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Last update: August 15, 2014.
1

Helical peptide arrays for lead identification and interaction site mapping.  

PubMed

Libraries composed of linear and cyclic peptides cannot fully represent the higher order structures of most antigenic sites. To map the binding site of ligands or antibodies, a larger part of the three-dimensional space should be sampled. Because parallel synthesis of large arrays of peptides on hydrogels is restricted to relatively small peptides, a simple and robust homodimeric helical system was chosen for antigen presentation. First, it was established in an heterodimeric system that the 26-mer peptide could be synthesized and that the helical coiled-coil peptides interact in the hydrogel in a predictable manner. Next, libraries of homodimeric coiled coils were synthesized into which the epitope was grafted. Using dedicated helical dimeric and trimeric coiled-coil libraries, the epitopes of two anti-HIV-1 gp41 monoclonal antibodies known to interact with helical structures were mapped at high resolution. These mappings precisely reflect existing X-ray data, and the arrays can be applied to lead identification, epitope mapping, and systematic analysis of amino acid contribution to coiled-coil systems. PMID:21708118

Langedijk, Johannes P M; Zekveld, Maria J; Ruiter, Mariska; Corti, Davide; Back, Jaap W

2011-10-01

2

Site Map  

Cancer.gov

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

3

Reverse Footprinting to Map Sites of RNA-Protein Interactions.  

PubMed

Nuclease protection of a site-specifically labeled RNA by an RNA-binding protein is an extremely powerful method for determining the site of an RNA-protein interaction. If a protein binds to the region that contains the site-specific label, it will protect the label and adjoining sequences from nuclease digestion. The protected region, or "footprint," can then be characterized by extensive fragmentation and gel electrophoresis. As the name implies, reverse footprinting produces a mirror image of a conventional footprint; the footprint is revealed by the presence, not the absence, of bands. This method has a distinct advantage over conventional footprinting in that only a small fraction of the labeled RNA must be bound. PMID:24890211

Nilsen, Timothy W

2014-01-01

4

RNase Footprinting to Map Sites of RNA-Protein Interactions.  

PubMed

The binding of a protein to an RNA sequence protects that the region of the RNA from ribonuclease (RNase) digestion; this protected region is known as the protein's "footprint." In this protocol, end-labeled RNAs with and without bound protein are digested with RNase, and the products of digestion are analyzed by gel electrophoresis on denaturing polyacrylamide gels. If the experiment is performed properly, a comparison of the banding patterns from the two samples will reveal the binding site of the protein. The binding site-or footprint-will be detected as a region without bands in the protein-bound sample. In the sample without bound protein, the bands should cover the entirety of the RNA molecule. To establish appropriate digestion conditions for the procedure (i.e., ?1 cleavage event per molecule), it is necessary to titrate the amount of RNase under a range of time and temperature conditions. RNase I cleaves after every nucleotide of RNA and works well under many assay conditions, but other enzymes with different cleavage specificities can also be used. RNase VI is preferable when analyzing structured RNA; RNase A is preferable when using pyrimidine-rich RNAs; and RNase T1 is useful for G-rich RNAs. Choosing enzymes with preference for double-stranded (such as RNase VI) versus single-stranded (such as RNase I) RNA may be helpful. Often, a combination of nucleases is advantageous. PMID:24890210

Nilsen, Timothy W

2014-01-01

5

Mapping of the interaction sites of galanthamine: a quantitative analysis through pairwise potentials and quantum chemistry.  

