These are representative sample records from related to your search topic.
For comprehensive and current results, perform a real-time search at

Site Map

Site Map Programs & Resources Research Groups Foundations of Prevention Biometry Publications Statistical Software Clinical Trials Research Training Internships About the Research Group Cancer Biomarkers Funding Opportunities Key Programs


Site Map

Search:  Site Map Whats New NBIA Application Collaborators NCI Cancer Imaging Program (CIP) Cancer Therapy Evaluation Program (CTEP) Division of Cancer Prevention(DCP) QUICK LINKS National Cancer Institute cancer Biomedical Informatics Grid (caBIG) NCI


Protein–protein interaction site mapping using NMR-detected mutational scanning  

Microsoft Academic Search

We demonstrate a novel NMR method for the mapping of protein–protein interaction sites. In our approach protein–protein binding\\u000a sites are mapped by competition binding experiments using indirect NMR reporter technology and Ala positional scanning. The\\u000a methodology provides high sensitivity, ease of implementation and high-throughput capabilities. The feasibility of the technique\\u000a is demonstrated with an application to the ?-Catenin\\/Tcf4 complex.

Bettina Baminger; Martin L. Ludwiczek; Georg Kontaxis; Stefan Knapp; Robert Konrat



Site Map

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


Human migrations map, interactive 2D animationSite: DNA Interactive (  

NSDL National Science Digital Library

The red lines show the possible migration pathway of the ancient human Homo erectus (sometimes known as Homo ergaster). There is little controversy about the travels of H. erectus. This possible path was mapped using fossil evidence that spans more than 1.5 million years. Many researchers believe that H. erectus lived until approximately 300,000 years ago. However, H. erectus may have survived in Indonesia until 40,000 years ago.



Mapping a Study Site  

NSDL National Science Digital Library

In this outdoor activity, learners use a mapping technique to become oriented to the major features of an outdoor site. Learners become aware of both physical and biological features including trees, rocks, water, signs of human activity. After completing this activity, learners can try the OBIS Terrestrial Hi-Lo Hunt and add more detail to their map.

Science, Lawrence H.



Molecular simulations with solvent competition quantify water displaceability and provide accurate interaction maps of protein binding sites.  


Binding sites present well-defined interaction patterns that putative ligands must meet. Knowing them is essential to guide structure-based drug discovery projects. However, complex aspects of molecular recognition-such as protein flexibility or the effect of aqueous solvation-hinder accurate predictions. This is particularly true for polar contacts, which are heavily influenced by the local environment and the behavior of discrete water molecules. Here we present and validate MDmix (Molecular Dynamics simulations with mixed solvents) as a method that provides much more accurate interaction maps than ordinary potentials (e.g., GRID). Additionally, MDmix also affords water displaceability predictions, with advantages over methods that use pure water as solvent (e.g., inhomogeneous fluid solvation theory). With current MD software and hardware solutions, predictions can be obtained in a matter of hours and visualized in a very intuitive manner. Thus, MDmix is an ideal complement in everyday structure-based drug discovery projects. PMID:25275946

Alvarez-Garcia, Daniel; Barril, Xavier



Importance of genetic maps, Mary-Claire KingSite: DNA Interactive (  

NSDL National Science Digital Library

Interviewee: Mary-Claire King DNAi Location:Applications>Genes and medicine>gene hunting>Markers Moving slowly Mary-Claire King talks about the tedious process of hunting for genes in the days before genetic maps (based on thousands of markers) were readily available.



Usability Evaluation of Public Web Mapping Sites  

NASA Astrophysics Data System (ADS)

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.

Wang, C.



NCI: SBIR & STTR - Site Map

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


Interactive Cardiovascular System Map  

NSDL National Science Digital Library

The cardiovascular portion of the InnerBody website is a road map to the human cardiovascular system. It displays all of the main veins and arteries of the human body allowing the user to click on various parts of body and dozens of links to the many different systems appear. Users can hover over the links to discover what each part is named, or click on the link to be brought to a thorough definition and description of the selected system. Users may also �zoom in� on certain parts to view more detail. In addition to the interactive �map,� InnerBody also has images and descriptions about common issues that arise within the cardiovascular system.



Multi-resolution approach for interactively locating functionally linked ion binding sites by steering small molecules into electrostatic potential maps using a haptic device.  


Metal ions drive important parts of biology, yet it remains experimentally challenging to locate their binding sites. Here we present an innovative computational approach. We use interactive steering of charged ions or small molecules in an electrostatic potential map in order to identify potential binding sites. The user interacts with a haptic device and experiences tactile feedback related to the strength of binding at a given site. The potential field is the first level of resolution used in this model. Any type of potential field can be used, implicitly taking into account various conditions such as ionic strength, dielectric constants or the presence of a membrane. At a second level, we represent the accessibility of all binding sites by modelling the shape of the target macromolecule via non-bonded van der Waals interactions between its static atomic or coarse-grained structure and the probe molecule(s). The third independent level concerns the representation of the molecular probe itself. Ion selectivity can be assessed by using multiple interacting ions as probes. This method was successfully applied to the DNase I enzyme, where we recently identified two new cation binding sites by computationally expensive extended molecular dynamics simulations. PMID:19908373

Delalande, Olivier; Ferey, Nicolas; Laurent, Benoist; Gueroult, Marc; Hartmann, Brigitte; Baaden, Marc



Digital Soil Mapping: Interactions with  

E-print Network

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

Grunwald, Sabine


Mapping Targetable Sites on Human Telomerase RNA Pseudoknot/Template Domain Using 2?-OMe RNA-interacting Polynucleotide (RIPtide) Microarrays*  

PubMed Central

Most cellular RNAs engage in intrastrand base-pairing that gives rise to complex three-dimensional folds. This self-pairing presents an impediment toward binding of the RNA by nucleic acid-based ligands. An important step in the discovery of RNA-targeting ligands is therefore to identify those regions in a folded RNA that are accessible toward the nucleic acid-based ligand. Because the folding of RNA targets can involve interactions between nonadjacent regions and employ both Watson-Crick and non-Watson-Crick base-pairing, screening of candidate binder ensembles is typically necessary. Microarray-based screening approaches have shown great promise in this regard and have suggested that achieving complete sequence coverage would be a valuable attribute of a next generation system. Here, we report a custom microarray displaying a library of RNA-interacting polynucleotides comprising all possible 2?-OMe RNA sequences from 4- to 8-nucleotides in length. We demonstrate the utility of this array in identifying RNA-interacting polynucleotides that bind tightly and specifically to the highly conserved, functionally essential template/pseudoknot domain of human telomerase RNA and that inhibit telomerase function in vitro. PMID:22451672

Gude, Lourdes; Berkovitch, Shaunna S.; Santos, Webster L.; Kutchukian, Peter S.; Pawloski, Adam R.; Kuimelis, Robert; McGall, Glenn; Verdine, Gregory L.



Site Map | Radiation Research Program (RRP)

Skip to Content Search this site Radiation Research Program (RRP) Last Updated: 05/15/14 Site Map Home About RRP Organizational Structure Clinical Radiation Oncology Branch Medical Physics Radiotherapy Development Branch Molecular Radiation Therapeutics


Site Map | Translational Research Program (TRP)

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


Site Map | Clinical Assay Development Program (CADP)

Skip to Content Search this site Site Map Home About CADP Mission Background CADP Resources for Assay Development CADN — Clinical Assay Development Network CADC — Clinical Assay Development Center SRS — Specimen Retrieval System Access to CADP Resources Eligibility Instructions Submit


Quantitative Trait Locus Mapping of Genes Under Selection Across Multiple Years and Sites in Avena barbata: Epistasis, Pleiotropy, and Genotype-by-Environment Interactions  

PubMed Central

The genetic architecture of variation in evolutionary fitness determines the trajectory of adaptive change. We identified quantitative trait loci (QTL) affecting fitness in a mapping population of recombinant inbred lines (RILs) derived from a cross between moist- and dry- associated ecotypes of Avena barbata. We estimated fitness in 179 RILs in each of two natural environments in each of 4 years. Two loci account for over half of the variation in geometric mean fitness across environments. These loci are associated in repulsion phase in the wild ecotypes, suggesting the potential for strong transgressive segregation, but also show significant epistasis giving hybrid breakdown. This epistasis is the result of sharply lower fitness in only one of the recombinant genotypes, suggesting that the loci may contain synergistically acting mutations. Within each trial (year/site combination), we can explain less of the variation than for geometric mean fitness, but the two major loci are associated with variation in fitness in most environments. Tests for pleiotropic effects of QTL on fitness in different environments reveal that the same loci are under selection in all trials. Genotype-by-environment interactions are significant for some loci, but this reflects variation in the strength, not the direction of selection. PMID:20194964

Latta, Robert G.; Gardner, Kyle M.; Staples, David A.



Quantitative trait locus mapping of genes under selection across multiple years and sites in Avena barbata: epistasis, pleiotropy, and genotype-by-environment interactions.  


The genetic architecture of variation in evolutionary fitness determines the trajectory of adaptive change. We identified quantitative trait loci (QTL) affecting fitness in a mapping population of recombinant inbred lines (RILs) derived from a cross between moist- and dry- associated ecotypes of Avena barbata. We estimated fitness in 179 RILs in each of two natural environments in each of 4 years. Two loci account for over half of the variation in geometric mean fitness across environments. These loci are associated in repulsion phase in the wild ecotypes, suggesting the potential for strong transgressive segregation, but also show significant epistasis giving hybrid breakdown. This epistasis is the result of sharply lower fitness in only one of the recombinant genotypes, suggesting that the loci may contain synergistically acting mutations. Within each trial (year/site combination), we can explain less of the variation than for geometric mean fitness, but the two major loci are associated with variation in fitness in most environments. Tests for pleiotropic effects of QTL on fitness in different environments reveal that the same loci are under selection in all trials. Genotype-by-environment interactions are significant for some loci, but this reflects variation in the strength, not the direction of selection. PMID:20194964

Latta, Robert G; Gardner, Kyle M; Staples, David A



Interaction site for soluble cytochromes on the tetraheme cytochrome subunit bound to the bacterial photosynthetic reaction center mapped by site-directed mutagenesis.  


The crystallographic structure of the Blastochloris (formerly called Rhodopseudomonas) viridis tetraheme cytochrome subunit bound to the photosynthetic reaction center (RC) suggests that all four hemes are located close enough to the surface of the protein to accept electrons from soluble cytochrome c2. To identify experimentally the site of this reaction we prepared site-directed mutants of Rubrivivax gelatinosus RCs with surface charge substitutions in the bound cytochrome subunit and studied the kinetics of their reduction by soluble cytochromes (mitochondrial horse cytochrome c, Blc. viridis cytochrome c2, and Rvi. gelatinosus cytochrome c8). In comparison with the wild-type, the mutants E79K (glutamate-79 substituted by lysine), E93K (glutamate-93 substituted by lysine), and E85K (glutamate-85 substituted by lysine) located near the solvent-exposed edge of low-potential heme 1, the fourth heme from the special pair of bacteriochlorophyll, exhibited decreased second-order rate constants for the reaction between the tetraheme subunit and the soluble cytochromes. Double charge substitutions in this region: E79K/E85K (glutamate-79 and -85 both replaced by lysine) and E93K/E85K (glutamate-93 and -85 both replaced by lysine) appeared to show an additive inhibitory effect. Mutations in other charged regions did not alter the kinetics of electron transfer between bound and soluble cytochromes. In light of the available structural information on Blc. viridis RC, these results indicate that the cluster of acidic residues immediately surrounding the distal heme 1 of the RC-bound tetraheme subunit forms an electrostatically favorable binding site for soluble cytochromes. Thus, all four hemes in the subunit seem to be directly involved in the electron transfer toward the photo-oxidized special pair of bacteriochlorophyll. On the basis of these findings, a model is proposed for the hypothetical cytochrome c2-RC transient complex for Blc. viridis. PMID:9718296

Osyczka, A; Nagashima, K V; Sogabe, S; Miki, K; Yoshida, M; Shimada, K; Matsuura, K



The Interactive Nolli Map of Rome  

NSDL National Science Digital Library

Born in 1701, Giambattista Nolli was an architect who was enamored of Rome in a way that few people have ever experienced. He spent thousands of hours creating his La Pianta Grande di Roma ("the great plan of Rome"), which became his remarkable 1748 map of the Eternal City. The actual map consists of twelve engraved copper plates that measure six feet high and seven feet wide when combined. Nolli was very careful to record the streets, squares, and various other public spaces throughout the city. This website, created by a team of dedicated scholars at the University of Oregon, allows users to examine the map in all its glory, along with a number of interactive layers that document specific building types and census data. First time visitors can launch the map engine from the homepage, and after that, they may wish to look at some of the thematic sections, which include "Natural Features", "Architecture", and "Cartography". The site also includes some fine articles on the map and its legacy, including "The Walls of Rome" and "The Nolli Map as Artifact".


Site maps and facilities listings  

SciTech Connect

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.

Not Available



Sense of Place Evoked by Interactive Maps  

E-print Network

, 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...

Go, Hanyoung



Designing interactive maps for crisis management  

Microsoft Academic Search

This paper describes the design, implementation, and evaluati on of pen input recognition systems that are suited for so-called interactive maps. Such systems provide the possibili ty to enter handwriting, drawings, sketches and other modes of pen input. Typically, interactive maps are used to an notate objects or mark situations that are depicted on the display of video walls, handhelds,

D. J. M. Willems; Louis Vuurpijl



Mapping of interaction sites of the Schizosaccharomyces pombe protein Translin with nucleic acids and proteins: a combined molecular genetics and bioinformatics study  

PubMed Central

Translin is a single-stranded RNA- and DNA-binding protein, which has been highly conserved in eukaryotes, from man to Schizosaccharomyces pombe. TRAX is a Translin paralog associated with Translin, which has coevolved with it. We generated structural models of the S. pombe Translin (spTranslin), based on the solved 3D structure of the human ortholog. Using several bioinformatics computation tools, we identified in the equatorial part of the protein a putative nucleic acids interaction surface, which includes many polar and positively charged residues, mostly arginines, surrounding a shallow cavity. Experimental verification of the bioinformatics predictions was obtained by assays of nucleic acids binding to amino acid substitution variants made in this region. Bioinformatics combined with yeast two-hybrid assays and proteomic analyses of deletion variants, also identified at the top of the spTranslin structure a region required for interaction with spTRAX, and for spTranslin dimerization. In addition, bioinformatics predicted the presence of a second protein-protein interaction site at the bottom of the spTranslin structure. Similar nucleic acid and protein interaction sites were also predicted for the human Translin. Thus, our results appear to generally apply to the Translin family of proteins, and are expected to contribute to a further elucidation of their functions. PMID:20081200

Eliahoo, Elad; Ben Yosef, Ron; Perez-Cano, Laura; Fernandez-Recio, Juan; Glaser, Fabian; Manor, Haim



A Protein Interaction Map of Drosophila melanogaster  

Microsoft Academic Search

Drosophila melanogaster is a proven model system for many aspects of human biology. Here we present a two-hybrid-based protein-interaction map of the fly proteome. A total of 10,623 predicted transcripts were isolated and screened against standard and normalized complementary DNA libraries to produce a draft map of 7048 proteins and 20,405 interactions. A computational method of rating two-hybrid interaction confidence

L. Giot; J. S. Bader; C. Brouwer; A. Chaudhuri; B. Kuang; Y. Li; Y. L. Hao; C. E. Ooi; B. Godwin; E. Vitols; G. Vijayadamodar; P. Pochart; H. Machineni; M. Welsh; Y. Kong; B. Zerhusen; R. Malcolm; Z. Varrone; A. Collis; M. Minto; S. Burgess; L. McDaniel; E. Stimpson; F. Spriggs; J. Williams; K. Neurath; N. Ioime; M. Agee; E. Voss; K. Furtak; R. Renzulli; N. Aanensen; S. Carrolla; E. Bickelhaupt; Y. Lazovatsky; A. DaSilva; J. Zhong; C. A. Stanyon; R. L. Finley; K. P. White; M. Braverman; T. Jarvie; S. Gold; M. Leach; J. Knight; R. A. Shimkets; M. P. McKenna; J. Chant; J. M. Rothberg



Interactive Map of 1906 Earthquake Photos  

NSDL National Science Digital Library

An interactive map of the city that allows the Bancroft's photographic archive of the quake to be searched by region of the city. The map is divided into regions, and points of interest are highlighted. By comparing photographs taken in each region, it's possible to compare how different areas of the city were affected by the earthquake.

Library, The B.


3D interactive pictorial maps  

E-print Network

. . . . . . . . . . . . . . . . . . . . . 23 11 A bar graph shows comparison of data. . . . . . . . . . . . . . . . . . 26 12 Simplififed shapes of states of USA with changing heights. . . . . . . 28 13 The slider interface in Maya for changing heights of models. . . . . . 29 14 Melscript... for creating the slider interface. . . . . . . . . . . . . . . . 30 15 Polygonal text in Maya for statistical maps. . . . . . . . . . . . . . . 31 16 Dome of light and hypershade option in Maya. . . . . . . . . . . . . 32 17 3D models with baked shadow...

Naz, Asma



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


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


Interactive Multimedia, Concept Mapping, and Cultural Context.  

ERIC Educational Resources Information Center

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…

Henderson, L.; And Others


An improved map of conserved regulatory sites for Saccharomyces cerevisiae  

PubMed Central

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 discovery programs to analyze genome-wide chromatin immunoprecipitation data for 203 transcription factors. The programs were used to identify sequence motifs that were likely to correspond to the DNA-binding specificity of the immunoprecipitated proteins. We report improved versions of two conservation-based motif discovery algorithms, PhyloCon and Converge. Using these programs, we create a refined regulatory map for S. cerevisiae by reanalyzing the same chromatin immunoprecipitation data. Results Applying the same conservative criteria that were applied in the original study, we find that PhyloCon and Converge each separately discover more known specificities than the combination of all six programs in the previous study. Combining the results of PhyloCon and Converge, we discover significant sequence motifs for 36 transcription factors that were previously missed. The new set of motifs identifies 636 more regulatory interactions than the previous one. The new network contains 28% more regulatory interactions among transcription factors, evidence of greater cross-talk between regulators. Conclusion Combining two complementary computational strategies for conservation-based motif discovery improves the ability to identify the specificity of transcriptional regulators from genome-wide chromatin immunoprecipitation data. The increased sensitivity of these methods significantly expands the map of yeast regulatory sites without the need to alter any of the thresholds for statistical significance. The new map of regulatory sites reveals a more elaborate and complex view of the yeast genetic regulatory network than was observed previously. PMID:16522208

MacIsaac, Kenzie D; Wang, Ting; Gordon, D Benjamin; Gifford, David K; Stormo, Gary D; Fraenkel, Ernest



Matter & Interactions: Textbook Web Site  

NSDL National Science Digital Library

This two-volume modern textbook for introductory calculus-based college physics courses emphasizes qualitative as well as quantitative reasoning, and puts heavy emphasis on atomic-level description and analysis. The 3rd edition, published in 2010, features a larger collection of problems and numerical examples, plus a new section on geometric optics. The Matter & Interactions approach focuses on the importance of basic principles of physics, engages students in modeling, and integrates the atomic nature of matter throughout the curriculum. The web site also provides extensive resources for instructors using the texts, including software, discussion forums, instructional activities, and lecture notes.

Chabay, Ruth; Sherwood, Bruce



Outline Map Sites: The Perry-Castaneda Library Map Collection  

NSDL National Science Digital Library

This website provides an extensive list of links to outline maps of the world, continents, countries, and counties, as well as some historical and thematic maps. Maps are presented as they were originally published, and the original publisher/source and date is provided.


An improved map of conserved regulatory sites for Saccharomyces cerevisiae  

E-print Network

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 ...

Wang, Ting


Data visualization in interactive maps and time series  

NASA Astrophysics Data System (ADS)

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 ( 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.

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



Soil Survey and Ecological Sites: Integrated Map Unit Design and  

E-print Network

Soil Survey and Ecological Sites: Integrated Map Unit Design and Interpretation Arlene J. Tugel Soil Scientist, Liasion to ARS Natural Resources Conservation Service Las Cruces, NM #12;Objectives · Soil maps- a review · Soil survey legend development · Data collection · Soil-Site correlation


Ontology-Based Web Site Mapping for Information Exploration1  

E-print Network

Ontology-Based Web Site Mapping for Information Exploration1 Xiaolan Zhu Susan Gauch Lutz Gerhard Nicholas Kral Alexander Pretschner Department of Electrical Engineering and Computer Science University. In this article, we introduce an ontology-based web site mapping method used to produce conceptual meta

Kansas, University of


Interactive State of Metropolitan America Indicator Map  

NSDL National Science Digital Library

How quickly have the suburbs in the American southeast grown over the past decade? This question, and many others, are answered in fine visual form on this website, created by staff members at The Brookings Institution. Visitors can use the interactive maps to look over population, ethnicity, age, and educational attainment distributions across the United States. Each map contains a zoom feature, and visitors can use the subject indicators to look at different variables. Also, visitors can toggle through different geographic scales of focus, including metro areas, center cities, suburbs, and states. Finally, visitors can also download and read "The State of Metropolitan America" report which provides additional perspective on some of these recent demographic trends.


Molecular mapping of the chloride-binding site in von Willebrand factor (VWF): energetics and conformational effects on the VWF/ADAMTS-13 interaction.  


Physiological concentrations of NaCl inhibit the hydrolysis of von Willebrand factor (VWF) by ADAMTS-13. This effect is because of the specific binding of chloride ions to VWF. Urea-induced unfolding was measured in the presence of NaCl, CH3COONa, and NaClO4 at pH 8.0, 25 degrees C, for multimeric VWF, the recombinant A1-A2-A3 VWF domains, and the A1 domain. Chloride stabilizes the folded conformation of the A1-A2-A3 and A1 domains more efficiently than acetate but less strongly than perchlorate. Spectroscopic evidence showed that chloride binds to both the A1 and A1-A2 domain but not to the isolated A2 domain. Binding of Cl- to both wild type (WT) and the natural mutant p.R1306W A1-A2-A3 domains of VWF has a large heat capacity change equal to -1 and -0.4 kcal mol(-1) K(-1) for WT and p.R1306W A1-A2-A3 domains, respectively. This result implies that a burial of a vast apolar surface area is caused by conformational transitions linked to chloride binding. At any temperature, chloride affinity was higher for WT than for the mutant p.R1306W form. Chloride ions inhibit hydrolysis by ADAMTS-13 of the A1-A2-A3 and A1-A2 domains in the presence of either urea or high shear stress, whereas this effect was either absent or negligible in experiments using A2 and A2-A3 domains. These findings show that the A1 domain contains the binding site of chloride ions that control allosterically the proteolysis by ADAMTS-13 of the Tyr1605-Met1606 bond in the A2 domain and that the R1306W mutation of type 2B VWD quenches the binding of chloride ion to the A1 domain. PMID:16899464

De Cristofaro, Raimondo; Peyvandi, Flora; Baronciani, Luciano; Palla, Roberta; Lavoretano, Silvia; Lombardi, Rossana; Di Stasio, Enrico; Federici, Augusto B; Mannucci, Pier Mannuccio



Restriction site and genetic map of Cucurbita pepo chloroplast DNA  

Microsoft Academic Search

A detailed restriction map of squash chloroplast DNA (cpDNA) was constructed with five restriction endonuclease, SalI, PvuII, BglI, SacII, and PstI. The cleavage sites were mapped by sequential digestion of cpDNA using low-gelling temperature agarose. The restriction map shows that squash cpDNA is an approximately 153 kilobase (kb) circle with a large inverted repeat sequence of 23.3 kb, separated by

H. Lim; I. Gounaris; R. C. Hardison; C. D. Boyer



National Cancer Institute - Cancer Prevention Fellowship Program - Site Map

Skip Navigation Site Map Cancer Prevention Fellowship Program Home About Us About Us Staff Listing Our Catalog Our Catalog Table of Contents Director's Message Staff Profiles Program Description Program Information Guidelines for Application Preceptorships Bibliography Post-Fellowship


Interactive Web Sites for Teens  

ERIC Educational Resources Information Center

Eighty-three percent of teenagers are online. The average teen spends 5 to 10 hours a week on the Web. When using Web sites, teenagers are easily bored. Teenagers are also not nearly as skilled as adults at navigating the Web and do not really care for glitzy graphics. Insufficient reading skills, immature research strategies, and unwillingness to…

Haycock, Ken



Docking Motif Interactions in MAP Kinases Revealed by Hydrogen Exchange Mass Spectrometry  

Microsoft Academic Search

Protein interactions between MAP kinases and substrates, activators, and scaffolding proteins are regulated by docking site motifs, one containing basic residues proximal to Leu-X-Leu (DEJL) and a second containing Phe-X-Phe (DEF). Hydrogen exchange mass spectrometry was used to identify regions in MAP kinases protected from solvent by docking motif interactions. Protection by DEJL peptide binding was observed in loops spanning

Thomas Lee; Andrew N Hoofnagle; Yukihito Kabuyama; James Stroud; Xiaoshan Min; Elizabeth J Goldsmith; Lin Chen; Katheryn A Resing; Natalie G Ahn



The interactive multisensor snow and ice mapping system  

Microsoft Academic Search

The interactive multisensor snow and ice mapping system (IMS) was developed to give snow and ice analysts the tools, on one platform, to inspect visually the imagery and mapped data from various sensor sources to determine the presence of snow and ice and to depict snow- and ice-covered areas on a map on a daily basis, in one hour or

Bruce H. Ramsay



Virtual reality mapping system for Chernobyl accident site assessment  

NASA Astrophysics Data System (ADS)

Initiated by the Department of Energy's International Nuclear Safety Program, an effort in underway to deliver and employ a telerobotic diagnostic system for structural evaluation and monitoring within the Chornobyl Unit-4 shelter. A mobile robot, named Pioneer, will enter the damaged Chornobyl structure and employ devices to measure radiation, temperature and humidity; acquire core samples of concrete structures for subsequent engineering analysis; and make photo-realistic 3D maps of the building interior. This paper details the latter element, dubbed 'C-Map', the Chornobyl Mapping System. C-Map consists of an automated 3D modeling system using stereo computer vision along with an interactive, virtual reality software program to acquire and analyze the photo-realistic 3D maps of the damaged building interior.

Blackmon, Theodore T.; Ngyuen, Laurent; Neveu, Charles F.; Rasmussen, Daryl; Zbinden, Eric; Maimone, Mark; Matthies, Larry H.; Thayer, Scott M.; Teza, James; Broz, Vince; Osborn, James; Hebert, Martial; Steele, Jerry; Thomas, Geb



An interactive method for digitizing zone maps  

NASA Technical Reports Server (NTRS)

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.

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



Global Mapping of the Yeast Genetic Interaction Network  

Microsoft Academic Search

A genetic interaction network containing ~1000 genes and ~4000 interactions was mapped by crossing mutations in 132 different query genes into a set of ~4700 viable gene yeast deletion mutants and scoring the double mutant progeny for fitness defects. Network connectivity was predictive of function because interactions often occurred among functionally related genes, and similar patterns of interactions tended to

Amy Hin Yan Tong; Guillaume Lesage; Gary D. Bader; Huiming Ding; Hong Xu; Xiaofeng Xin; James Young; Gabriel F. Berriz; Renee L. Brost; Michael Chang; YiQun Chen; Xin Cheng; Gordon Chua; Helena Friesen; Debra S. Goldberg; Jennifer Haynes; Christine Humphries; Grace He; Shamiza Hussein; Lizhu Ke; Nevan Krogan; Zhijian Li; Joshua N. Levinson; Hong Lu; Patrice Ménard; Christella Munyana; Ainslie B. Parsons; Owen Ryan; Raffi Tonikian; Tania Roberts; Anne-Marie Sdicu; Jesse Shapiro; Bilal Sheikh; Bernhard Suter; Sharyl L. Wong; Lan V. Zhang; Hongwei Zhu; Christopher G. Burd; Sean Munro; Chris Sander; Jasper Rine; Jack Greenblatt; Matthias Peter; Anthony Bretscher; Graham Bell; Frederick P. Roth; Grant W. Brown; Brenda Andrews; Howard Bussey; Charles Boone



Map Quality for Site-Specific Fertility Management  

Microsoft Academic Search

M aps are fundamental to SSFM because they rep- The quality of soil fertility maps affects the efficacy of site-specific resent either the spatial state of a condition of soil fertility management (SSFM). The purpose of this study was to interest, the prescription of inputs needed to manage a evaluate how different soil sampling approaches and grid interpolation particular condition

T. G. Mueller; F. J. Pierce; O. Schabenberger; D. D. Warncke



Restriction site and genetic map of Cucurbita pepo chloroplast DNA.  


A detailed restriction map of squash chloroplast DNA (cpDNA) was constructed with five restriction endonucleases, SalI, PvuII, BglI, SacII, and PstI. The cleavage sites were mapped by sequential digestion of cpDNA using low-gelling temperature agarose. The restriction map shows that squash cpDNA is an approximately 153 kilobase (kb) circle with a large inverted repeat sequence of 23.3 kb, separated by a large (83.7 kb) and a small (22.7 kb) single copy region. Genes for a number of chloroplast polypeptides were localized on the map by hybridizing the cpDNA restriction fragments to heterologous gene-specific probes from tobacco, pea, tomato, maize, and spinach chloroplasts. The gene locations and organization of squash cpDNA are highly conserved and similar to chloroplast genomes of tomato, pepper, and Ginkgo. PMID:2249258

Lim, H; Gounaris, I; Hardison, R C; Boyer, C D



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

PubMed Central

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

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



Is tilt interaction better than keypad interaction for mobile map-based applications?  

Microsoft Academic Search

Map-based applications are becoming standard features of most smart phones. Keypad and touch-screen interaction have traditionally been used to interact with maps on mobile phones, but both these interaction techniques have several shortcomings. Tilt interaction offers an alternative approach with several advantages. Tilt interaction is intuitive and can be performed one-handed. Previous research has shown that tilt interaction offers equivalent

Bradley van Tonder; Janet Wesson



Context Modeling with Evolutionary Fuzzy Cognitive Map in Interactive Storytelling  

E-print Network

Context Modeling with Evolutionary Fuzzy Cognitive Map in Interactive Storytelling Yundong Cai is a great challenge in interactive storytelling. In this paper, we propose a model, namely Evolutionary. INTRODUCTION In recent years, interactive storytelling in the virtual envi- ronment has gain a lot of interests

Tan, Ah-Hwee


MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures.  


Mutation position imaging toolbox (MuPIT) interactive is a browser-based application for single-nucleotide variants (SNVs), which automatically maps the genomic coordinates of SNVs onto the coordinates of available three-dimensional (3D) protein structures. The application is designed for interactive browser-based visualization of the putative functional relevance of SNVs by biologists who are not necessarily experts either in bioinformatics or protein structure. Users may submit batches of several thousand SNVs and review all protein structures that cover the SNVs, including available functional annotations such as binding sites, mutagenesis experiments, and common polymorphisms. Multiple SNVs may be mapped onto each structure, enabling 3D visualization of SNV clusters and their relationship to functionally annotated positions. We illustrate the utility of MuPIT interactive in rationalizing the impact of selected polymorphisms in the PharmGKB database, somatic mutations identified in the Cancer Genome Atlas study of invasive breast carcinomas, and rare variants identified in the exome sequencing project. MuPIT interactive is freely available for non-profit use at . PMID:23793516

Niknafs, Noushin; Kim, Dewey; Kim, Ryangguk; Diekhans, Mark; Ryan, Michael; Stenson, Peter D; Cooper, David N; Karchin, Rachel




Microsoft Academic Search

We show that a compactum is locally connected if and only if every semimonotone mapping onto it is also monotone. If we put open in place of monotone, we obtain the finite compacta; if we put in confluent, we obtain a large class of compacta, the connected members of which are connected im kleinen at each of their cut points.




Microtubule Interaction Site of the Kinesin Motor  

Microsoft Academic Search

Kinesin and myosin are motor proteins that share a common structural core and bind to microtubules and actin filaments, respectively. While the actomyosin interface has been well studied, the location of the microtubule-binding site on kinesin has not been identified. Using alanine-scanning mutagenesis, we have found that microtubule-interacting kinesin residues are located in three loops that cluster in a patch

Günther Woehlke; Aaron K Ruby; Cynthia L Hart; Bernice Ly; Nora Hom-Booher; Ronald D Vale



An in-depth map of polyadenylation sites in cancer  

PubMed Central

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

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



Quantitative genetic-interaction mapping in mammalian cells  

PubMed Central

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

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



Tools for Glycomics: Mapping Interactions of Carbohydrates in Biological Systems  

E-print Network

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

Ratner, Daniel M.


Phylogeny-guided interaction mapping in seven eukaryotes  

Microsoft Academic Search

BACKGROUND: The assembly of reliable and complete protein-protein interaction (PPI) maps remains one of the significant challenges in systems biology. Computational methods which integrate and prioritize interaction data can greatly aid in approaching this goal. RESULTS: We developed a Bayesian inference framework which uses phylogenetic relationships to guide the integration of PPI evidence across multiple datasets and species, providing more

Janusz Dutkowski; Jerzy Tiuryn



Cartographic Mapping of Mars Landing Sites: A Historical Perspective  

NASA Technical Reports Server (NTRS)

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.

Duxbury, Thomas C.



The interaction map of yeast: terra incognita?  

PubMed Central

A systematic curation of the literature on Saccharomyces cerevisiae has yielded a comprehensive collection of experimentally observed interactions. This new resource augments current views of the topological structure of yeast's physical and genetic networks, but also reveals that existing studies cover only a fraction of the cell. PMID:16762048

Mellor, Joe; DeLisi, Charles



Building protein interaction maps for Down's syndrome.  


Now that the complete sequences for human chromosome 21 and the orthologous mouse genomic regions are known, reasonably complete, conserved, protein-coding gene catalogues are also available. The central issue now facing Down's syndrome researchers is the correlation of increased expression of specific, normal, chromosome 21 genes with the development of specific deficits in learning and memory. Because of the number of candidate genes involved, the number of alternative splice variants of individual genes and the number of pathways in which these genes function, a pathway analysis approach will be critical to success. Here, three examples, both gene specific and pathway related, that would benefit from pathway analysis are discussed: (1) the potential roles of eight chromosome 21 proteins in RNA processing pathways; (2) the chromosome 21 protein intersectin 1 and its domain composition, alternative splicing, protein interactions and functions; and (3) the interactions of ten chromosome 21 proteins with components of the mitogen-activated protein kinase and the calcineurin signalling pathways. A productive approach to developing gene-phenotype correlations in Down's syndrome will make use of known and predicted functions and interactions of chromosome 21 genes to predict pathways that may be perturbed by their increased levels of expression. Investigations may then be targeted in animal models to specific interactions, intermediate steps or end-points of such pathways and the downstream - perhaps amplified - consequences of gene dosage directly assessed. Once pathway perturbations have been identified, the potential for rational design of therapeutics becomes practical. PMID:15355596

Gardiner, Katheleen; Davisson, Muriel T; Crnic, Linda S



Site classification map for Tbilisi using seismic prospecting methods  

NASA Astrophysics Data System (ADS)

This aspect deserves major attention since it plays considerable role in the definition of the seismic impact to be considered in the design and retrofitting of structures. The most important parameter of soil maps of seismic site conditions, the shear wave velocity in the upper 30 m section of the ground (VS30) on regional scales are relatively rare since they require substantial investment in geological and geotechnical data acquisition and interpretation. Work presented here was initiated by working package wp5 of regional projects EMME (Earthquake Model for Middle East Region). In the frame of the project geophysical field work were done in some parts of Tbilisi. Seismic prospecting measurements were done along some profiles. In seismic= prospecting RAS-24 was used and obtained data is processed by Winsism V.12 (refraction analysis ). Second version of soil classification for Tbilisi city was done on the basis of new geo-engineering map of 1: 25 000 scales. For this the number of engineering-geological researches and generalization on the territory of Tbilisi were processed, All the Geological and Engineer-geological reports, that were collected and processed. Since in the geological reports less attention is paid to the genesis of the quaternary sediments and their lithological description, and in this regard the territory of Tbilisi is very difficult and multi-spectrum, it was necessary to conduct additional field surveys in 10 districts to specify information. Finely combining information that comes from seismoprospecting measurements and geo-engineering map the new site classification map expressed in Vs30 were derived for Tbilisi city.

