massachusetts. The site is located in the headwaters of the Aberjona Watershed. In order to support assessments of the risk posed by off-site migration of ar...

  7. Novel Genes Affecting the Interaction between the Cabbage Whitefly and Arabidopsis Uncovered by Genome-Wide Association Mapping

    PubMed Central

    Broekgaarden, Colette; Bucher, Johan; Bac-Molenaar, Johanna; Keurentjes, Joost J. B.; Kruijer, Willem; Voorrips, Roeland E.; Vosman, Ben

    2015-01-01

    Plants have evolved a variety of ways to defend themselves against biotic attackers. This has resulted in the presence of substantial variation in defense mechanisms among plants, even within a species. Genome-wide association (GWA) mapping is a useful tool to study the genetic architecture of traits, but has so far only had limited exploitation in studies of plant defense. Here, we study the genetic architecture of defense against the phloem-feeding insect cabbage whitefly (Aleyrodes proletella) in Arabidopsis thaliana. We determined whitefly performance, i.e. the survival and reproduction of whitefly females, on 360 worldwide selected natural accessions and subsequently performed GWA mapping using 214,051 SNPs. Substantial variation for whitefly adult survival and oviposition rate (number of eggs laid per female per day) was observed between the accessions. We identified 39 candidate SNPs for either whitefly adult survival or oviposition rate, all with relatively small effects, underpinning the complex architecture of defense traits. Among the corresponding candidate genes, i.e. genes in linkage disequilibrium (LD) with candidate SNPs, none have previously been identified as a gene playing a role in the interaction between plants and phloem-feeding insects. Whitefly performance on knock-out mutants of a number of candidate genes was significantly affected, validating the potential of GWA mapping for novel gene discovery in plant-insect interactions. Our results show that GWA analysis is a very useful tool to gain insight into the genetic architecture of plant defense against herbivorous insects, i.e. we identified and validated several genes affecting whitefly performance that have not previously been related to plant defense against herbivorous insects. PMID:26699853

  8. Improving the Understanding of Pathogenesis of Human Papillomavirus 16 via Mapping Protein-Protein Interaction Network

    PubMed Central

    Dong, Yongcheng; Kuang, Qifan; Dai, Xu; Li, Rong; Wu, Yiming; Leng, Weijia; Li, Yizhou; Li, Menglong

    2015-01-01

    The human papillomavirus 16 (HPV16) has high risk to lead various cancers and afflictions, especially, the cervical cancer. Therefore, investigating the pathogenesis of HPV16 is very important for public health. Protein-protein interaction (PPI) network between HPV16 and human was used as a measure to improve our understanding of its pathogenesis. By adopting sequence and topological features, a support vector machine (SVM) model was built to predict new interactions between HPV16 and human proteins. All interactions were comprehensively investigated and analyzed. The analysis indicated that HPV16 enlarged its scope of influence by interacting with human proteins as much as possible. These interactions alter a broad array of cell cycle progression. Furthermore, not only was HPV16 highly prone to interact with hub proteins and bottleneck proteins, but also it could effectively affect a breadth of signaling pathways. In addition, we found that the HPV16 evolved into high carcinogenicity on the condition that its own reproduction had been ensured. Meanwhile, this work will contribute to providing potential new targets for antiviral therapeutics and help experimental research in the future. PMID:25961044

  9. Google Maps: You Are Here

    ERIC Educational Resources Information Center

    Jacobsen, Mikael

    2008-01-01

    Librarians use online mapping services such as Google Maps, MapQuest, Yahoo Maps, and others to check traffic conditions, find local businesses, and provide directions. However, few libraries are using one of Google Maps most outstanding applications, My Maps, for the creation of enhanced and interactive multimedia maps. My Maps is a simple and…

  10. Interactions of the Julia Set with Critical and (Un)Stable Sets in an Angle-Doubling Map on ?\\{0}

    NASA Astrophysics Data System (ADS)

    Hittmeyer, Stefanie; Krauskopf, Bernd; Osinga, Hinke M.

    We study a nonanalytic perturbation of the complex quadratic family z ? z2 + c in the form of a two-dimensional noninvertible map that has been introduced by Bamón et al. [2006]. The map acts on the plane by opening up the critical point to a disk and wrapping the plane twice around it; points inside the disk have no preimages. The bounding critical circle and its images, together with the critical point and its preimages, form the so-called critical set. For parameters away from the complex quadratic family we define a generalized notion of the Julia set as the basin boundary of infinity. We are interested in how the Julia set changes when saddle points along with their stable and unstable sets appear as the perturbation is switched on. Advanced numerical techniques enable us to study the interactions of the Julia set with the critical set and the (un)stable sets of saddle points. We find the appearance and disappearance of chaotic attractors and dramatic changes in the topology of the Julia set; these bifurcations lead to three complicated types of Julia sets that are given by the closure of stable sets of saddle points of the map, namely, a Cantor bouquet and what we call a Cantor tangle and a Cantor cheese. We are able to illustrate how bifurcations of the nonanalytic map connect to those of the complex quadratic family by computing two-parameter bifurcation diagrams that reveal a self-similar bifurcation structure near the period-doubling route to chaos in the complex quadratic family.