PubMed

A quantitative analysis of the interaction sites of the anti-Alzheimer drug galanthamine with molecular probes (water and benzene molecules) representative of its surroundings in the binding site of acetylcholinesterase (AChE) has been realized through pairwise potentials calculations and quantum chemistry. This strategy allows a full and accurate exploration of the galanthamine potential energy surface of interaction. Significantly different results are obtained according to the distances of approaches between the various molecular fragments and the conformation of the galanthamine N-methyl substituent. The geometry of the most relevant complexes has then been fully optimized through MPWB1K/6-31 + G(d,p) calculations, final energies being recomputed at the LMP2/aug-cc-pVTZ(-f) level of theory. Unexpectedly, galanthamine is found to interact mainly from its hydrogen-bond donor groups. Among those, CH groups in the vicinity of the ammonium group are prominent. The trends obtained provide rationales to the predilection of the equatorial orientation of the galanthamine N-methyl substituent for binding to AChE. The analysis of the interaction energies pointed out the independence between the various interaction sites and the rigid character of galanthamine. The comparison between the cluster calculations and the crystallographic observations in galanthamine-AChE co-crystals allows the validation of the theoretical methodology. In particular, the positions of several water molecules appearing as strongly conserved in galanthamine-AChE co-crystals are predicted by the calculations. Moreover, the experimental position and orientation of lateral chains of functionally important aminoacid residues are in close agreement with the ones predicted theoretically. Our study provides relevant information for a rational drug design of galanthamine based AChE inhibitors. PMID:22972560

Galland, Nicolas; Kone, Soleymane; Le Questel, Jean-Yves

2012-10-01

6

Predicting Interaction Sites from the Energetics of Isolated Proteins: A New Approach to Epitope Mapping  

PubMed Central

Abstract An increasing number of functional studies of proteins have shown that sequence and structural similarities alone may not be sufficient for reliable prediction of their interaction properties. This is particularly true for proteins recognizing specific antibodies, where the prediction of antibody-binding sites, called epitopes, has proven challenging. The antibody-binding properties of an antigen depend on its structure and related dynamics. Aiming to predict the antibody-binding regions of a protein, we investigate a new approach based on the integrated analysis of the dynamical and energetic properties of antigens, to identify nonoptimized, low-intensity energetic interaction networks in the protein structure isolated in solution. The method is based on the idea that recognition sites may correspond to localized regions with low-intensity energetic couplings with the rest of the protein, which allows them to undergo conformational changes, to be recognized by a binding partner, and to tolerate mutations with minimal energetic expense. Upon analyzing the results on isolated proteins and benchmarking against antibody complexes, it is found that the method successfully identifies binding sites located on the protein surface that are accessible to putative binding partners. The combination of dynamics and energetics can thus discriminate between epitopes and other substructures based only on physical properties. We discuss implications for vaccine design.

Scarabelli, Guido; Morra, Giulia; Colombo, Giorgio

2010-01-01

7

Native genomic blotting: high-resolution mapping of DNase I-hypersensitive sites and protein-DNA interactions  

SciTech Connect

DNase I-hypersensitive sites are observed in the promoter regions of actively expressed genes, potentially active genes, and genes that were once active. The authors have developed an approach that greatly increases the resolution for mapping these sites by electrophoresing genomic DNA on native polyacrylamide gels prior to electroblotting and hybridization. This improved method has been used to scan the promoter and coding region of a cell-cycle-dependent human histone H4 gene with an accuracy of +/- 5-10 base pairs. Protein-DNA interactions can be seen in the autoradiograph as light areas and DNase I-hypersensitive sites as dark bands. Therefore, this method provides a rapid and relatively simple means to accurately localize protein-DNA interactions as well as DNase I-hypersensitive sites, thus directly displaying DNase I hypersensitivity and protein-DNA complexes on one autoradiograph. It also potentially allows the analysis of small changes in DNase I-hypersensitive sites under various biological conditions. With this technique rather large regions of DNA can be screened to determine areas that should be analyzed by more sophisticated methods, such as genomic sequencing or gel retardation assays.

Pauli, U.; Chrysogelos, S.; Stein, J.; Stein, G.