Goguadze, Nino; Gventcadze, Aleko; Arabidze, Vakhtang; Tsereteli, Emil; Gaphrindashvili, Giorgi



Evaluation of Mapping Methodologies at a Legacy Test Site  

NASA Astrophysics Data System (ADS)

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.

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.



Interactive computer methods for generating mineral-resource maps  

USGS Publications Warehouse

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.

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



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


Glycosaminoglycans (GAGs) are complex polysaccharides involved in a wide range of biological signaling events, as well as being important as biological structural materials. Despite the ubiquity and importance of GAG-protein interactions in biological systems and potentially as therapeutic targets, detailed structures of such interactions are sparse in availability. Computational methods can provide detailed structural knowledge of these interactions; however, they should be evaluated against suitable test systems prior to their widespread use. In this study, we have investigated the application of automated molecular docking and interaction mapping techniques to characterizing GAG-protein interactions. A series of high-resolution X-ray crystal structures of GAGs in complex with proteins was used to evaluate the approaches. Accurately scoring the pose fitting best with the crystal structure was a challenge for all docking programs evaluated. The site mapping technique offered excellent prediction of the key residues involved in ligand recognition, comparable to the best pose and improved over the top-ranked pose. A design protocol incorporating site- and ligand-based mapping techniques was developed and applied to identify GAGs capable of binding to acidic fibroblast growth factor (aFGF). The protocol was able to identify ligands known to bind to aFGF and accurately able to predict the binding modes of those ligands when using a known ligand-binding conformation of the protein. This study demonstrates the value of mapping-based techniques in identifying specific GAG epitopes recognized by proteins and for GAG-based drug design. PMID:24859723

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



Mapping the phase diagram of strongly interacting matter  

SciTech Connect

We employ a conformal mapping to explore the thermodynamics of strongly interacting matter at finite values of the baryon chemical potential {mu}. This method allows us to identify the singularity corresponding to the critical point of a second-order phase transition at finite {mu}, given information only at {mu}=0. The scheme is potentially useful for computing thermodynamic properties of strongly interacting hot and dense matter in lattice gauge theory. The technique is illustrated by an application to a chiral effective model.

Skokov, V.; Morita, K.; Friman, B. [GSI Helmholtzzentrum fuer Schwerionenforschung, D-64291 Darmstadt (Germany)



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.


Interactive Decal Compositing with Discrete Exponential Maps Ryan Schmidt  

E-print Network

Interactive Decal Compositing with Discrete Exponential Maps Ryan Schmidt University of Calgary an hour. Abstract A method is described for texturing surfaces using decals, images placed on the surface using local parameterizations. Decal pa- rameterizations are generated with a novel O(N logN) discrete

Grimm, Cindy


Protein-Protein Interaction Site Predictions with Three-Dimensional Probability Distributions of Interacting Atoms on Protein Surfaces  

PubMed Central

Protein-protein interactions are key to many biological processes. Computational methodologies devised to predict protein-protein interaction (PPI) sites on protein surfaces are important tools in providing insights into the biological functions of proteins and in developing therapeutics targeting the protein-protein interaction sites. One of the general features of PPI sites is that the core regions from the two interacting protein surfaces are complementary to each other, similar to the interior of proteins in packing density and in the physicochemical nature of the amino acid composition. In this work, we simulated the physicochemical complementarities by constructing three-dimensional probability density maps of non-covalent interacting atoms on the protein surfaces. The interacting probabilities were derived from the interior of known structures. Machine learning algorithms were applied to learn the characteristic patterns of the probability density maps specific to the PPI sites. The trained predictors for PPI sites were cross-validated with the training cases (consisting of 432 proteins) and were tested on an independent dataset (consisting of 142 proteins). The residue-based Matthews correlation coefficient for the independent test set was 0.423; the accuracy, precision, sensitivity, specificity were 0.753, 0.519, 0.677, and 0.779 respectively. The benchmark results indicate that the optimized machine learning models are among the best predictors in identifying PPI sites on protein surfaces. In particular, the PPI site prediction accuracy increases with increasing size of the PPI site and with increasing hydrophobicity in amino acid composition of the PPI interface; the core interface regions are more likely to be recognized with high prediction confidence. The results indicate that the physicochemical complementarity patterns on protein surfaces are important determinants in PPIs, and a substantial portion of the PPI sites can be predicted correctly with the physicochemical complementarity features based on the non-covalent interaction data derived from protein interiors. PMID:22701576

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



Nemitin, a Novel Map8/Map1s Interacting Protein with Wd40 Repeats  

PubMed Central

In neurons, a highly regulated microtubule cytoskeleton is essential for many cellular functions. These include axonal transport, regional specialization and synaptic function. Given the critical roles of microtubule-associated proteins (MAPs) in maintaining and regulating microtubule stability and dynamics, we sought to understand how this regulation is achieved. Here, we identify a novel LisH/WD40 repeat protein, tentatively named nemitin (neuronal enriched MAP interacting protein), as a potential regulator of MAP8-associated microtubule function. Based on expression at both the mRNA and protein levels, nemitin is enriched in the nervous system. Its protein expression is detected as early as embryonic day 11 and continues through adulthood. Interestingly, when expressed in non-neuronal cells, nemitin displays a diffuse pattern with puncta, although at the ultrastructural level it localizes along the microtubule network in vivo in sciatic nerves. These results suggest that the association of nemitin to microtubules may require an intermediary protein. Indeed, co-expression of nemitin with microtubule-associated protein 8 (MAP8) results in nemitin losing its diffuse pattern, instead decorating microtubules uniformly along with MAP8. Together, these results imply that nemitin may play an important role in regulating the neuronal cytoskeleton through an interaction with MAP8. PMID:22523538

Wang, Wei; Lundin, Victor F.; Millan, Ivan; Zeng, Anne; Chen, Xinyu; Yang, Jie; Allen, Elizabeth; Chen, Ningna; Bach, Gillian; Hsu, Andrew; Maloney, Michael T.; Kapur, Mridu; Yang, Yanmin



Imputing and Predicting Quantitative Genetic Interactions in Epistatic MAPs  

PubMed Central

Mapping epistatic (or genetic) interactions has emerged as an important network biology approach for establishing functional relationships among genes and proteins. Epistasis networks are complementary to physical protein interaction networks, providing valuable insight into both the function of individual genes and the overall wiring of the cell. A high-throughput method termed “epistatic mini array profiles” (E-MAPs) was recently developed in yeast to quantify alleviating or aggravating interactions between gene pairs. The typical output of an E-MAP experiment is a large symmetric matrix of interaction scores. One problem with this data is the large amount of missing values – interactions that cannot be measured during the high-throughput process or whose measurements were discarded due to quality filtering steps. These missing values can reduce the effectiveness of some data analysis techniques and prevent the use of others. Here, we discuss one solution to this problem, imputation using nearest neighbors, and give practical examples of the use of a freely available implementation of this method. PMID:21877290

Ryan, Colm; Cagney, Gerard; Krogan, Nevan; Cunningham, Padraig; Greene, Derek



An Interaction Map of Endoplasmic Reticulum Chaperones and Foldases*  

PubMed Central

Chaperones and foldases in the endoplasmic reticulum (ER) ensure correct protein folding. Extensive protein-protein interaction maps have defined the organization and function of many cellular complexes, but ER complexes are under-represented. Consequently, chaperone and foldase networks in the ER are largely uncharacterized. Using complementary ER-specific methods, we have mapped interactions between ER-lumenal chaperones and foldases and describe their organization in multiprotein complexes. We identify new functional chaperone modules, including interactions between protein-disulfide isomerases and peptidyl-prolyl cis-trans-isomerases. We have examined in detail a novel ERp72-cyclophilin B complex that enhances the rate of folding of immunoglobulin G. Deletion analysis and NMR reveal a conserved surface of cyclophilin B that interacts with polyacidic stretches of ERp72 and GRp94. Mutagenesis within this highly charged surface region abrogates interactions with its chaperone partners and reveals a new mechanism of ER protein-protein interaction. This ability of cyclophilin B to interact with different partners using the same molecular surface suggests that ER-chaperone/foldase partnerships may switch depending on the needs of different substrates, illustrating the flexibility of multichaperone complexes of the ER folding machinery. PMID:22665516

Jansen, Gregor; Maattanen, Pekka; Denisov, Alexey Y.; Scarffe, Leslie; Schade, Babette; Balghi, Haouaria; Dejgaard, Kurt; Chen, Leanna Y.; Muller, William J.; Gehring, Kalle; Thomas, David Y.



Combining different 'omics' technologies to map and validate protein-protein interactions in humans  

Microsoft Academic Search

The mapping of protein-protein interactions is key to understanding biological processes. Many technologies have been reported to map interactions and these have been systematically applied in yeast. To date, the number of reported yeast protein interactions that have been truly validated by at least one other approach is low. The mapping of human protein interaction networks is even more complicated.

Daniel Figeys




NSDL National Science Digital Library

This collection presents maps of blast and fire damage to Hiroshima and Nagasaki, Japan, and the radioactive fallout levels from the Trinity and BRAVO tests. The collection also includes maps of Manhattan Project Era Sites (Hanford, Washington, Oak Ridge, Tennessee, and Los Alamos, New Mexico).

Griffith, Christopher


Magnetic mapping and interpretation of an archaeological site in Syria  

NASA Astrophysics Data System (ADS)

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.

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



Learning to merge: a new tool for interactive mapping  

NASA Astrophysics Data System (ADS)

The task of turning raw imagery into semantically meaningful maps and overlays is a key area of remote sensing activity. Image analysts, in applications ranging from environmental monitoring to intelligence, use imagery to generate and update maps of terrain, vegetation, road networks, buildings and other relevant features. Often these tasks can be cast as a pixel labeling problem, and several interactive pixel labeling tools have been developed. These tools exploit training data, which is generated by analysts using simple and intuitive paint-program annotation tools, in order to tailor the labeling algorithm for the particular dataset and task. In other cases, the task is best cast as a pixel segmentation problem. Interactive pixel segmentation tools have also been developed, but these tools typically do not learn from training data like the pixel labeling tools do. In this paper we investigate tools for interactive pixel segmentation that also learn from user input. The input has the form of segment merging (or grouping). Merging examples are 1) easily obtained from analysts using vector annotation tools, and 2) more challenging to exploit than traditional labels. We outline the key issues in developing these interactive merging tools, and describe their application to remote sensing.

Porter, Reid B.; Lundquist, Sheng; Ruggiero, Christy



Mapping of heparin/heparan sulfate binding sites on ?v?3 integrin by molecular docking.  


Heparin/heparan sulfate interact with growth factors, chemokines, extracellular proteins, and receptors. Integrins are ?? heterodimers that serve as receptors for extracellular proteins, regulate cell behavior, and participate in extracellular matrix assembly. Heparin binds to RGD-dependent integrins (?IIb?3, ?5?1, ?v?3, and ?v?5) and to RGD-independent integrins (?4?1, ?X?2, and ?M?2), but their binding sites have not been located on integrins. We report the mapping of heparin binding sites on the ectodomain of ?v?3 integrin by molecular modeling. The surface of the ectodomain was scanned with small rigid probes mimicking the sulfated domains of heparan sulfate. Docking results were clustered into binding spots. The best results were selected for further docking simulations with heparin hexasaccharide. Six potential binding spots containing lysine and/or arginine residues were identified on the ectodomain of ?v?3 integrin. Heparin would mostly bind to the top of the genu domain, the Calf-I domain of the ? subunit, and the top of the ? subunit of RGD-dependent integrins. Three spots were close enough from each other on the integrin surface to form an extended binding site that could interact with heparin/heparan sulfate chains. Because heparin does not bind to the same integrin site as protein ligands, no steric hindrance prevents the formation of ternary complexes comprising the integrin, its protein ligand, and heparin/heparan sulfate. The basic amino acid residues predicted to interact with heparin are conserved in the sequences of RGD-dependent but not of RGD-independent integrins suggesting that heparin/heparan sulfate could bind to different sites on these two integrin subfamilies. PMID:23334915

Ballut, Lionel; Sapay, Nicolas; Chautard, Emilie; Imberty, Anne; Ricard-Blum, Sylvie



Application of structured light imaging for high resolution mapping of underwater archaeological sites  

Microsoft Academic Search

This paper presents results from recent work using structured light laser profile imaging to create high resolution bathymetric maps of underwater archaeological sites. Documenting the texture and structure of submerged sites is a difficult task and many applicable acoustic and photographic mapping techniques have recently emerged. This effort was completed to evaluate laser profile imaging in comparison to stereo imaging

Chris Roman; Gabrielle Inglis; James Rutter



FAW-AAIM 2012 Program Sunday, May 13th at Zhongguanyuan Global Village, map site F  

E-print Network

Siu Lin Center for International Studies on campus, map site 2 8:40am-9:00am: Opening Address Chair-Jie Wang and Xin He Succinct Strictly Convex Greedy Drawing of 3-Connected Plane Graphs Longcheng Liu at Tan Siu Lin Center for International Studies on campus, map site 2 9:00am-10:00am: Invited Talk II

Gu, Qianping


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

E-print Network

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

Holberton, Rebecca L.


PTRcombiner: mining combinatorial regulation of gene expression from post-transcriptional interaction maps  

PubMed Central

Background The progress in mapping RNA-protein and RNA-RNA interactions at the transcriptome-wide level paves the way to decipher possible combinatorial patterns embedded in post-transcriptional regulation of gene expression. Results Here we propose an innovative computational tool to extract clusters of mRNA trans-acting co-regulators (RNA binding proteins and non-coding RNAs) from pairwise interaction annotations. In addition the tool allows to analyze the binding site similarity of co-regulators belonging to the same cluster, given their positional binding information. The tool has been tested on experimental collections of human and yeast interactions, identifying modules that coordinate functionally related messages. Conclusions This tool is an original attempt to uncover combinatorial patterns using all the post-transcriptional interaction data available so far. PTRcombiner is available at PMID:24758252



Ecoregions of North Dakota and South Dakota: Interactive Map  

NSDL National Science Digital Library

Ecoregions denote areas of general similarity in ecosystems and in the type, quality, and quantity of environmental resources. They are designed to serve as a spatial framework for the research, assessment, management, and monitoring of ecosystems and ecosystem components. This interactive map shows the ecoregions of North and South Dakota in increasing levels of detail (from level III to level IV). Clicking on the legend shows information for each type of ecoregion, including a photo and description, physiography, geology, soils type, climate, natural vegetation types, and land use/land cover. A downloadable version is available.


Genome-wide map of regulatory interactions in the human genome  

PubMed Central

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

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



Dissection of DNA Damage Responses Using Multiconditional Genetic Interaction Maps  

PubMed Central

SUMMARY To protect the genome, cells have evolved a diverse set of pathways designed to sense, signal, and repair multiple types of DNA damage. To assess the degree of coordination and crosstalk among these pathways, we systematically mapped changes in the cell's genetic network across a panel of different DNA-damaging agents, resulting in ~1,800,000 differential measurements. Each agent was associated with a distinct interaction pattern, which, unlike single-mutant phenotypes or gene expression data, has high statistical power to pinpoint the specific repair mechanisms at work. The agent-specific networks revealed roles for the histone acetyltranferase Rtt109 in the mutagenic bypass of DNA lesions and the neddylation machinery in cell-cycle regulation and genome stability, while the network induced by multiple agents implicates Irc21, an uncharacterized protein, in checkpoint control and DNA repair. Our multiconditional genetic interaction map provides a unique resource that identifies agent-specific and general DNA damage response pathways. PMID:23273983

Guenole, Aude; Srivas, Rohith; Vreeken, Kees; Wang, Ze Zhong; Wang, Shuyi; Krogan, Nevan J.; Ideker, Trey; van Attikum, Haico



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

PubMed Central

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

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



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  

Microsoft Academic Search

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 http:\\/\\/\\/GoogleMapsAPI\\/

Maged N Kamel Boulos



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

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 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.

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



Towards a proteome-scale map of the human protein-protein interaction network  

Microsoft Academic Search

Systematic mapping of protein-protein interactions, or `interactome' mapping, was initiated in model organisms, starting with defined biological processes and then expanding to the scale of the proteome. Although far from complete, such maps have revealed global topological and dynamic features of interactome networks that relate to known biological properties, suggesting that a human interactome map will provide insight into development

Jean-François Rual; Kavitha Venkatesan; Tong Hao; Tomoko Hirozane-Kishikawa; Amélie Dricot; Ning Li; Gabriel F. Berriz; Francis D. Gibbons; Matija Dreze; Nono Ayivi-Guedehoussou; Niels Klitgord; Christophe Simon; Mike Boxem; Stuart Milstein; Jennifer Rosenberg; Debra S. Goldberg; Lan V. Zhang; Sharyl L. Wong; Giovanni Franklin; Siming Li; Joanna S. Albala; Janghoo Lim; Carlene Fraughton; Estelle Llamosas; Sebiha Cevik; Camille Bex; Philippe Lamesch; Robert S. Sikorski; Jean Vandenhaute; Huda Y. Zoghbi; Alex Smolyar; Stephanie Bosak; Reynaldo Sequerra; Lynn Doucette-Stamm; Michael E. Cusick; David E. Hill; Frederick P. Roth; Marc Vidal



Demographic differences among populations of Northern Map Turtles ( Graptemys geographica ) in intact and fragmented sites  

Microsoft Academic Search

Habitat fragmentation is a leading cause of reptile declines worldwide. We examined demographic differences between populations of Northern Map Turtles, Graptemys geographica (Le Sueur, 1817), inhabiting intact and fragmented sites along the Trent-Severn Waterway (TSW) in Ontario over two field seasons. We examined population densities, sex ratios, body size, and growth rates in two control sites and two fragmented sites

A. M. Bennett; M. Keevil; J. D. Litzgus



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

PubMed Central

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

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



Preliminary analysis of Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) for mineralogic mapping at sites in Nevada and Colorado  

NASA Technical Reports Server (NTRS)

Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) data for sites in Nevada and Colorado were evaluated to determine their utility for mineralogical mapping in support of geologic investigations. Equal energy normalization is commonly used with imaging spectrometer data to reduce albedo effects. Spectra, profiles, and stacked, color-coded spectra were extracted from the AVIRIS data using an interactive analysis program (QLook) and these derivative data were compared to Airborne Imaging Spectrometer (AIS) results, field and laboratory spectra, and geologic maps. A feature extraction algorithm was used to extract and characterize absorption features from AVIRIS and laboratory spectra, allowing direct comparison of the position and shape of absorption features. Both muscovite and carbonate spectra were identified in the Nevada AVIRIS data by comparison with laboratory and AIS spectra, and an image was made that showed the distribution of these minerals for the entire site. Additional, distinctive spectra were located for an unknown mineral. For the two Colorado sites, the signal-to-noise problem was significantly worse and attempts to extract meaningful spectra were unsuccessful. Problems with the Colorado AVIRIS data were accentuated by the IAR reflectance technique because of moderate vegetation cover. Improved signal-to-noise and alternative calibration procedures will be required to produce satisfactory reflectance spectra from these data. Although the AVIRIS data were useful for mapping strong mineral absorption features and producing mineral maps at the Nevada site, it is clear that significant improvements to the instrument performance are required before AVIRIS will be an operational instrument.

Kruse, Fred A.; Taranik, Dan L.; Kierein-Young, Kathryn S.



Simultaneous single-molecule mapping of protein-DNA interactions and DNA methylation by MAPit  

PubMed Central

Sites of protein binding to DNA are inferred from footprints or spans of protection against a probing reagent. In most protocols, sites of accessibility to a probe are detected by mapping breaks in DNA strands. As discussed in this unit, such methods obscure molecular heterogeneity by averaging cuts at a given site over all DNA strands in sample population. DNA methyltransferase accessibility protocol for individual templates (MAPit), an alternative method described in this unit, localizes protein-DNA interactions by probing with cytosine-modifying DNA methyltransferases followed by bisulfite sequencing. Sequencing individual DNA products after amplification of bisulfite-converted sequences permits assignment of the methylation status of every enzyme target site along a single DNA strand. Use of the GC-methylating enzyme M.CviPI allows simultaneous mapping of chromatin accessibility and endogenous CpG methylation. MAPit is therefore the only footprinting method that can detect subpopulations of molecules with distinct patterns of protein binding or chromatin architecture, and correlate them directly with the occurrence of endogenous methylation. Additional advantages of MAPit methylation footprinting as well as considerations for experimental design and potential sources of error are discussed. PMID:21732317

Pardo, Carolina E.; Darst, Russell P.; Nabilsi, Nancy H.; Delmas, Amber L.; Kladde, Michael P.



Thermal interaction effect on nucleation site distribution in subcooled boiling  

SciTech Connect

An experimental work on subcooled boiling of refrigerant, R134a, to examine nucleation site distributions on both copper and stainless steel heating surfaces was performed. In order to obtain high fidelity active nucleation site density and distribution data, a high-speed digital camera was utilized to record bubble emission images from a view normal to heating surfaces. Statistical analyses on nucleation site data were done and their statistical distributions were obtained. Those experimentally observed nucleation site distributions were compared to the random spatial Poisson distribution. The comparisons showed that, rather than purely random, active nucleation site distributions on boiling surfaces are relatively more uniform. Experimental results also showed that on the copper heating surface, nucleation site distributions are slightly more uniform than on the stainless steel surface. This was concluded as the results of thermal interactions between nucleation sites with different solid thermal conductivities. A two dimensional thermal interaction model was then developed to quantitatively examine the thermal interactions between nucleation sites. The results give a reasonable explanation to the experimental observation on nucleation site distributions.

Ling Zou; Barclay Joned



Interactive Maps of Science and Technology Dr. Katy Brner  

E-print Network

(2011) Science Maps for Kids (2012) Science Forecasts (2013) How to Lie with Science Maps (2014) Exhibit, Ann Arbor, MI Mapping Science Exhibit ­ 10 Iterations in 10 years 7 #12;Richard Klavans & Kevin W. Boyack. 2007. Maps of Science: Forecasting Large Trends in Science 10 Today used

Bustamante, Fabián E.


A Global Map of p53 Transcription-Factor Binding Sites in the Human Genome  

E-print Network

Resource A Global Map of p53 Transcription-Factor Binding Sites in the Human Genome Chia-Lin Wei,1 to map p53 tar- gets in the human genome. From a satu- rated sampling of over half a million PET se completion of human genome sequencing (Inter- national Human Genome Sequencing Consortium, 2004) marked

Weng, Zhiping


The Shark-Search Algorithm. An Application: Tailored Web Site Mapping  

Microsoft Academic Search

This paper introduces the “shark search” algorithm, a refined version of one of the first dynamic Web search algorithms, the “fish search”. The shark-search has been embodied into a dynamic Web site mapping that enables users to tailor Web maps to their interests. Preliminary experiments show significant improvements over the original fish-search algorithm.

Michael Herscovici; Michal Jacovi; Yoëlle S. Maarek; Dan Pelleg; Menachem Shtalhaim; Ur Sigalit



Retrovirus integration and chromatin structure: Moloney murine leukemia proviral integration sites map near DNase I-hypersensitive sites.  

PubMed Central

The chromatin conformation of mouse genome regions containing Moloney murine leukemia proviral intergration sites in two Mov mouse strains and randomly selected integration sites in virus-infected mouse 3T3 fibroblasts was analyzed. All integrations have occurred into chromosomal regions containing several DNase-hypersensitive sites, and invariably the proviral integration sites map within a few hundred base pairs of a DNase-hypersensitive site. The probability that this close association between proviral integration sites and DNase-hypersensitive sites was due to chance was calculated to be extremely low (2 X 10(-4]. Because the proviral integrations analyzed were not selected for an altered phenotype, our results suggest that DNase-hypersensitive regions are preferred targets for retrovirus integration. Images PMID:3027365

Rohdewohld, H; Weiher, H; Reik, W; Jaenisch, R; Breindl, M



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

USGS Publications Warehouse

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.

Lucchitta, Baerbel Koesters



GATA-1 binding sites mapped in the ?-globin locus by using mammalian chIp-chip analysis  

PubMed Central

The expression of the ?-like globin genes is intricately regulated by a series of both general and tissue-restricted transcription factors. The hemapoietic lineage-specific transcription factor GATA-1 is important for erythroid differentiation and has been implicated in regulating the expression of the erythroid-specific genes including the genes of the ?-globin locus. In the human erythroleukemic K562 cell line, only one DNA region has been identified previously as a putative site of GATA-1 interaction by in vivo footprinting studies. We mapped GATA-1 binding throughout the ?-globin locus by using chIp-chip analysis of K562 cells. We found that GATA-1 binds in a region encompassing the HS2 core element, as was previously identified, and an additional region of GATA-1 binding upstream of the ?G gene. This approach will be of general utility for mapping transcription factor binding sites within the ?-globin locus and throughout the genome. PMID:11867748

Horak, Christine E.; Mahajan, Milind C.; Luscombe, Nicholas M.; Gerstein, Mark; Weissman, Sherman M.; Snyder, Michael



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

USGS Publications Warehouse

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.

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



Halogenated naphthyl methoxy piperidines for mapping serotonin transporter sites  


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.

Goodman, M.M.; Faraj, B.



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

NASA Technical Reports Server (NTRS)

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

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



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

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…

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



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

SciTech Connect

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

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



Classification and mapping forest sites using geographic information system (GIS): a case study in Artvin Province.  


The productivity of forest sites has been indirectly determined with solo wood production objective in forest management. Forest site productivity should, however, be determined directly in order to implement ecosystem based multipurpose forest management philosophy. This article tackles the problem in distinguishing and mapping forest sites using both direct method and indirect method in Genya Mountain located in central of Artvin State Forest Enterprise. About 112 sample plots were designed and distributed over the area. In each sample plot, soil samples were collected and the classical timber inventory measurements were taken. According to direct method, Soil Moisture Regime (SMR) method is preferred due to a water deficiency in the study area. Water holding capacity was used as an essential criterion for the classification of the forest site. Forest site classifications were assigned regarding the physiographic factors such as landform, aspect, and slope. Five different forest sites classes; dry, moderate fresh, fresh, humid and hygric were determined. According to direct method, the guiding curve was used to generate anamorphic site index (SI) equations and three site index classes; good (SI=I-II), medium (SI=III) and low (SI=IV-V) were determined. Some important differences between the methods were realized. The forest sites determined with site index estimation method indicate that site index I and II is 505.99 ha, III 1095.79 ha and IV and V 992.95 ha, whereas forest sites determined with direct method related to dry site of 937.58 ha, moderate fresh site of 931.90 ha, fresh site of 1,797.71 ha, humid site of 80.48 ha and hygric site of 356.55 ha. The forest site maps of both methods were created using GIS functions. The forest sites of open and degraded areas should be determined according to direct method. PMID:17564804

Altun, Lokman; Baskent, Emin Zeki; Gunlu, Alkan; Kadiogullari, Ali Ihsan



Map model for nonlinear alpha particle interaction with toroidal Alfven waves  

SciTech Connect

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.

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



Mapping the binding site on small ankyrin 1 for obscurin.  


Small ankyrin 1 (sAnk1), an integral protein of the sarcoplasmic reticulum encoded by the ANK1 gene, binds with nanomolar affinity to the C terminus of obscurin, a giant protein surrounding the contractile apparatus in striated muscle. We used site-directed mutagenesis to characterize the binding site on sAnk1, specifically addressing the role of two putative amphipathic, positively charged helices. We measured binding qualitatively by blot overlay assays and quantitatively by surface plasmon resonance and showed that both positively charged sequences are required for activity. We showed further that substitution of a lysine or arginine with an alanine or glutamate located at the same position along either of the two putative helices has similar inhibitory or stimulatory effects on binding and that the effects of a particular mutation depended on the position of the mutated amino acid in each helix. We modeled the structure of the binding region of sAnk1 by homology with ankyrin repeats of human Notch1, which have a similar pattern of charged and hydrophobic residues. Our modeling suggested that each of the two positively charged sequences forms pairs of amphipathic, anti-parallel alpha-helices flanked by beta-hairpin-like turns. Most of the residues in homologous positions along each helical unit have similar, though not identical, orientations. CD spectroscopy confirmed the alpha-helical content of sAnk1, approximately 33%, predicted by the model. Thus, structural and mutational studies of the binding region on sAnk1 for obscurin suggest that it consists of two ankyrin repeats with very similar structures. PMID:17720975

Borzok, Maegen A; Catino, Dawn H; Nicholson, James D; Kontrogianni-Konstantopoulos, Aikaterini; Bloch, Robert J



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

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

Boulos, Maged N Kamel



Crop water stress mapping for site-specific irrigation by thermal imagery and artificial reference surfaces  

Microsoft Academic Search

Variable-rate irrigation by machines or solid set systems has become technically feasible, however mapping crop water status\\u000a is necessary to match irrigation quantities to site-specific crop water demands. Remote thermal sensing can provide such maps\\u000a in sufficient detail and in a timely way. In a set of aerial and ground scans at the Hula Valley, Israel, digital crop water\\u000a stress

M. Meron; J. Tsipris; Valerie Orlov; V. Alchanatis; Yafit Cohen



HomozygosityMapper - an interactive approach to homozygosity mapping  

Microsoft Academic Search

Homozygosity mapping is a common method for mapping recessive traits in consanguineous families. In most studies, applications for multipoint linkage analyses are applied to determine the geno- mic region linked to the disease. Unfortunately, these are neither suited for very large families nor for the inclusion of tens of thousands of SNPs. Even if less than 10 000 markers are

Dominik Seelow; Markus Schuelke; Friedhelm Hildebrandt; Peter Nürnberg



Mapping protein interactions by combining antibody affinity maturation and mass spectrometry  

PubMed Central

Mapping protein interactions by immunoprecipitation is limited by the availability of antibodies recognizing available native epitopes within protein complexes with sufficient affinity. Here we demonstrate a scalable approach for generation of such antibodies using phage display and affinity maturation. We combined antibody variable heavy (VH) genes from target-specific clones (recognizing Src homology 2 (SH2) domains of LYN, VAV1, NCK1, ZAP70, PTPN11, CRK, LCK, and SHC1) with a repertoire of 108 to 109 new variable light (VL) genes. Improved binders were isolated by stringent selections from these new “chain-shuffled” libraries. We also developed a predictive 96-well immunocapture screen and found that only 12% of antibodies had sufficient affinity/epitope availability to capture endogenous target from lysates. Using antibodies of different affinities to the same epitope, we show that affinity improvement was a key determinant for success and identified a clear affinity threshold value (60 nM for SHC1) that must be breached for success in immunoprecipitation. By combining affinity capture using matured antibodies to SHC1 with mass spectrometry, we identified seven known binding partners and two known SHC1 phosphorylation sites in epidermal growth factor (EGF)-stimulated human breast cancer epithelial cells. These results demonstrate that antibodies capable of immunoprecipitation can be generated by chain shuffling, providing a scalable approach to mapping protein–protein interaction networks. PMID:21704603

Dyson, Michael R.; Zheng, Yong; Zhang, Cunjie; Colwill, Karen; Pershad, Kritika; Kay, Brian K.; Pawson, Tony; McCafferty, John



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

SciTech Connect

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.

Bechtel Nevada



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

NASA Technical Reports Server (NTRS)

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.

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



Chaotic scattering in solitary wave interactions: A singular iterated-map description  

SciTech Connect

We derive a family of singular iterated maps--closely related to Poincare maps--that describe chaotic interactions between colliding solitary waves. The chaotic behavior of such solitary-wave collisions depends on the transfer of energy to a secondary mode of oscillation, often an internal mode of the pulse. This map allows us to go beyond previous analyses and to understand the interactions in the case when this mode is excited prior to the first collision. The map is derived using Melnikov integrals and matched asymptotic expansions and generalizes a ''multipulse'' Melnikov integral. It allows one to find not only multipulse heteroclinic orbits, but exotic periodic orbits. The maps exhibit singular behavior, including regions of infinite winding. These maps are shown to be singular versions of the conservative Ikeda map from laser physics and connections are made with problems from celestial mechanics and fluid mechanics.

Goodman, Roy H. [Department of Mathematical Sciences, New Jersey Institute of Technology, Newark, New Jersey 07102 (United States)



Predicting peptide binding sites on protein surfaces by clustering chemical interactions.  


Short peptides play important roles in cellular processes including signal transduction, immune response, and transcription regulation. Correct identification of the peptide binding site on a given protein surface is of great importance not only for mechanistic investigation of these biological processes but also for therapeutic development. In this study, we developed a novel computational approach, referred to as ACCLUSTER, for predicting the peptide binding sites on protein surfaces. Specifically, we use the 20 standard amino acids as probes to globally scan the protein surface. The poses forming good chemical interactions with the protein are identified, followed by clustering with the density-based spatial clustering of applications with noise technique. Finally, these clusters are ranked based on their sizes. The cluster with the largest size is predicted as the putative binding site. Assessment of ACCLUSTER was performed on a diverse test set of 251 nonredundant protein-peptide complexes. The results were compared with the performance of POCASA, a pocket detection method for ligand binding site prediction. Peptidb, another protein-peptide database that contains both bound structures and unbound or homologous structures was used to test the robustness of ACCLUSTER. The performance of ACCLUSTER was also compared with PepSite2 and PeptiMap, two recently developed methods developed for identifying peptide binding sites. The results showed that ACCLUSTER is a promising method for peptide binding site prediction. Additionally, ACCLUSTER was also shown to be applicable to nonpeptide ligand binding site prediction. © 2014 Wiley Periodicals, Inc. PMID:25363279

Yan, Chengfei; Zou, Xiaoqin



Core Site-Moiety Maps Reveal Inhibitors and Binding Mechanisms of Orthologous Proteins by Screening Compound Libraries  

PubMed Central

Members of protein families often share conserved structural subsites for interaction with chemically similar moieties despite low sequence identity. We propose a core site-moiety map of multiple proteins (called CoreSiMMap) to discover inhibitors and mechanisms by profiling subsite-moiety interactions of immense screening compounds. The consensus anchor, the subsite-moiety interactions with statistical significance, of a CoreSiMMap can be regarded as a “hot spot” that represents the conserved binding environments involved in biological functions. Here, we derive the CoreSiMMap with six consensus anchors and identify six inhibitors (IC50<8.0 µM) of shikimate kinases (SKs) of Mycobacterium tuberculosis and Helicobacter pylori from the NCI database (236,962 compounds). Studies of site-directed mutagenesis and analogues reveal that these conserved interacting residues and moieties contribute to pocket-moiety interaction spots and biological functions. These results reveal that our multi-target screening strategy and the CoreSiMMap can increase the accuracy of screening in the identification of novel inhibitors and subsite-moiety environments for elucidating the binding mechanisms of targets. PMID:22393385

Chen, Yen-Fu; Wang, Hung-Jung; Li, Ling-Ting; Wang, Wen-Ching; Yang, Jinn-Moon



Chloroplast DNA restriction site mapping and the phylogeny of Ranunculus ( Ranunculaceae )  

Microsoft Academic Search

A chloroplast DNA restriction site map forRanunculus sceleratus (Ranunculaceae) was constructed using 14 restriction endonucleases. The total size of the chloroplast genome is 152.4kb. No inversions were detected relative to the tobacco chloroplast DNA. Cladistic analyses of chloroplast DNA restriction site polymorphism were employed in order to elucidate the phylogeny among 76 species of the genusRanunculus in a wide sense

Jan Thomas Johansson



Expansion of Protein Farnesyltransferase Specificity Using "Tunable" Active Site Interactions  

PubMed Central

Post-translational modifications play essential roles in regulating protein structure and function. Protein farnesyltransferase (FTase) catalyzes the biologically relevant lipidation of up to several hundred cellular proteins. Site-directed mutagenesis of FTase coupled with peptide selectivity measurements demonstrates that molecular recognition is determined by a combination of multiple interactions. Targeted randomization of these interactions yields FTase variants with altered and, in some cases, bio-orthogonal selectivity. We demonstrate that FTase specificity can be “tuned” using a small number of active site contacts that play essential roles in discriminating against non-substrates in the wild-type enzyme. This tunable selectivity extends in vivo, with FTase variants enabling the creation of bioengineered parallel prenylation pathways with altered substrate selectivity within a cell. Engineered FTase variants provide a novel avenue for probing both the selectivity of prenylation pathway enzymes and the effects of prenylation pathway modifications on the cellular function of a protein. PMID:22992747

Hougland, James L.; Gangopadhyay, Soumyashree A.; Fierke, Carol A.