  11. Exploring Students' Mapping Behaviors and Interactive Discourses in a Case Diagnosis Problem: Sequential Analysis of Collaborative Causal Map Drawing Processes

    ERIC Educational Resources Information Center

    Lee, Woon Jee

    2012-01-01

    The purpose of this study was to explore the nature of students' mapping and discourse behaviors while constructing causal maps to articulate their understanding of a complex, ill-structured problem. In this study, six graduate-level students were assigned to one of three pair groups, and each pair used the causal mapping software program,…

  12. An active site–tail interaction in the structure of hexahistidine-tagged Thermoplasma acidophilum citrate synthase

    SciTech Connect

    Murphy, Jesse R.; Donini, Stefano; Kappock, T. Joseph

    2015-09-23

    Citrate synthase from the thermophilic euryarchaeon T. acidophilum fused to a hexahistidine tag was purified and biochemically characterized. The structure of the unliganded enzyme at 2.2 Ĺ resolution contains tail–active site contacts in half of the active sites. Citrate synthase (CS) plays a central metabolic role in aerobes and many other organisms. The CS reaction comprises two half-reactions: a Claisen aldol condensation of acetyl-CoA (AcCoA) and oxaloacetate (OAA) that forms citryl-CoA (CitCoA), and CitCoA hydrolysis. Protein conformational changes that ‘close’ the active site play an important role in the assembly of a catalytically competent condensation active site. CS from the thermoacidophile Thermoplasma acidophilum (TpCS) possesses an endogenous Trp fluorophore that can be used to monitor the condensation reaction. The 2.2 Ĺ resolution crystal structure of TpCS fused to a C-terminal hexahistidine tag (TpCSH6) reported here is an ‘open’ structure that, when compared with several liganded TpCS structures, helps to define a complete path for active-site closure. One active site in each dimer binds a neighboring His tag, the first nonsubstrate ligand known to occupy both the AcCoA and OAA binding sites. Solution data collectively suggest that this fortuitous interaction is stabilized by the crystalline lattice. As a polar but almost neutral ligand, the active site–tail interaction provides a new starting point for the design of bisubstrate-analog inhibitors of CS.

  13. Radial position of single-site gamma-ray interactions from a parametric pulse shape analysis of germanium detector signals

    E-print Network

    John L. Orrell; Craig E. Aalseth; Matthew W. Cooper; Jeremy D. Kephart; Carolyn E. Seifert

    2007-03-14

    Pulse shape analysis of germanium gamma-ray spectrometer signals can yield information on the radial position of individual gamma-ray interactions within the germanium crystal. A parametric pulse shape analysis based on calculation of moments of the reconstructed current pulses from a closed-ended coaxial germanium detector is used to preferentially select single-site gamma-ray interactions. The double escape peak events from the 2614.5 keV gamma-ray of 208-Tl are used as a training set to optimize the single-site event selection region in the pulse shape parameter space. A collimated source of 320.1 keV gamma-rays from 51-Cr is used to scan different radial positions of the same semi-coaxial germanium detector. The previously trained single-site selection region is used to preferentially identify the single-site photoelectric absorption events from the 320.1 keV full-energy peak. From the identified events, a comparison of the pulse shape parameter space distributions between different scan positions allows radial interaction location information to be collected.

  14. X-ray Structure and Nuclear Magnetic Resonance Analysis of the Interaction Sites of the Ga-Substituted Cyanobacterial Ferredoxin.

    PubMed

    Mutoh, Risa; Muraki, Norifumi; Shinmura, Kanako; Kubota-Kawai, Hisako; Lee, Young-Ho; Nowaczyk, Marc M; Rögner, Matthias; Hase, Toshiharu; Ikegami, Takahisa; Kurisu, Genji

    2015-10-01

    In chloroplasts, ferredoxin (Fd) is reduced by Photosystem I (PSI) and oxidized by Fd-NADP(+) reductase (FNR) that is involved in NADP(+) reduction. To understand the structural basis for the dynamics and efficiency of the electron transfer reaction via Fd, we complementary used X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy. In the NMR analysis of the formed electron transfer complex with Fd, the paramagnetic effect of the [2Fe-2S] cluster of Fd prevented us from detecting the NMR signals around the cluster. To solve this problem, the paramagnetic iron-sulfur cluster was replaced with a diamagnetic metal cluster. We determined the crystal structure of the Ga-substituted Fd (GaFd) from Synechocystis sp. PCC6803 at 1.62 Ĺ resolution and verified its functional complementation using affinity chromatography. NMR analysis of the interaction sites on GaFd with PSI (molecular mass of ?1 MDa) and FNR from Thermosynechococcus elongatus was achieved with high-field NMR spectroscopy. With reference to the interaction sites with FNR of Anabaena sp. PCC 7119 from the published crystal data, the interaction sites of Fd with FNR and PSI in solution can be classified into two types: (1) the core hydrophobic residues in the proximity of the metal center and (2) the hydrophilic residues surrounding the core. The former sites are shared in the Fd:FNR and Fd:PSI complex, while the latter ones are target-specific and not conserved on the residual level. PMID:26348494

  15. Identification of protein O-glycosylation site and corresponding glycans using liquid chromatography-tandem mass spectrometry via mapping accurate mass and retention time shift.