1988-01-01

8

Carboxyl terminal sequences of ?-tubulin involved in the interaction of HMW-MAPs. Studies using site-specific antibodies  

Microsoft Academic Search

After the finding of the involvement of the C-terminal moieties of tubulin subunits in the interaction of MAPs, different studies have focused on the substructure of the binding domains for the different MAPs. Current biochemical evidence point to the role of a low-homology sequence between a and ß-subunits within the conserved region of the C-terminal domain of tubulin, in the

Daniel Cross; Gustavo Farías; Jorge Domínguez; Jestis Avila; Ricardo B. Maccioni

1994-01-01

9

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.

2014-04-01

10

Policy Manual Site Map  

Cancer.gov

 CCR Home   About CCR   CCR Intranet        Laboratory of Pathology LP Home Clinical Services Basic Sciences Training LP Staff Accessibility of Web Site Policy Manual Main Page LP Forms and Checklists Download Manual POLICY MANUAL SECTIONS General

11

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

PubMed Central

Recent global proteomic and genomic studies have determined that lysine acetylation is a highly abundant posttranslational modification. The next challenge is connecting lysine acetyltransferases (KATs) to their cellular targets. We hypothesize that proteins that physically interact with KATs may not only predict the cellular function of the KATs but may be acetylation targets. We have developed a mass spectrometry-based method that generates a KAT protein interaction network from which we simultaneously identify both in vivo acetylation sites and in vitro acetylation sites. This modified chromatin-immunopurification coupled to an in vitro KAT assay with mass spectrometry (mChIP-KAT-MS) was applied to the Saccharomyces cerevisiae KAT nucleosome acetyltransferase of histone H4 (NuA4). Using mChIP-KAT-MS, we define the NuA4 interactome and in vitro-enriched acetylome, identifying over 70 previously undescribed physical interaction partners for the complex and over 150 acetyl lysine residues, of which 108 are NuA4-specific in vitro sites. Through this method we determine NuA4 acetylation of its own subunit Epl1 is a means of self-regulation and identify a unique link between NuA4 and the spindle pole body. Our work demonstrates that this methodology may serve as a valuable tool in connecting KATs with their cellular targets.

Mitchell, Leslie; Huard, Sylvain; Cotrut, Michael; Pourhanifeh-Lemeri, Roghayeh; Steunou, Anne-Lise; Hamza, Akil; Lambert, Jean-Philippe; Zhou, Hu; Ning, Zhibin; Basu, Amrita; Cote, Jacques; Figeys, Daniel A.; Baetz, Kristin

2013-01-01

12

One-dimensional mapping, modulated phases and Lyapunov exponent for the antiferromagnetic Q-state Potts and multi-site exchange interaction Ising models  

NASA Astrophysics Data System (ADS)

We describe the bifurcation structure, period doubling and chaos for the antiferromagnetic Q-state Potts model on the Bethe lattice and three-site interaction Ising model on Husimi one in a magnetic field, by using the recursion relation technique. A chaotic behavior of the magnetic susceptibility for the models is observed at low temperatures. The resulting one-dimensional rational mapping has a positive Lyapunov exponent in the region of the chaotic regime for the antiferromagnetic Q-state Potts ( Q<2) and three-site interaction Ising models. We discuss modulated phases for the antiferromagnetic Q-state Potts ( Q<2 and Q?2) and three-site interaction Ising model. At low temperatures the Q-state Potts model ( Q?2) has only one modulated phase with {1}/{2} pinching corresponding to the 2-cycle. The Q-state Potts ( Q<2) and three-site interaction Ising models have an infinite number of modulated phases with different pinching numbers; we construct the first modulated phase after the first bifurcation point.

Ananikian, N. S.; Ananikyan, L. N.; Artuso, R.; Hovhannisyan, V. V.