Matrix model maps and reconstruction of AdS supergravity interactions  

SciTech Connect

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)

Cremonini, Sera; Mello Koch, Robert de; Jevicki, Antal [Michigan Center for Theoretical Physics, Randall Laboratory of Physics, University of Michigan, Ann Arbor, MI 48109 (United States); Department of Physics, University of Witwatersrand, Wits, 2050 (South Africa); Department of Physics, Brown University, Providence, RI 02912 (United States)



Interactions among localized corrosion sites investigated through experiments and models  

NASA Astrophysics Data System (ADS)

It has often been assumed that pitting events occur randomly in time and space and that there is no effect of one event upon another. However, when a pit begins to form and current flows, the local environment is altered. Changes can occur in the local concentration of aggressive species, the potential field and damage can occur to the passivating oxide film. These three competing effects work on different time scales and can affect electrode areas through different distances. Therefore, pitting events can have some influence on the probability of future nearby events. Current time series data collected on a single working electrode experiencing metastable pitting corrosion was first analyzed. The metastable pitting events were found to have correlation and were not randomly distributed in time. Further investigation was performed on an array of 25 working electrodes in order to obtain information on the spatial interactions among metastable and stable pitting sites. The 5-by-5 array consisted of closely spaced, 0.025 cm diameter 316 stainless steel wires. The flush-mounted wire tips were exposed to 0.05 M NaCl solution at 47°C. To examine the environmental changes created by a stable pitting site, one or more electrodes in the array were held at a 1 V vs. SCE causing the entire electrode to corrode at a high rate simulating a single large pit. Two types of interactions were observed when a pit was created in the center of the array. First, inhibition of pitting on nearby electrodes occurred due to ohmic potential drop near the actively corroding pit site. Second, enhancement of pitting was observed due to alternations in the local solution composition and oxide film created by a deactivated pitting site. The ohmic shielding effect was dominant near the active site, however, it dissipated almost immediately after the pit site was deactivated. The other two interactive effects increased pitting probabilities as they endured for a longer time after the current ceased to flow, with oxide film changing lasting more than 10 minutes. The information obtained about the interactions among corrosion sites were then used to develop a spatial metastable pitting model that simulated the behavior found experimentally.

Lunt, Tracy T.



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

ERIC Educational Resources Information Center

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…

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



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

USGS Publications Warehouse

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

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



DNA repair gets physical: mapping a XPA binding site on ERCC1  

PubMed Central

Two recent reports provide new physical information on how the XPA protein recruits the ERCC1-XPF heterodimer to the site of damage during the process of mammalian nucleotide excision repair (NER). Using chemical shift perturbation NMR experiments, the contact sites between a central fragment of ERCC1 and a XPA fragment have been mapped. While both studies agree with regard to the XPA binding site, they differ on whether the ERCC1-XPA complex can simultaneously bind DNA. These studies have important implications for both the molecular process and the design of potential inhibitors of NER. PMID:18343204

Croteau, Deborah L.; Peng, Ye; Van Houten, Bennett



Mars Landing Site Selection: An exercise in reading geologic maps and other geologic data sets  

NSDL National Science Digital Library

Upon arrival in the lab, students are designated as an engineer, a biologist, or a geologist. Working in these groups, each group uses available Mars data (including, but not limited to, Mars geologic maps, topography, thermal inertia data) to identify their top three landing sites on the basis of provided criteria. In jig-saw fashion, new groups are generated consisting of one geologist, one engineer, and one geologist. These new groups must agree on their top three landing sites. Finally, the entire class must agree on a landing site.

Gregg, Tracy


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

NASA Astrophysics Data System (ADS)

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.

Chorianopoulos, Konstantinos; Rieniets, Tim


Interactive Computer Programs for Sorting and Mapping Dialect Data.  

ERIC Educational Resources Information Center

This computer program, a mechanization of the handsorted techniques which geographical dialectology has been using, increases the number of hypotheses that can be explored and the various correlations that can be made. It can draw several of the kinds of maps that dialectologists have used in direct atlases. The hardware, software, and program…

Herrick, Earl M.


Environmental Research Translation: enhancing interactions with communities at contaminated sites.  


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

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



Mapping protein interactions by combining antibody affinity maturation and mass spectrometry  

E-print Network

Mapping protein interactions by combining antibody affinity maturation and mass spectrometry Accepted 3 May 2011 Available online 31 May 2011 Keywords: Antibody phage display Affinity maturation epitopes within protein complexes with sufficient affinity. Here we demonstrate a scalable approach

Kay, Brian K.



Microsoft Academic Search

Image mapping in a 2-dimensional plane has been used as a method to understand design trends at an early stage of the design process. This method could also be very useful in the process of kids robot design. This study focused on the application of interactive image mapping as an advanced technique for analyzing the trend of kids robot design.

Jonghwan Seo; Jaehyung Byun; Sungho Yang; Myungseok Kim


Synchronization of globally coupled non-identical maps with inhomogeneous delayed interactions  

Microsoft Academic Search

We study the synchronization of a coupled map lattice consisting of a one-dimensional chain of logistic maps. We consider global coupling with a time-delay that takes into account the finite velocity of propagation of interactions. We recently showed that clustering occurs for weak coupling, while for strong coupling the array synchronizes into a global state where each element sees all

Arturo C. Mart??; C. Masoller



FLS2-BAK1 Extracellular Domain Interaction Sites Required for Defense Signaling Activation  

PubMed Central

Signaling initiation by receptor-like kinases (RLKs) at the plasma membrane of plant cells often requires regulatory leucine-rich repeat (LRR) RLK proteins such as SERK or BIR proteins. The present work examined how the microbe-associated molecular pattern (MAMP) receptor FLS2 builds signaling complexes with BAK1 (SERK3). We first, using in vivo methods that validate separate findings by others, demonstrated that flg22 (flagellin epitope) ligand-initiated FLS2-BAK1 extracellular domain interactions can proceed independent of intracellular domain interactions. We then explored a candidate SERK protein interaction site in the extracellular domains (ectodomains; ECDs) of the significantly different receptors FLS2, EFR (MAMP receptors), PEPR1 (damage-associated molecular pattern (DAMP) receptor), and BRI1 (hormone receptor). Repeat conservation mapping revealed a cluster of conserved solvent-exposed residues near the C-terminus of models of the folded LRR domains. However, site-directed mutagenesis of this conserved site in FLS2 did not impair FLS2-BAK1 ECD interactions, and mutations in the analogous site of EFR caused receptor maturation defects. Hence this conserved LRR C-terminal region apparently has functions other than mediating interactions with BAK1. In vivo tests of the subsequently published FLS2-flg22-BAK1 ECD co-crystal structure were then performed to functionally evaluate some of the unexpected configurations predicted by that crystal structure. In support of the crystal structure data, FLS2-BAK1 ECD interactions were no longer detected in in vivo co-immunoprecipitation experiments after site-directed mutagenesis of the FLS2 BAK1-interaction residues S554, Q530, Q627 or N674. In contrast, in vivo FLS2-mediated signaling persisted and was only minimally reduced, suggesting residual FLS2-BAK1 interaction and the limited sensitivity of co-immunoprecipitation data relative to in vivo assays for signaling outputs. However, Arabidopsis plants expressing FLS2 with the Q530A+Q627A double mutation were impaired both in detectable interaction with BAK1 and in FLS2-mediated responses, lending overall support to current models of FLS2 structure and function. PMID:25356676

Koller, Teresa; Bent, Andrew F



Brief Genetics Report Fine-Mapping Gene-by-Diet Interactions on Chromosome  

E-print Network

intercross line (AIL) from the SM/J and LG/J inbred strains. Half of our sample was fed a low-fat (15% energyBrief Genetics Report Fine-Mapping Gene-by-Diet Interactions on Chromosome 13 in a LG/J SM/J Murine strains reveals locus-by-diet interactions for all previously mapped loci. Adip7, located on proximal

Hrbek, Tomas - Department of Biology, Universidad de Puerto Rico


High Precision Topographic Mapping at Chang'E-3 Landing Site with Multi-Source Data  

NASA Astrophysics Data System (ADS)

Chang'e-3 (CE-3) is the first lander and rover of China following the success of Chang'e-1 and Chang'e-2 (CE-2) orbiters. High precision topographic mapping can provide detailed terrain information to ensure the safety of the rover as well as to support scientific investigations. In this research, multi-source data are co-registered into a uniform geographic framework for high precision topographic mapping at the CE-3 landing site. CE-2 CCD images with 7 m- and 1.5 m- resolutions are registered using selfcalibration bundle adjustment method with ground control points (GCPs) selected from LRO WAC mosaic map and LOLA DTM. The trajectory of CE-3 descent images are recovered using self-calibration free net bundle adjustment, and then the topographic data is rectified by absolute orientation with GCPs selected from the adjusted CE-2 DEM and DOM. Finally, these topographic data are integrated into the same geographic framework for unified, multi-scale, high precision mapping of the CE-3 landing site. Key technologies and the mapping products of this research have been used to support the surface operations of CE-3 mission.

Liu, Y.; Liu, B.; Xu, B.; Liu, Z.; Di, K.; Zhou, J.



Deconstructing the DGAT1 enzyme: Binding sites and substrate interactions.  


Diacylglycerol acyltransferase 1 (DGAT1) is a microsomal membrane enzyme responsible for the final step in the synthesis of triacylglycerides. Although DGATs from a wide range of organisms have nearly identical sequences, there is little structural information available for these enzymes. The substrate binding sites of DGAT1 are predicted to be in its large luminal extramembranous loop and to include common motifs with acyl-CoA cholesterol acyltransferase enzymes and the diacylglycerol binding domain found in protein kinases. In this study, synthetic peptides corresponding to the predicted binding sites of DGAT1 enzyme were examined using synchrotron radiation circular dichroism spectroscopy, fluorescence emission and adsorption onto lipid monolayers to determine their interactions with substrates associated with triacylglyceride synthesis (oleoyl-CoA and dioleoylglycerol). One of the peptides, Sit1, which includes the FYxDWWN motif common to both DGAT1 and acyl-CoA cholesterol acyltransferase, changes its conformation in the presence of both substrates, suggesting its capability to bind their acyl chains. The other peptide (Sit2), which includes the putative diacylglycerol binding domain HKWCIRHFYKP found in protein kinase C and diacylglycerol kinases, appears to interact with the charged headgroup region of the substrates. Moreover, in an extended-peptide which contains Sit1 and Sit2 sequences separated by a flexible linker, larger conformational changes were induced by both substrates, suggesting that the two binding sites may bring the substrates into close proximity within the membrane, thus catalyzing the formation of the triacylglyceride product. PMID:25152299

Lopes, José L S; Nobre, Thatyane M; Cilli, Eduardo M; Beltramini, Leila M; Araújo, Ana P U; Wallace, B A



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

SciTech Connect

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.

Lemiszki, P.J.



Repeated mapping of reefs constructed by Sabellaria spinulosa Leuckart 1849 at an offshore wind farm site  

NASA Astrophysics Data System (ADS)

Sabellaria spinulosa reefs are considered to be sensitive and of high conservation status. This article evaluates the feasibility of using remote sensing technology to delineate S. spinulosa reefs. S. spinulosa reef habitats associated with the Thanet Offshore Windfarm site were mapped using high resolution sidescan sonar (410 kHz) and multibeam echo sounder (<1 m2) data in 2005 (baseline), 2007 (pre-construction baseline) and 2012 (post-construction). The S. spinulosa reefs were identified in the acoustic data as areas of distinct irregular texturing. Maps created using acoustic data were validated using quantitative measures of reef quality, namely tube density (as a proxy for the density of live S. spinulosa), percentage cover of S. spinulosa structures (both living and dead) and associated macrofauna derived from seabed images taken across the development site. Statistically significant differences were observed in all physical measures of S. spinulosa as well the number (S) and diversity (H') of associated species, derived from seabed images classified according to the presence or absence of reef, validating the use of high resolution sidescan sonar to map these important biogenic habitats. High precision mapping in the early stages allowed for the micro-siting of wind turbines in a way that caused minimal damage to S. spinulosa reefs during construction. These habitats have since recovered and expanded in extent. The surveys undertaken at the Thanet Offshore Windfarm site demonstrate the importance of repeat mapping for this emerging industry, allowing habitat enhancement to be attributed to the development whilst preventing background habitat degradation from being wrongly attributed to the development.

Pearce, Bryony; Fariñas-Franco, Jose M.; Wilson, Christian; Pitts, Jack; deBurgh, Angela; Somerfield, Paul J.



Analysis of protein binding sites by computational solvent mapping David R. Hall, Dima Kozakov, and Sandor Vajda  

E-print Network

Analysis of protein binding sites by computational solvent mapping David R. Hall, Dima Running Head: Solvent mapping #12;Summary Computational solvent mapping globally samples the surface transform (FFT) correlation approach. Identifying regions of low free energy rather than individual low

Vajda, Sandor


Reproductive parameters in female yellow-blotched map turtles (Graptemys flavimaculata) from a historically contaminated site vs. a reference site.  


Graptemys flavimaculata, the yellow-blotched map turtle, is a long-lived, threatened, species, endemic to the Pascagoula River drainage in Mississippi. During the 1980s, one branch of the drainage (i.e. the Leaf River) was impacted by effluent from a wood pulp processing plant known to contain endocrine disrupters. A decade later, we examined seasonal reproductive parameters (i.e. monthly plasma estradiol-17beta (E(2)), testosterone (T), vitellogenin (VTG) and follicular development) in adult female turtles from historically polluted and reference sites in the drainage to determine if legacy exposure to pollution impacts reproduction . We found no seasonal patterns in E(2) or T and these patterns did not differ between sites. However, E(2) differed significantly among ovarian stages for the reference, but not pollutant exposed females. A significantly greater percentage of reference site females were able to produce a second clutch than females from the historically polluted site (50% and 17%). Additionally, there was a significant positive correlation between E(2) with VTG levels for reference, but not pollutant exposed females. Body and yolk tissue contaminant analysis indicated that exposure to pollutants is presently minimal and unlikely the cause of the reproductive differences observed between sites; instead, differences are potentially due to exposure history. PMID:19651226

Shelby-Walker, Jennifer A; Ward, Chelsea K; Mendonça, Mary T



Catalonia Maps  

NSDL National Science Digital Library

As an autonomous community within the kingdom of Spain, Catalonia has a rich and diverse history. It includes the cosmopolitan city of Barcelona and also has a rather diverse agricultural base that includes crops like maize, potatoes, and olives. Maps of this lovely region of Spain may be found in abundance on this site, which is provided courtesy of the Institut Cartografica de Catalunya. Visitors can search the collection by place name or they can also search the collection through an interactive map of the entire region which will return individual geological and topographic maps. Finally, it is worth noting that the site is also available in Spanish and Catalan.



The distribution of transgene insertion sites in barley determined by physical and genetic mapping.  

PubMed Central

The exact site of transgene insertion into a plant host genome is one feature of the genetic transformation process that cannot, at present, be controlled and is often poorly understood. The site of transgene insertion may have implications for transgene stability and for potential unintended effects of the transgene on plant metabolism. To increase our understanding of transgene insertion sites in barley, a detailed analysis of transgene integration in independently derived transgenic barley lines was carried out. Fluorescence in situ hybridization (FISH) was used to physically map 23 transgene integration sites from 19 independent barley lines. Genetic mapping further confirmed the location of the transgenes in 11 of these lines. Transgene integration sites were present only on five of the seven barley chromosomes. The pattern of transgene integration appeared to be nonrandom and there was evidence of clustering of independent transgene insertion events within the barley genome. In addition, barley genomic regions flanking the transgene insertion site were isolated for seven independent lines. The data from the transgene flanking regions indicated that transgene insertions were preferentially located in gene-rich areas of the genome. These results are discussed in relation to the structure of the barley genome. PMID:15280249

Salvo-Garrido, Haroldo; Travella, Silvia; Bilham, Lorelei J; Harwood, Wendy A; Snape, John W



p38 MAP kinase interacts with and stabilizes pancreatic and duodenal homeobox-1.  


Pancreatic and duodenal homeobox-1 (PDX-1) is a homeodomain-containing transcription factor that plays a critical role in pancreatic development, ?-cell differentiation, maintenance of normal ?-cell function and tumorigenesis. PDX-1 is subjected to extensive post-translational modifications for its stability, subcellular location and transactivity. We report here that PDX-1 expression is up-regulated by p38 MAP kinase. Antibody array screen identified p38 as a candidate PDX-1-interacting protein in GFP-PDX-1 stable HEK293 cells. The p38-PDX-1 interaction was confirmed by immunoprecipitation/Western blotting analysis in both transient transfection system of HEK293 cells and endogenous system of ?-TC-6 cells stimulated by glucagon-like peptide 1 (GLP-1). Co-transfection of p38 with PDX-1 resulted in increased PDX-1 expression in HEK293 cells, which was accompanied by a decreased PDX-1 ubiquitination. Mass spectrometry analysis showed that Ser 268 of human PDX-1 was phosphorylated in GFP-PDX-1 stable HEK293 cells. Functional mutagenesis analysis showed that mutation of Ser 269 of mouse PDX-1 (corresponding to Ser 268 of human PDX-1) into nonphosphorylatable alanine abolished the stabilizing effect of p38 on PDX-1, which was in line with enhanced PDX-1 ubiquitination and shortened half-life of PDX-1. p38 showed kinase activity towards PDX-1 in vitro, suggesting that Ser 269 is a potential p38-regulated phosphorylation site within PDX-1. GLP-1-stimulated PDX-1 expression was accompanied by p38 kinase activation in mouse insulinoma ?-TC-6 cells and p38 inhibitor SB202190 inhibited GLP-1-stimulated PDX-1 expression with accompanied inhibition of p38 kinase activation. Taken together, our studies indicated that p38 MAP kinase is a positive regulator of PDX-1 stability and that p38 exerts its stabilizing effect on PDX-1 through a phosphorylation-dependent inhibition of PDX-1 ubiquitination. PMID:23331010

Zhou, G; Wang, H; Liu, S-H; Shahi, K M; Lin, X; Wu, J; Feng, X-H; Qin, J; Tan, T-H; Brunicardi, F C



Quantitative maps of genetic interactions in yeast - Comparative evaluation and integrative analysis  

PubMed Central

Background High-throughput genetic screening approaches have enabled systematic means to study how interactions among gene mutations contribute to quantitative fitness phenotypes, with the aim of providing insights into the functional wiring diagrams of genetic interaction networks on a global scale. However, it is poorly known how well these quantitative interaction measurements agree across the screening approaches, which hinders their integrated use toward improving the coverage and quality of the genetic interaction maps in yeast and other organisms. Results Using large-scale data matrices from epistatic miniarray profiling (E-MAP), genetic interaction mapping (GIM), and synthetic genetic array (SGA) approaches, we carried out here a systematic comparative evaluation among these quantitative maps of genetic interactions in yeast. The relatively low association between the original interaction measurements or their customized scores could be improved using a matrix-based modelling framework, which enables the use of single- and double-mutant fitness estimates and measurements, respectively, when scoring genetic interactions. Toward an integrative analysis, we show how the detections from the different screening approaches can be combined to suggest novel positive and negative interactions which are complementary to those obtained using any single screening approach alone. The matrix approximation procedure has been made available to support the design and analysis of the future screening studies. Conclusions We have shown here that even if the correlation between the currently available quantitative genetic interaction maps in yeast is relatively low, their comparability can be improved by means of our computational matrix approximation procedure, which will enable integrative analysis and detection of a wider spectrum of genetic interactions using data from the complementary screening approaches. PMID:21435228



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

SciTech Connect

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.

Todd Jaffe



Network Physiology: Mapping Interactions Between Networks of Physiologic Networks  

NASA Astrophysics Data System (ADS)

The human organism is an integrated network of interconnected and interacting organ systems, each representing a separate regulatory network. The behavior of one physiological system (network) may affect the dynamics of all other systems in the network of physiologic networks. Due to these interactions, failure of one system can trigger a cascade of failures throughout the entire network. We introduce a systematic method to identify a network of interactions between diverse physiologic organ systems, to quantify the hierarchical structure and dynamics of this network, and to track its evolution under different physiologic states. We find a robust relation between network structure and physiologic states: every state is characterized by specific network topology, node connectivity and links strength. Further, we find that transitions from one physiologic state to another trigger a markedly fast reorganization in the network of physiologic interactions on time scales of just a few minutes, indicating high network flexibility in response to perturbations. This reorganization in network topology occurs simultaneously and globally in the entire network as well as at the level of individual physiological systems, while preserving a hierarchical order in the strength of network links. Our findings highlight the need of an integrated network approach to understand physiologic function, since the framework we develop provides new information which can not be obtained by studying individual systems. The proposed system-wide integrative approach may facilitate the development of a new field, Network Physiology.

Ivanov, Plamen Ch.; Bartsch, Ronny P.


Mapping adaptation opportunities and activities in an interactive atlas.  


The need for transparency is taking more prominence in international climate negotiations as developed countries pledge large sums of money to foster adaptation efforts in developing countries. Tools that provide accurate and up-to-date spatial information that can be easily used and vetted by local practitioners may provide effective and affordable ways to improve transparency. The Global Adaptation Atlas is such a tool, combining vetted, publicly available climate impact data with timely maps of on the ground adaptation projects to highlight confluences of effects of climate change with actions taken to address those effects. Here, we describe the structure and general functions of the Global Adaptation Atlas and explain how it may be utilized to track short-term investments in adaptation. Over longer time scales, it may also help gauge the effectiveness of specific adaptation investments as well as reveal how different climate impacts affect long-term investment in differing regions. PMID:22314858

Morris, Daniel F; Krishnan, Nisha



Curcuminoids as inhibitors of thioredoxin reductase: a receptor based pharmacophore study with distance mapping of the active site.  


Curcumin is the yellow pigment of turmeric that interacts irreversibly forming an adduct with thioredoxin reductase (TrxR), an enzyme responsible for redox control of cell and defence against oxidative stress. Docking at both the active sites of TrxR was performed to compare the potency of three naturally occurring curcuminoids, namely curcumin, demethoxy curcumin and bis-demethoxy curcumin. Results show that active sites of TrxR occur at the junction of E and F chains. Volume and area of both cavities is predicted. It has been concluded by distance mapping of the most active conformations that Se atom of catalytic residue SeCYS498, is at a distance of 3.56 from C13 of demethoxy curcumin at the E chain active site, whereas C13 carbon atom forms adduct with Se atom of SeCys 498. We report that at least one methoxy group in curcuminoids is necessary for interation with catalytic residues of thioredoxin. Pharmacophore of both active sites of the TrxR receptor for curcumin and demethoxy curcumin molecules has been drawn and proposed for design and synthesis of most probable potent antiproliferative synthetic drugs. PMID:20461157

Singh, Durg Vijay; Misra, Krishna



Interacting damage models mapped onto ising and percolation models  

SciTech Connect

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.

Toussaint, Renaud; Pride, Steven R.



Interactive Web Interface to the Global Strain Rate Map Project  

Microsoft Academic Search

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

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



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.  


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

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



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

USGS Publications Warehouse

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.

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



Vibrations on the Roll - MANA, a Roll Along Array Experiment to map Local Site Effects Across a Fault System  

Microsoft Academic Search

The effects of surficial geology on seismic motion (site effects) are considered one of the major controlling factors to the damage distribution during earthquakes. Qualitative and quantitative estimates of local site amplifications provide important information for the identification of potential high risk areas. In this context, the analysis of ambient vibrations is an attractive tool for the mapping of site

M. Ohrnberger; F. Scherbaum; K. G. Hinzen; S. K. Reamer; B. Weber



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

SciTech Connect

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.

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



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

SciTech Connect

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

Madueno, E.; Modolell, J. [Universidad Autonoma de Madrid (Spain); Papagiannakis, G. [Institute of Molecular Biology and Biotechnology, Heraklion (Greece)] [and others



A Physical Map of the X Chromosome of Drosophila Melanogaster: Cosmid Contigs and Sequence Tagged Sites  

PubMed Central

A physical map of the euchromatic X chromosome of Drosophila melanogaster has been constructed by assembling contiguous arrays of cosmids that were selected by screening a library with DNA isolated from microamplified chromosomal divisions. This map, consisting of 893 cosmids, covers ~64% of the euchromatic part of the chromosome. In addition, 568 sequence tagged sites (STS), in aggregate representing 120 kb of sequenced DNA, were derived from selected cosmids. Most of these STSs, spaced at an average distance of ~35 kb along the euchromatic region of the chromosome, represent DNA tags that can be used as entry points to the fruitfly genome. Furthermore, 42 genes have been placed on the physical map, either through the hybridization of specific probes to the cosmids or through the fact that they were represented among the STSs. These provide a link between the physical and the genetic maps of D. melanogaster. Nine novel genes have been tentatively identified in Drosophila on the basis of matches between STS sequences and sequences from other species. PMID:7789765

Madueno, E.; Papagiannakis, G.; Rimmington, G.; Saunders, RDC.; Savakis, C.; Siden-Kiamos, I.; Skavdis, G.; Spanos, L.; Trenear, J.; Adam, P.; Ashburner, M.; Benos, P.; Bolshakov, V. N.; Coulson, D.; Glover, D. M.; Herrmann, S.; Kafatos, F. C.; Louis, C.; Majerus, T.; Modolell, J.



Bundling of microtubules in transfected cells does not involve an autonomous dimerization site on the MAP2 molecule.  

PubMed Central

We have searched for putative dimerization sites in microtubule-associated protein 2 (MAP2) that may be involved in the bundling of microtubules. An overlapping series of fragments of the embryonic form MAP2c were created and immunologically "tagged" with an 11 amino acid sequence from human c-myc. Nonneuronal cells were transfected simultaneously with one of these myc-tagged fragments and with full-length native MAP2c. Immunolabeling with site-specific antibodies allowed the two transgene products to be located independently within the cytoplasm of a single double-transfected cell. All transfected cells contained bundled microtubules to which the full-length native MAP2 was bound. The distribution of the tagged MAP2 fragment relative to these MAP2-induced bundles was determined by the anti-myc staining. None of the fragments tested, representing all of the MAP2c sequence in overlapping pieces, were associated with MAP2-induced microtubule bundles. These results suggest that MAP2-induced bundle formation in cells does not involve an autonomous dimerization site within the MAP2 sequence. Images PMID:7919534

Burgin, K E; Ludin, B; Ferralli, J; Matus, A



Mapping of the second tetracycline binding site on the ribosomal small subunit of E.coli  

PubMed Central

Tetracycline blocks stable binding of aminoacyl-tRNA to the bacterial ribosomal A-site. Various tetracycline binding sites have been identified in crystals of the 30S ribosomal small subunit of Thermus thermophilus. Here we describe a direct photo- affinity modification of the ribosomal small subunits of Escherichia coli with 7-[3H]-tetracycline. To select for specific interactions, an excess of the 30S subunits over tetracycline has been used. Primer extension analysis of the 16S rRNA revealed two sites of the modifications: C936 and C948. Considering available data on tetracycline interactions with the prokaryotic 30S subunits, including the presented data (E.coli), X-ray data (T.thermophilus) and genetic data (Helicobacter pylori, E.coli), a second high affinity tetracycline binding site is proposed within the 3?-major domain of the 16S rRNA, in addition to the A-site related tetracycline binding site. PMID:15141029

Anokhina, Maria M.; Barta, Andrea; Nierhaus, Knud H.; Spiridonova, Vera A.; Kopylov, Alexei M.



Mapping genome-wide transcription factor binding sites in frozen tissues  

PubMed Central

Background Genome-wide maps of transcription factor binding sites in primary tissues can expand our understanding of genome function, transcriptional regulation, and genetic alterations that contribute to disease risk. However, almost all genome-wide studies of transcription factors have been in cell lines, and performing these experiments in tissues has been technically challenging and limited in throughput. Results Here we outline a simple strategy for mapping transcription factor binding sites in frozen tissues that utilizes dry pulverization of samples and is scalable for high-throughput analyses. We show that the method leads to accurate and reproducible chromatin immunoprecipitation next-generation sequencing (ChIP-seq) data, and is highly sensitive, identifying high-quality transcription factor binding sites from chromatin corresponding to only 5 mg of liver tissue. Conclusions The enhanced reproducibility, robustness, and sensitivity of the dry pulverization method, in addition to the ease of implementation and scalability, makes ChIP-seq in primary tissues a widely accessible assay. PMID:24279905



Invariants, Attractors and Bifurcation in Two Dimensional Maps with Polynomial Interaction  

NASA Astrophysics Data System (ADS)

This work will present an extended discrete-time analysis on maps and their generalizations including iteration in order to better understand the resulting enrichment of the bifurcation properties. The standard concepts of stability analysis and bifurcation theory for maps will be used. Both iterated maps and flows are used as models for chaotic behavior. It is well known that when flows are converted to maps by discretization, the equilibrium points remain the same but a richer bifurcation scheme is observed. For example, the logistic map has a very simple behavior as a differential equation but as a map fold and period doubling bifurcations are observed. A way to gain information about the global structure of the state space of a dynamical system is investigating invariant manifolds of saddle equilibrium points. Studying the intersections of the stable and unstable manifolds are essential for understanding the structure of a dynamical system. It has been known that the Lotka-Volterra map and systems that can be reduced to it or its generalizations in special cases involving local and polynomial interactions admit invariant manifolds. Bifurcation analysis of this map and its higher iterates can be done to understand the global structure of the system and the artifacts of the discretization by comparing with the corresponding results from the differential equation on which they are based.

Hacinliyan, Avadis Simon; Aybar, Orhan Ozgur; Aybar, Ilknur Kusbeyzi


Mapping Site Remediation with Electrical Resistivity Tomography Explored via Coupled-Model Simulations  

NASA Astrophysics Data System (ADS)

Remediation programs for sites contaminated with dense non-aqueous phase liquids (DNAPLs) would benefit from an ability to non-intrusively map the evolving volume and extent of the DNAPL source zone. Electrical resistivity tomography (ERT) is a well-established geophysical tool, widely used outside the remediation industry, that has significant potential for mapping DNAPL source zones. However, that potential has not been realized due to challenges in data interpretation from contaminated sites - in either a qualitative or quantitative way. The objective of this study is to evaluate the potential of ERT to map realistic, evolving DNAPL source zones within complex subsurface environments during remedial efforts. For this purpose, a novel coupled model was developed that integrates a multiphase flow model (DNAPL3D-MT), which generates realistic DNAPL release scenarios, with 3DINV, an ERT model which calculates the corresponding resistivity response. This presentation will describe the developed model coupling methodology, which integrates published petrophysical relationships to generate an electrical resistivity field that accounts for both the spatial heterogeneity of subsurface soils and the evolving spatial distribution of fluids (including permeability, porosity, clay content and air/water/DNAPL saturation). It will also present an example in which the coupled model was employed to explore the ability of ERT to track the remediation of a DNAPL source zone. A field-scale, three-dimensional release of chlorinated solvent DNAPL into heterogeneous clayey sand was simulated, including the subsurface migration and subsequent removal of the DNAPL source zone via dissolution in groundwater. Periodic surveys of this site via ERT applied at the surface were then simulated and inversion programs were used to calculate the subsurface distribution of electrical properties. This presentation will summarize this approach and its potential as a research tool exploring the range of site conditions under which ERT may prove useful in aiding DNAPL site remediation. Moreover, it is expected to provide a cost-effective avenue to test optimum ERT data acquisition, inversion and interpretative tools at contaminated sites.

Power, C.; Gerhard, J. I.; Tsourlos, P.; Giannopoulos, A.



Mapping the lethal factor and edema factor binding sites on oligomeric anthrax protective antigen  

PubMed Central

Assembly of anthrax toxin complexes at the mammalian cell surface involves competitive binding of the edema factor (EF) and lethal factor (LF) to heptameric oligomers and lower order intermediates of PA63, the activated carboxyl-terminal 63-kDa fragment of protective antigen (PA). We used sequence differences between PA63 and homologous PA-like proteins to delineate a region within domain 1? of PA that may represent the binding site for these ligands. Substitution of alanine for any of seven residues in or near this region (R178, K197, R200, P205, I207, I210, and K214) strongly inhibited ligand binding. Selected mutations from this set were introduced into two oligomerization-deficient PA mutants, and the mutants were used in various combinations to map the single ligand site within dimeric PA63. The site was found to span the interface between two adjacent subunits, explaining the dependence of ligand binding on PA oligomerization. The locations of residues comprising the site suggest that a single ligand molecule sterically occludes two adjacent sites, consistent with the finding that the PA63 heptamer binds a maximum of three ligand molecules. These results elucidate the process by which the components of anthrax toxin, and perhaps other binary bacterial toxins, assemble into toxic complexes. PMID:11997439

Cunningham, Kristina; Lacy, D. Borden; Mogridge, Jeremy; Collier, R. John



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

SciTech Connect

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.

Kinney, Teena M.; McDonald, John P.



Large-scale mapping of human protein-protein interactions by mass spectrometry  

PubMed Central

Mapping protein–protein interactions is an invaluable tool for understanding protein function. Here, we report the first large-scale study of protein–protein interactions in human cells using a mass spectrometry-based approach. The study maps protein interactions for 338 bait proteins that were selected based on known or suspected disease and functional associations. Large-scale immunoprecipitation of Flag-tagged versions of these proteins followed by LC-ESI-MS/MS analysis resulted in the identification of 24 540 potential protein interactions. False positives and redundant hits were filtered out using empirical criteria and a calculated interaction confidence score, producing a data set of 6463 interactions between 2235 distinct proteins. This data set was further cross-validated using previously published and predicted human protein interactions. In-depth mining of the data set shows that it represents a valuable source of novel protein–protein interactions with relevance to human diseases. In addition, via our preliminary analysis, we report many novel protein interactions and pathway associations. PMID:17353931

Ewing, Rob M; Chu, Peter; Elisma, Fred; Li, Hongyan; Taylor, Paul; Climie, Shane; McBroom-Cerajewski, Linda; Robinson, Mark D; O'Connor, Liam; Li, Michael; Taylor, Rod; Dharsee, Moyez; Ho, Yuen; Heilbut, Adrian; Moore, Lynda; Zhang, Shudong; Ornatsky, Olga; Bukhman, Yury V; Ethier, Martin; Sheng, Yinglun; Vasilescu, Julian; Abu-Farha, Mohamed; Lambert, Jean-Philippe; Duewel, Henry S; Stewart, Ian I; Kuehl, Bonnie; Hogue, Kelly; Colwill, Karen; Gladwish, Katharine; Muskat, Brenda; Kinach, Robert; Adams, Sally-Lin; Moran, Michael F; Morin, Gregg B; Topaloglou, Thodoros; Figeys, Daniel



Mapping Hsp47 binding site(s) using CNBr peptides derived from type I and type II collagen  

PubMed Central

As a crucial molecular chaperone in collagen biosynthesis, Hsp47 interacts with the nascent form as well as the mature triple-helical form of procollagen. The location(s) of Hsp47 binding sites on the collagen molecule are, as yet, unknown. We have examined the substrate specificity of Hsp47 in vitro using well-characterized CNBr peptide fragments of type I and type II collagen along with radiolabeled, recombinant Hsp47. Interaction of these peptides with Hsp47 bound to collagen-coated microtiter wells showed several binding sites for Hsp47 along the length of the ?1 and ?2 chains of type I collagen and the ?1 chain of type II collagen, with the N-terminal regions showing the strongest affinities. The latter observation was also supported by the results of a ligand-blot assay. Except for two peptides in the ?2(I) chain, peptides that showed substantial binding to Hsp47 did so in their triple-helical and not random-coil form. Unlike earlier studies that used peptide models for collagen, the results obtained here on fragments of type I and type II collagen identify, for the first time, binding of Hsp47 to specific regions of the collagen molecule. They also point to additional structural requirements for Hsp47 binding besides the known preference for third-position Arg residues and the triple-helical conformation. PMID:12876328

Thomson, Christy A.; Tenni, Ruggero; Ananthanarayanan, Vettai S.