    PubMed

    Huang, Li-Juan; Lin, Jen-Hui; Tsai, Jung-Heng; Chu, Yen-Yin; Chen, Yen-Wen; Chen, Shun-Li; Chen, Shu-Hui

    2014-12-01

    We reported an improved combinatorial approach for identifying site-specific O-glycosylation using both glycan cleaved and non-cleaved methods. In this approach, a non-reducing ?-elimination kit coupled with non-specific enzymes performed efficient digestion, O-glycan cleavage, and partial dephosphorylation without significant side reactions, thus enabling an automatic database search for the cleaved O-glycosylation or serine/threonine (S/T) phosphorylation sites. From the same sample concurrently prepared without ?-elimination, the corresponding intact O-glycopeptides were mapped by accurate precursor ion mass using an in-house glycan database majorly composed of GalNAc (mucin-type) core and the retention-time shift (?Rt). Each glycopeptide assignment was verified by the detection of glycan-specific fragments using collision-induced dissociation (CID) to estimate False Discovery Rate (FDR). Using fetuin as a model, all identified S/T elimination sites were matched to multiple intact glycopeptides with a 31% FDR. This considerably reduced to 0% FDR by ?Rt filtering. This approach was then applied to a protein mixture composed of therapeutic Factor IX and Enbrel(®) mixed with fetuin and kappa-casein. A total of 26 glycosylation sites each of which corresponds to 1-4 glycans were positively mapped and confirmed. The FDR decreased from 33% to 3.3% by ?Rt filtering and exclusion of repeated peptide tags that covered the same glycosylation sites. Moreover, the phosphorylation and O-glycosylation on the same site such as T159 of Factor IX and T170 of kappa-casein were able to be unambiguously differentiated. Thus, our approach is useful for in-depth characterization of site-specific O-glycosylation of a simple mixture such as protein-based therapeutics. PMID:25456591

  16. Phosphorus-bearing phases as archaeopetrogenetic indicator for possible bone-rock interactions in pyrometamorphic slags from ritual immolation sites

    NASA Astrophysics Data System (ADS)

    Tropper, Peter; Spielmann, Magdalena

    2015-04-01

    Although 200 ritual immolation sites occur throughout the Eastern Alps only 2 have been investigated from a mineralogical/petrological point of view. The investigated sites (Oetz, Goldbichl/Igls) are located on hill-tops and show abundant ceramic and bone fragments. In these sites pyrometamorphic slags occur (in Oetz only little, at the Goldbichl, massive amounts). The textures within these slags indicate strongly disequilibrium conditions. Investigations of slags from two ritual immolation sites in the Eastern Alps, the La-Tčne (450 - 15 B.C.) age site in Oetz and the Bronze-Age site at the Goldbichl/Igls yielded the occurrence of phosphorus-rich olivines and phosphates such as whitlockite (Oetz) and stanfieldite (Goldbichl). Temperatures derived from the slags are >1000-1100°C under highly reducing (QFM) conditions. On the other hand bone apatite crystallinity of calcinated bones yields much lower temperatures this might be due to their position in "cooler" spots of the fire (e.g. at the surface). The high temperatures deduced from the slags are compatible with core temperatures (>1100°C) of large bone fires with a possible wind-driven air circulation. Experimental investigations using DTA-TG to study chlorite breakdown verify these temperatures. In order to verify the presence of P-bearing phases during bone-rock interactions experiments were carried out at 1100-1300°C and highly-reducing conditions in graphite crucibles. Experiments concerning the interaction of bone material and three different rock types such as paragneiss, quartzphyllite and granite led to the formation of whitlockite and P-bearing olivine. Olivine contains 0-4.6 wt.%, P2O5 where the highest P-contents were observed in the quartzphyllite experiments. The occurrence of P-rich olivine and whitlockite in the quartzphyllite experiments is therefore diagnostic for bone-rock interaction at high temperatures. Based on the mineralogical observations from the two sites P-rich minerals which indicate the presence of a P-source (bone or detrital apatite) in the fire are the following: whitlockite, P-rich olivine, P-rich clinopyroxene and stanfieldite. The following mineral assemblage has experimentally shown to be associated with bone-rock interactions is: P-rich olivine ± P-rich clinopyroxene only when coexisting with whitlockite, which was found in the Oetz site.