2010-09-01

13

Dynamic and Interactive Mapping Syllabus  

NSDL National Science Digital Library

From Foothill College and the Using a Web-Based GIS to Teach Problem-Based Science in High School and College project, this pdf contains a syllabus on Dynamic and Interactive Mapping. The objective of the course is to introduce students to "maps for the World-Wide Web, animation, multimedia presentation, and interactive interfaces for presenting geographic information." The syllabus includes lectures, discussions, and laboratory exercises on "computer mapping, GIS, and computer graphics."

2012-05-07

14

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

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

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

15

Mapping functional interaction sites of human prune C-terminal domain by NMR spectroscopy in human cell lysates.  

PubMed

Get well prune: The C-terminal third domain of h-prune is largely unfolded and involved in relevant protein-protein interactions, particularly with Nm23-H1 (see figure), GSK-3? and gelsolin. This study shows that protein functions mediated by protein-protein interactions can be accurately followed in cell lysates by using fast NMR spectroscopy, which could be easily used for a very efficient NMR drug-discovery strategy. PMID:23939913

Diana, Donatella; Smaldone, Giovanni; De Antonellis, Pasquale; Pirone, Luciano; Carotenuto, MariaNeve; Alonzi, Alessandro; Di Gaetano, Sonia; Zollo, Massimo; Pedone, Emilia M; Fattorusso, Roberto

2013-09-01

16

Site Map | Cancer Diagnosis Program (CDP)  

Cancer.gov

Skip to Content Search this site Last Updated: 06/03/13 Site Map Home About CDP Mission Statement Staff Directory Office of the Associate Director (OAD) Biorepository and Biospecimen Research Branch (BBRB) Diagnostic Biomarkers and Technology Branch

17

Yellowstone National Park Interactive Map  

NSDL National Science Digital Library

This Yellowstone National Park Map is a handy way to quickly find locations and buildings located in the park. It is currently the most detailed map of Yellowstone national park that can be viewed online. The pull down menu has Yellowstone features such as geyser basins, campgrounds, trails, mountains, and historical points and park structures. Popular geysers, and park locations such as Norris geyser basin, Yellowstone visitor centers, park housing, lodging, and park dining can be easily found. All Yellowstone National Park named structures are indexed so you can easily find the sites that you want to locate.

Census, Nps S.

18

Interactive Geophysical Mapping on the Web  

NASA Astrophysics Data System (ADS)

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

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

2002-12-01

19

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".

20

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

1993-11-01

21

Localisation and Interaction for Augmented Maps  

Microsoft Academic Search

Paper-based cartographic maps provide highly detailed information visualisation with unrivalled fidelity and infor- mation density. Moreover, the physical properties of paper afford simple interactions for browsing a map or focusing on individual details, managing concurrent access for mul- tiple users and general malleability. However, printed maps are static displays and while computer-based map displays can support dynamic information, they lack

Gerhard Reitmayr; Ethan Eade; Tom Drummond

2005-01-01

22

Mapping the elusive neonicotinoid binding site  

PubMed Central

Two types of structurally similar nicotinic agonists have very different biological and physicochemical properties. Neonicotinoids, important insecticides including imidacloprid and thiacloprid, are nonprotonated and selective for insects and their nicotinic receptors, whereas nicotinoids such as nicotine and epibatidine are cationic and selective for mammalian systems. We discovered that a mollusk acetylcholine binding protein (AChBP), as a structural surrogate for the extracellular ligand-binding domain of the nicotinic receptor, is similarly sensitive to neonicotinoids and nicotinoids. It therefore seemed possible that the proposed very different interactions of the neonicotinoids and nicotinoids might be examined with a single AChBP by using optimized azidochloropyridinyl photoaffinity probes. Two azidoneonicotinoids with a nitro or cyano group were compared with the corresponding desnitro or descyano azidonicotinoids. The four photoactivated nitrene probes modified AChBP with up to one agonist for each subunit based on analysis of the intact derivatized protein. Identical modification sites were observed by collision-induced dissociation analysis for the neonicotinoids and nicotinoids with similar labeling frequency of Tyr-195 of loop C and Met-116 of loop E at the subunit interface. The nitro- or cyano-substituted guanidine/amidine planes of the neonicotinoids provide a unique electronic conjugation system to interact with loop C Tyr-188. The neonicotinoid nitro oxygen and cyano nitrogen contact loop C Cys-190/Ser-189, whereas the cationic head of the corresponding nicotinoids is inverted for hydrogen-bonding and cation-? contact with Trp-147 and Tyr-93. These structural models based on AChBP directly map the elusive neonicotinoid binding site and further describe the molecular determinants of agonists on nicotinic receptors.