High Resolution Multibeam Sonar Mapping of the Lost City Hydrothermal Site with the Autonomous Benthic Explorer  

NASA Astrophysics Data System (ADS)

The Autonomous Benthic Explorer (ABE) of the Woods Hole Oceanographic Institution (WHOI) collected high-resolution multibeam sonar bathymetry of the Atlantis Massif and the Lost City vent site in May 2003. A Simrad Mesotech SM 2000 multibeam sonar has been fully integrated into the vehicle for this purpose. The challenging topography of the Lost City site demanded careful AUV survey planning, but also afforded the opportunity to try new survey techniques, particularly side-looking surveys along steep slopes. The quality of post-processed navigation has been improved with the addition of a model-based smoother. To aid in processing the large volume of sonar data generated during surveys, we have developed a high-level user interface in the form of a MATLAB GUI that allows users to inspect sonar images and the corresponding bathymetry concurrently. Using these techniques, bathymetric maps gridded on 2 m regular grids are visually free of trackline artifacts.

Jakuba, M. V.; Yoerger, D. R.; Bradley, A. M.; Kelley, D. S.; Karson, J. A.



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

SciTech Connect

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.

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. (Abbott)



High-quality binary protein interaction map of the yeast interactome network.  


Current yeast interactome network maps contain several hundred molecular complexes with limited and somewhat controversial representation of direct binary interactions. We carried out a comparative quality assessment of current yeast interactome data sets, demonstrating that high-throughput yeast two-hybrid (Y2H) screening provides high-quality binary interaction information. Because a large fraction of the yeast binary interactome remains to be mapped, we developed an empirically controlled mapping framework to produce a "second-generation" high-quality, high-throughput Y2H data set covering approximately 20% of all yeast binary interactions. Both Y2H and affinity purification followed by mass spectrometry (AP/MS) data are of equally high quality but of a fundamentally different and complementary nature, resulting in networks with different topological and biological properties. Compared to co-complex interactome models, this binary map is enriched for transient signaling interactions and intercomplex connections with a highly significant clustering between essential proteins. Rather than correlating with essentiality, protein connectivity correlates with genetic pleiotropy. PMID:18719252

Yu, Haiyuan; Braun, Pascal; Yildirim, Muhammed A; Lemmens, Irma; Venkatesan, Kavitha; Sahalie, Julie; Hirozane-Kishikawa, Tomoko; Gebreab, Fana; Li, Na; Simonis, Nicolas; Hao, Tong; Rual, Jean-François; Dricot, Amélie; Vazquez, Alexei; Murray, Ryan R; Simon, Christophe; Tardivo, Leah; Tam, Stanley; Svrzikapa, Nenad; Fan, Changyu; de Smet, Anne-Sophie; Motyl, Adriana; Hudson, Michael E; Park, Juyong; Xin, Xiaofeng; Cusick, Michael E; Moore, Troy; Boone, Charlie; Snyder, Michael; Roth, Frederick P; Barabási, Albert-László; Tavernier, Jan; Hill, David E; Vidal, Marc



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} ABSTRACT First working prototypes of mobile phones with integrated pico projectors have already been of the mobile phone, the projection or a combination of both. These three options were compared in a user study


Fine Mapping Reveals Multiple Loci and a Possible Epistatic Interaction within the Mammary Carcinoma Susceptibility  

E-print Network

Fine Mapping Reveals Multiple Loci and a Possible Epistatic Interaction within the Mammary developed a rat genetic model that uses the Wistar-Kyoto (WKy) inbred strain, resistant to developing 7-Furth (WF) strain as the recipient. Here, data from congenic rat lines containing smaller WKy genomic

Gould, Michael N.


iGMT: Interactive Mapping of Geoscientific Datasets. User manual for version 1.0  

E-print Network

GMT: Interactive Mapping of Geoscientific Datasets. # # Easy access to GMT via a Tcl/Tk GUI # # # # Copyright (C) and the Tcl/Tk toolkit by John Ousterhout. Small parts of the routines and templates were taken directly from the Tcl/Tk book by Ousterhout (1993) or the GMT documentation. Some of the initial Tk frame packing

Taylor, Mark A J


UBC Social Ecological Economic Development Studies (SEEDS) Student Report Interactive Map of the UBC Food System  

E-print Network

UBC Social Ecological Economic Development Studies (SEEDS) Student Report Interactive Map can have a variety of indirect and direct effects on the environment. Informing consumers of the availability and accessibility of green products in their community encourages green consumerism. While UBC


Using Process Mining to Generate Accurate and Interactive Business Process Maps  

E-print Network

(cf. TomTom HD Traffic is calculating the best route based on cell phone information provided by Vodafone, i.e., the locations and directions of cell phones are used to predict traffic jams on these interactive maps (e.g., traffic jams, four-bedroom apartments for sale, etc.). Process models can be seen

van der Aalst, Wil


An Interactive Map Viewer for the Urban Geology of Ottawa (Canada): an Example of Web Publishing  

Microsoft Academic Search

Developed by the Terrain Sciences Division (TSD) of the Geological Survey of Canada (GSC), an interactive map viewer, called GEOSERV (, is now available on the Internet. The purpose of this viewer is to provide engineers, planners, decision makers, and the general public with the geoscience information required for sound regional planning in densely populated areas, such as Canada's national

D. Giroux; R. Bélanger



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.



NSDL National Science Digital Library

These are a list of links about maps. ACTIVITIES I like to start off with Cardinal Directions Acitivity and Using a Map Grid with grades K-2. I even show the grid activity to the older students for a second so that they can remember what to do with them. I use ...

B, Miss



Mapping of SPARC/BM-40/Osteonectin-binding Sites on Fibrillar Collagens*S?  

PubMed Central

The 33-kDa matrix protein SPARC (BM-40, osteonectin) binds several collagen types with moderate affinity. The collagen-binding site resides in helix ?A of the extracellular calcium-binding domain of SPARC and is partially masked by helix ?C. Previously, we found that the removal of helix ?C caused a 10-fold increase in the affinity of SPARC for collagen, and we identified amino acids crucial for binding by site-directed mutagenesis. In this study, we used rotary shadowing, CNBr peptides, and synthetic peptides to map binding sites of SPARC onto collagens I, II, and III. Rotary shadowing and electron microscopy of SPARC-collagen complexes identified a major binding site ?180 nm from the C terminus of collagen. SPARC binding was also detected with lower frequency near the matrix metalloproteinase cleavage site. These data fit well with our analysis of SPARC binding to CNBr peptides, denaturation of which abolished binding, indicating triple-helical conformation of collagen to be essential. SPARC binding was substantially decreased in two of seven ?2(I) mutant procollagen I samples and after N-acetylation of Lys/Hyl side chains in wild-type collagen. Synthetic peptides of collagen III were used to locate the binding sites, and we found SPARC binding activity in a synthetic triple-helical peptide containing the sequence GPOGPSGPRGQOGVMGFOGPKGNDGAO (where O indicates 4-hydroxyproline), with affinity for SPARC comparable with that of procollagen III. This sequence is conserved among ? chains of collagens I, II, III, and V. In vitro collagen fibrillogenesis was delayed in the presence of SPARC, suggesting that SPARC might modulate collagen fibril assembly in vivo. PMID:18487610

Giudici, Camilla; Raynal, Nicolas; Wiedemann, Hanna; Cabral, Wayne A.; Marini, Joan C.; Timpl, Rupert; Bachinger, Hans Peter; Farndale, Richard W.; Sasaki, Takako; Tenni, Ruggero



Environmental Maps  

NSDL National Science Digital Library

The US Housing and Urban Development (HUD) Environmental Maps Web site is a free Internet service that combines information on HUD's community development and housing programs with Environmental Protection Agency (EPA) environmental data. The maps "provide: location, type, and performance of HUD-funded activities in every neighborhood across the country; and select EPA information on brownfields, hazardous wastes, air pollution and waste water discharges." The Geographic Information Systems (GIS)-based mapping interface is easily manipulated and users can locate theirs, or an interested neighborhood, in no time and browse the information provided. This powerful application is one of the best online interactive GIS mapping sites online for both its content and ease of use, making it a must visit.


NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps  

PubMed Central

Background Molecular biology knowledge can be formalized and systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist an increasing number of maps of molecular interactions containing detailed and step-wise description of various cell mechanisms. It is difficult to explore these large maps, to organize discussion of their content and to maintain them. Several efforts were recently made to combine these capabilities together in one environment, and NaviCell is one of them. Results NaviCell is a web-based environment for exploiting large maps of molecular interactions, created in CellDesigner, allowing their easy exploration, curation and maintenance. It is characterized by a combination of three essential features: (1) efficient map browsing based on Google Maps; (2) semantic zooming for viewing different levels of details or of abstraction of the map and (3) integrated web-based blog for collecting community feedback. NaviCell can be easily used by experts in the field of molecular biology for studying molecular entities of interest in the context of signaling pathways and crosstalk between pathways within a global signaling network. NaviCell allows both exploration of detailed molecular mechanisms represented on the map and a more abstract view of the map up to a top-level modular representation. NaviCell greatly facilitates curation, maintenance and updating the comprehensive maps of molecular interactions in an interactive and user-friendly fashion due to an imbedded blogging system. Conclusions NaviCell provides user-friendly exploration of large-scale maps of molecular interactions, thanks to Google Maps and WordPress interfaces, with which many users are already familiar. Semantic zooming which is used for navigating geographical maps is adopted for molecular maps in NaviCell, making any level of visualization readable. In addition, NaviCell provides a framework for community-based curation of maps. PMID:24099179



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

USGS Publications Warehouse

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).

Torresan, Michael E.; Gardner, James V.



Cross-modal soundscape mapping: Integrating ambisonic field recordings with high dynamic range spherical panoramic photography to produce interactive maps.  


We cannot "measure" the soundscape any more than we can "measure" the ocean, the city, or the wilderness. Being comprised of myriad complex elements, conditions, and relationships between sound sources and sound perceivers, the soundscape-and any sufficient description of it-must account for several different, but significantly interrelated, dimensions: physical, spatial, temporal, perceptual, cultural, and historical. How, then, are we to meaningfully document the soundscape? If we are to begin to understand the soundscape's impact on us-and our impact upon it-we need new methods to capture and represent the multisensory extents of a soundscape without reverting to one-dimensional quantitative abstractions. This project proposes an interdisciplinary method to record a soundscape's multisensory attributes by combining aural and visual information in a structured way which links the directionality of view and sound arrival. This method integrates multi-directional Ambisonic audio recordings with high dynamic range (HDR) spherical panoramic photography in the form of interactive maps and virtual tours. Case studies using the cross-modal soundscape mapping method will be presented. PMID:25235181

Carter, J Parkman; Braasch, Jonas



Mapping Single Cell-Substrate Interactions by Surface Plasmon Resonance Microscopy  

PubMed Central

We report on imaging of cell-substrate adhesion of a single cell with sub-cellular spatial resolution. Osmotic pressure was introduced to provide a controllable mechanical stimulation to the cell attached to a substrate, and high-resolution surface plasmon resonance microscopy was used to map the response of the cell, from which local cell-substrate adhesion was determined. In addition to high spatial resolution, the approach is non-invasive and fast, and allows for continuously mapping of cell-substrate interactions and single cell movements. PMID:22920036

Wang, Wei; Wang, Shaopeng; Liu, Qiang; Wu, Jie; Tao, Nongjian



Mapping of promoter sites on the genome of bacteriophage M13.  


With the aid of transcription studies on restriction fragments of bacteriophage M13 DNA it has been demonstrated that at least eight promoter sites are located on the M13 genome. Five of these promoters initiate the synthesis of RNA chains which contain at their 5'-terminal end pppG (G promoters), while the other three promoters initiate RNA chains which start exclusively with pppA (A promoters). The positions of these promoter sites on the physical map are: 0.82 (G0.82), 0.88 (G0.88), 0.94 (G0.94), 0.01 (G0.01), 0.08 (G0.08), 0.36 (A0.36), 0.51 (A0.51) and 0.56 (A0.56). The G promoters were found to be clustered within a distance of one-third of the genome length from the central termination site for transcription (map position 0.77). The A promoters, however, were found at greater distances from this termination signal. Based upon the incorporation of [gamma-32P]ATP or [gamma-32P]GTP, the capacity of these promoters to initiate the synthesis of RNA chains varies. The strongest G promoters are G0.82, G0.94 and G0.08 and the strongest A promoter is A0.36. As judged from their position on the genetic map, it is postulated that two promoters, namely G0.94 and G0.01, are located within gene II. The other promoters are most probably located immediately in front of the gene VIII/VII boundary (G0.82), and immediately in front of gene V (G0.88), gene II (G0.08), gene IV (A0.36), gene I (A0.51) and gene VI (A0.56). No evidence has been obtained so far for the existence of a promoter immediately in front of gene III. PMID:795656

Edens, L; van Wezenbeek, P; Konings, N H; Schoenmakers, J G



Health 2.0: how interactive Web sites are changing the healthcare industry.  


Having a Web site is no longer a luxury or perk for your practice and your patients. A Web site is a basic necessity that patients are expecting firom their physicians and their practices. But patients want more than a mere Internet presence. They are expecting an interactive Web site, and they want to be able to communicate with the practice and the physicians. This article will discuss the creation of an interactive Web site and why it is necessary for doctors to enhance their Web site so that patients can interact with the practice. PMID:21506467

Lombardi, Glenn; Baum, Neil



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

USGS Publications Warehouse

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).

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.



Mapping the complex morphology of cell interactions with nanowire substrates using FIB-SEM.  


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

Wierzbicki, Rafa?; Købler, Carsten; Jensen, Mikkel R B; Lopaci?ska, Joanna; Schmidt, Michael S; Skolimowski, Maciej; Abeille, Fabien; Qvortrup, Klaus; Mølhave, Kristian



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


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

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



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

PubMed Central

The frequency-dependent ultrasound backscatter from tissues contains information about the microstructure that can be quantified. In many cases, the anatomic microstructure details responsible for ultrasonic scattering remain unidentified. However, their identification would lead to potentially improved methodologies for characterizing tissue and diagnosing disease from ultrasonic backscatter measurements. Recently, three-dimensional (3D) acoustic models of tissue microstructure, termed 3D impedance maps (3DZMs), were introduced to help to identify scattering sources [J. Mamou, M. L. Oelze, W. D. O’Brien, Jr., and J. F. Zachary, “Identifying ultrasonic scattering sites from 3D impedance maps,” J. Acoust. Soc. Am. 117, 413–423 (2005)]. In the current study, new 3DZM methodologies are used to model and identify scattering structures. New processing procedures (e.g., registration, interpolations) are presented that allow more accurate 3DZMs to be constructed from histology. New strategies are proposed to construct scattering models [i.e., form factor (FF)] from 3DZMs. These new methods are tested on simulated 3DZMs, and then used to evaluate 3DZMs from three different rodent tumor models. Simulation results demonstrate the ability of the extended strategies to accurately predict FFs and estimate scatterer properties. Using the 3DZM methods, distinct FFs and scatterer properties were obtained for each tumor examined. PMID:18247919

Mamou, Jonathan; Oelze, Michael L.; O'Brien, William D.; Zachary, James F.



Mapping air pollution using Earth observation techniques for cultural heritage sites  

NASA Astrophysics Data System (ADS)

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

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



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


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

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



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

PubMed Central

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



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

PubMed Central

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



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

NASA Astrophysics Data System (ADS)

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 if you are interested.

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



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

PubMed Central

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

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



Short Co-occurring Polypeptide Regions Can Predict Global Protein Interaction Maps  

PubMed Central

A goal of the post-genomics era has been to elucidate a detailed global map of protein-protein interactions (PPIs) within a cell. Here, we show that the presence of co-occurring short polypeptide sequences between interacting protein partners appears to be conserved across different organisms. We present an algorithm to automatically generate PPI prediction method parameters for various organisms and illustrate that global PPIs can be predicted from previously reported PPIs within the same or a different organism using protein primary sequences. The PPI prediction code is further accelerated through the use of parallel multi-core programming, which improves its usability for large scale or proteome-wide PPI prediction. We predict and analyze hundreds of novel human PPIs, experimentally confirm protein functions and importantly predict the first genome-wide PPI maps for S. pombe (?9,000 PPIs) and C. elegans (?37,500 PPIs). PMID:22355752

Pitre, Sylvain; Hooshyar, Mohsen; Schoenrock, Andrew; Samanfar, Bahram; Jessulat, Matthew; Green, James R.; Dehne, Frank; Golshani, Ashkan



A Strategy for Interaction Site Prediction between Phospho-binding Modules and their Partners Identified from Proteomic Data*  

PubMed Central

Small and large scale proteomic technologies are providing a wealth of potential interactions between proteins bearing phospho-recognition modules and their substrates. Resulting interaction maps reveal such a dense network of interactions that the functional dissection and understanding of these networks often require to break specific interactions while keeping the rest intact. Here, we developed a computational strategy, called STRIP, to predict the precise interaction site involved in an interaction with a phospho-recognition module. The method was validated by a two-hybrid screen carried out using the ForkHead Associated (FHA)1 domain of Rad53, a key protein of Saccharomyces cerevisiae DNA checkpoint, as a bait. In this screen we detected 11 partners, including Cdc7 and Cdc45, essential components of the DNA replication machinery. FHA domains are phospho-threonine binding modules and the threonines involved in both interactions could be predicted using the STRIP strategy. The threonines T484 and T189 in Cdc7 and Cdc45, respectively, were mutated and loss of binding could be monitored experimentally with the full-length proteins. The method was further tested for the analysis of 63 known Rad53 binding partners and provided several key insights regarding the threonines likely involved in these interactions. The STRIP method relies on a combination of conservation, phosphorylation likelihood, and binding specificity criteria and can be accessed via a web interface at PMID:20733106

Aucher, Willy; Becker, Emmanuelle; Ma, Emilie; Miron, Simona; Martel, Arnaud; Ochsenbein, Francoise; Marsolier-Kergoat, Marie-Claude; Guerois, Raphael



Genetic Mapping of Social Interaction Behavior in B6\\/MSM Consomic Mouse Strains  

Microsoft Academic Search

Genetic studies are indispensable for understanding the mechanisms by which individuals develop differences in social behavior.\\u000a We report genetic mapping of social interaction behavior using inter-subspecific consomic strains established from MSM\\/Ms\\u000a (MSM) and C57BL\\/6J (B6) mice. Two animals of the same strain and sex, aged 10 weeks, were introduced into a novel open-field\\u000a for 10 min. Social contact was detected by an

Aki TakahashiKazuya Tomihara; Kazuya Tomihara; Toshihiko Shiroishi; Tsuyoshi Koide



INTERACTIVE MAPS By R.M. Flores and G.L. Gunther  

E-print Network

. Gunther GIS MANAGEMENT AND DEVELOPMENT By G.L. Gunther, M.E. Ellis, G.S. Rossi, S.A. Kinney, T.T. Taber, S.B. Roberts COAL RESOURCES By M.E. Ellis, G.L. Gunther, and S.B. Roberts METADATA By G.S. Rossi, S.A. KinneyINTERACTIVE MAPS By R.M. Flores and G.L. Gunther In U.S. Geological Survey Professional Paper 1625


Maps That Teach: US and World Geography  

NSDL National Science Digital Library

Created by Owl and Mouse Educational Software, this resource uses interactive maps to teach geography. The site provides both Map Puzzles and Interactive Maps. Map Puzzles are downloadable and must be run on Windows. They challenge users to piece together the States of the United States or the countries of the world's continents, depending on the puzzle used. Interactive Maps allow users to move their cursor over a basic regional map. As the cursor hits each country, its name appears. The page also provides resources for printing large maps using only a single printer and a discussion of how these resources can be used in the classroom.



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

SciTech Connect

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.

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



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

NASA Astrophysics Data System (ADS)

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

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



Site-specific mapping and quantification of protein S-sulphenylation in cells.  


Cysteine S-sulphenylation provides redox regulation of protein functions, but the global cellular impact of this transient post-translational modification remains unexplored. We describe a chemoproteomic workflow to map and quantify over 1,000 S-sulphenylation sites on more than 700 proteins in intact cells. Quantitative analysis of human cells stimulated with hydrogen peroxide or epidermal growth factor measured hundreds of site selective redox changes. Different cysteines in the same proteins displayed dramatic differences in susceptibility to S-sulphenylation. Newly discovered S-sulphenylations provided mechanistic support for proposed cysteine redox reactions and suggested novel redox mechanisms, including S-sulphenyl-mediated redox regulation of the transcription factor HIF1A by SIRT6. S-sulphenylation is favored at solvent-exposed protein surfaces and is associated with sequence motifs that are distinct from those for other thiol modifications. S-sulphenylations affect regulators of phosphorylation, acetylation and ubiquitylation, which suggest regulatory crosstalk between redox control and signalling pathways. PMID:25175731

Yang, Jing; Gupta, Vinayak; Carroll, Kate S; Liebler, Daniel C



Odorant binding by a pheromone binding protein: active site mapping by photoaffinity labeling.  


The bacterially expressed recombinant pheromone binding protein (PBP) of Antheraea polyphemus was photoaffinity labeled with (6E,11Z)-[3H]hexadecadienyl diazoacetate, a photoactivatable analog of the naturally occurring acetate pheromone. Radiolabeled peptides were separated from an endoproteinase Lys-C digestion by HPLC and characterized by Edman degradation. The label was exclusively found in the Asp39-Lys58 fragment. Cleavage of this peptide (DDYVMTDRLAGCAINCLATK) with Arg-C gave a single radiolabeled peptide (DDYVMTDR), which was predicted to be alpha-helical. The adjoining LAGCAINCLATK fragment, which is highly conserved in PBP sequences, was predicted to be a hydrophobic beta-strand and has been proposed to be important in recognition of the alkadienyl chain. Edman degradation confirmed the location of the covalently attached ligand at Thr44 of the smaller hydrophilic peptide. In addition, the synthesis of the newly identified pheromone component (4E,9Z)-tetradecadienyl acetate and its photoaffinity analog, (4E,9Z)-[3H]tetradecadienyl diazoacetate, is also described. Mapping of PBP photoaffinity labeled by (4E,9Z)-[3H]14:Dza revealed that the hydrophobic region Asp21-Lys38 adjacent to the primary binding domain Asp39-Lys58 contained a second modification site. The 14-carbon odorant molecule thus had two binding positions within the recognition site, while only a single binding position was available to the 16-carbon pheromone. PMID:8161541

Du, G; Ng, C S; Prestwich, G D



Mapping of contamination at Savannah River Site FBWU by INEEL trolley  

SciTech Connect

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

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



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

ERIC Educational Resources Information Center

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…

Ko, Moo Nam



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

SciTech Connect

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.

Molecke, M.A. [Sandia National Lab., Albuquerque, NM (United States); Carney, K.R.; Autin, W.J.; Overton, E.B. [Louisiana State Univ., Baton Rouge, LA (United States)



Barbara WeberSite: DNA Interactive (  

NSDL National Science Digital Library

Barbara Weber is Director of the Breast Cancer Program at the Abramson Cancer Center at the University of Pennsylvania. Barbara Weber based her gene-mapping work on studies of families with a high incidence of breast cancer. Dr. Weber was startled to realize that her study had yielded crucial information about whether her patient VickyÃÂÃÂôs sister Denise was at high risk for developing the disease.



Mapping the Vif-A3G interaction using peptide arrays: a basis for anti-HIV lead peptides.  


Human apolipoprotein-B mRNA-editing catalytic polypeptide-like 3G (A3G) is a cytidine deaminase that restricts retroviruses, endogenous retro-elements and DNA viruses. A3G plays a key role in the anti-HIV-1 innate cellular immunity. The HIV-1 Vif protein counteracts A3G mainly by leading A3G towards the proteosomal machinery and by direct inhibition of its enzymatic activity. Both activities involve direct interaction between Vif and A3G. Disrupting the interaction between A3G and Vif may rescue A3G antiviral activity and inhibit HIV-1 propagation. Here, mapping the interaction sites between A3G and Vif by peptide array screening revealed distinct regions in Vif important for A3G binding, including the N-terminal domain (NTD), C-terminal domain (CTD) and residues 83-99. The Vif-binding sites in A3G included 12 different peptides that showed strong binding to either full-length Vif, Vif CTD or both. Sequence similarity was found between Vif-binding peptides from the A3G CTD and NTD. A3G peptides were synthesized and tested for their ability to counteract Vif action. A3G 211-225 inhibited HIV-1 replication in cell culture and impaired Vif dependent A3G degradation. In vivo co-localization of full-length Vif with A3G 211-225 was demonstrated by use of FRET. This peptide has the potential to serve as an anti-HIV-1 lead compound. Our results suggest a complex interaction between Vif and A3G that is mediated by discontinuous binding regions with different affinities. PMID:23545135

Reingewertz, Tali H; Britan-Rosich, Elena; Rotem-Bamberger, Shahar; Viard, Mathias; Jacobs, Amy; Miller, Abigail; Lee, Ji Youn; Hwang, Jeeseong; Blumenthal, Robert; Kotler, Moshe; Friedler, Assaf



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


The residue C221 on pyruvate decarboxylase (EC. 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

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



A pilot study of an interactive web site in the workplace for reducing alcohol consumption  

Microsoft Academic Search

An interactive web-site-based intervention for reducing alcohol consumption was pilot tested. Participants were 145 employees of a work site in the Silicon Valley region of California, categorized as low or moderate risk for alcohol problems. All participants were given access to a web site that provided feedback on their levels of stress and use of coping strategies. Participants randomized to

Robert A. Matano; Cheryl Koopman; Stanley F. Wanat; Andrew J. Winzelberg; Shelly D. Whitsell; Darrah Westrup; Kristine Futa; Justin B. Clayton; Lisa Mussman; C. Barr Taylor



New description of protein-ligand interactions using a spherical self-organizing map.  


In a previous report, we studied the mapping ability of the spherical self-organizing map (SSOM). The original 3D structure of the active site of the ?2 protein structure was well reproduced by the SSOM. To validate the geometrical transformation and the resulting molecular electrostatic potential (MEP) distribution, the molecular surfaces of 20 ?2 ligands were mapped onto the protein SSOM sphere. The MEP values of the two spheres derived from the ligand and the ?2 receptor protein were compared. In most cases involving potent ligands, the two spheres had a moderate negative correlation. This indicates that the SSOM approach has excellent potential to represent a complex protein surface as a simple spherical structure. In this study, we perform a quantitative structure-activity relationship (QSAR) study of caspase-3 inhibitors based on the SSOM technique. Initially, the active site of the protein structure 'caspase-3' was characterized by the SSOM using the MEP values. Each inhibitor was then projected onto the protein SSOM sphere and the chemical descriptors were derived from the ligand SSOM sphere. The correlation of the chemical descriptors and the inhibitory activities was investigated using the support vector regression (SVR) method. Finally, the important MEP descriptors from the final SVR model were examined. The structural requirements of caspase-3 inhibitors are discussed from the perspectives of both the ligand and protein structures. PMID:22503362

Hasegawa, Kiyoshi; Funatsu, Kimito



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

NASA Astrophysics Data System (ADS)

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 ( 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.

Wirkus, Lars; Strunck, Alexander



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

PubMed Central

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



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

PubMed Central

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



Mapping the Putative G Protein-coupled Receptor (GPCR) Docking Site on GPCR Kinase 2  

PubMed Central

G protein-coupled receptor kinases (GRKs) phosphorylate agonist-occupied receptors initiating the processes of desensitization and ?-arrestin-dependent signaling. Interaction of GRKs with activated receptors serves to stimulate their kinase activity. The extreme N-terminal helix (?N), the kinase small lobe, and the active site tether (AST) of the AGC kinase domain have previously been implicated in mediating the allosteric activation. Expanded mutagenesis of the ?N and AST allowed us to further assess the role of these two regions in kinase activation and receptor phosphorylation in vitro and in intact cells. We also developed a bioluminescence resonance energy transfer-based assay to monitor the recruitment of GRK2 to activated ?2A-adrenergic receptors (?2AARs) in living cells. The bioluminescence resonance energy transfer signal exhibited a biphasic response to norepinephrine concentration, suggesting that GRK2 is recruited to G?? and ?2AAR with EC50 values of 15 nm and 8 ?m, respectively. We show that mutations in ?N (L4A, V7E, L8E, V11A, S12A, Y13A, and M17A) and AST (G475I, V477D, and I485A) regions impair or potentiate receptor phosphorylation and/or recruitment. We suggest that a surface of GRK2, including Leu4, Val7, Leu8, Val11, and Ser12, directly interacts with receptors, whereas residues such as Asp10, Tyr13, Ala16, Met17, Gly475, Val477, and Ile485 are more important for kinase domain closure and activation. Taken together with data on GRK1 and GRK6, our data suggest that all three GRK subfamilies make conserved interactions with G protein-coupled receptors, but there may be unique interactions that influence selectivity. PMID:25049229

Beautrait, Alexandre; Michalski, Kevin R.; Lopez, Thomas S.; Mannix, Katelynn M.; McDonald, Devin J.; Cutter, Amber R.; Medina, Christopher B.; Hebert, Aaron M.; Francis, Charnelle J.; Bouvier, Michel; Tesmer, John J. G.; Sterne-Marr, Rachel



Seismic Hazard Mapping and Microzonation in the Sikkim Himalaya through GIS Integration of Site Effects and Strong Ground Motion Attributes  

Microsoft Academic Search

The seismic ground motion hazard is mapped in the Sikkim Himalaya with local and regional site conditions incorporated through geographic information system. A strong motion network in Sikkim comprising of 9 digital accelerographs recorded more than 100 events during 1998–2002, of which 41 events are selected with signal-to-noise ratio =3 for the estimation of site response (SR), peak ground acceleration

Sankar Kumar Nath



Mapping of subaqueous glacier topography in Greenland with multibeam sonars to document ice-ocean interactions  

NASA Astrophysics Data System (ADS)

Very few attempts have been made to map the submerged calving face of tidewater glaciers in the past. Here, we present results from the August 2012 and 2013 campaigns in West Greenland where we visited several glaciers in Atasund, Torssukataq, Uummannaq and Upernavik Fjords. We employ a low frequency multibeam sonar tilted to the side to image the side walls of the glacial fjords, including the submerged calving faces. The results reveal the true depth of the grounding line of these glaciers, which is typically unknown - or known with enormous uncertainties - from traditional ship soundings or from the mapping of glacier thickness, the general shape and slope of the submerged calving fronts, and the presence and spatial distribution of channels of subglacial water discharge that fuel high rates of ice face melting. By repeating the mapping over time on a few glaciers and compensating the data for ice motion, we are able to calculate calving rates and ice melt rates over periods of a few days and compare the ice melt production results with estimates derived from hydrographic surveys. In most examples, knowledge of the sea floor topography is the principal information retrieved from these surveys because it determines whether subsurface warm waters can access the glacier face, but the spatial imaging of the submerged calving face reveals spatial details about ice-ocean interactions that are fundamental to the process of ice melt and complex. Such mappings should be extended to other glaciers and eventually to all tidewater glaciers in Greenland.

Rignot, E. J.; Fenty, I. G.; Xu, Y.; Cai, C.; Aykutlug, E.; Dupont, T. K.



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

NASA Astrophysics Data System (ADS)

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.

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



An Online Interactive Map Service for Displaying Ground-Water Conditions in Arizona  

USGS Publications Warehouse

Monitoring the availability of the nation's ground-water supplies is of critical importance to planners and water managers. The general public also has an interest in understanding the status of ground-water conditions, especially in the semi-arid Southwestern United States where much of the water used by municipalities and agriculture comes from the subsurface. Unlike surface-water indicators such as stage or discharge, ground-water conditions may be more difficult to assess and present. Individual well observations may only represent conditions in a limited area surrounding the well and wells may be screened over single or multiple aquifers, further complicating single-well measurement interpretations. Additionally, changes in ground-water conditions may involve time scales ranging from days to many years, depending on recharge, soil properties and depth to the water table. This lack of an easily identifiable ground-water property indicative of current conditions combined with differing time scales of water-level changes makes the presentation of ground-water conditions a difficult task, particularly on a regional basis. One approach is to spatially present several indicators of ground-water conditions that address different time scales and attributes of the aquifer systems. In this report, we describe a publicly-available online interactive map service that presents several different layers of ground-water-conditions information for the alluvial basins in the Lower Colorado River Basin in Arizona ( These data layers include wells experiencing water-level decline, wells experiencing water-level rise, recent trends in ground-water levels, change in water level since predevelopment and change in storage since predevelopment. Recent pumpage totals and projected population numbers are also provided for ground-water basins and counties in the region of the Lower Colorado River in Arizona along with a bibliography of U.S. Geological Survey reports for those seeking further information. The methods used to create these data layers are explained with illustrations of example information available on the Web site.

Tillman, Fred D; Leake, Stanley A.; Flynn, Marilyn E.; Cordova, Jeffrey T.; Schonauer, Kurt T.



REVIEW ARTICLE Enabling cross-site interactions in social networks  

E-print Network

application that shares user's photos between Facebook and MySpace based on the cross-site access control network services, including Facebook, MySpace, Twitter, LinkedIn, Hi5, and Orkut have gained user adoption of services and experiences, for example, Facebook and MySpace allow users to create photo albums, fan clubs

Shehab, Mohamed


Comprehensive Human Transcription Factor Binding Site Map for Combinatory Binding Motifs Discovery  

PubMed Central

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

Muller-Molina, Arnoldo J.; Scholer, Hans R.; Arauzo-Bravo, Marcos J.



Dynamic map of protein interactions in the Escherichia coli chemotaxis pathway  

PubMed Central

Protein–protein interactions play key roles in virtually all cellular processes, often forming complex regulatory networks. A powerful tool to study interactions in vivo is fluorescence resonance energy transfer (FRET), which is based on the distance-dependent energy transfer from an excited donor to an acceptor fluorophore. Here, we used FRET to systematically map all protein interactions in the chemotaxis signaling pathway in Escherichia coli, one of the most studied models of signal transduction, and to determine stimulation-induced changes in the pathway. Our FRET analysis identified 19 positive FRET pairs out of the 28 possible protein combinations, with 9 pairs being responsive to chemotactic stimulation. Six stimulation-dependent and five stimulation-independent interactions were direct, whereas other interactions were apparently mediated by scaffolding proteins. Characterization of stimulation-induced responses revealed an additional regulation through activity dependence of interactions involving the adaptation enzyme CheB, and showed complex rearrangement of chemosensory receptors. Our study illustrates how FRET can be efficiently employed to study dynamic protein networks in vivo. PMID:19156130

Kentner, David; Sourjik, Victor



Interaction Between Two Rows of Localized Adsorption Sites in a 2D One-Component Plasma  

E-print Network

We compute the free energy for two rows of localized adsorption sites embedded in a two dimensional one-component plasma with neutralizing background density $\\rho$. The interaction energy between the adsorption sites is repulsive. We also compute the average occupation number of the adsorption sites and compare it to the result for a single row of sites. The exact result indicates that the discretization does not induce charge asymmetry and no attractive forces occur.

Christian D. Santangelo; Lesser Blum



Gill microsomal (Na+,K+)-ATPase from the blue crab Callinectes danae: Interactions at cationic sites.  


Euryhaline crustaceans tolerate exposure to a wide range of dilute media, using compensatory, ion regulatory mechanisms. However, data on molecular interactions occurring at cationic sites on the crustacean gill (Na+,K+)-ATPase, a key enzyme in this hyperosmoregulatory process, are unavailable. We report that Na+ binding at the activating site leads to cooperative, heterotropic interactions that are insensitive to K+. The binding of K+ ions to their high affinity sites displaces Na+ ions from their sites. The increase in Na+ ion concentrations increases heterotropic interactions with the K+ ions, with no changes in K0.5 for K+ ion activation at the extracellular sites. Differently from mammalian (Na+,K+)-ATPases, that from C. danae exhibits additional NH4+ ion binding sites that synergistically activate the enzyme at saturating concentrations of Na+ and K+ ions. NH4+ binding is cooperative, and heterotropic NH4+ ion interactions are insensitive to Na+ ions, but Na+ ions displace NH4+ ions from their sites. NH4+ ions also displace Na+ ions from their sites. Mg2+ ions modulate enzyme stimulation by NH4+ ions, displacing NH4+ ion from its sites. These interactions may modulate NH4+ ion excretion and Na+ ion uptake by the gill epithelium in euryhaline crustaceans that confront hyposmotic media. PMID:16055367

Masui, D C; Furriel, R P M; Silva, E C C; Mantelatto, F L M; McNamara, J C; Barrabin, H; Scofano, H M; Fontes, C F L; Leone, F A



A remote characterization system for subsurface mapping of buried waste sites  

SciTech Connect

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.

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



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

NASA Astrophysics Data System (ADS)

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

Jasper, Cameron A.


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

USGS Publications Warehouse

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.

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



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


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 Ca(2+) responses in the vasculature, it was found that this tissue contributes to flg22-induced Ca(2+) 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

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



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

USGS Publications Warehouse

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.

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, A.; Kirk, R.L.; Maimone, M.; Matthies, L.H.; Malin, M.; Parker, T.; Sims, M.; Thompson, S.; Squyres, S.W.; Soderblom, L.A.



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

E-print Network

invests more into thermonuclear reaction study China's announced Friday in to invest 50 million yuan (6 Help Site Map languages China World Opinion Business Sci-Edu Culture/Life Sports Photos Services - - - - - - - Newsletter Online Community China Biz Info News Archive Feedback Voices of Readers Weather Forecast RSS Feeds


Mapping of a mouse mammary tumor virus integration site by retroviral LTR—arbitrary polymerase chain reaction  

Microsoft Academic Search

The de novo integration of retroviral genomes within the mammalian genome is believed to contribute to the tumorigenic process. Integration may result in the disruption or inappropriate transcription of key regulatory genes. We describe the application of an arbitrarily primed PCR method for the mapping and cloning of genomic integration sites of the mouse mammary tumor virus (MMTV). We have

Claus Casper; Christine Leib-Mösch; Brian Salmons; Walter H Günzburg; Gaby Baumann; Heinz Höfler; Volker Erfle; Michael J Atkinson



High-resolution mapping of transcription factor binding sites on native chromatin  

PubMed Central

Sequence-specific DNA-binding proteins including transcription factors (TFs) are key determinants of gene regulation and chromatin architecture. Formaldehyde cross-linking and sonication followed by Chromatin ImmunoPrecipitation (X-ChIP) is widely used for profiling of TF binding, but is limited by low resolution and poor specificity and sensitivity. We present a simple protocol that starts with micrococcal nuclease-digested uncross-linked chromatin and is followed by affinity purification of TFs and paired-end sequencing. The resulting ORGANIC (Occupied Regions of Genomes from Affinity-purified Naturally Isolated Chromatin) profiles of Saccharomyces cerevisiae Abf1 and Reb1 provide highly accurate base-pair resolution maps that are not biased toward accessible chromatin, and do not require input normalization. We also demonstrate the high specificity of our method when applied to larger genomes by profiling Drosophila melanogaster GAGA Factor and Pipsqueak. Our results suggest that ORGANIC profiling is a widely applicable high-resolution method for sensitive and specific profiling of direct protein-DNA interactions. PMID:24336359

Kasinathan, Sivakanthan; Orsi, Guillermo A.; Zentner, Gabriel E.; Ahmad, Kami; Henikoff, Steven



Mapping of single-site magnetic anisotropy tensors in weakly coupled spin clusters by torque magnetometry.  


Single-crystal torque magnetometry performed on weakly-coupled polynuclear systems provides access to a complete description of single-site anisotropy tensors. Variable-temperature, variable-field torque magnetometry was used to investigate triiron(III) complex [Fe3La(tea)2(dpm)6] (Fe3La), a lanthanum(III)-centred variant of tetrairon(III) single molecule magnets (Fe4) (H3tea = triethanolamine, Hdpm = dipivaloylmethane). Due to the presence of the diamagnetic lanthanoid, magnetic interactions among iron(III) ions (si = 5/2) are very weak (<0.1 cm(?1)) and the magnetic response of Fe3La is predominantly determined by single-site anisotropies. The local anisotropy tensors were found to have Di > 0 and to be quasi-axial with |Ei/Di| ~ 0.05. Their hard axes form an angle of approximately 70° with the threefold molecular axis, which therefore corresponds to an easy magnetic direction for the molecule. The resulting picture was supported by a High Frequency EPR investigation and by DFT calculations. Our study confirms that the array of peripheral iron(III) centres provides substantially noncollinear anisotropy contributions to the ground state of Fe4 complexes, which are of current interest in molecular magnetism and spintronics. PMID:25014192

Rigamonti, Luca; Cornia, Andrea; Nava, Andrea; Perfetti, Mauro; Boulon, Marie-Emmanuelle; Barra, Anne-Laure; Zhong, Xiaoliang; Park, Kyungwha; Sessoli, Roberta



Interactions between cochlear implant electrode insertion depth and frequency-place mapping  

NASA Astrophysics Data System (ADS)

While new electrode designs allow deeper insertion and wider coverage in the cochlea, there is still considerable variation in the insertion depth of the electrode array among cochlear implant users. The present study measures speech recognition as a function of insertion depth, varying from a deep insertion of 10 electrodes at 28.8 mm to a shallow insertion of a single electrode at 7.2 mm, in four Med-El Combi 40+ users. Short insertion depths were simulated by inactivating apical electrodes. Speech recognition increased with deeper insertion, reaching an asymptotic level at 21.6 or 26.4 mm depending on the frequency-place map used. Ba?kent and Shannon [J. Acoust. Soc. Am. 116, 3130-3140 (2004)] showed that speech recognition by implant users was best when the acoustic input frequency was matched onto the cochlear location that normally processes that frequency range, minimizing the spectral distortions in the map. However, if an electrode array is not fully inserted into the cochlea, a matched map will result in the loss of considerable low-frequency information. The results show a strong interaction between the optimal frequency-place mapping and electrode insertion depth. Consistent with previous studies, frequency-place matching produced better speech recognition than compressing the full speech range onto the electrode array for full insertion ranges (20 to 25 mm from the round window). For shallower insertions (16.8 and 19.2 mm) a mild amount of frequency-place compression was better than truncating the frequency range to match the basal cochlear location. These results show that patients with shallow electrode insertions might benefit from a map that assigns a narrower frequency range than patients with full insertions. .

Ba?kent, Deniz; Shannon, Robert V.



The actin binding site of thymosin beta 4 mapped by mutational analysis.  

PubMed Central

We characterized in detail the actin binding site of the small actin-sequestering protein thymosin beta 4 (T beta 4) using chemically synthesized full-length T beta 4 variants. The N-terminal part (residues 1-16) and a hexapeptide motif (residues 17-22) form separate structural entities. In both, we identified charged and hydrophobic residues that participate in the actin interaction using chemical cross-linking, complex formation in native gels and actin-sequestering experiments. Quantitative data on the activity of the variants and circular dichroism experiments allow to present a model in which the N-terminal part needs to adopt an alpha-helix for actin binding and interacts through a patch of hydrophobic residues (6M-I-F12) on one side of this helix. Also, electrostatic contacts between actin and lysine residues 18, in the motif, and 14, in the N-terminal alpha-helix, appear important for binding. The residues critical for contacting actin are conserved throughout the beta-thymosin family and in addition to this we identify a similar pattern in the C-terminal headpiece of villin and dematin. Images PMID:8617195

Van Troys, M; Dewitte, D; Goethals, M; Carlier, M F; Vandekerckhove, J; Ampe, C



Genome-wide mapping of cellular protein-RNA interactions enabled by chemical crosslinking.  


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

Li, Xiaoyu; Song, Jinghui; Yi, Chengqi



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

SciTech Connect

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.

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



Snowpack: Decadal Averages Map  

NSDL National Science Digital Library

This is an interactive map of California and the Sierra Nevada mountains, showing projected variations in water stored in snowpack, from 1950 to 2090, assuming low or high emission scenarios over that period of time. Interactive can be adjusted to show different months of the year and various climate models, graphed by site.

Commission, California E.


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

NASA Astrophysics Data System (ADS)

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.

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



California Geological Survey: Geologic Maps  

NSDL National Science Digital Library

This index provides access to a selection of geologic maps of California, as well as an overview of geologic and other mapping activities in the state. The index, which can be accessed by clicking on an interactive map of the state, contains lists of selected geologic maps in California prepared by the Regional Geologic Mapping Project (RGMP). The RGMP staff monitors the literature and collects references that contain geologic mapping that may be useful for future compilations. In addition, the site has information about Caltrans Highway Corridor Mapping, The Mineral Resources and Mineral Hazards Mapping Program, North Coast Watersheds Assessment Program, The Timber Harvesting Plan Enforcement Program, and The Seismic Hazards Mapping Program. A set of links is provided to other sources of geologic maps and map information.


VESGEN 2D: Automated, User-Interactive Software for Vascular Quantification and Mapping of Angiogenic and Lymphangiogenic Trees and Networks  

PubMed Central

Quantification of microvascular remodeling as a meaningful discovery tool requires mapping and measurement of site-specific changes within vascular trees and networks. Vessel density and other critical vascular parameters are often modulated by molecular regulators as determined by local vascular architecture. For example, enlargement of vessel diameter by vascular endothelial growth factor (VEGF) is restricted to specific generations of vessel branching (Microvascular Research 72(3):91, 2006). The averaging of vessel diameter over many successively smaller generations is therefore not particularly useful. The newly automated, user-interactive software VESGEN (VESsel GENeration Analysis) quantifies major vessel parameters within two-dimensional (2D) vascular trees, networks, and tree-network composites. This report reviews application of VESGEN 2D to angiogenic and lymphangiogenic tissues that includes the human and murine retina, embryonic coronary vessels, and avian chorioallantoic membrane (CAM). Software output includes colorized image maps with quantification of local vessel diameter, fractal dimension, tortuosity and avascular spacing. The density of parameters such as vessel area, length, number and branch point are quantified according to site-specific generational branching within vascular trees. The sole user input requirement is a binary (black/white) vascular image. Future applications of VESGEN will include analysis of 3D vascular architecture and bioinformatic dimensions such as blood flow and receptor localization. Branching analysis by VESGEN has demonstrated that numerous regulators including VEGF165, basic fibroblast growth factor (bFGF), transforming growth factor ?-1 (TGF?-1), angiostatin and the clinical steroid triamcinolone acetonide induce ‘fingerprint’ or ‘signature’ changes in vascular patterning that provide unique readouts of dominant molecular signaling. PMID:19248164

Vickerman, Mary B.; Keith, Patricia A.; McKay, Terri L.; Gedeon, Dan J.; Watanabe, Michiko; Montano, Monica; Karunamuni, Ganga; Kaiser, Peter K.; Sears, Jonathan E.; Ebrahem, Quteba; Ribita, Daniela; Hylton, Alan G.; Parsons-Wingerter, Patricia



Method of predicting Splice Sites based on signal interactions  

PubMed Central

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

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



Multiple magnetic interactions in A-site-ordered perovskite-structure oxides.  


Multiple magnetic interactions in A-site-ordered perovskite-structure oxides AA'3B2B'2O12 with A'-site Cu and B-site Fe ions are highlighted here. Several new compounds with this structure type were obtained by high-pressure synthesis and have been given unusual magnetic properties due to multiple interactions of Cu and Fe ions (A'-A', A'-B, A'-B', B-B, B-B', and B'-B' interactions). The magnetic interaction is discussed here in light of the results of magnetic structure analysis with neutron powder diffraction data and x-ray magnetic circular dichroism spectra obtained in x-ray absorption experiments. The characteristic structural framework with ordered cation arrangements and the variation in the oxidation state of the ions at the A' and B sites are shown to play roles crucial for the diverse and intriguing physical properties of these new compounds. PMID:25352258

Shimakawa, Yuichi; Mizumaki, Masaichiro



Multiple magnetic interactions in A-site-ordered perovskite-structure oxides  

NASA Astrophysics Data System (ADS)

Multiple magnetic interactions in A-site-ordered perovskite-structure oxides AA?3B2B?2O12 with A?-site Cu and B-site Fe ions are highlighted here. Several new compounds with this structure type were obtained by high-pressure synthesis and have been given unusual magnetic properties due to multiple interactions of Cu and Fe ions (A?–A?, A?–B, A?–B?, B–B, B–B?, and B?–B? interactions). The magnetic interaction is discussed here in light of the results of magnetic structure analysis with neutron powder diffraction data and x-ray magnetic circular dichroism spectra obtained in x-ray absorption experiments. The characteristic structural framework with ordered cation arrangements and the variation in the oxidation state of the ions at the A? and B sites are shown to play roles crucial for the diverse and intriguing physical properties of these new compounds.

Shimakawa, Yuichi; Mizumaki, Masaichiro



Rapid Mapping and Identification of Mutations in Caenorhabditis elegans by Restriction Site-Associated DNA Mapping and Genomic Interval Pull-Down Sequencing  

PubMed Central

Forward genetic screens provide a powerful approach for inferring gene function on the basis of the phenotypes associated with mutated genes. However, determining the causal mutation by traditional mapping and candidate gene sequencing is often the rate-limiting step, especially when analyzing many mutants. We report two genomic approaches for more rapidly determining the identity of the affected genes in Caenorhabditis elegans mutants. First, we report our use of restriction site-associated DNA (RAD) polymorphism markers for rapidly mapping mutations after chemical mutagenesis and mutant isolation. Second, we describe our use of genomic interval pull-down sequencing (GIPS) to selectively capture and sequence megabase-sized portions of a mutant genome. Together, these two methods provide a rapid and cost-effective approach for positional cloning of C. elegans mutant loci, and are also applicable to other genetic model systems. PMID:21900274

O'Rourke, Sean M.; Yochem, John; Connolly, Amy A.; Price, Meredith H.; Carter, Luke; Lowry, Joshua B.; Turnbull, Douglas W.; Kamps-Hughes, Nick; Stiffler, Nicholas; Miller, Michael R.; Johnson, Eric A.; Bowerman, Bruce



Kentucky Mine Mapping Information System  

NSDL National Science Digital Library

This Geographic Information System (GIS) allows users to view and download all known mined out areas (polygons) digitized by the Kentucky Revenue Cabinet; individual reports from the Mines and Minerals database; and scanned images of engineering drawings (mine maps) submitted since January 2002, plus selected earlier maps. The maps can be viewed directly online with the use of an interactive viewer, or they can be downloaded from an FTP site. The interactive viewer shows all scanned maps and oil/gas wells (where available) for a selected area, overlain on a base map or imagery.


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

PubMed Central

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

Boulos, Maged N Kamel; Burden, David



Mars Exploration Rover (MER) 2003 Data Maps  

NSDL National Science Digital Library

This NASA website provides links to maps for all potential Mars Exploration Rover landing sites. The site includes maps showing MOC (Mars Orbiter Camera )/MOLA (Mars Orbiting Laser Altimeter) images, TES (Thermal Emission Spectrometer) thermal inertia, Geology/MOLA, TES mineral abundances (basalt, andesite, hematite), vertical roughness, and data from the Viking Infrared Thermal Mapper. These maps can also be viewed using the interactive map and data browser.

Marsoweb; Administration, National A.


A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities  

PubMed Central

Improved efforts are necessary to define the functional product of cancer mutations currently being revealed through large-scale sequencing efforts. Using genome-scale pooled shRNA screening technology, we mapped negative genetic interactions across a set of isogenic cancer cell lines and confirmed hundreds of these interactions in orthogonal co-culture competition assays to generate a high-confidence genetic interaction network of differentially essential or differential essentiality (DiE) genes. The network uncovered examples of conserved genetic interactions, densely connected functional modules derived from comparative genomics with model systems data, functions for uncharacterized genes in the human genome and targetable vulnerabilities. Finally, we demonstrate a general applicability of DiE gene signatures in determining genetic dependencies of other non-isogenic cancer cell lines. For example, the PTEN?/? DiE genes reveal a signature that can preferentially classify PTEN-dependent genotypes across a series of non-isogenic cell lines derived from the breast, pancreas and ovarian cancers. Our reference network suggests that many cancer vulnerabilities remain to be discovered through systematic derivation of a network of differentially essential genes in an isogenic cancer cell model. PMID:24104479

Vizeacoumar, Franco J; Arnold, Roland; Vizeacoumar, Frederick S; Chandrashekhar, Megha; Buzina, Alla; Young, Jordan T F; Kwan, Julian H M; Sayad, Azin; Mero, Patricia; Lawo, Steffen; Tanaka, Hiromasa; Brown, Kevin R; Baryshnikova, Anastasia; Mak, Anthony B; Fedyshyn, Yaroslav; Wang, Yadong; Brito, Glauber C; Kasimer, Dahlia; Makhnevych, Taras; Ketela, Troy; Datti, Alessandro; Babu, Mohan; Emili, Andrew; Pelletier, Laurence; Wrana, Jeff; Wainberg, Zev; Kim, Philip M; Rottapel, Robert; O'Brien, Catherine A; Andrews, Brenda; Boone, Charles; Moffat, Jason



The Importance of Synchronous Interaction for Student Satisfaction with Course Web Sites  

ERIC Educational Resources Information Center

As more affordable synchronous communications are becoming available, the use of synchronous interactions has not been noted in course Web sites as often as asynchronous communications. Previous research indicated that the integration of synchronous tools into course Web sites has made a positive impact on students. While most of the previous…

Cao, Qidong; Griffin, Thomas E.; Bai, Xue



Regulatory Interactions between Ubiquinol Oxidation and Ubiquinone Reduction Sites in the Dimeric Cytochrome  

E-print Network

transports one electron from the QH2 oxidation site (center P) in cytochrome b to cytochrome c1 between the cytochrome b subunits would favor the formation of SQ with oxidized bH heme at each center NRegulatory Interactions between Ubiquinol Oxidation and Ubiquinone Reduction Sites in the Dimeric

Trumpower, Bernard L.


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

ERIC Educational Resources Information Center

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…

Braun, Linda W.



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

SciTech Connect

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.

Yow, J.L. Jr.



Using a sentiment map for visualizing credibility of news sites on the web  

Microsoft Academic Search

We have developed a visualizing news system that shows the trend of the news site on the Web for credibility. If users know the trend of the news site, users can evaluate the credibility of each news topic. This system detects and uses sentiments of each news article to resolve the trend of Web site. The trend of Web sites

Yukiko Kawai; Yusuke Fujita; Tadahiko Kumamoto; Jianwei Jianwei; Katsumi Tanaka




SciTech Connect

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.

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



Homology Inference of Protein-Protein Interactions via Conserved Binding Sites  

Microsoft Academic Search

The coverage and reliability of protein-protein interactions determined by high-throughput experiments still needs to be improved, especially for higher organisms, therefore the question persists, how interactions can be verified and predicted by computational approaches using available data on protein structural complexes. Recently we developed an approach called IBIS (Inferred Biomolecular Interaction Server) to predict and annotate protein-protein binding sites and

Manoj Tyagi; Ratna R. Thangudu; Dachuan Zhang; Stephen H. Bryant; Thomas Madej; Anna R. Panchenko



A simple thermal mapping method for seasonal spatial patterns of groundwater-surface water interaction  

NASA Astrophysics Data System (ADS)

SummaryA simple thermal mapping method for simulating seasonal and spatial patterns of groundwater-surface water interaction is developed and tested for a segment of the Aa River, Belgium. Spatially distributed temperature profiles in the hyporheic zone of the river are measured in winter and summer seasons of three consecutive years. Inverse modeling of the one-dimensional heat transport equation is applied to estimate vertical advective fluxes using the numerical STRIVE model and an analytical model. Results of the study show that seasonal flux estimates for summer and winter can be derived with a minimum data input and simulation effort. The estimated fluxes are analyzed via non-parametric statistical tests, while spatial interpolation techniques are used to generate maps of distributed flux exchange. The estimated seepage is compared with volumetric flux obtained from piezometer measurements and output of a groundwater model. The thermal method shows higher discharge rates in winter and that the relative contribution of exfiltration to the river discharge is higher in summer. A higher flux and a more heterogeneous flow pattern are observed in the upper reach of the river compared to the lower reach. This spatial difference shows the importance of the local geomorphology and to a lesser extent the hydrogeologic setting on hyporheic flux exchange in the river. A significantly higher flux is noted on the banks than in the center of the river, which is driven by the relatively high hydraulic conductivity of the river banks. It is concluded that bank flow in groundwater-surface water interaction deserves more attention. The main channel of the Aa River alone accounts for about 15% of the total river discharge at its outlet. As the developed thermal method is cost-effective, simple and fast, it is recommended for use in identifying zones of interest in initial stages of field investigations of groundwater-surface water interaction.

Anibas, Christian; Buis, Kerst; Verhoeven, Ronny; Meire, Patrick; Batelaan, Okke



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

USGS Publications Warehouse

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.

Wilhelms, Don E.



Accurate Thermodynamics for Short-Ranged Truncations of Coulomb Interactions in Site-Site Molecular Models  

E-print Network

Coulomb interactions are present in a wide variety of all-atom force fields. Spherical truncations of these interactions permit fast simulations but are problematic due to their incorrect thermodynamics. Herein we demonstrate that simple analytical corrections for the thermodynamics of uniform truncated systems are possible. In particular results for the SPC/E water model treated with spherically-truncated Coulomb interactions suggested by local molecular field theory [Proc. Nat. Acad. Sci. USA 105, 19136 (2008)] are presented. We extend results developed by Chandler [J. Chem. Phys. 65, 2925 (1976)] so that we may treat the thermodynamics of mixtures of flexible charged and uncharged molecules simulated with spherical truncations. We show that the energy and pressure of spherically-truncated bulk SPC/E water are easily corrected using exact second-moment-like conditions on long-ranged structure. Furthermore, applying the pressure correction as an external pressure removes the density errors observed by other research groups in NPT simulations of spherically-truncated bulk species.

Jocelyn M. Rodgers; John D. Weeks



Interaction of antiparallel microtubules in the phragmoplast is mediated by the microtubule-associated protein MAP65-3 in Arabidopsis.  


In plant cells, microtubules (MTs) in the cytokinetic apparatus phragmoplast exhibit an antiparallel array and transport Golgi-derived vesicles toward MT plus ends located at or near the division site. By transmission electron microscopy, we observed that certain antiparallel phragmoplast MTs overlapped and were bridged by electron-dense materials in Arabidopsis thaliana. Robust MT polymerization, reported by fluorescently tagged End Binding1c (EB1c), took place in the phragmoplast midline. The engagement of antiparallel MTs in the central spindle and phragmoplast was largely abolished in mutant cells lacking the MT-associated protein, MAP65-3. We found that endogenous MAP65-3 was selectively detected on the middle segments of the central spindle MTs at late anaphase. When MTs exhibited a bipolar appearance with their plus ends placed in the middle, MAP65-3 exclusively decorated the phragmoplast midline. A bacterially expressed MAP65-3 protein was able to establish the interdigitation of MTs in vitro. MAP65-3 interacted with antiparallel microtubules before motor Kinesin-12 did during the establishment of the phragmoplast MT array. Thus, MAP65-3 selectively cross-linked interdigitating MTs (IMTs) to allow antiparallel MTs to be closely engaged in the phragmoplast. Although the presence of IMTs was not essential for vesicle trafficking, they were required for the phragmoplast-specific motors Kinesin-12 and Phragmoplast-Associated Kinesin-Related Protein2 to interact with MT plus ends. In conclusion, we suggest that the phragmoplast contains IMTs and highly dynamic noninterdigitating MTs, which work in concert to bring about cytokinesis in plant cells. PMID:21873565

Ho, Chin-Min Kimmy; Hotta, Takashi; Guo, Fengli; Roberson, Robert W; Lee, Yuh-Ru Julie; Liu, Bo



Automated analysis of viral integration sites in gene therapy research using the SeqMap web resource.  


Research in gene therapy involving genome-integrating vectors now often includes analysis of vector integration sites across the genome using methods such as ligation-mediated PCR (LM-PCR) or linear amplification-mediated PCR (LAM-PCR). To help researchers analyze these sites and the functions of nearby genes, we have developed SeqMap ( a secure, web-based comprehensive vector integration site management tool that automatically analyzes and annotates large numbers of vector integration sites derived from LM-PCR experiments in human and model organisms upon a common genome database. We believe the use of this resource will enable better reproducibility and understanding of this important data. PMID:18580967

Peters, B; Dirscherl, S; Dantzer, J; Nowacki, J; Cross, S; Li, X; Cornetta, K; Dinauer, M C; Mooney, S D



Body composition and gene expression QTL mapping in mice reveals imprinting and interaction effects  

PubMed Central

Background Shifts in body composition, such as accumulation of body fat, can be a symptom of many chronic human diseases; hence, efforts have been made to investigate the genetic mechanisms that underlie body composition. For example, a few quantitative trait loci (QTL) have been discovered using genome-wide association studies, which will eventually lead to the discovery of causal mutations that are associated with tissue traits. Although some body composition QTL have been identified in mice, limited research has been focused on the imprinting and interaction effects that are involved in these traits. Previously, we found that Myostatin genotype, reciprocal cross, and sex interacted with numerous chromosomal regions to affect growth traits. Results Here, we report on the identification of muscle, adipose, and morphometric phenotypic QTL (pQTL), translation and transcription QTL (tQTL) and expression QTL (eQTL) by applying a QTL model with additive, dominance, imprinting, and interaction effects. Using an F2 population of 1000 mice derived from the Myostatin-null C57BL/6 and M16i mouse lines, six imprinted pQTL were discovered on chromosomes 6, 9, 10, 11, and 18. We also identified two IGF1 and two Atp2a2 eQTL, which could be important trans-regulatory elements. pQTL, tQTL and eQTL that interacted with Myostatin, reciprocal cross, and sex were detected as well. Combining with the additive and dominance effect, these variants accounted for a large amount of phenotypic variation in this study. Conclusions Our study indicates that both imprinting and interaction effects are important components of the genetic model of body composition traits. Furthermore, the integration of eQTL and traditional QTL mapping may help to explain more phenotypic variation than either alone, thereby uncovering more molecular details of how tissue traits are regulated. PMID:24165562



A study of ternary element site substitution in Ni{sub 3}Al using pseudopotential orbital radii based structure maps  

SciTech Connect

It is well known that ternary alloying additions are usually added in small quantities to structural intermetallics with a view to optimize their structural, physical, chemical and mechanical properties. Since structural intermetallics are highly ordered alloys, the added ternary solutes often reveal a preponderant tendency to substitute preferentially one of the sublattices. A knowledge of the basic factors governing the preferential site substitution behavior is useful in elucidating the role of ternary additions in controlling the materials properties. In this paper, the authors apply the concept of structure maps for explaining the site substitution behavior of ternary alloying additions in Ni{sub 3}Al.

Raju, S.; Mohandas, E.; Raghunathan, V.S. [Indira Gandhi Centre for Atomic Research, Kalpakkam (India). Metallurgy Div.] [Indira Gandhi Centre for Atomic Research, Kalpakkam (India). Metallurgy Div.



Using 15N-Ammonium to Characterise and Map Potassium Binding Sites in Proteins by NMR Spectroscopy  

PubMed Central

A variety of enzymes are activated by the binding of potassium ions. The potassium binding sites of these enzymes are very specific, but ammonium ions can often replace potassium ions in vitro because of their similar ionic radii. In these cases, ammonium can be used as a proxy for potassium to characterise potassium binding sites in enzymes: the 1H,15N spin-pair of enzyme-bound 15NH4+ can be probed by 15N-edited heteronuclear NMR experiments. Here, we demonstrate the use of NMR spectroscopy to characterise binding of ammonium ions to two different enzymes: human histone deacetylase 8 (HDAC8), which is activated allosterically by potassium, and the bacterial Hsp70 homologue DnaK, for which potassium is an integral part of the active site. Ammonium activates both enzymes in a similar way to potassium, thus supporting this non-invasive approach. Furthermore, we present an approach to map the observed binding site onto the structure of HDAC8. Our method for mapping the binding site is general and does not require chemical shift assignment of the enzyme resonances. PMID:24520048

Werbeck, Nicolas D; Kirkpatrick, John; Reinstein, Jochen; Hansen, D Flemming



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

PubMed Central

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



Geologic mapping and characterization of Gale Crater and implications for its potential as a Mars Science Laboratory landing site  

NASA Astrophysics Data System (ADS)

We mapped the geomorphologic units of the Gale crater central mound and the proposed Mars Science Laboratory landing site, developed an inferred stratigraphy, and assessed hypotheses for the origin of the mound. Key findings include: sinuous inverted channels in the landing ellipse, cemented fractures in the lower mound, and possible cross-beds in the upper mound unit suggesting an aeolian origin for the upper mound.

Anderson, Ryan B.; Bell, James F., III


Modular Robotics for Delivering On-Site contamination Sensors and Mapping Systems to Difficult-to-Access Locations  

SciTech Connect

Presently, characterization operations are scheduled for thousands of facilities and pieces of equipment throughout DOE sites, each of which requires manual surveying with handheld instruments and manual record keeping. Such work, particularly in difficult-to-access-areas, results in significant amounts of worker exposure, long timelines and additional secondary waste generation. Therefore, a distinct need exists for remote tools that can quickly deploy sensors and automated contamination mapping systems into these areas.

Geisinger, Joseph



Mapping Density Response in Maize: A Direct Approach for Testing Genotype and Treatment Interactions  

PubMed Central

Maize yield improvement has been strongly linked to improvements in stress tolerance, particularly to increased interplant competition. As a result, modern hybrids are able to produce kernels at high plant population densities. Identification of the genetic factors responsible for density response in maize requires direct testing of interactions between genetic effects and density and evaluation of that response in multiple traits. In this article we take a broad view of the problem and use a general approach based upon mixed models to analyze data from eight segmental inbred lines in a B73 background and their crosses to the unrelated parent Mo17 (hybrids). We directly test for the interaction between treatment effects and genetic effects instead of the commonly used overlaying of results on a common map. Additionally, we demonstrate one way to handle heteroscedasticity of variances common in stress responses. We find that some SILs are consistently different from the recurrent parent regardless of the density, while others differ from the recurrent parent in one density level but not in the other. Thus, we find positive evidence for both main effects and interaction between genetic loci and density in cases where the approach of overlapping results fails to find significant results. Furthermore, our study clearly identifies segments that respond differently to density depending upon the inbreeding level (inbred/hybrid). PMID:16489238

Gonzalo, Martin; Vyn, Tony J.; Holland, James B.; McIntyre, Lauren M.



Mapping Ultra-weak Protein-Protein Interactions between Heme Transporters of Staphylococcus aureus  

PubMed Central

Iron is an essential nutrient for the proliferation of Staphylococcus aureus during bacterial infections. The iron-regulated surface determinant (Isd) system of S. aureus transports and metabolizes iron porphyrin (heme) captured from the host organism. Transportation of heme across the thick cell wall of this bacterium requires multiple relay points. The mechanism by which heme is physically transferred between Isd transporters is largely unknown because of the transient nature of the interactions involved. Herein, we show that the IsdC transporter not only passes heme ligand to another class of Isd transporter, as previously known, but can also perform self-transfer reactions. IsdA shows a similar ability. A genetically encoded photoreactive probe was used to survey the regions of IsdC involved in self-dimerization. We propose an updated model that explicitly considers self-transfer reactions to explain heme delivery across the cell wall. An analogous photo-cross-linking strategy was employed to map transient interactions between IsdC and IsdE transporters. These experiments identified a key structural element involved in the rapid and specific transfer of heme from IsdC to IsdE. The resulting structural model was validated with a chimeric version of the homologous transporter IsdA. Overall, our results show that the ultra-weak interactions between Isd transporters are governed by bona fide protein structural motifs. PMID:22427659

Abe, Ryota; Caaveiro, Jose M. M.; Kozuka-Hata, Hiroko; Oyama, Masaaki; Tsumoto, Kouhei



Large-scale mapping of transposable element insertion sites using digital encoding of sample identity.  


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

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



Ground Sites: Mapping of Solar Wind KHI Periodicities and the Subsequent Generation of Compressional/Breathing Pc5 Modes  

NASA Astrophysics Data System (ADS)

Herein we present the on the impact of multiple high speed solar streams, stemming from co-rotating interaction regions, on the Earth's magnetospheric system as observed during the summer of 2008. Utilizing ACE, GOES, and ground-based fluxgate magnetometer data, we map ULF activity in the the solar wind to the ground. These ULF signatures are shown to be highly correlated and exhibit coupled spectra structures. The generation of compressional/breathing Pc5 modes in the magnetosphere is discussed.

Teti, A. J.; Gerrard, A. J.; Olsztyn, J.; Dupiano, P.; Bhattacharya, Y.; Jeffer, G.; Urban, K. D.; Lanzerotti, L. J.; Weatherwax, A. T.



An improved interolog mapping-based computational prediction of protein-protein interactions with increased network coverage.  


Automated and efficient methods that map ortholog interactions from several organisms and public databases (pDB) are needed to identify new interactions in an organism of interest (interolog mapping). When computational methods are applied to predict interactions, it is important that these methods be validated and their efficiency proven. In this study, we compare six Blast+ metrics over three datasets to identify the best metric for protein-protein interaction predictions. Using Blast+ to align the protein pairs, the ortholog interactions from DIP were mapped to String, Intact and Psibase pDBs. For each interaction mapped to each pDBs, we retrieved the alignment score, e-value, bitscore, similarity, identity and coverage. We evaluated these Blast+ values, and combinations thereof, with the Receiver Operating Characteristic (ROC) curves and computed the Area Under Curve (AUC). To validate these predictions, we used a subset of the Database of Interacting Proteins (DIP) composed of experimental interactions curated by the International Molecular Exchange (IMEx). The cut-off point for each metric/pDB was computed aiming to identify the best one that separates the true and false predicted interactions. In contrast to other methods that only compute the first Blast hit, we considered the first 20 hits, thus increasing the number of predicted interaction pairs. In addition, we identified the contribution of each individual pDB, as well as their combined contribution to the prediction. The best metric had an AUC of 0.96 for a single pDB and AUC of 0.93 for combined pDBs. Compared to other studies, with a cut-off point of 0.70 representing a specificity of 0.95 and a sensitivity of 0.90 for individual pDB, our method efficiently predicts protein-protein interactions. PMID:25209055

Folador, Edson Luiz; Hassan, Syed Shah; Lemke, Ney; Barh, Debmalya; Silva, Artur; Ferreira, Rafaela Salgado; Azevedo, Vasco



Reference map technique for finite-strain elasticity and fluid-solid interaction  

NASA Astrophysics Data System (ADS)

The reference map, defined as the inverse motion function, is utilized in an Eulerian-frame representation of continuum solid mechanics, leading to a simple, explicit finite-difference method for solids undergoing finite deformations. We investigate the accuracy and applicability of the technique for a range of finite-strain elasticity laws under various geometries and loadings. Capacity to model dynamic, static, and quasi-static conditions is shown. Specifications of the approach are demonstrated for handling irregularly shaped and/or moving boundaries, as well as shock solutions. The technique is also integrated within a fluid-solid framework using a level-set to discern phases and using a standard explicit fluid solver for the fluid phases. We employ a sharp-interface method to institute the interfacial conditions, and the resulting scheme is shown to efficiently capture fluid-solid interaction solutions in several examples.

Kamrin, Ken; Rycroft, Chris H.; Nave, Jean-Christophe


274 - Interactive High-Resolution Digital Brain Atlases and Virtual Microscopy.  

PubMed 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

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



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

USGS Publications Warehouse

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.

Pouch, G.W.