Tomizawa, Motohiro; Talley, Todd T.; Maltby, David; Durkin, Kathleen A.; Medzihradszky, Katalin F.; Burlingame, Alma L.; Taylor, Palmer; Casida, John E.

2007-01-01

23

EMP Simulator - Site Interaction.  

National Technical Information Service (NTIS)

EMP simulators interact with test objects and subsequently do not provide a test excitation environment that equals that of the threat EMP. This study compares the excitation from a horizontal simulator (TEMPS) to that from a horizontal EMP (HEMP). This c...

A. L. Whitson W. E. Scharfman

1978-01-01

24

Creating an Interactive Videodisc on Mapping.  

ERIC Educational Resources Information Center

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

Andrews, Sona Karentz; Grozik, John

1994-01-01

25

Accuracy of MER landing site maps  

Microsoft Academic Search

Continuous and precision controlled photomosaic maps of the MER A Meridiani Planum and the MER B Gusev Crater landing sites were used for mission operations to target the incoming rovers to the surface of Mars during Mars approach. Sets of photomosaics were composed from Viking Orbiter images (60 m\\/pixel) and also from Odyssey THEMIS Infrared images (100 m\\/pixel). After landing,

T. Duxbury

2004-01-01

26

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

PubMed

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; Pérez-Cano, Laura; Fernández-Recio, Juan; Glaser, Fabian; Manor, Haim

2010-05-01

27

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

2007-01-01

28

Mapping the interaction sites of Aspergillus nidulans phytochrome FphA with the global regulator VeA and the White Collar protein LreB.  

PubMed

Aspergillus nidulans senses red and blue-light and employs a phytochrome and a Neurospora crassa White Collar (WC) homologous system for light perception and transmits this information into developmental decisions. Under light conditions it undergoes asexual development and in the dark it develops sexually. The phytochrome FphA consists of a light sensory domain and a signal output domain, consisting of a histidine kinase and a response regulator domain. Previously it was shown that the phytochrome FphA directly interacts with the WC-2 homologue, LreB and another regulator, VeA. In this paper we mapped the interaction of FphA with LreB to the histidine kinase and the response regulator domain at the C-terminus in vivo using the bimolecular fluorescence complementation assay and in vitro by co-immunoprecipitation. In comparison, VeA interacted with FphA only at the histidine kinase domain. We present evidence that VeA occurs as a phosphorylated and a non-phosphorylated form in the cell. The phosphorylation status of the protein was independent of the light receptors FphA, LreB and the WC-1 homologue LreA. PMID:18936976

Purschwitz, Janina; Müller, Sylvia; Fischer, Reinhard

2009-01-01

29

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

2003-01-01

30

Mapping the Interaction Site for a ?-Scorpion Toxin in the Pore Module of Domain III of Voltage-gated Na+ Channels*  