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

NASA Astrophysics Data System (ADS)

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

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


Cytogenomic mapping and bioinformatic mining reveal interacting brain expressed genes for intellectual disability  

PubMed Central

Background Microarray analysis has been used as the first-tier genetic testing to detect chromosomal imbalances and copy number variants (CNVs) for pediatric patients with intellectual and developmental disabilities (ID/DD). To further investigate the candidate genes and underlying dosage-sensitive mechanisms related to ID, cytogenomic mapping of critical regions and bioinformatic mining of candidate brain-expressed genes (BEGs) and their functional interactions were performed. Critical regions of chromosomal imbalances and pathogenic CNVs were mapped by subtracting known benign CNVs from the Databases of Genomic Variants (DGV) and extracting smallest overlap regions with cases from DatabasE of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources (DECIPHER). BEGs from these critical regions were revealed by functional annotation using Database for Annotation, Visualization, and Integrated Discovery (DAVID) and by tissue expression pattern from Uniprot. Cross-region interrelations and functional networks of the BEGs were analyzed using Gene Relationships Across Implicated Loci (GRAIL) and Ingenuity Pathway Analysis (IPA). Results Of the 1,354 patients analyzed by oligonucleotide array comparative genomic hybridization (aCGH), pathogenic abnormalities were detected in 176 patients including genomic disorders in 66 patients (37.5%), subtelomeric rearrangements in 45 patients (25.6%), interstitial imbalances in 33 patients (18.8%), chromosomal structural rearrangements in 17 patients (9.7%) and aneuploidies in 15 patients (8.5%). Subtractive and extractive mapping defined 82 disjointed critical regions from the detected abnormalities. A total of 461 BEGs was generated from 73 disjointed critical regions. Enrichment of central nervous system specific genes in these regions was noted. The number of BEGs increased with the size of the regions. A list of 108 candidate BEGs with significant cross region interrelation was identified by GRAIL and five significant gene networks involving cell cycle, cell-to-cell signaling, cellular assembly, cell morphology, and gene expression regulations were denoted by IPA. Conclusions These results characterized ID related cross-region interrelations and multiple networks of candidate BEGs from the detected genomic imbalances. Further experimental study of these BEGs and their interactions will lead to a better understanding of dosage-sensitive mechanisms and modifying effects of human mental development. PMID:24410907



Superstable cycles for antiferromagnetic Q-state Potts and three-site interaction Ising models on recursive lattices  

NASA Astrophysics Data System (ADS)

We consider the superstable cycles of the Q-state Potts (QSP) and the three-site interaction antiferromagnetic Ising (TSAI) models on recursive lattices. The rational mappings describing the models’ statistical properties are obtained via the recurrence relation technique. We provide analytical solutions for the superstable cycles of the second order for both models. A particular attention is devoted to the period three window. Here we present an exact result for the third order superstable orbit for the QSP and a numerical solution for the TSAI model. Additionally, we point out a non-trivial connection between bifurcations and superstability: in some regions of parameters a superstable cycle is not followed by a doubling bifurcation. Furthermore, we use symbolic dynamics to understand the changes taking place at points of superstability and to distinguish areas between two consecutive superstable orbits.

Ananikian, N.; Artuso, R.; Chakhmakhchyan, L.



Mutated primer binding sites interacting with different tRNAs allow efficient murine leukemia virus replication.  

PubMed Central

Two Akv murine leukemia virus-based retroviral vectors with primer binding sites matching tRNA(Gln-1) and tRNA(Lys-3) were constructed. The transduction efficiency of these mutated vectors was found to be comparable to that of a vector carrying the wild-type primer binding site matching tRNA(Pro). Polymerase chain reaction amplification and sequence analysis of transduced proviruses confirmed the transfer of vectors with mutated primer binding sites and further showed that tRNA(Gln-2) may act efficiently in conjunction with the tRNA(Gln-1) primer binding site. We conclude that murine leukemia virus can replicate by using various tRNA molecules as primers and propose primer binding site-tRNA primer interactions to be of major importance for tRNA primer selection. However, efficient primer selection does not require perfect Watson-Crick base pairing at all 18 positions of the primer binding site. PMID:7693968

Lund, A H; Duch, M; Lovmand, J; Jørgensen, P; Pedersen, F S



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

USGS Publications Warehouse

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)

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



Near-field spatial mapping of strongly interacting multiple plasmonic infrared antennas.  


Near-field dipolar plasmon interactions of multiple infrared antenna structures in the strong coupling limit are studied using scattering-type scanning near-field optical microscope (s-SNOM) and theoretical finite-difference time-domain (FDTD) calculations. We monitor in real-space the evolution of plasmon dipolar mode of a stationary antenna structure as multiple resonantly matched dipolar plasmon particles are closely approaching it. Interparticle separation, length and polarization dependent studies show that the cross geometry structure favors strong interparticle charge-charge, dipole-dipole and charge-dipole Coulomb interactions in the nanometer scale gap region, which results in strong field enhancement in cross-bowties and further allows these structures to be used as polarization filters. The nanoscale local field amplitude and phase maps show that due to strong interparticle Coulomb coupling, cross-bowtie structures redistribute and highly enhance the out-of-plane (perpendicular to the plane of the sample) plasmon near-field component at the gap region relative to ordinary bowties. PMID:24097054

Grefe, Sarah E; Leiva, Daan; Mastel, Stefan; Dhuey, Scott D; Cabrini, Stefano; Schuck, P James; Abate, Yohannes



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

SciTech Connect

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.




Bayesian model choice and search strategies for mapping interacting quantitative trait Loci.  

PubMed Central

Most complex traits of animals, plants, and humans are influenced by multiple genetic and environmental factors. Interactions among multiple genes play fundamental roles in the genetic control and evolution of complex traits. Statistical modeling of interaction effects in quantitative trait loci (QTL) analysis must accommodate a very large number of potential genetic effects, which presents a major challenge to determining the genetic model with respect to the number of QTL, their positions, and their genetic effects. In this study, we use the methodology of Bayesian model and variable selection to develop strategies for identifying multiple QTL with complex epistatic patterns in experimental designs with two segregating genotypes. Specifically, we develop a reversible jump Markov chain Monte Carlo algorithm to determine the number of QTL and to select main and epistatic effects. With the proposed method, we can jointly infer the genetic model of a complex trait and the associated genetic parameters, including the number, positions, and main and epistatic effects of the identified QTL. Our method can map a large number of QTL with any combination of main and epistatic effects. Utility and flexibility of the method are demonstrated using both simulated data and a real data set. Sensitivity of posterior inference to prior specifications of the number and genetic effects of QTL is investigated. PMID:14573494

Yi, Nengjun; Xu, Shizhong; Allison, David B




EPA Science Inventory

This report considers several issues related to the preparation of isopleth maps for the display of spatial patterns of wet deposition. The valid sample criteria and data completeness rating used in the data summarization process are described. The data interpolation technique, k...


Drought mapping using Geoinformation technology for some sites in the Iraqi Kurdistan region  

Microsoft Academic Search

Iraq has suffered severely from drought in recent years and the year 2008 was the driest, particularly in the Iraqi Kurdistan region. This study incorporated Geoinformation technology into mapping the drought that severely affected the Kurdistan region in the years 2007–2008. Geoinformation technology provides support in the theories, methods and techniques for building, and development of Digital Earth aspect. Five

Ayad Mohammed Fadhil



Targeting the Tcf4 G13ANDE17 binding site to selectively disrupt ?-catenin/T-cell factor protein-protein interactions.  


Selective disruption of protein-protein interactions by small molecules is important for probing the structure and dynamic aspects of cellular network. It can also provide new therapeutic targets. ?-Catenin of the canonical Wnt signaling pathway uses the same positively charged groove to bind with T-cell factor (Tcf), cadherin, and adenomatous polysis coli (APC). The extravagant formation of ?-catenin/Tcf interactions drives the initiation and progression of many cancers and fibroses, while ?-catenin/cadherin and ?-catenin/APC interactions are essential for cell-cell adhesion and ?-catenin degradation. In this study, a selective binding site that can differentiate ?-catenin/Tcf, ?-catenin/cadherin, and ?-catenin/APC interactions was identified by alanine scanning and biochemical assays. A new peptidomimetic strategy that incorporates SiteMap and multiple-copy simultaneous search was used to design selective small-molecule inhibitors for ?-catenin/Tcf interactions. A potent inhibitor was discovered to bind with ?-catenin and completely disrupt ?-catenin/Tcf interactions. It also exhibits dual selectivity for ?-catenin/Tcf over ?-catenin/cadherin and ?-catenin/APC interactions in both biochemical and cell-based assays. This study provides a proof of concept for designing selective inhibitors for ?-catenin/Tcf interactions. PMID:24191653

Huang, Zheng; Zhang, Min; Burton, Shawn D; Katsakhyan, Levon N; Ji, Haitao



High Resolution Multibeam Sonar Mapping of the Lost City Hydrothermal Site with the Autonomous Benthic Explorer  

Microsoft Academic Search

The Autonomous Benthic Explorer (ABE) of the Woods Hole Oceanographic Institution (WHOI) collected high-resolution multibeam sonar bathymetry of the Atlantis Massif and the Lost City vent site in May 2003. A Simrad Mesotech SM 2000 multibeam sonar has been fully integrated into the vehicle for this purpose. The challenging topography of the Lost City site demanded careful AUV survey planning,

M. V. Jakuba; D. R. Yoerger; A. M. Bradley; D. S. Kelley; J. A. Karson



The use of interactive graphical maps for browsing medical/health Internet information resources  

PubMed Central

As online information portals accumulate metadata descriptions of Web resources, it becomes necessary to develop effective ways for visualising and navigating the resultant huge metadata repositories as well as the different semantic relationships and attributes of described Web resources. Graphical maps provide a good method to visualise, understand and navigate a world that is too large and complex to be seen directly like the Web. Several examples of maps designed as a navigational aid for Web resources are presented in this review with an emphasis on maps of medical and health-related resources. The latter include HealthCyberMap maps , which can be classified as conceptual information space maps, and the very abstract and geometric Visual Net maps of PubMed (for demos). Information resources can be also organised and navigated based on their geographic attributes. Some of the maps presented in this review use a Kohonen Self-Organising Map algorithm, and only HealthCyberMap uses a Geographic Information System to classify Web resource data and render the maps. Maps based on familiar metaphors taken from users' everyday life are much easier to understand. Associative and pictorial map icons that enable instant recognition and comprehension are preferred to geometric ones and are key to successful maps for browsing medical/health Internet information resources. PMID:12556244

Boulos, Maged N Kamel



Mapping of immunogenic and protein-interacting regions at the surface of the seven-bladed ?-propeller domain of the HIV-1 cellular interactor EED  

PubMed Central

Background The human EED protein, a member of the superfamily of Polycomb group proteins, is involved in multiple cellular protein complexes. Its C-terminal domain, which is common to the four EED isoforms, contains seven repeats of a canonical WD-40 motif. EED is an interactor of three HIV-1 proteins, matrix (MA), integrase (IN) and Nef. An antiviral activity has been found to be associated with isoforms EED3 and EED4 at the late stage of HIV-1 replication, due to a negative effect on virus assembly and genomic RNA packaging. The aim of the present study was to determine the regions of the EED C-terminal core domain which were accessible and available to protein interactions, using three-dimensional (3D) protein homology modelling with a WD-40 protein of known structure, and epitope mapping of anti-EED antibodies. Results Our data suggested that the C-terminal domain of EED was folded as a seven-bladed ?-propeller protein. During the completion of our work, crystallographic data of EED became available from co-crystals of the EED C-terminal core with the N-terminal domain of its cellular partner EZH2. Our 3D-model was in good congruence with the refined structural model determined from crystallographic data, except for a unique ?-helix in the fourth ?-blade. More importantly, the position of flexible loops and accessible ?-strands on the ?-propeller was consistent with our mapping of immunogenic epitopes and sites of interaction with HIV-1 MA and IN. Certain immunoreactive regions were found to overlap with the EZH2, MA and IN binding sites, confirming their accessibility and reactivity at the surface of EED. Crystal structure of EED showed that the two discrete regions of interaction with MA and IN did not overlap with each other, nor with the EZH2 binding pocket, but were contiguous, and formed a continuous binding groove running along the lateral face of the ?-propeller. Conclusion Identification of antibody-, MA-, IN- and EZH2-binding sites at the surface of the EED isoform 3 provided a global picture of the immunogenic and protein-protein interacting regions in the EED C-terminal domain, organized as a seven-bladed ?-propeller protein. Mapping of the HIV-1 MA and IN binding sites on the 3D-model of EED core predicted that EED-bound MA and IN ligands would be in close vicinity at the surface of the ?-propeller, and that the occurrence of a ternary complex MA-EED-IN would be possible. PMID:18302803

Rakotobe, Dina; Violot, Sebastien; Hong, Saw See; Gouet, Patrice; Boulanger, Pierre



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

USGS Publications Warehouse

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.

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



Three-dimensional mapping of equiprobable hydrostratigraphic units at the Frenchman Flat Corrective Action Unit, Nevada Test Site  

SciTech Connect

Geological and geophysical data are used with the sequential indicator simulation algorithm of Gomez-Hernandez and Srivastava to produce multiple, equiprobable, three-dimensional maps of informal hydrostratigraphic units at the Frenchman Flat Corrective Action Unit, Nevada Test Site. The upper 50 percent of the Tertiary volcanic lithostratigraphic column comprises the study volume. Semivariograms are modeled from indicator-transformed geophysical tool signals. Each equiprobable study volume is subdivided into discrete classes using the ISIM3D implementation of the sequential indicator simulation algorithm. Hydraulic conductivity is assigned within each class using the sequential Gaussian simulation method of Deutsch and Journel. The resulting maps show the contiguity of high and low hydraulic conductivity regions.

Shirley, C.; Pohlmann, K.; Andricevic, R.



COREMAP: Graphical user interface for displaying reactor core data in an interactive hexagon map  

SciTech Connect

COREMAP is a Graphical User Interface (GUI) designed to assist users read and check reactor core data from multidimensional neutronic simulation models in color and/or as text in an interactive 2D planar grid of hexagonal subassemblies. COREMAP is a complete GEODST/RUNDESC viewing tool which enables the user to access multi data set files (e.g. planes, moments, energy groups ,... ) and display up to two data sets simultaneously, one as color and the other as text. The user (1) controls color scale characteristics such as type (linear or logarithmic) and range limits, (2) controls the text display based upon conditional statements on data spelling, and value. (3) chooses zoom features such as core map size, number of rings and surrounding subassemblies, and (4) specifies the data selection for supplied popup subwindows which display a selection of data currently off-screen for a selected cell, as a list of data and/or as a graph. COREMAP includes a RUNDESC file editing tool which creates ``proposed`` Run-description files by point and click revisions to subassembly assignments in an existing EBRII Run-description file. COREMAP includes a fully automated printing option which creates high quality PostScript color or greyscale images of the core map independent of the monitor used, e.g. color prints can be generated with a session from a color or monochrome monitor. The automated PostScript output is an alternative to the xgrabsc based printing option. COREMAP includes a plotting option which creates graphs related to a selected cell. The user specifies the X and Y coordinates types (planes, moment, group, flux ,... ) and a parameter, P, when displaying several curves for the specified (X, Y) pair COREMAP supports hexagonal geometry reactor core configurations specified by: the GEODST file and binary Standard Interface Files and the RUNDESC ordering.

Muscat, F.L.; Derstine, K.L.



Concordance of experimentally mapped or predicted Z-DNA sites with positions of selected alternating purine-pyrimidine tracts.  

PubMed Central

The recent electronmicroscopic and biochemical mapping of Z-DNA sites in phi X174, SV40, pBR322 and PM2 DNAs has been used to determine two sets of criteria for identification of potential Z-DNA sequences in natural DNA genomes. The prediction of potential Z-DNA tracts and corresponding statistical analysis of their occurrence have been made on a sample of 14 DNA genomes. Alternating purine and pyrimidine tracts longer than 5 base pairs in length and their clusters (quasi alternating fragments) in the 14 genomes studied are under-represented compared to the expectation from corresponding random sequences. The fragments [d(G X C)]n and [d(C X G)]n (n greater than or equal to 3) in general do not occur in circular DNA genomes and are under-represented in the linear DNAs of phages lambda and T7, whereas in linear genomes of adenoviruses they are strongly over-represented. With minor exceptions, potential Z-DNA sites are also under-represented compared to random sequences. In the 14 genomes studied, predicted Z-DNA tracts occur in non-coding as well as in protein coding regions. The predicted Z-DNA sites in phi X174, SV40, pBR322 and PM2 correspond well with those mapped experimentally. A complete listing together with a compact graphical representation of alternating purine-pyrimidine fragments and their Z-forming potential are presented. PMID:4000942

Konopka, A K; Reiter, J; Jung, M; Zarling, D A; Jovin, T M



Antibody-Array Interaction Mapping, a New Method to Detect Protein Complexes Applied to the Discovery and Study of Serum Amyloid P Interactions with Kininogen in Human Plasma*  

PubMed Central

Protein-protein interactions are fundamentally important in biological processes, but the existing analytical tools have limited ability to sensitively and precisely measure the dynamic composition of protein complexes in biological samples. We report here the development of antibody-array interaction mapping (AAIM) to address that need. We used AAIM to probe interactions among a set of 48 proteins in serum and found several known interactions as well potentially novel interactions, including multiprotein clusters of interactions. A novel interaction initially identified between the innate immune system protein C-reactive protein and the inflammatory protein kininogen (KNG) was confirmed in subsequent experiments to involve serum amyloid P instead of its highly related family member, C-reactive protein. AAIM was used in a variety of formats to further study this interaction. In vitro studies confirmed the ability of the purified proteins to interact and revealed a zinc dependence of the interaction. Studies using plasma samples collected longitudinally following a controlled myocardial infarction revealed no consistent changes in the serum amyloid P-KNG interaction levels but consistent changes in KNG activation and interactions with plasma prekallikrein. These results demonstrate a versatile platform for measuring the dynamic composition of protein complexes in biological samples that should have value for studies of normal and disease-related signaling networks, multiprotein clusters, or enzymatic cascades. PMID:20023212

Bergsma, Derek; Chen, Songming; Buchweitz, John; Gerszten, Robert; Haab, Brian B.



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

USGS Publications Warehouse

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.

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.




PubMed Central

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 mitotic kinesin-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 [1]. 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 [1], which X-ray structures suggest stabilizes a 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 be located 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 ribose hydroxyls, consistent with the EPR spectroscopy results. Taken together, these data provide support for the hypothesis that L5 modulates Eg5 function via interaction with the nucleotide-binding site. PMID:21872609

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



Short cell-penetrating peptides: a model of interactions with gene promoter sites.  


Analysis of the main parameters of molecular mechanics (number of hydrogen bonds, hydrophobic and electrostatic interactions, DNA-peptide complex minimization energy) provided the data to validate the previously proposed qualitative models of peptide-DNA interactions and to evaluate their quantitative characteristics. Based on these estimations, a three-dimensional model of Lys-Glu and Ala-Glu-Asp-Gly peptide interactions with DNA sites (GCAG and ATTTC) located in the promoter zones of genes encoding CD5, IL-2, MMP2, and Tram1 signal molecules. PMID:23484211

Khavinson, V Kh; Tarnovskaya, S I; Linkova, N S; Pronyaeva, V E; Shataeva, L K; Yakutseni, P P



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

PubMed Central

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

Li, Yaoguo; He, Maoxian



The Effectiveness of Interactive Computer Assisted Modeling in Teaching Study Strategies and Concept Mapping of College Textbook Material.  

ERIC Educational Resources Information Center

A study evaluated the effectiveness of a series of print materials and interactive computer-guided study programs designed to lead undergraduate students to apply basic textbook reading and concept mapping strategies to the study of science and social science textbooks. Following field testing with 25 learning skills students, 50 freshman biology…

Mikulecky, Larry


Mapping Fiber and Yield QTLs with Main, Epistatic, and QTL × Environment Interaction Effects in Recombinant Inbred Lines of Upland Cotton  

Microsoft Academic Search

Most agronomic traits of cotton (Gossypium hirsutum L.) are quan- titatively inherited and affected by environment. The importance of epistasis as the genetic basis for complex traits has been reported in many crops. In this study, a linkage map was constructed by means of a recombinant inbred line (RIL) population derived from 72353TM-1. Main effects, epistatic effects, and environmental interaction

Xinlian Shen; Tianzhen Zhang; Wangzhen Guo; Xiefei Zhu; Xiaoyang Zhang



Interactive computer support in decision conferencing: Two cases on off-site nuclear emergency management  

Microsoft Academic Search

In this paper, we study the new opportunities offered by the interactive use of advanced multicriteria software in decision conferencing. We analyze and make observations on this approach in two one-day decision conferences on the planning of later phase countermeasures in off-site nuclear emergency management. The participants' individual use of the software in the preference elicitation phase was an essential

Jyri Mustajoki; Raimo P. Hämäläinen; Kari Sinkko



On the Digital Reconstruction and Interactive Presentation of Heritage Sites through Time  

Microsoft Academic Search

Virtual time travel from existing remains of a heritage site to its previous states and original condition is an educational and interesting experience and can provide better understanding of history. However, digitally reconstructing non-existing objects is a challenge. The interaction and navigation within virtual 4D worlds (adding time to 3D worlds) is also problematical due to the time dimension. In

Sabry F. El-Hakim; George MacDonald; Jean-François Lapointe; Lorenzo Gonzo; Michael Jemtrud



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

NASA Technical Reports Server (NTRS)

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.

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



Understanding Patterns of User Visits to Web Sites: Interactive Star eld Visualizations of WWW Log Data  

E-print Network

those of traditional web log analysis tools. We in- troduce a series of interactive star eld providers, understanding of user visit patterns is essential for e ective design of sites involving online issues such as depth vs. breadth of tree structures, incidental learning patterns, utilityofgraphics

Shneiderman, Ben


Using Interactive Visualizations of WWW Log Data to Characterize Access Patterns and Inform Site Design  

E-print Network

that exceed those of traditional web log analysis tools. We introduce a series of interactive visualizations providers, understanding of user visit patterns is essential for effective design of sites involving online issues such as depth vs. breadth of tree structures, incidental learning patterns, utility of graphics

Shneiderman, Ben


Using Interactive Visualizations of WWW Log Data to Characterize Access Patterns and Inform Site Design  

E-print Network

that exceed those of traditional web log analysis tools. We introduce a series of interactive visualizations for effective design of sites involving online communities, government services, digital libraries, and electronic commerce. Such understanding helps resolve issues such as depth vs. breadth of tree structures

Golbeck, Jennifer


Where Do Web Sites Come From? Capturing and Interacting with Design History  

E-print Network

Time, By Note, or By Author). We employ a branched history, presenting the current branch to the userWhere Do Web Sites Come From? Capturing and Interacting with Design History Scott R. ABSTRACT To form a deep understanding of the present; we need to Ã?nd and engage history. We present

Klemmer, Scott


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

E-print Network

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

Brutlag, Doug


Understanding and Designing for Interactional Privacy Needs within Social Networking Sites  

ERIC Educational Resources Information Center

"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…

Wisniewski, Pamela J.



Photoreactive stapled peptides to identify and characterize BCL-2 family interaction sites by mass spectrometry.  


Protein interactions dictate a myriad of cellular activities that maintain health or cause disease. Dissecting these binding partnerships, and especially their sites of interaction, fuels the discovery of signaling pathways, disease mechanisms, and next-generation therapeutics. We previously applied all-hydrocarbon peptide stapling to chemically restore ?-helical shape to bioactive motifs that become unfolded when taken out of context from native signaling proteins. For example, we developed stabilized alpha-helices of BCL-2 domains (SAHBs) to dissect and target protein interactions of the BCL-2 family, a critical network that regulates the apoptotic pathway. SAHBs are ?-helical surrogates that bind both stable and transient physiologic interactors and have effectively uncovered novel sites of BCL-2 family protein interaction. To leverage stapled peptides for proteomic discovery, we describe our conversion of SAHBs into photoreactive agents that irreversibly capture their protein targets and facilitate rapid identification of the peptide helix binding sites. We envision that the development of photoreactive stapled peptides will accelerate the discovery of novel and unanticipated protein interactions and how they impact health and disease. PMID:24974285

Lee, Susan; Braun, Craig R; Bird, Gregory H; Walensky, Loren D



In vivo protein-interaction mapping of a mitochondrial translocator protein Tom22 at work.  


Mitochondrial protein import requires cooperation of the machineries called translocators in the outer and inner mitochondrial membranes. Here we analyze the interactions of Tom22, a multifunctional subunit of the outer membrane translocator TOM40 complex, with other translocator subunits such as Tom20, Tom40, and Tim50 and with substrate precursor proteins at a spatial resolution of the amino acid residue by in vivo and in organello site-specific photocross-linking. Changes in cross-linking patterns caused by excess substrate precursor proteins or presequence peptides indicate how the cytosolic receptor domain of Tom22 accepts substrate proteins and how the intermembrane space domain of Tom22 transfers them to Tim50 of the inner-membrane translocator. PMID:21896724

Shiota, Takuya; Mabuchi, Hide; Tanaka-Yamano, Sachiko; Yamano, Koji; Endo, Toshiya



IQGAP1 scaffold-kinase interaction blockade selectively targets RAS-MAP kinase-driven tumors  

PubMed Central

Upregulation of the ERK1 and ERK2 (ERK1/2) MAP kinase (MAPK) cascade occurs in >30% of cancers1, often through mutational activation of receptor tyrosine kinases or other upstream genes, including KRAS and BRAF 2. Efforts to target endogenous MAPKs are challenged by the fact that these kinases are required for viability in mammals3,4. Additionally, the effectiveness of new inhibitors of mutant BRAF has been diminished by acquired tumor resistance through selection for BRAF-independent mechanisms of ERK1/2 induction2,5,6. Furthermore, recently identified ERK1/2-inducing mutations in MEK1 and MEK2 (MEK1/2) MAPK genes in melanoma confer resistance to emerging therapeutic MEK inhibitors, underscoring the challenges facing direct kinase inhibition in cancer7,8. MAPK scaffolds, such as IQ motif–containing GTPase activating protein 1 (IQGAP1)9,10, assemble pathway kinases to affect signal transmission11–13, and disrupting scaffold function therefore offers an orthogonal approach to MAPK cascade inhibition. Consistent with this, we found a requirement for IQGAP1 in RAS-driven tumorigenesis in mouse and human tissue. In addition, the ERK1/2-binding14 IQGAP1 WW domain peptide disrupted IQGAP1-ERK1/2 interactions, inhibited RAS- and RAF-driven tumorigenesis, bypassed acquired resistance to the BRAF inhibitor vemurafenib (PLX-4032) and acted as a systemically deliverable therapeutic to significantly increase the lifespan of tumor-bearing mice. Scaffold-kinase interaction blockade acts by a mechanism distinct from direct kinase inhibition and may be a strategy to target overactive oncogenic kinase cascades in cancer. PMID:23603816

Zehnder, Ashley M; Zhang, Jiajing; Zarnegar, Brian; Sage, Julien; Khavari, Paul A



Neural network approximations for nonlinear interactions in wind wave spectra: direct mapping for wind seas in deep water  

NASA Astrophysics Data System (ADS)

The potential of Neural Networks (NN) to provide accurate estimates of nonlinear interactions for wind wave spectra by means of direct mapping is considered. Expanding on a previously reported feasibility study, an Empirical Orthogonal Functions (EOF) based NN for single peaked spectra is shown to be much more accurate than the well known Discrete Interaction Approximation (DIA), at the expense of a moderate increase of computational costs. This Neural Network Interaction Approximation (NNIA) gives reasonable results for modeled wave spectra, but is not yet capable of providing acceptable model integrations. Methods to expand the NNIA to be suitable for model integration are discussed.

Tolman, Hendrik L.; Krasnopolsky, Vladimir M.; Chalikov, Dmitry V.


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

NASA Astrophysics Data System (ADS)

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.

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.



iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution  

PubMed Central

The unique composition and spatial arrangement of RNA-binding proteins (RBPs) on a transcript guide the diverse aspects of post-transcriptional regulation1. Therefore, an essential step towards understanding transcript regulation at the molecular level is to gain positional information on the binding sites of RBPs2. Protein-RNA interactions can be studied using biochemical methods, but these approaches do not address RNA binding in its native cellular context. Initial attempts to study protein-RNA complexes in their cellular environment employed affinity purification or immunoprecipitation combined with differential display or microarray analysis (RIP-CHIP)3-5. These approaches were prone to identifying indirect or non-physiological interactions6. In order to increase the specificity and positional resolution, a strategy referred to as CLIP (UV cross-linking and immunoprecipitation) was introduced7,8. CLIP combines UV cross-linking of proteins and RNA molecules with rigorous purification schemes including denaturing polyacrylamide gel electrophoresis. In combination with high-throughput sequencing technologies, CLIP has proven as a powerful tool to study protein-RNA interactions on a genome-wide scale (referred to as HITS-CLIP or CLIP-seq)9,10. Recently, PAR-CLIP was introduced that uses photoreactive ribonucleoside analogs for cross-linking11,12. Despite the high specificity of the obtained data, CLIP experiments often generate cDNA libraries of limited sequence complexity. This is partly due to the restricted amount of co-purified RNA and the two inefficient RNA ligation reactions required for library preparation. In addition, primer extension assays indicated that many cDNAs truncate prematurely at the crosslinked nucleotide13. Such truncated cDNAs are lost during the standard CLIP library preparation protocol. We recently developed iCLIP (individual-nucleotide resolution CLIP), which captures the truncated cDNAs by replacing one of the inefficient intermolecular RNA ligation steps with a more efficient intramolecular cDNA circularization (Figure 1)14. Importantly, sequencing the truncated cDNAs provides insights into the position of the cross-link site at nucleotide resolution. We successfully applied iCLIP to study hnRNP C particle organization on a genome-wide scale and assess its role in splicing regulation14. PMID:21559008

Konig, Julian; Zarnack, Kathi; Rot, Gregor; Curk, Tomaz; Kayikci, Melis; Zupan, Blaz; Turner, Daniel J.; Luscombe, Nicholas M.; Ule, Jernej



iCLIP--transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution.  


The unique composition and spatial arrangement of RNA-binding proteins (RBPs) on a transcript guide the diverse aspects of post-transcriptional regulation. Therefore, an essential step towards understanding transcript regulation at the molecular level is to gain positional information on the binding sites of RBPs. Protein-RNA interactions can be studied using biochemical methods, but these approaches do not address RNA binding in its native cellular context. Initial attempts to study protein-RNA complexes in their cellular environment employed affinity purification or immunoprecipitation combined with differential display or microarray analysis (RIP-CHIP). These approaches were prone to identifying indirect or non-physiological interactions. In order to increase the specificity and positional resolution, a strategy referred to as CLIP (UV cross-linking and immunoprecipitation) was introduced. CLIP combines UV cross-linking of proteins and RNA molecules with rigorous purification schemes including denaturing polyacrylamide gel electrophoresis. In combination with high-throughput sequencing technologies, CLIP has proven as a powerful tool to study protein-RNA interactions on a genome-wide scale (referred to as HITS-CLIP or CLIP-seq). Recently, PAR-CLIP was introduced that uses photoreactive ribonucleoside analogs for cross-linking. Despite the high specificity of the obtained data, CLIP experiments often generate cDNA libraries of limited sequence complexity. This is partly due to the restricted amount of co-purified RNA and the two inefficient RNA ligation reactions required for library preparation. In addition, primer extension assays indicated that many cDNAs truncate prematurely at the crosslinked nucleotide. Such truncated cDNAs are lost during the standard CLIP library preparation protocol. We recently developed iCLIP (individual-nucleotide resolution CLIP), which captures the truncated cDNAs by replacing one of the inefficient intermolecular RNA ligation steps with a more efficient intramolecular cDNA circularization (Figure 1). Importantly, sequencing the truncated cDNAs provides insights into the position of the cross-link site at nucleotide resolution. We successfully applied iCLIP to study hnRNP C particle organization on a genome-wide scale and assess its role in splicing regulation. PMID:21559008

Konig, Julian; Zarnack, Kathi; Rot, Gregor; Curk, Tomaz; Kayikci, Melis; Zupan, Blaz; Turner, Daniel J; Luscombe, Nicholas M; Ule, Jernej



Newsletter Forums Store About Us Contact Us Memewatch News Features Resources Topics Site Map Search  

E-print Network

Search Site Web Google Search Home » News Latest News Alter Your DNA: Exercise Meditation Linked that align themselves on a chip of glass have been used to create rudimentary electronic devices that provide a glass substrate and following this with normal photolithography to etch a circuit pattern. "By using

Ham, Donhee


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

USGS Publications Warehouse

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.

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



Development of a Subsurface Flow Path Observational Site to Connect Agricultural Land Management with Groundwater-Surface Water Interactions  

NASA Astrophysics Data System (ADS)

The San Joaquin Valley, California is one of the most productive agricultural areas in the world. The application of fertilizer and manure to the land over decades has led to extensive nitrate contamination in Valley aquifer. Groundwater-surface water exchanges in the region have can result in significant nitrate fluxes into Valley rivers. This work examines groundwater-surface water interactions at a USGS NAWQA site on the Merced River, near Livingston, CA. Hydrologic infrastructure at the site includes deep observation wells leading to shallow riparian wells and sampling points. The infrastructure is being instrumented as an agricultural flow path sensor network linking agricultural management practices to chemical transport and fate along a flow path through the vadose zone, groundwater and surface water. This work examines the movement of nitrate rich water into the Merced River through the hyporheic zone, and the denitrification rates associated with this transfer. Small inexpensive loggers self-logging thermistors are used to map temperature gradients in the streambed which are used estimate spatially distributed groundwater losses and gains within a roughly 300 m reach of the Merced River. In addition, samples collected from drive points installed at multiple depths in the riverbed are used to characterize the nitrate gradient across two transects within the same reach.

Butler, C.; Fisher, J.; Pai, H.; Villamizar Amaya, S.; Harmon, T. C.



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

NASA Astrophysics Data System (ADS)

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 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.

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



Interaction of antibiotics with A- and P-site-specific bases in 16S ribosomal RNA.  


We have studied the interactions of the antibiotics apramycin, kasugamycin, myomycin, neamine and pactamycin with 16S rRNA by chemical probing of drug-ribosome complexes. Kasugamycin and pactamycin, which are believed to affect translational initiation, protect bases in common with P-site-bound tRNA. While kasugamycin protects A794 and G926, and causes enhanced reactivity of C795, pactamycin protects G693 and C795. All four of these bases were previously shown to be protected by P-site tRNA or by edeine, another P-site inhibitor. Apramycin and neamine, which both induce miscoding and inhibit translocation, protect A1408, G1419 and G1494, as was also found earlier for neomycin, gentamicin, kanamycin and paromomycin. A1408 and G1494 were previously shown to be protected by A-site tRNA. Surprisingly, myomycin fails to give strong protection of any bases in 16S rRNA, in spite of having an apparently identical target site and mode of action to streptomycin, which protects several bases in the 915 region. Instead, myomycin gives only weak protection of A1408. These results suggest that the binding site(s) of streptomycin and myomycin have yet to be identified. PMID:1915283

Woodcock, J; Moazed, D; Cannon, M; Davies, J; Noller, H F



Acid-base site detection and mapping on solid surfaces by Kelvin force microscopy (KFM).  


Electrostatic potential at the surface of acidic or basic solids changes under higher relative humidity (RH), as determined by using Kelvin force microscopy (KFM). The potential on acid surfaces becomes more negative as the water vapor pressure increases, while it becomes more positive on basic solids. These results verify the following hypothesis: OH(-) or H(+) ions associated with atmospheric water ion clusters are selectively adsorbed on solid surfaces, depending on the respective Brønsted acid or base character. Therefore, Kelvin microscopy, under variable humidity, is a rigorous but convenient alternative to determine the acid-base character of solid surfaces, with a great advantage: it uses only one amphoteric and simple reagent to determine both the acid and base sites. Moreover, this technique provides information on the spatial distribution of acid-base sites, which is currently inaccessible to any other method. PMID:23126418

Gouveia, Rubia F; Bernardes, Juliana S; Ducati, Telma R D; Galembeck, Fernando



Mapping of MCP-1 functional domains by peptide analysis and site-directed mutagenesis  

Microsoft Academic Search

Monocyte chemoattractant protein-1 (MCP-1) is a member of the ? chemokine family which acts through specific seven transmembrane receptors to recruit monocytes, basophils, and T lymphocytes to sites of inflammation. To identify regions of the human MCP-1 protein which are important for its biological activity, we have synthesized domain-specific peptides and tested their ability to antagonize MCP-1 binding and chemotaxis

Susan A Steitz; Ko Hasegawa; Shiu-Lan Chiang; Ronald R Cobb; Mary A Castro; Thomas J Lobl; Masaki Yamada; Elias Lazarides; Pina M Cardarelli



Mapping of antigenic sites on the bovine ephemeral fever virus glycoprotein using monoclonal antibodies  

Microsoft Academic Search

Monoclonal antibodies (MAbs) were produced against the G, M2 and N proteins of bovine ephemeral fever virus (BEFV) and 29 were selected for further study. Thirteen neutralizing MAbs were assigned to one conformation-independent and at least two conforma- tion-dependent antigenic sites on the G protein by a competitive binding ELISA. The panel of MAbs were tested by neutralization and immunofluorescence

D. H. Cybinski; P. J. Walker; K. A. Byrne; H. Zakrzewski



Allosteric interactions between the nucleotide-binding sites and the ssDNA-binding site in the PriA helicase-ssDNA complex. 3.  


Allosteric interactions between the strong and weak nucleotide-binding sites and the total and proper single-stranded (ss)DNA-binding sites of the Escherichia coli PriA helicase have been analyzed using the fluorescence titration technique. Binding of the DNA exclusively to the proper DNA-binding site of the helicase, profoundly affects the intrinsic affinities of both nucleotide-binding sites, indicating a direct communication between the nucleotide-binding sites and the proper DNA-binding site. The communication involves conformational changes of the entire protein molecule. Nevertheless, the bound DNA differently affects the structures of the strong and weak nucleotide-binding sites. While the polarity of the strong site is moderately diminished, the polarity of the weak site is dramatically increased, indicating an intimate involvement of the weak site in controlling the helicase interactions with the DNA. The strong site does not directly control the DNA affinity of the enzyme. Only when the helicase has both nucleotide-binding sites saturated with ADP but not with ATP analogues does the enzyme have an increased affinity for the ssDNA, indicating that the control of ssDNA affinity involves a coordinated action of both nucleotide-binding sites and depends upon the phosphate group of the bound cofactor. A dramatic increase of the DNA affinity, when the DNA encompasses the total DNA-binding site of the enzyme, with both nucleotide-binding sites saturated with ADP or NDP, indicates that an additional area of the protein within the total DNA-binding site becomes engaged in interactions with the DNA. The significance of these results for the enzyme activities in the DNA unwinding and recognition is discussed. PMID:16752913

Lucius, Aaron L; Jezewska, Maria J; Bujalowski, Wlodzimierz



Interactive learning for congregate nutrition site nutrition education: a pilot study.  


Older adults who participate in the Older Americans Act Title III-C Elderly Nutrition Program often are at moderate to high nutritional risk. Although nutrition education is a component of the Elderly Nutrition Program, there are numerous barriers to promoting behavior change in older adults. Nutrition education programs targeted to congregate nutrition site participants must address their unique nutritional needs, while engaging them in activities that promote learning and motivate them to make positive behavior changes. This paper describes a pilot study of a theory-driven, five-lesson educational module designed to promote healthful eating behaviors among congregate nutrition site participants through interactive learning. PMID:14650554

Bobroff, Linda B; Turner, Elaine; Weddle, Dian O; Brake, Julie H; Lieberman, Leslie Sue; Allen, Tina B



Experimental analysis of bubble growth, departure and interactions during pool boiling on artificial nucleation sites  

SciTech Connect

The present work describes experimental results of pentane pool boiling, simplified to the cases of boiling on a single or on two adjacent nucleation sites. Bubbles growths have been recorded by a high speed camera under various wall superheat conditions. Bubble volume has been plotted as a function of time, and an experimental growth law has been proposed. Oscillations were observed during growth, showing the interaction of one bubble with the preceding bubble released from the same nucleation site. Lateral coalescence has been visualized and the images have brought to the fore the capillary effects on the distortion of the interface. (author)

Siedel, S.; Cioulachtjian, S.; Bonjour, J. [CETHIL - UMR5008 CNRS INSA-Lyon Univ. Lyon1, Bat. Sadi Carnot, 9 rue de la Physique, INSA-Lyon, F-69621 Villeurbanne Cedex (France)



Mapping the complement C1q binding site in Haemonchus contortus calreticulin  

Microsoft Academic Search

Haemonchus contortus is an economically important gastrointestinal parasite of domestic animals. The parasite secretes calreticulin (CalR), a Ca++ binding protein which modulates the host immune response. One way by which this protein acts is by inhibiting the classical complement pathway by binding to complement C1q protein. Understanding CalR–C1q interaction is important to develop methods to enhance host immune response. In

S. Naresha; A. Suryawanshi; M. Agarwal; B. P. Singh; P. Joshi



Cloning and epitope mapping of Cry11Aa-binding sites in the Cry11Aa-receptor alkaline phosphatase from Aedes aegypti.  


Cry11Aa is the most active Bacillus thuringiensis israelensis toxin against Aedes aegypti larvae. Ae. aegypti alkaline phosphatase (ALP) was previously identified as a Cry11Aa receptor mediating toxicity. Here we report the cloning and functional characterization of this Ae. aegypti Cry11Aa-ALP receptor. Of three ALP's cDNA clones, the recombinant produced ALP1 isoform was shown to bind Cry11Aa and P1.BBMV peptide phage that specifically binds the midgut ALP-Cry11Aa receptor. An anti-ALP1 antibody inhibited binding to brush border membrane vesicles and toxicity of Cry11Aa in isolated cultured guts. Two ALP1 Cry11Aa binding regions (R59-G102 and N257-I296) were mapped by characterizing binding of Cry11Aa to nine recombinant overlapping peptides covering the ALP1 sequence. Finally, by using a peptide spot array of Cry11Aa domain III and site-directed mutagenesis, we show that the ALP1 R59-G102 region binds Cry11Aa through domain II loop alpha-8 while ALP1 N257-I296 interacts with Cry11Aa through domain III 561RVQSQNSGNN570 located in beta18-beta19. Our results show that Cry11Aa domain II and domain III are involved in the binding with two distinct binding sites in the ALP1 receptor. PMID:19697959

Fernandez, Luisa E; Martinez-Anaya, Claudia; Lira, Erandi; Chen, Jianwu; Evans, Amy; Hernández-Martínez, Salvador; Lanz-Mendoza, Humberto; Bravo, Alejandra; Gill, Sarjeet S; Soberón, Mario



mMAPS: A Flow-Proteometric Technique to Analyze Protein-Protein Interactions in Individual Signaling Complexes  

PubMed Central

Signal transduction is a dynamic process that regulates cellular functions through multiple types of biomolecular interactions, such as the interactions between proteins and between proteins and nucleic acids. However, the techniques currently available for identifying protein-protein or protein–nucleic acid complexes typically provide information about the overall population of signaling complexes in a sample instead of information about the individual signaling complexes therein. We developed a technique called “microchannel for multiparameter analysis of proteins in a single complex” (mMAPS) that simultaneously detected individual target proteins either singly or in a multicomponent complex in cell or tissue lysates. We detected the target proteins labeled with fluorophores by flow proteometry, which provided quantified data in the form of multidimensional fluorescence plots. Using mMAPS, we quantified individual complexes of epidermal growth factor (EGF) with its receptor EGFR, EGFR with signal transducer and activator of transcription 3 (STAT3), and STAT3 with the acetylase p300 and DNA in lysates from cultured cells with and without treatment with EGF, as well as in lysates from tumor xenograft tissue. Consistent with the ability of this method to reveal the dynamics of signaling protein interactions, we observed that cells treated with EGF induced the interaction of EGF with EGFR and the autophosphorylation of EGFR, but this interaction decreased with longer treatment time. Thus, we expect that this technique may reveal new aspects of molecular interaction dynamics. PMID:24595109

Chou, Chao-Kai; Lee, Heng-Huan; Tsou, Pei-Hsiang; Chen, Chun-Te; Hsu, Jung-Mao; Yamaguchi, Hirohito; Wang, Ying-Nai; Lee, Hong-Jen; Hsu, Jennifer L.; Lee, Jin-Fong; Kameoka, Jun; Hung, Mien-Chie



Force Mapping during the Formation and Maturation of Cell Adhesion Sites with Multiple Optical Tweezers  

PubMed Central

Focal contacts act as mechanosensors allowing cells to respond to their biomechanical environment. Force transmission through newly formed contact sites is a highly dynamic process requiring a stable link between the intracellular cytoskeleton and the extracellular environment. To simultaneously investigate cellular traction forces in several individual maturing adhesion sites within the same cell, we established a custom-built multiple trap optical tweezers setup. Beads functionalized with fibronectin or RGD-peptides were placed onto the apical surface of a cell and trapped with a maximum force of 160 pN. Cells form adhesion contacts around the beads as demonstrated by vinculin accumulation and start to apply traction forces after 30 seconds. Force transmission was found to strongly depend on bead size, surface density of integrin ligands and bead location on the cell surface. Highest traction forces were measured for beads positioned on the leading edge. For mouse embryonic fibroblasts, traction forces acting on single beads are in the range of 80 pN after 5 minutes. If two beads were positioned parallel to the leading edge and with a center-to-center distance less than 10 µm, traction forces acting on single beads were reduced by 40%. This indicates a spatial and temporal coordination of force development in closely related adhesion sites. We also used our setup to compare traction forces, retrograde transport velocities, and migration velocities between two cell lines (mouse melanoma and fibroblasts) and primary chick fibroblasts. We find that maximal force development differs considerably between the three cell types with the primary cells being the strongest. In addition, we observe a linear relation between force and retrograde transport velocity: a high retrograde transport velocity is associated with strong cellular traction forces. In contrast, migration velocity is inversely related to traction forces and retrograde transport velocity. PMID:23372781

Schwingel, Melanie; Bastmeyer, Martin



Interactive Weather Information Network  

NSDL National Science Digital Library

Offered by the National Oceanic and Atmospheric Administration (NOAA), the Interactive Weather Information Network (IWIN) is a collection of interactive weather maps and satellite images that is updated every five seconds. Visitors can see cloud cover animation loops, NEXRAD Radar images of precipitation, a map of all current weather fronts, and an interactive national map to see information about any particular state. Other information on the site includes a listing of any active weather warnings, a link for world weather data, and more, making this a must-see site for all those users interested in the most current weather happenings anywhere.



Field-mapping and petrographic analysis of volcanoes surrounding the Lake Natron Homo sapiens footprint site, northern Tanzania  

NASA Astrophysics Data System (ADS)

The Lake Natron Homo sapiens footprint site is located in northern Tanzania along the East African Rift escarpment. The site is positioned south of Lake Natron within an ephemeral channel of the Engare Sero River. The hominid footprints are preserved in a tuff, which originated from one of the volcanic centers surrounding the site. Two large volcanoes in the surrounding region, including the active carbonatite producing Oldoinyo L’engai and the now extinct Kerimasi are possible sources. This area also contains over 30 smaller tuff cones and tuff rings that have been poorly mapped and not analyzed in detail. The site is significant as it is the oldest modern human trackway in East Africa and one of the largest collections of hominid footprints in the world. Determining the source of the footprinted volcanic ash requires detailed field mapping, and both petrographic and geochemical analyses. Extensive field-mapping of the region revealed multiple regional beds that stratigraphically overlay the footprinted layer. Age dating as well as geochemical analysis is being conducted to relate these beds to the footprinted layer. Field-mapping showed that the footprinted tuff is over 35 cm thick, suggesting a large, sustained eruption. The bulk of the tuff cones examined in the field visibly varied in composition to the footprinted tuff and, based on proximity to the footprint site, are too small to produce the requisite volume of ash. Field analysis of samples collected from Oldoinyo L’engai reveal the most similar mineral assemblages to the footprinted layer, and the large volcano provides a source substantial enough to create a thick ash bed 10 km north of the summit. Preliminary research reveals that the footprinted tuff is a phonolite, characterized by silica depletion and the presence of sanidine, augite, and annite with interstitial calcite. XRD analysis of samples collected from Oldoinyo L’engai reveal a nepheline-rich phonolite with zeolites (ie. phillipsite) and calcite, both of which are likely secondary. Work by Dawson (1993)1 suggests that Oldoinyo L’engai had a phonolitic composition, which has evolved into a carbonatite. Samples collected from the two major volcanoes, including both modern and ancient samples, as well as numerous tuff cones will be analyzed with X-ray diffraction (XRD), scanning-electron microscopy (SEM), and both cathodoluminescence (CL) and transmitted light petrography, and then compared to the footprinted tuff. The goals of the geochemical and petrographic analyses are to determine similarities in bulk mineral composition between the target ash and the surrounding volcanics, find the source of the target ash, and confirm that Oldoinyo L’engai produced the footprinted tuff. 1Dawson, J.B., 1993. The Geology of Oldoinyo Lengai: Tanganyika Geological Survey, p. 350-387.

Hewitt, S. M.; Zimmer, B.; Liutkus, C.; Carmichael, S. K.; McGinnis, K.



The nano-bio interface mapped by oxidative footprinting of the adsorption sites of myoglobin.  


Oxidative footprinting has been used to study the structure of macromolecular assemblies such as protein-protein and protein-ligand complexes. We propose a novel development of this technique to probe the protein corona that forms at the surface of nanoparticles in any biological medium. Indeed, very few techniques allow studying this interface at the molecular and residue level. Based on hydroxyl radical-mediated oxidation of proteins and analysis by nanoscale liquid chromatography coupled to tandem mass spectrometry (nanoLC-MS/MS), two sites of adsorption of myoglobin on silica nanoparticles are identified. This method gives new insights in the understanding of protein adsorption on nanomaterials. PMID:25245420

Devineau, Stéphanie; Mathé, Christelle; Legros, Véronique; Gonnet, Florence; Daniel, Régis; Renault, Jean Philippe; Pin, Serge



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

E-print Network

transformation The promoter of FLS2 (988 bp) was used from pFLS2::FLS2–GFP (Robatzek et al., 2006) and fused to the GUS gene, which was iso- lated from pGUS Topo via BamHI and HindIII restriction sites and inserted into pFLS2::pCAMBIA2300, resulting in pFLS2... of bacteria in Arabidopsis leaves, Col-0 plants were incubated with a GFP-transformed Pto DC3000 strain (Supplementary Fig. S4A at JXB online). The GFP-labelled bacteria were clearly visible in epidermal cells and within the openings of stomata...

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



Interactive Texture Mapping Jer^ome Maillot , Hussein Yahiaz, Anne Verroustz  

E-print Network

. This program could be used, for example, by fashion designers to map woven or leather textures onto polygonal objects. CR Categories and subject descriptors: I.3.3 [Computer Graphics] Pic- ture/Image Generation. I.3.7 [Computer Graphics] Graphics and Realism - Color, Shading and Texture. Additional Keywords: Texture Mapping

Frey, Pascal


The density and strength of proteoglycan-proteoglycan interaction sites in concentrated solutions.  


Rheological flow properties of link-stable and link-free proteoglycan (PG) aggregates in concentrated solutions were measured using a cone-on-plate viscometer. A second-order constitutive model, based upon the statistical-network theories of Lodge, [Rheol. Acta 7, 379-392 (1968)] and De Kee and Carreau [J. Non-Newtonian Fluid Mech. 6, 127-143 (1979)], was developed to describe the measured steady and transient flow responses exhibited by the PG solutions. Our measurements confirmed previous experimental findings that the complex shear modulus of PG solutions depends on the frequency of the imposed small-amplitude oscillatory shear, and the apparent viscosity and primary normal-stress difference depend nonlinearly on the shear rate under steady-shear flow conditions [Mow et al., J. Biomechanics 17, 325-338 (1984b); Hardingham et al., J. orthop. Res. 5, 36-46 (1987)]. In the present study, we found that PG solutions exhibit pronounced stress overshoot responses and large hysteresis loop effects. These transient responses were shown to be sensitive to acceleration strain (i.e. the second rate of strain) as well as PG structure (i.e. link-protein stabilization). The model parameters were determined by curvefitting of the second-order constitutive model and experimental data from steady, oscillatory and transient shear flow measurements. Using this network model, we calculated the density of the idealized interaction sites existing in the PG network, and the average strength of these interaction sites. The results indicate that link-protein stabilization of PG aggregates does not change the density of interaction sites formed in the PG network, rather, it increases the average strength of these interaction sites. PMID:1761579

Zhu, W; Lai, W M; Mow, V C



Genome-wide Mapping of Transcriptional Start Sites Defines an Extensive Leaderless Transcriptome in Mycobacterium tuberculosis  

PubMed Central

Summary Deciphering physiological changes that mediate transition of Mycobacterium tuberculosis between replicating and nonreplicating states is essential to understanding how the pathogen can persist in an individual host for decades. We have combined RNA sequencing (RNA-seq) of 5? triphosphate-enriched libraries with regular RNA-seq to characterize the architecture and expression of M. tuberculosis promoters. We identified over 4,000 transcriptional start sites (TSSs). Strikingly, for 26% of the genes with a primary TSS, the site of transcriptional initiation overlapped with the annotated start codon, generating leaderless transcripts lacking a 5? UTR and, hence, the Shine-Dalgarno sequence commonly used to initiate ribosomal engagement in eubacteria. Genes encoding proteins with active growth functions were markedly depleted from the leaderless transcriptome, and there was a significant increase in the overall representation of leaderless mRNAs in a starvation model of growth arrest. The high percentage of leaderless genes may have particular importance in the physiology of nonreplicating M. tuberculosis. PMID:24268774

Cortes, Teresa; Schubert, Olga T.; Rose, Graham; Arnvig, Kristine B.; Comas, Iñaki; Aebersold, Ruedi; Young, Douglas B.



Calculating the Habitable Zones of Multiple Star Systems with a New Interactive Web Site  

NASA Astrophysics Data System (ADS)

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 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.

Müller, Tobias W. A.; Haghighipour, Nader



Mapping the Binding Site of TRPV1 on AKAP79: Implications for Inflammatory Hyperalgesia  

PubMed Central

Inflammation causes hyperalgesia, an enhanced sensitivity to noxious stimuli. Transient receptor potential vanilloid 1 (TRPV1), a thermo-TRP ion channel activated by painful levels of heat, is an important contributor because hyperalgesia is reduced when TRPV1 is either genetically deleted or pharmacologically blocked. Inflammatory mediators such as prostaglandin-E2 or bradykinin cause hyperalgesia by activating cellular kinases that phosphorylate TRPV1, a process that has recently been shown to rely on a scaffolding protein, AKAP79, to target the kinases to TRPV1. Here we use Förster resonance energy transfer, immunoprecipitation, and TRPV1 membrane trafficking experiments to identify a key region on AKAP79, between amino acids 326–336, which is responsible for its interaction with TRPV1. A peptide identical to this domain inhibited sensitization of TRPV1 in vitro, and when covalently linked to a TAT peptide to promote uptake across the cell membrane the peptide inhibited in vivo inflammatory hyperalgesia in mice. Critically, it did so without affecting pain thresholds in the absence of inflammation. These results suggest that antagonizing the TRPV1–AKAP79 interaction will be a useful strategy for inhibiting inflammatory hyperalgesia. PMID:23699529

Stott, Katherine; McNaughton, Peter A.



Basaltic Magma-Water Interaction on Earth: Recognition Criteria To Aid Planetary Mapping on Mars (Invited)  

NASA Astrophysics Data System (ADS)

The interaction of basaltic magma with frozen/liquid water or wet sediment is a very common process on Earth, resulting in a wide array of explosively and non-explosively generated products at the micron to kilometre scale. A variety of products and edifices on Mars have also been interpreted as having formed by such interaction, but with the exception of rootless cones, such interpretations are rarely unequivocal. This talk focuses on terrestrial process recognition criteria at a scale, orientation (vertical) and erosion level that is relevant to Mars geological mapping. In this context, we emphasise intrusions with peperite margins and wide hydrothermal haloes, steep margins of ice-contact lava flows, subaerial-subaqueous lava delta transitions, lava domains with distinctive water-cooled jointing, edifices that are dominated by slumped and rotated beds, and the presence of surrounding fluvial deposits and erosion. The most common products of magma-water interaction on Earth are subaqueously emplaced lava flows, which are dominated by pillow lavas. Though pillows are not easy to distinguish from subaerial pahoehoe toes at the resolution of most remote imagery, they are commonly associated with distinctively jointed lava domains, which are usually on a larger scale, including areas of water-cooled jointing (curvicolumnar, blocky etc), lava-filled tubes, which often display radial jointing, and steep talus deposits of joint-block breccia. Subaqueous basaltic lavas emplaced in an ice-confined environment may also display near-vertical ice-contact margins, draped by curtains of elongate pillows or cavities formed from melting of included ice-blocks. Subaerial lava flows that transition into water also develop large-scale foreset-bedding close to the angle of repose, which should be easily visible, at least in oblique imagery. As the majority of the Martian surface is more deeply eroded than most areas of terrestrial basaltic volcanism, it is important to discuss intrusive processes in wet environments on Earth, where intrusions commonly mingle with surrounding unconsolidated clastic deposits, generating peperite. Such domains are typically on the metre to 100s metres scale and may be associated with wide (<25m) surrounding haloes of hydrothermal alteration. Basaltic peperite is often intimately associated with coherent domains, including dikes with pillowed margins, pillowed stringers, and irregular domains of water-cooled lava. Basaltic magma emplaced into ice-cemented deposits can also generate distinctive clastic dikes with coherent margins of chilled lava. Basaltic lavas emplaced in shallow (<500m) water may be draped with a variety of explosively-generated vitriclastic deposits and their reworked equivalents. A distinctive feature of these deposits that is relevant to planetary mappers, is that they are very susceptible to collapse, during or shortly after emplacement, generating rotated beds with bedding angles greater than the angle of repose and slump structures. In ice-confined environments the deposits may also be reworked as meltwater flood deposits in erosion channels

Skilling, I. P.; Graettinger, A. H.; Mercurio, E.; McGarvie, D.; Edwards, B. R.



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

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

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



Remote sensing techniques for mapping range sites and estimating range yield  

NASA Technical Reports Server (NTRS)

Image interpretation procedures for determining range yield and for extrapolating range information were investigated for an area of the Pine Ridge Indian Reservation in southwestern South Dakota. Soil and vegetative data collected in the field utilizing a grid sampling design and digital film data from color infrared film and black and white films were analyzed statistically using correlation and regression techniques. The pattern recognition techniques used were K-class, mode seeking, and thresholding. The herbage yield equation derived for the detailed test site was used to predict yield for an adjacent similar field. The herbage yield estimate for the adjacent field was 1744 lbs. of dry matter per acre and was favorably compared to the mean yield of 1830 lbs. of dry matter per acre based upon ground observations. Also an inverse relationship was observed between vegetative cover and the ratio of MSS 5 to MSS 7 of ERTS-1 imagery.

Benson, L. A.; Frazee, C. J.; Waltz, F. A.; Reed, C.; Carey, R. L.; Gropper, J. L.



Mapping of antigenic sites on the bovine ephemeral fever virus glycoprotein using monoclonal antibodies.  


Monoclonal antibodies (MAbs) were produced against the G, M2 and N proteins of bovine ephemeral fever virus (BEFV) and 29 were selected for further study. Thirteen neutralizing MAbs were assigned to one conformation-independent and at least two conformation-dependent antigenic sites on the G protein by a competitive binding ELISA. The panel of MAbs were tested by neutralization and immunofluorescence with three strains of BEFV and three BEFV-related viruses. The results indicated that BEFV strains from different sources were not identical and that the M2 protein was the least variable of the proteins investigated. Passive protection studies in mice showed that the correlation between neutralizing titre and resistance to challenge was 0.85 (P less than 0.001). PMID:1698922

Cybinski, D H; Walker, P J; Byrne, K A; Zakrzewski, H



Mapping of a cholinergic binding site by means of synthetic peptides, monoclonal antibodies, and. alpha. -bungarotoxin  

SciTech Connect

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.

Conti-Tronconi, B.M.; Tang, Fen; Diethelm, B.M.; Spencer, S.R. (Univ. of Minnesota, St. Paul (USA)); Reinhardt-Maelicke, S.; Maelicke, A. (Max-Planck-Institut fur Ernahrungsphysiologie, Dortmund (West Germany))



Subunit interactions in ABC transporters: a conserved sequence in hydrophobic membrane proteins of periplasmic permeases defines an important site of interaction with the ATPase subunits.  


The cytoplasmic membrane proteins of bacterial binding protein-dependent transporters belong to the superfamily of ABC transporters. The hydrophobic proteins display a conserved, at least 20 amino acid EAA---G---------I-LP region exposed in the cytosol, the EAA region. We mutagenized the EAA regions of MalF and MalG proteins of the Escherichia coli maltose transport system. Substitutions at the same positions in MalF and MalG have different phenotypes, indicating that EAA regions do not act symmetrically. Mutations in malG or malF that slightly affect or do not affect transport, determine a completely defective phenotype when present together. This suggests that EAA regions of MalF and MalG may interact during transport. Maltose-negative mutants fall into two categories with respect to the cellular localization of the MalK ATPase: in the first, MalK is membrane-bound, as in wild-type strains, while in the second, it is cytosolic, as in strains deleted in the malF and malG genes. From maltose-negative mutants of the two categories, we isolated suppressor mutations within malK that restore transport. They map mainly in the putative helical domain of MalK, suggesting that EAA regions may constitute a recognition site for the ABC ATPase helical domain. PMID:9214624

Mourez, M; Hofnung, M; Dassa, E



Subunit interactions in ABC transporters: a conserved sequence in hydrophobic membrane proteins of periplasmic permeases defines an important site of interaction with the ATPase subunits.  

PubMed Central

The cytoplasmic membrane proteins of bacterial binding protein-dependent transporters belong to the superfamily of ABC transporters. The hydrophobic proteins display a conserved, at least 20 amino acid EAA---G---------I-LP region exposed in the cytosol, the EAA region. We mutagenized the EAA regions of MalF and MalG proteins of the Escherichia coli maltose transport system. Substitutions at the same positions in MalF and MalG have different phenotypes, indicating that EAA regions do not act symmetrically. Mutations in malG or malF that slightly affect or do not affect transport, determine a completely defective phenotype when present together. This suggests that EAA regions of MalF and MalG may interact during transport. Maltose-negative mutants fall into two categories with respect to the cellular localization of the MalK ATPase: in the first, MalK is membrane-bound, as in wild-type strains, while in the second, it is cytosolic, as in strains deleted in the malF and malG genes. From maltose-negative mutants of the two categories, we isolated suppressor mutations within malK that restore transport. They map mainly in the putative helical domain of MalK, suggesting that EAA regions may constitute a recognition site for the ABC ATPase helical domain. PMID:9214624

Mourez, M; Hofnung, M; Dassa, E



Human expressed tagged sites on the X chromosome: A mapping resource for heritable sex-linked chorioretinal disorders  

SciTech Connect

We have isolated a bank of human X-specific genomic clones which harbor chorioretinal expressed sequences using library to library cross-screening. The steps included (1) the creation of a {lambda}gt-10 library of human chorioretinal cDNA, (2) the creation of a human X-specific EMBL-3 genomic library from a somatic cell hybrid (82082a) containing the X chromosome as its only human component and lacking the hamster X, and (3) a PCR-based cross-screen to identify 78 clones expressed in choroid and retina. The characterization of one human X-specific EMBL-3 clone (XEH.8; DXS542) has provided a clear illustration of the feasibility of this approach. FISH mapping confirms the regional localization of XEH.8 to Xp11. Localization of additional clones, XEH.1, XEH.34, XEH.41, and XEH.52 will be presented along with partial sequencing and characterization. Our approach has focused on the search for expressed sequences which can serve as expressed tagged sites (ESTs) in mapping or candidate genes for heritable eye disorders.

MacDonald, I.M.; Nesslinger, N. [Univ. of Alberta, Edmonton (Canada); Wong, P. [National Eye Institute, Bethesda, MD (United States)



The HIV-1 5' LTR poly(A) site is inactivated by U1 snRNP interaction with the downstream major splice donor site.  

PubMed Central

The inactivity of the 5' long terminal repeat (LTR) poly(A) site immediately downstream of the cap site maximizes the production of HIV-1 transcripts. In this paper, we demonstrate that this inactivity is mediated by the interaction of the U1 snRNP with the major splice donor site (MSD). The inhibition of the HIV-1 poly(A) site by U1 snRNP relies on a series of delicately balanced RNA processing signals. These include the poly(A) site, the major splice donor site and the splice acceptor sites. The inherent efficiency of the HIV-1 poly(A) site allows maximal activity where there is no donor site (in the 3' LTR) but full inhibition by the downstream MSD (in the 5' LTR). The MSD must interact efficiently with U1 snRNP to completely inhibit the 5' LTR poly(A) site, whereas the splice acceptor sites are inefficient, allowing full-length genomic RNA production. PMID:9312033

Ashe, M P; Pearson, L H; Proudfoot, N J



High-throughput genomic mapping of vector integration sites in gene therapy studies.  


Gene therapy has enormous potential to treat a variety of infectious and genetic diseases. To date hundreds of patients worldwide have received hematopoietic cell products that have been gene-modified with retrovirus vectors carrying therapeutic transgenes, and many patients have been cured or demonstrated disease stabilization as a result (Adair et al., Sci Transl Med 4:133ra57, 2012; Biffi et al., Science 341:1233158, 2013; Aiuti et al., Science 341:1233151, 2013; Fischer et al., Gene 525:170-173, 2013). Unfortunately, for some patients the provirus integration dysregulated the expression of nearby genes leading to clonal outgrowth and, in some cases, cancer. Thus, the unwanted side effect of insertional mutagenesis has become a major concern for retrovirus gene therapy. The careful study of retrovirus integration sites (RIS) and the contribution of individual gene-modified clones to hematopoietic repopulating cells is of crucial importance for all gene therapy studies. Supporting this, the US Food and Drug Administration (FDA) has mandated the careful monitoring of RIS in all clinical trials of gene therapy. An invaluable method was developed: linear amplification mediated-polymerase chain reaction (LAM-PCR) capable of analyzing in vitro and complex in vivo samples, capturing valuable genomic information directly flanking the site of provirus integration. Linking this method and similar methods to high-throughput sequencing has now made possible an unprecedented understanding of the integration profile of various retrovirus vectors, and allows for sensitive monitoring of their safety. It also allows for a detailed comparison of improved safety-enhanced gene therapy vectors. An important readout of safety is the relative contribution of individual gene-modified repopulating clones. One limitation of LAM-PCR is that the ability to capture the relative contribution of individual clones is compromised because of the initial linear PCR common to all current methods. Here, we describe an improved protocol developed for efficient capture, sequencing, and analysis of RIS that preserves gene-modified clonal contribution information. We also discuss methods to assess dominant/overrepresented gene-modified clones in preclinical and clinical models. PMID:25062639

Beard, Brian C; Adair, Jennifer E; Trobridge, Grant D; Kiem, Hans-Peter



Mapping and Imaging Methodologies within the Comprehensive Test Ban Treaty's On-Site Inspection Framework  

NASA Astrophysics Data System (ADS)

On-site inspection (OSI) is the final verification measure of the Comprehensive Nuclear Test Ban Treaty (CTBT). OSIs rely heavily on geologic and geophysical investigations. The objective is to apply methods that are effective, efficient and minimally intrusive. We present a general overview of the OSI as provisioned in the CTBT, specifying the allowed techniques and the timeline for their application. A CTBT OSI relies on many geological, geophysical and radiological methods. The search area for an OSI is mostly defined by uncertainty in the location of a suspect event detected by the International Monitoring System (IMS) and reported through the International Data Center and can be as large as 1000 km2. Thus OSI methods are fundamentally divided into general survey methods that narrow the search area and more focused, detailed survey methods to look for evidence of a potential underground explosion and try to find its location within an area of several km2. The purpose and goal of a CTBT OSI, as specified in the Article IV of the Treaty, is 'to clarify whether a nuclear explosion has been carried out in violation of the Treaty' and to 'gather any facts which might assist in identifying any possible violator.' Through the use of visual, geophysical, and radiological techniques, OSIs can detect and characterize anomalies and artifacts related to the event that triggered the inspection. In the context of an OSI, an 'observable' is a physical property that is important to recognize and document because of its relevance to the purpose of the inspection. Potential observables include: (1) visual observables such as ground/environmental disturbances and manmade features, (2) geophysical techniques that provide measurements of altered and damaged ground and buried artifacts, and (3) radiological measurements on samples. Information provided in this presentation comes from observations associated with historical testing activities that were not intended to go undetected. Every CTBT OSI will be different, and the observables present and detectable within an Inspection Area (IA) will depend on many factors, such as location, geology, emplacement configuration, climate, and the time elapsed after the event before the deployment of the Inspection Team (IT). A successful OSI is contingent on familiarity with potential observables, the suitability of the equipment to detect and characterize relevant observables, and the team's ability to document and integrate all the information into comprehensive, logical, and factual reports. In preparation for an OSI, a variety of types, scales, and generations of open-source digital imagery can be compared using geographic information systems (GIS) to focus on areas of interest. Simple image comparison from various open sources within GIS afford the opportunity to view anthropogenic and natural changes to locations of interest over time, thus remotely elucidating information about a site's use and level of activity.

Hawkins, W.; Sussman, A. J.; Kelley, R. E.; Wohletz, K. H.; Schultz-Fellenz, E. S.



Interaction of Palmitic Acid with Metoprolol Succinate at the Binding Sites of Bovine Serum Albumin  

PubMed Central

Purpose: The aim of this study was to characterize the binding profile as well as to notify the interaction of palmitic acid with metoprolol succinate at its binding site on albumin. Methods: The binding of metoprolol succinate to bovine serum albumin (BSA) was studied by equilibrium dialysis method (ED) at 27°C and pH 7.4, in order to have an insight in the binding chemistry of the drug to BSA in presence and absence of palmitic acid. The study was carried out using ranitidine as site-1 and diazepam as site-2 specific probe. Results: Different analysis of binding of metoprolol succinate to bovine serum albumin suggested two sets of association constants: high affinity association constant (k1 = 11.0 x 105 M-1) with low capacity (n1 = 2) and low affinity association (k2 = 4.0×105 M-1) constant with high capacity (n2 = 8) at pH 7.4 and 27°C. During concurrent administration of palmitic acid and metoprolol succinate in presence or absence of ranitidine or diazepam, it was found that palmitic acid displaced metoprolol succinate from its binding site on BSA resulting reduced binding of metoprolol succinate to BSA. The increment in free fraction of metoprolol succinate was from 26.27% to 55.08% upon the addition of increased concentration of palmitic acid at a concentration of 0×10-5 M to 16×10-5 M. In presence of ranitidine and diazepam, palmitic acid further increases the free fraction of metoprolol succinate from 33.05% to 66.95% and 40.68% to 72.88%, respectively. Conclusion: This data provided the evidence of interaction at higher concentration of palmitic acid at the binding sites on BSA, which might change the pharmacokinetic properties of metoprolol succinate.

Rahman, Mashiur; Prianka, Farzana; Shohel, Mohammad; Mazid, Md. Abdul



Mapping of MCP-1 functional domains by peptide analysis and site-directed mutagenesis.  