PubMed Central

Activation of voltage-gated sodium (Nav) channels initiates and propagates action potentials in electrically excitable cells. ?-Scorpion toxins, including toxin IV from Centruroides suffusus suffusus (CssIV), enhance activation of NaV channels. CssIV stabilizes the voltage sensor in domain II in its activated state via a voltage-sensor trapping mechanism. Amino acid residues required for the action of CssIV have been identified in the S1-S2 and S3-S4 extracellular loops of domain II. The extracellular loops of domain III are also involved in toxin action, but individual amino acid residues have not been identified. We used site-directed mutagenesis and voltage clamp recording to investigate amino acid residues of domain III that are involved in CssIV action. In the IIISS2-S6 loop, five substitutions at four positions altered voltage-sensor trapping by CssIVE15A. Three substitutions (E1438A, D1445A, and D1445Y) markedly decreased voltage-sensor trapping, whereas the other two substitutions (N1436G and L1439A) increased voltage-sensor trapping. These bidirectional effects suggest that residues in IIISS2-S6 make both positive and negative interactions with CssIV. N1436G enhanced voltage-sensor trapping via increased binding affinity to the resting state, whereas L1439A increased voltage-sensor trapping efficacy. Based on these results, a three-dimensional model of the toxin-channel interaction was developed using the Rosetta modeling method. These data provide additional molecular insight into the voltage-sensor trapping mechanism of toxin action and define a three-point interaction site for ?-scorpion toxins on NaV channels. Binding of ?- and ?-scorpion toxins to two distinct, pseudo-symmetrically organized receptor sites on NaV channels acts synergistically to modify channel gating and paralyze prey.

Zhang, Joel Z.; Yarov-Yarovoy, Vladimir; Scheuer, Todd; Karbat, Izhar; Cohen, Lior; Gordon, Dalia; Gurevitz, Michael; Catterall, William A.

2012-01-01

31

Mapping the interaction site for a ?-scorpion toxin in the pore module of domain III of voltage-gated Na(+) channels.  

PubMed

Activation of voltage-gated sodium (Na(v)) channels initiates and propagates action potentials in electrically excitable cells. ?-Scorpion toxins, including toxin IV from Centruroides suffusus suffusus (CssIV), enhance activation of Na(V) channels. CssIV stabilizes the voltage sensor in domain II in its activated state via a voltage-sensor trapping mechanism. Amino acid residues required for the action of CssIV have been identified in the S1-S2 and S3-S4 extracellular loops of domain II. The extracellular loops of domain III are also involved in toxin action, but individual amino acid residues have not been identified. We used site-directed mutagenesis and voltage clamp recording to investigate amino acid residues of domain III that are involved in CssIV action. In the IIISS2-S6 loop, five substitutions at four positions altered voltage-sensor trapping by CssIV(E15A). Three substitutions (E1438A, D1445A, and D1445Y) markedly decreased voltage-sensor trapping, whereas the other two substitutions (N1436G and L1439A) increased voltage-sensor trapping. These bidirectional effects suggest that residues in IIISS2-S6 make both positive and negative interactions with CssIV. N1436G enhanced voltage-sensor trapping via increased binding affinity to the resting state, whereas L1439A increased voltage-sensor trapping efficacy. Based on these results, a three-dimensional model of the toxin-channel interaction was developed using the Rosetta modeling method. These data provide additional molecular insight into the voltage-sensor trapping mechanism of toxin action and define a three-point interaction site for ?-scorpion toxins on Na(V) channels. Binding of ?- and ?-scorpion toxins to two distinct, pseudo-symmetrically organized receptor sites on Na(V) channels acts synergistically to modify channel gating and paralyze prey. PMID:22761417

Zhang, Joel Z; Yarov-Yarovoy, Vladimir; Scheuer, Todd; Karbat, Izhar; Cohen, Lior; Gordon, Dalia; Gurevitz, Michael; Catterall, William A

2012-08-31

32

A protein interaction map of Drosophila melanogaster.  