Monocyte chemoattractant protein-1 (MCP-1) is a member of the beta chemokine family which acts through specific seven transmembrane receptors to recruit monocytes, basophils, and T lymphocytes to sites of inflammation. To identify regions of the human MCP-1 protein which are important for its biological activity, we have synthesized domain-specific peptides and tested their ability to antagonize MCP-1 binding and chemotaxis in THP-1 cells. We have found that an intercysteine first loop peptide encompassing amino acids 13-35 inhibits MCP-1 binding and chemotactic activity, while peptides representing the amino-terminus (amino acids 1-10), second loop (amino acids 37-51), and carboxy-terminus (amino acids 56-71) of MCP-1 have no effect. In addition, we have found that cyclization of the first loop peptide by disulfide linkage and blocking the C-terminus of the peptide by amidation increases the activity of this peptide to block MCP-1 binding and chemotaxis. In order to specifically identify amino acid residues within the first loop that are crucial for MCP-1 functional activity, we have substituted alanine for tyrosine (Y13A) or arginine (R18A) in MCP-1 recombinant proteins. While baculovirus produced wild type and R18A MCP-1 proteins are indistinguishable in their ability to induce THP-1 chemotaxis and show modest effects in binding activity compared to commercially available recombinant MCP-1 protein, the Y13A point mutation causes a dramatic loss in function. The identification of functional domains of MCP-1 will assist in the design of MCP-1 receptor antagonists which may be clinically beneficial in a number of inflammatory diseases. PMID:9688530

Steitz, S A; Hasegawa, K; Chiang, S L; Cobb, R R; Castro, M A; Lobl, T J; Yamada, M; Lazarides, E; Cardarelli, P M



Mapping the Active Site Helix-to-Strand Conversion of CxxxxC Peroxiredoxin Q Enzymes †  

PubMed Central

Peroxiredoxins (Prx) are a family of enzymes which reduce peroxides using a peroxidatic cysteine residue; among these, the PrxQ subfamily members are proposed to be the most ancestral-like yet are among the least characterized. In many PrxQ enzymes, a second “resolving” cysteine is located six residues downstream from the peroxidatic Cys, and these residues form a disulfide during the catalytic cycle. Here, we describe three hyperthermophilic PrxQ crystal structures originally solved by the RIKEN structural genomics group. We reprocessed the diffraction data and carried out further refinement to yield models with Rfree lowered by 2.3–7.2% and resolution extended by 0.2–0.3 Å, making one, at 1.4 Å, the best resolved peroxiredoxin to date. Comparisons of two matched thiol and disulfide forms reveal that the active site conformational change required for disulfide formation involves a transition of about 20 residues from a pair of ?-helices to a ?-hairpin and 310-helix. Each conformation has about 10 residues with high disorder providing slack that enables the dramatic shift, and the two conformations are anchored to the protein core by distinct non-polar side chains that fill three hydrophobic pockets. Sequence conservation patterns confirm the importance of these and a few additional residues for function. From a broader perspective, this study raises the provocative question of how to make use of the valuable information in the protein data bank generated by structural genomics projects but not described in the literature, perhaps remaining unrecognized and certainly underutilized. PMID:22928725

Perkins, Arden; Gretes, Michael C.; Nelson, Kimberly J.; Poole, Leslie B.; Karplus, P. Andrew



Expression profiling and mapping of defence response genes associated with the barley-Pyrenophora teres incompatible interaction.  


Barley net- and spot-form of net blotch disease are caused by two formae of the hemibiotrophic fungus Pyrenophora teres (P. t. f. teres and P. t. f. maculata). In the present study, suppression subtractive hybridization (SSH) was used in combination with quantitative real-time reverse transcriptase PCR to identify and profile the expression of defence response (DR) genes in the early stages of both barley-P. teres incompatible and compatible interactions. From a pool of 307 unique gene transcripts identified by SSH, 45 candidate DR genes were selected for temporal expression profiling in infected leaf epidermis. Differential expression profiles were observed for 28 of the selected candidates, which were grouped into clusters depending on their expression profiles within the first 48 h after inoculation. The expression profiles characteristic of each gene cluster were very similar in both barley-P. t. f. teres and barley-P. t. f. maculata interactions, indicating that resistance to both pathogens could be mediated by induction of the same group of DR genes. Chromosomal map locations for 21 DR genes were identified using four doubled-haploid mapping populations. The mapped DR genes were distributed across all seven barley chromosomes, with at least one gene mapping to within 15 cM of another on chromosomes 1H, 2H, 5H and 7H. Additionally, some DR genes appeared to co-localize with loci harbouring known resistance genes or quantitative trait loci for net blotch resistance on chromosomes 6H and 7H, as well as loci associated with resistance to other barley diseases. The DR genes are discussed with respect to their map locations and potential functional role in contributing to net blotch disease resistance. PMID:19018994

Bogacki, P; Oldach, K H; Williams, K J



Exploring Variation in the d N \\/d S Ratio Among Sites and Lineages Using Mutational Mappings: Applications to the Influenza Virus  

Microsoft Academic Search

We use a likelihood-based method for mapping mutations on a phylogeny in a way that allows for both site-specific and lineage-specific\\u000a variation in selection intensity. The method accounts for many of the potential sources of bias encountered in mapping of\\u000a mutations on trees while still being computationally efficient. We apply the method to a previously published influenza data\\u000a set to

Weiwei Zhai; Montgomery Slatkin; Rasmus Nielsen



A 3347Locus Genetic Recombination Map of Sequence-Tagged Sites Reveals Features of Genome Organization, Transmission and Evolution of Cotton (Gossypium)  

Microsoft Academic Search

We report genetic maps for diploid (D) and tetraploid (AtDt) Gossypium genomes composed of sequence-tagged sites (STS) that foster structural, functional, and evolutionary genomic studies. The maps include, respectively, 2584 loci at 1.72-cM (600 kb) intervals based on 2007 probes (AtDt) and 763 loci at 1.96-cM (500 kb) intervals detected by 662 probes (D). Both diploid and tetraploid cottons exhibit

Junkang Rong; Colette Abbey; John E. Bowers; Curt L. Brubaker; Charlene Chang; Peng W. Chee; Terrye A. Delmonte; Xiaoling Ding; Juan J. Garza; Barry S. Marler; Chan-hwa Park; Gary J. Pierce; Katy M. Rainey; Vipin K. Rastogi; Stefan R. Schulze; Norma L. Trolinder; Jonathan F. Wendel; Thea A. Wilkins; T. Dawn Williams-Coplin; Rod A. Wing; Robert J. Wright; Xinping Zhao; Linghua Zhu; Andrew H. Paterson



Proteomic quantification and site-mapping of S-nitrosylated proteins using isobaric iodoTMT reagents.  


S-Nitrosylation is a redox-based protein post-translational modification in response to nitric oxide signaling and is involved in a wide range of biological processes. Detection and quantification of protein S-nitrosylation have been challenging tasks due to instability and low abundance of the modification. Many studies have used mass spectrometry (MS)-based methods with different thiol-reactive reagents to label and identify proteins with S-nitrosylated cysteine (SNO-Cys). In this study, we developed a novel iodoTMT switch assay (ISA) using an isobaric set of thiol-reactive iodoTMTsixplex reagents to specifically detect and quantify protein S-nitrosylation. Irreversible labeling of SNO-Cys with the iodoTMTsixplex reagents enables immune-affinity detection of S-nitrosylated proteins, enrichment of iodoTMT-labeled peptides by anti-TMT resin, and importantly, unambiguous modification site-mapping and multiplex quantification by liquid chromatography-tandem MS. Additionally, we significantly improved anti-TMT peptide enrichment efficiency by competitive elution. Using ISA, we identified a set of SNO-Cys sites responding to lipopolysaccharide (LPS) stimulation in murine BV-2 microglial cells and revealed effects of S-allyl cysteine from garlic on LPS-induced protein S-nitrosylation in antioxidative signaling and mitochondrial metabolic pathways. ISA proved to be an effective proteomic approach for quantitative analysis of S-nitrosylation in complex samples and will facilitate the elucidation of molecular mechanisms of nitrosative stress in disease. PMID:24926564

Qu, Zhe; Meng, Fanjun; Bomgarden, Ryan D; Viner, Rosa I; Li, Jilong; Rogers, John C; Cheng, Jianlin; Greenlief, C Michael; Cui, Jiankun; Lubahn, Dennis B; Sun, Grace Y; Gu, Zezong



Magnificent Maps  

NSDL National Science Digital Library

The British Library has a few maps in its collection, and it is an institution that is well-positioned to create an exhibition with the title "Magnificent Maps: Power, Propaganda and Art". This digital exhibit is meant to complement an in situ exhibit that explores these main themes through 80 different maps. On this site, visitors can look over four of these marvelous maps in exquisite detail, and also watch and listen as the exhibit's curators talk about each work. The maps include the Psalter World Map from 1625, which is most likely a copy of the lost map which decorated King Henry III's bedchamber in Westminster Palace. "The Island" map shouldn't be missed either, as it satirizes "the London-centric view of the English capital and its commuter towns as independent from the rest of the country." The site is rounded out by a blog maintained by the curators, and it is worth a look.

Barber, Peter; Harper, Tom


Hydrogeologic Mapping  

NSDL National Science Digital Library

In this exercise, students learn how to make a preliminary evaluation of the hydrogeology of a site. Students map the location and elevation of important hydrogeologic features, then produce a hydrogeologic map of the site, including a water profile and estimated flow paths for groundwater. This type of map is crucial for evaluating potential sources of groundwater, as well as potential sources of groundwater contamination.

Brikowski, Tom


Genotype to phenotype maps: multiple input abiotic signals combine to produce growth effects via attenuating signaling interactions in maize.  


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

Makumburage, G Buddhika; Richbourg, H Lee; LaTorre, Kalindi D; Capps, Andrew; Chen, Cuixen; Stapleton, Ann E



Genotype to Phenotype Maps: Multiple Input Abiotic Signals Combine to Produce Growth Effects via Attenuating Signaling Interactions in Maize  

PubMed Central

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

Makumburage, G. Buddhika; Richbourg, H. Lee; LaTorre, Kalindi D.; Capps, Andrew; Chen, Cuixen; Stapleton, Ann E.



Cyclin-dependent kinase inhibitor dinaciclib interacts with the acetyl-lysine recognition site of bromodomains.  


Bromodomain-containing proteins are considered atypical kinases, but their potential to interact with kinase inhibitors is unknown. Dinaciclib is a potent inhibitor of cyclin-dependent kinases (CDKs), which recently advanced to Phase III clinical trials for the treatment of leukemia. We determined the crystal structure of dinaciclib in complex with CDK2 at 1.7 Å resolution, revealing an elaborate network of binding interactions in the ATP site, which explains the extraordinary potency and selectivity of this inhibitor. Remarkably, dinaciclib also interacted with the acetyl-lysine recognition site of the bromodomain testis-specific protein BRDT, a member of the BET family of bromodomains. The binding mode of dinaciclib to BRDT at 2.0 Å resolution suggests that general kinase inhibitors ("hinge binders") possess a previously unrecognized potential to act as protein-protein inhibitors of bromodomains. The findings may provide a new structural framework for the design of next-generation bromodomain inhibitors using the vast chemical space of kinase inhibitors. PMID:24007471

Martin, Mathew P; Olesen, Sanne H; Georg, Gunda I; Schönbrunn, Ernst



Alaska Geothermal Sites Map and Database: Bringing together legacy and new geothermal data for research, exploration and development  

NASA Astrophysics Data System (ADS)

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.

Clough, J. G.; Harun, N. T.; Hughes, C. A.; Weakland, J. R.; Cameron, C. E.



Genome-wide mapping of DNase I hypersensitive sites and association analysis with gene expression in MSB1 cells  

PubMed Central

DNase I hypersensitive sites (DHSs) mark diverse classes of cis-regulatory regions, such as promoters and enhancers. MSB-1 derived from chicken Marek's disease (MD) lymphomas is an MDV-transformed CD4+ T-cell line for MD study. Previously, DNase I HS sites were studied mainly in human cell types for mammalian. To capture the regulatory elements specific to MSB1 cells and explore the molecular mechanisms of T-cell transformation caused by MDV in MD, we generated high-quality of DHSs map and gene expression profile for functional analysis in MSB1 cell line. The total of 21,724 significant peaks of DHSs was identified from around 40 million short reads. DHSs distribution varied between chromosomes and they preferred to enrich in the gene-rich chromosomes. More interesting, DHSs enrichments appeared to be scarce on regions abundant in CpG islands. Besides, we integrated DHSs into the gene expression data and found that DHSs tended to enrich on high expressed genes throughout whole gene regions while DHSs did not show significant changes for low and silent expressed genes. Furthermore, the correlation of DHSs with lincRNAs expression was also calculated and it implied that enhancer-associated lincRNAs probably originated from enhancer-like regions of DHSs. Together, our results indicated that DNase I HS sites highly correlate with active genes expression in MSB1 cells, suggesting DHSs can be considered as markers to identify the cis-regulatory elements associated with chicken Marek's disease. PMID:25352859

He, Yanghua; Carrillo, Jose A.; Luo, Juan; Ding, Yi; Tian, Fei; Davidson, Irit; Song, Jiuzhou



iSOIL: Interactions between soil related sciences - Linking geophysics, soil science and digital soil mapping  

NASA Astrophysics Data System (ADS)

High-resolution soil property maps are one major prerequisite for the specific protection of soil functions and restoration of degraded soils as well as sustainable land use, water and environmental management. To generate such maps the combination of digital soil mapping approaches and remote as well as proximal soil sensing techniques is most promising. However, a feasible and reliable combination of these technologies for the investigation of large areas (e.g. catchments and landscapes) and the assessment of soil degradation threats is missing. Furthermore, there is insufficient dissemination of knowledge on digital soil mapping and proximal soil sensing in the scientific community, to relevant authorities as well as prospective users. As one consequence there is inadequate standardization of techniques. At the poster we present the EU collaborative project iSOIL within the 7th framework program of the European Commission. iSOIL focuses on improving fast and reliable mapping methods of soil properties, soil functions and soil degradation risks. This requires the improvement and integration of advanced soil sampling approaches, geophysical and spectroscopic measuring techniques, as well as pedometric and pedophysical approaches. The focus of the iSOIL project is to develop new and to improve existing strategies and innovative methods for generating accurate, high resolution soil property maps. At the same time the developments will reduce costs compared to traditional soil mapping. ISOIL tackles the challenges by the integration of three major components: (i)high resolution, non-destructive geophysical (e.g. Electromagnetic Induction EMI; Ground Penetrating Radar, GPR; magnetics, seismics) and spectroscopic (e.g., Near Surface Infrared, NIR) methods, (ii)Concepts of Digital Soil Mapping (DSM) and pedometrics as well as (iii)optimized soil sampling with respect to profound soil scientific and (geo)statistical strategies. A special focus of iSOIL lies on the sustainable dissemination of technologies and concepts developed in the projects through workshops for stakeholders and the publication of a handbook "Methods and Technologies for Mapping of Soil Properties, Function and Threat Risks". Besides, the CEN Workshop offers a new mechanism and approach to standardization. During the project we decided that the topic of the CEN Workshop should focus on a voluntary standardization of electromagnetic induction measurement to ensure that results can be evaluated and processed under uniform circumstances and can be comparable. At the poster we will also present the idea and the objectives of our CEN Workshop "Best Practice Approach for electromagnetic induction measurements of the near surface"and invite every interested person to participate.

Dietrich, Peter; Werban, Ulrike; Sauer, Uta



The RFX family interacts at the collagen (COL1A2) start site and represses transcription.  


The transcription start site of the collagen alpha2(1) gene (COL1A2) has a sequence-specific binding site for a DNA methylation-responsive binding protein called regulatory factor for X-box 1 (RFX1) (Sengupta, P. K., Erhlich, M., and Smith, B. D. (1999) J. Biol. Chem. 274, 36649-36655). In this report, we demonstrate that RFX1 forms homodimers as well as heterodimers with RFX2 spanning the collagen transcription start site. Methylation at +7 on the coding strand increases RFX1 complex formation in gel shift assays. Methylation on the template strand, however, does not increase RFX1 complex formation. DNA from human fibroblasts contains minimal methylation on the coding strand (<4%) with variable methylation on the template strand. RFX1 acts as a repressor of collagen transcription as judged by in vitro transcription and co-transfection assays with an unmethylated collagen promoter-reporter construct. In addition, an RFX5 complex present in human fibroblasts interacts with the collagen RFX site, which is not sensitive to methylation. This is the first demonstration of RFX5 complex formation on a gene other than major histocompatibility complex (MHC) promoters. Also, RFX5 represses transcription of a collagen promoter-reporter construct in rat fibroblasts that have no detectable RFX5 complex formation or protein. RFX5 complex activates MHC II transcription by interacting with an interferon-gamma (IFN-gamma)-inducible protein, major histocompatibility class II trans-activator (CIITA). Collagen transcription is repressed by IFN-gamma in a dose-dependent manner in human but not in rat fibroblasts. IFN-gamma enhances RFX5 binding activity, and CIITA is present in the RFX5 complex of IFN-gamma-treated human fibroblasts. CIITA repressed collagen gene transcription more effectively in human fibroblasts than in rat fibroblasts, suggesting that the RFX5 complex may, in part, recruit CIITA protein to the collagen transcription start site. Thus the RFX family may be important repressors of collagen gene transcription through a RFX binding site spanning the transcription start site. PMID:11986307

Sengupta, Pritam K; Fargo, John; Smith, Barbara D



Denosumab mimics the natural decoy receptor osteoprotegerin by interacting with its major binding site on RANKL  

PubMed Central

Bone homeostasis critically relies on the RANKL-RANK-OPG axis which can be targeted by the fully human monoclonal antibody denosumab in conditions with increased bone resporption such as bone metastases. The binding site and therefore the molecular mechanism by which this antibody inhibits RANKL has not been characterized so far. Here, we used random peptide phage display library screenings to identify the denosumab epitope on RANKL. Alignments of phage derived peptide sequences with RANKL suggested that this antibody recognized a linear epitope between position T233 and Y241. Mutational analysis confirmed the core residues as critical for this interaction. The spatial localization of this epitope on a 3-dimensional model of RANKL showed that it overlapped with the major binding sites of OPG and RANK on RANKL. We conclude that denosumab inhibits RANKL by both functional and molecular mimicry of the natural decoy receptor OPG. PMID:25138051

Schieferdecker, Aneta; Voigt, Mareike; Riecken, Kristoffer; Braig, Friederike; Schinke, Thorsten; Loges, Sonja; Bokemeyer, Carsten; Fehse, Boris; Binder, Mascha



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


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

Huang, Edgar; Chang, Chiu-Chi Angela



Multiple sites of interaction between prostaglandins and non-steroidal anti-inflammatory agents.  


Several non-steroidal anti-inflammatory agents (NSAIA) are shown to inhibit the net production of prostaglandin (PG)- like activity from arachidonic acid by a cell-free preparation of guinea-pig lung. Moreover, these agents also antagonize PGE-1-induced contractions of the isolated gerbil colon. The anti-spasmogenic effects are reversible and specific. At high concentrations, indomethacin and mefenamic acid interfere with the binding of PGE-1 to a broken cell preparation of rat epididymal adipocytes. Taken together the data indicate that NSAIA interact with prostaglandins at multiple sites and are consistent with the suggestions reported previously that NSAIA may have multiple in vivo actions. PMID:1138291

Tolman, E L; Partridge, R



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

PubMed Central

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 PMID:24880689

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



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


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 PMID:24880689

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



Molecular dynamics study of active-site interactions with tetracoordinate transients in acetylcholinesterase and its mutants.  

PubMed Central

The role of active-site residues in the dealkylation reaction in the P(S)C(S) diastereomer of 2-(3,3-dimethylbutyl)methylphosphonofluoridate (soman)-inhibited Torpedo californica acetylcholinesterase (AChE) was investigated by full-scale molecular dynamics simulations using CHARMM: >400 ps equilibration was followed by 150-200 ps production runs with the fully solvated tetracoordinate phosphonate adduct of the wild-type, Trp84Ala and Gly199Gln mutants of AChE. Parallel simulations were carried out with the tetrahedral intermediate formed between serine-200 Ogamma of AChE and acetylcholine. We found that the NepsilonH in histidine H(+)-440 is positioned to protonate the oxygen in choline and thus promote its departure. In contrast, NepsilonH in histidine H(+)-440 is not aligned for a favourable proton transfer to the pinacolyl O to promote dealkylation, but electrostatic stabilization by histidine H(+)-440 of the developing anion on the phosphonate monoester occurs. Destabilizing interactions between residues and the alkyl fragment of the inhibitor enforce methyl migration from Cbeta to Calpha concerted with C-O bond breaking in soman-inhibited AChE. Tryptophan-84, phenyalanine-331 and glutamic acid-199 are within 3.7-3.9 A (1 A=10(-10) m) from a methyl group in Cbeta, 4.5-5.1 A from Cbeta and 4.8-5.8 A from Calpha, and can better stabilize the developing carbenium ion on Cbeta than on Calpha. The Trp84Ala mutation eliminates interactions between the incipient carbenium ion and the indole ring, but also reduces its interactions with phenylalanine-331 and aspartic acid-72. Tyrosine-130 promotes dealkylation by interacting with the indole ring of tryptophan-84. Glutamic acid-443 can influence the orientation of active-site residues through tyrosine-421, tyrosine-442 and histidine-440 in soman-inhibited AChE, and thus facilitate dealkylation. PMID:11171062

Enyedy, I J; Kovach, I M; Bencsura, A



Mapping and Characterization of the Interaction Interface between Two Polypyrimidine-Tract Binding Proteins and a Nova-Type Protein of Solanum tuberosum  

PubMed Central

Polypyrimidine tract-binding (PTB) proteins are RNA-binding proteins that generally contain four RNA recognition motifs (RRMs). In potato, six cDNAs encoding full-length PTB proteins have been identified. In the present study Nova1-like protein, designated StNova1, was identified as a potential interacting partner of the StPTB proteins via yeast two-hybrid screening. Nova protein is a RNA-binding protein that contains three K-homology (KH) domains. In humans, these proteins are involved in regulation of neuronal RNA metabolism but the role of Nova-like proteins in plants is poorly understood. We have validated this interaction and mapped the protein binding region on StNova1 and StPTB1 and ?6 using a novel domain interaction phage display (DIPP) technique. The interaction between the two RNA-binding proteins StPTB1/6 and StNova1 is mediated through linker regions that are distinctly separated from the RRMs. Furthermore, using a random 21-mer phage-peptide library, we have identified a number of peptides with the consensus sequence motif [S/G][V/I][L/V]G that recognize the StPTB proteins. One over-represented peptide that recognizes StPTB6 contains the GVLGPWP sequence that is similar to the GIGGRYP sequence in the glycine-rich linker region between the KH2 and KH3 domains of StNova1. We show, through site-specific mutations, the importance of glycine and proline residues in StNova1-StPTB interactions. PMID:23717658

Shah, Shweta; Butler, Nathaniel M.; Hannapel, David J.; Rao, A. Gururaj



FISH HABITAT MAPPING Results of a short study of interactions of cetaceans  

E-print Network

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

Pierce, Graham


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

E-print Network

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 ...

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



Integrated platform for genome-wide screening and construction of high-density genetic interaction maps in mammalian cells.  


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

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



Digital photogrammetric analysis of the IMP camera images: Mapping the Mars Pathfinder landing site in three dimensions  

USGS Publications Warehouse

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.

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.



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

PubMed Central

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

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



Site Map - SEER

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.


Functional mapping of the neural circuitry of rat maternal motivation: effects of site-specific transient neural inactivation  

PubMed Central

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

Pereira, Mariana; Morrell, Joan I.



New fields of investigation in the earth sciences opened up by spot: borehole siting and landslide mapping  

NASA Astrophysics Data System (ADS)

The extensive use of remote sensing in the field of Earth Sciences is described. Three points are emphasized and considered as prerequisites for a successful use of remote sensing: it is a tool and not a goal in itself; it is not exclusive and should be used in combination with other tools, and ground control is always necessary. Spot data have enables new kinds of study. An example is presented of a breakthrough, owing to improved accuracy, concerning the siting of wells in New Caledonia. The main results of this study are: the integration of remote sensing into the logical sequence of methods used by the hydrogeologist; the improvement of structural analysis; a time saving in the selection phase and an increased rate of sucessful borehole locations. A second example of a breakthrough, owing to stereoscopic capability and 3D models, is taken from Bolivia. The main results of this study are the [ossibility of composing landslide maps with an accuracy similar to those made using aerial photographs at 1:25 000 scale and to improve the perception of risks in the La Paz area at two different levels: neotectonic and potential high risk zones.

Coudert, Jean-Michel; Dutartre, Philippe; Scanvic, Jean-Yves


Sub-crop geologic map of pre-Tertiary rocks in the Yucca Flat and northern Frenchman Flat areas, Nevada Test Site, southern Nevada  

Microsoft Academic Search

This map displays interpreted structural and stratigraphic relations among the Paleozoic and older rocks of the Nevada Test Site region beneath the Miocene volcanic rocks and younger alluvium in the Yucca Flat and northern Frenchman Flat basins. These interpretations are based on a comprehensive examination and review of data for more than 77 drillholes that penetrated part of the pre-Tertiary

J. C. Cole; A. G. Harris; R. R. Wahl



Substantial prevalence of microdeletions of the Y-chromosome in infertile men with idiopathic azoospermia and oligozoospermia detected using a sequence-tagged site-based mapping strategy  

Microsoft Academic Search

Genes on the long arm of Y (Yq), particularly within interval 6, are believed to play a critical role in human spermatogenesis. Cytogenetically detectable deletions of this region are associated with azoospermia in men, but are relatively uncommon. The objective of this study was to validate a sequence-tagged site (STS)-mapping strategy for the detection of Yq microdeletions and to use

H. Najmabadi; V. Huang; D. Bhasin



Home Site Map Make Your Home Page Suggestions Enquiry Rope Car to be set up in city to attract tourists 20 childre  

E-print Network

Home Site Map Make Your Home Page Suggestions Enquiry Rope Car to be set up in city to attract monitor tested Dallas | May 30, 2007 12:01:13 AM IST U.S. medical engineers are developing a wireless the use of radio frequency identification, or RFID impulses, with impedance monitoring. We always want

Chiao, Jung-Chih


ACES 2012 2012 Awards Presenters Publicity Past ACES Site Map Congratulations to all of the award recipients and thank you to all of the presenters!  

E-print Network

ACES 2012 2012 Awards Presenters Publicity Past ACES Site Map Congratulations to all of the award Energy for Emergent Use after Major Earthquakes Faculty Mentor(s): Dr. Shih-Ho (Simon) Chao Provost President's Award ($200) Name: Joshuah Beach-Letendre (Biology) Title: Are increasing global temperatures

Chiao, Jung-Chih


Music via motion: transdomain mapping of motion and sound for interactive performances  

Microsoft Academic Search

This paper presents a framework called Music via Motion (MvM) designed for the transdomain mapping between physical movements of the performer(s) and multimedia events, translating activities from one creative domain to another-for example, from physical gesture to audio output. With a brief background of this domain and prototype designs, the paper describes a number of inter- and multidisciplinary collaborative works




The Evolution of the MAP Kinase Pathways: Coduplication of Interacting Proteins Leads to New Signaling Cascades  

Microsoft Academic Search

.   The MAP-kinase pathways are intracellular signaling modules that are likely to exist in all eukaryotes. We provide an evolutionary\\u000a model for these signaling pathways by focusing on the gene duplications that have occurred since the divergence of animals\\u000a from yeast. Construction of evolutionary trees with confidence assessed by bootstrap clearly shows that the mammalian JNK\\u000a and p38 pathways arose

Daniel R. Caffrey; Luke A. J. O'Neill; Denis C. Shields



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

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.

Rine, J.M.; Berg, R.C.; Shafer, J.M.; Covington, E.R.; Reed, J.K.; Bennett, C.B.; Trudnak, J.E.



Large, motile epifauna interact strongly with harpacticoid copepods and polychaetes at a bathyal site  

NASA Astrophysics Data System (ADS)

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.

Thistle, David; Eckman, James E.; Paterson, Gordon L. J.



Revealing interaction between sulfobutylether-?-cyclodextrin and reserpine by chemiluminescence and site-directed molecular docking.  


The host-guest interaction between sulfobutylether-?-cyclodextrin (SBE-?-CD) and reserpine (RSP) is described using flow injection-chemiluminescence (FI-CL) and site-directed molecular docking methods. It was found that RSP could inhibit the CL intensity produced by a luminol/SBE-?-CD system. The decrease in CL intensity was logarithmic over an RSP concentration range of 0.03 to 700.0 nM, giving a regression equation of ?I?=?107.1lgCRES ?+?186.1 with a detection limit of 10 pM (3?). The CL assay was successfully applied in the determination of RSP in injection, saliva and urine samples with recoveries in the range 93.5-106.1%. Using the proposed CL model, the binding constant (KCD-R ) and the stoichiometric ratio of SBE-?-CD/RSP were calculated to be 7.4?×?10(6) ?M(-1) and 1 : 1, respectively. Using molecular docking, it was confirmed that luminol binds to the small cavity of SBE-?-CD with a nonpolar interaction, while RSP targeted the larger cavity of SBE-?-CD and formed a 1 : 1 complex with hydrogen bonds. The proposed new CL method has the potential to become a powerful tool for revealing the host-guest interaction between CDs and drugs, as well as monitoring drugs with high sensitivity. PMID:24127401

Xiong, Xunyu; Wu, Min; Zhao, Xinfeng; Song, Zhenghua



Pro Region C-Terminus:Protease Active Site Interactions Are Critical in Catalyzing the Folding of R-Lytic Protease  

E-print Network

substrate/inhibitor complexes. Further, mutation of two protease residues near the active site havePro Region C-Terminus:Protease Active Site Interactions Are Critical in Catalyzing the Folding of R-Lytic Protease Reuben J. Peters, Andrew K. Shiau, Julie L. Sohl,§ D. Eric Anderson, Gale Tang,| Joy L. Silen

Agard, David


Cytokine gene expression profiles of bovine dendritic cells after interaction with Mycobacterium avium ssp. paratuberculosis (M.a.p.), Escherichia coli (E. coli) or recombinant M.a.p. heat shock protein 70.  


Mycobacterium avium paratuberculosis (M.a.p.) resides and replicates in macrophages. Many of the of immune mechanisms aiding M.a.p. survival in the host's cells are known. However, little is known about interactions of M.a.p. with dendritic cells (DC). As DC are important for the induction of protective immunity against infectious diseases, we investigated the interaction of M.a.p. with these cells. Quantitative real-time PCR (RT-PCR) was used to analyse differential expression of cytokine genes after 6 h and 24 h of incubation by immature DC that phagocytosed either M.a.p. or Escherichia coli (E. coli). We hypothesized that phagocytosis of E. coli would induce pro-inflammatory cytokines due to abundant presence of lipopolysaccharide (LPS) and that the cytokine expression profile induced by phagocytosis of live M.a.p. would differ. In addition we hypothesized that incubation of immature DC with rHsp70, an immunodominant antigen of M.a.p., would induce a similar profile of cytokine gene expression as phagocytosis of intact M.a.p. However, phagocytosis of both E. coli and M.a.p. resulted in a cytokine gene expression pattern representative of a (pro-)inflammatory reaction, dominated by strong induction of IL-12 gene expression, that was higher after 24 h than after 6 h of incubation, although the response to M.a.p. was less vigorous than to E. coli. Incubation with rHsp70 resulted in a more inhibitory type of cytokine gene expression, with delayed IL-12 gene expression and downregulation of the genes for IL-1beta and IL-6 after 24 h of incubation. We conclude that bovine DC produce an immuno-stimulatory, anti-mycobacterial response to infection with M.a.p., while Hsp70 potentially contributes to pathogen virulence by allowing the bacteria to invade the host cell. PMID:15946745

Langelaar, Merel F M; Weber, Corinna N; Overdijk, Marije B; Müller, Kerstin E; Koets, Ad P; Rutten, Victor P M G



The Binding Sites for the Chromatin Insulator Protein CTCF Map to DNA Methylation-Free Domains Genome-Wide  

PubMed Central

All known vertebrate chromatin insulators interact with the highly conserved, multivalent 11-zinc finger nuclear factor CTCF to demarcate expression domains by blocking enhancer or silencer signals in a position-dependent manner. Recent observations document that the properties of CTCF include reading and propagating the epigenetic state of the differentially methylated H19 imprinting control region. To assess whether these findings may reflect a universal role for CTCF targets, we identified more than 200 new CTCF target sites by generating DNA microarrays of clones derived from chromatin-immunopurified (ChIP) DNA followed by ChIP-on-chip hybridization analysis. Target sites include not only known loci involved in multiple cellular functions, such as metabolism, neurogenesis, growth, apoptosis, and signalling, but potentially also heterochromatic sequences. Using a novel insulator trapping assay, we also show that the majority of these targets manifest insulator functions with a continuous distribution of stringency. As these targets are generally DNA methylation-free as determined by antibodies against 5-methylcytidine and a methyl-binding protein (MBD2), a CTCF-based network correlates with genome-wide epigenetic states. PMID:15256511

Mukhopadhyay, Rituparna; Yu, WenQiang; Whitehead, Joanne; Xu, JunWang; Lezcano, Magda; Pack, Svetlana; Kanduri, Chandrasekhar; Kanduri, Meena; Ginjala, Vasudeva; Vostrov, Alexander; Quitschke, Wolfgang; Chernukhin, Igor; Klenova, Elena; Lobanenkov, Victor; Ohlsson, Rolf



A Rearrangement of the Guanosine-Binding Site Establishes an Extended Network of Functional Interactions in the Tetrahymena Group I Ribozyme Active Site†  

PubMed Central

Protein enzymes appear to use extensive packing and hydrogen-bonding interactions to precisely position catalytic groups within active sites. Due to their inherent backbone flexibility and limited side chain repertoire, RNA enzymes face additional challenges relative to proteins in precisely positioning substrates and catalytic groups. Here, we use the group I ribozyme to probe the existence, establishment, and functional consequences of an extended network of interactions in an RNA active site. The group I ribozyme catalyzes a site-specific attack of guanosine on an oligonucleotide substrate. We previously determined that the hydrogen bond between the exocyclic amino group of guanosine and the 2?-hydroxyl group at position A261 of the Tetrahymena group I ribozyme contributes to overall catalysis. We now use functional data, aided by double-mutant cycles, to probe this hydrogen bond in the individual reaction steps of the catalytic cycle. Our results indicate that this hydrogen bond is not formed upon guanosine binding to the ribozyme but instead forms at a later stage of the catalytic cycle. Formation of this hydrogen bond is correlated to other structural rearrangements in the ribozyme's active site that are promoted by docking of the oligonucleotide substrate into the ribozyme's active site, and disruption of this interaction has deleterious consequences for the chemical transformation within the ternary complex. These results, combined with earlier results, provide insight into the nature of the multiple conformational steps used by the Tetrahymena group I ribozyme to achieve its active structure and reveal an intricate, extended network of interactions that is used to establish catalytic interactions within this RNA's active site. PMID:20175542

Forconi, Marcello; Sengupta, Raghuvir N.; Piccirilli, Joseph A.; Herschlag, Daniel



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

E-print Network

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 ...

Fan, Yue


Redrawing the Map of Great Britain from a Network of Human Interactions  

E-print Network

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 ...

Ratti, Carlo


Maps: Finding Our Place in the World  

NSDL National Science Digital Library

How do we find our way through the world, geographically speaking? Do we all carry around a type of "mental map" in our head, formed through experience and repetition? Some would say yes, some would beg to differ. Maps remain a powerful way to represent the world in all its spatial glory, and this online exhibit from The Field Museum explores the history of maps and their history over the millennia. Designed to complement an ongoing exhibition at the Museum, the site includes a photo gallery, information about the participating institutions, and about researchers at the Museum who use maps and mapping technology in their own work. The interactive feature is definitely worth a look, as visitors can examine two dozen different maps in detail from Chicago to the Marshall Islands. One can imagine that this remarkable site could also be used in classrooms to expose students to the wide variety of maps that have been created by human hands.



Ecotin: a serine protease inhibitor with two distinct and interacting binding sites 1 1 Edited by J. Wells  

Microsoft Academic Search

The interaction between ecotin and target proteases with trypsin-like specificity has been systematically dissected to understand the structural basis of ecotin’s broad inhibitory specificity and the role of the secondary binding site. Site-directed and region-specific mutagenesis were preformed at ecotin’s primary site P1 residue (84), the C-terminal dimer interface (133 to 142), and two surface loops of the secondary binding

Steve Q Yang; Cheng-I Wang; Sarah A Gillmor; Robert J Fletterick; Charles S Craik



Persuasion Map  

NSDL National Science Digital Library

The Persuasion Map is an interactive graphic organizer that enables students to map out their arguments for a persuasive essay or debate. Students begin by determining their goal or thesis. They then identify three reasons to support their argument, and three facts or examples to validate each reason. The map graphic in the upper right-hand corner allows students to move around the map, instead of having to work in a linear fashion. The finished map can be saved, e-mailed, or printed.