PubMed

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 was developed to refine this draft map to a higher confidence map of 4679 proteins and 4780 interactions. Statistical modeling of the network showed two levels of organization: a short-range organization, presumably corresponding to multiprotein complexes, and a more global organization, presumably corresponding to intercomplex connections. The network recapitulated known pathways, extended pathways, and uncovered previously unknown pathway components. This map serves as a starting point for a systems biology modeling of multicellular organisms, including humans. PMID:14605208

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

2003-12-01

33

A Protein Interaction Map of Drosophila melanogaster  

NASA Astrophysics Data System (ADS)

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 was developed to refine this draft map to a higher confidence map of 4679 proteins and 4780 interactions. Statistical modeling of the network showed two levels of organization: a short-range organization, presumably corresponding to multiprotein complexes, and a more global organization, presumably corresponding to intercomplex connections. The network recapitulated known pathways, extended pathways, and uncovered previously unknown pathway components. This map serves as a starting point for a systems biology modeling of multicellular organisms, including humans.

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

2003-12-01

34

Specifying Interaction Surfaces Using Interaction Maps.  

National Technical Information Service (NTIS)

Defining how 3D models respond to user actions is a crucial step in building an interactive 3D world. Unfortunately, existing tools make it very difficult for interaction designers to assign responses to any part of a 3D model that is not a pre-defined gr...

J. S. Pierce R. Pausch

2001-01-01

35

Interactive Maps for Community in Online Learning  

ERIC Educational Resources Information Center

The online courses studied here used the visual medium of the interactive geographic map as a form of dialogue to reduce students' sense of transactional distance during the course, build their skills with Web 2.0 media, and increase their motivation. Using the dynamic map and the related online spreadsheet, the course participants created digital…

Cavanaugh, Terence W.; Cavanaugh, Cathy

2008-01-01

36

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.

37

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

38

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

39

Mapping glycans onto specific N-linked glycosylation sites of Pyrus communis PGIP redefines the interface for EPG-PGIP interactions.  

PubMed

Polygalacturonase inhibiting proteins (PGIPs) are members of the leucine rich repeat family of proteins, involved in plant defense against fungal pathogens. PGIPs exhibit a remarkable degree of specificity in terms of their ability to bind and inhibit their target molecules, the endopolygalacturonases (EPGs). This specificity has been attributed for certain EPG/PGIP combinations to differences in primary sequence, but this explanation is unable to account for the full range of binding and inhibitory activities observed. In this paper, we have fully characterized the glycosylation on the PGIP derived from Pyrus communis and demonstrated, using a combination of PNGaseF and PNGaseA in (18)O-water, that the Pyrus communis PGIP utilizes all seven potential sites of N-linked glycosylation. Further, we demonstrate that certain sites appear to be modified only by glycans bearing alpha3-linked core fucosylation, while others are occupied by a mixture of fucosylated and nonfucosylated glycans. Modeling of the carbohydrates onto a homologous structure of PGIP indicates potential roles for glycosylation in mediating the interactions of PGIPs with EPGs. PMID:19072240

Lim, Jae-Min; Aoki, Kazuhiro; Angel, Peggi; Garrison, Derek; King, Daniel; Tiemeyer, Michael; Bergmann, Carl; Wells, Lance

2009-02-01

40

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.

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

2006-01-01

41

Geographic Information System Interactive Map Server  

NSDL National Science Digital Library

Cornell University's Institute for the Study of the Continents (INSTOC) has launched this interactive, data-rich Website to provide regional "maps showing major geographic features of a region, along with such information as the location of earthquake faults, a record of earthquake occurrences and technical data about the events." The Geoscience Interactive Database (Java applet with accompanying User Guide) enables users to interact dynamically with "large volumes of organized digital data sets, map and display any parts of selected data," and create unique maps for download (in postscript or JPEG formats). In addition to the database, INSTOC offers information about their current projects, highlighted at the Webpage, including Building the Digital Earth, Active Tectonics Studies in the Dead Sea Fault Zone, and The Saudi Arabia Seismology Project, among others.

42

Topographic Map of Pathfinder Landing Site  

NASA Technical Reports Server (NTRS)

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

NOTE: original caption as published in Science Magazine

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

1997-01-01

43

Interaction network mapping among IL-32 isoforms.  

PubMed

IL-32 has been studied for its pleiotropic effects ranging from host immune responses to cell differentiation. Although several IL-32 isoforms have been characterized for their effects on cells, the roles of the others remain unclear. We previously reported that IL-32? interacted with IL-32? and inhibited IL-32?-mediated IL-10 production. Thus, we performed comprehensive analyses to reveal more interactions between IL-32 isoforms in this study. We screened the interactions of 81 combinations of nine IL-32 isoforms by using a yeast two-hybrid assay, which identified 13 heterodimeric interactions. We verified these results by using reciprocal immunoprecipitation assays and reconfirmed 10 interactions, and presented the interaction network map between IL-32 isoforms. Our data suggest that IL-32 may have diverse intracellular effects through the interactions with its different isoforms. PMID:24472437

Kang, Jeong-Woo; Park, Yun Sun; Lee, Dong Hun; Kim, Man Sub; Bak, Yesol; Ham, Sun Young; Park, Su Ho; Kim, Heejong; Ahn, Joong Hoon; Hong, Jin Tae; Yoon, Do-Young

2014-06-01

44

Interactive mapping on 3-D terrain models  

NASA Astrophysics Data System (ADS)

We present an interactive, real-time mapping system for use with digital elevation models and remotely sensed multispectral imagery that aids geoscientists in the creation and interpretation of geologic/neotectonic maps at length scales of 10 m to 1000 km. Our system provides a terrain visualization of the surface of the Earth or other terrestrial planets by displaying a virtual terrain model generated from a digital elevation model overlain by a color texture generated from orthophotos or satellite imagery. We use a quadtree-based, multiresolution display method to render in real time high-resolution virtual terrain models that span large spatial regions. The system allows users to measure the orientations of geologic surfaces and record their observations by drawing lines directly on the virtual terrain model. In addition, interpretive surfaces can be generated from these drawings and displayed to facilitate understanding of the three-dimensional geometry of geologic surfaces. The main strength of our system is the combination of real-time rendering and interactive mapping performed directly on the virtual terrain model with the ability to navigate the scene while changing viewpoints arbitrarily during mapping. User studies and comparisons with commercially available mapping software show that our system improves mapping accuracy and efficiency and also yields observations that cannot be made with existing systems.

Bernardin, T.; Cowgill, E.; Gold, R.; Hamann, B.; Kreylos, O.; Schmitt, A.

2006-10-01

45

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 (http://www.globalcarbonatlas.org): a web portal to explore, visualize, and interpret global and regional carbon fluxes from various model simulations arising from both human activities and natural processes, a work led by the Global Carbon Project.

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

2014-05-01

46

Mapping of a yeast G protein betagamma signaling interaction.  

PubMed Central

The mating pathway of Saccharomyces cerevisiae is widely used as a model system for G protein-coupled receptor-mediated signal transduction. Following receptor activation by the binding of mating pheromones, G protein betagamma subunits transmit the signal to a MAP kinase cascade, which involves interaction of Gbeta (Ste4p) with the MAP kinase scaffold protein Ste5p. Here, we identify residues in Ste4p required for the interaction with Ste5p. These residues define a new signaling interface close to the Ste20p binding site within the Gbetagamma coiled-coil. Ste4p mutants defective in the Ste5p interaction interact efficiently with Gpa1p (Galpha) and Ste18p (Ggamma) but cannot function in signal transduction because cells expressing these mutants are sterile. Ste4 L65S is temperature-sensitive for its interaction with Ste5p, and also for signaling. We have identified a Ste5p mutant (L196A) that displays a synthetic interaction defect with Ste4 L65S, providing strong evidence that Ste4p and Ste5p interact directly in vivo through an interface that involves hydrophobic residues. The correlation between disruption of the Ste4p-Ste5p interaction and sterility confirms the importance of this interaction in signal transduction. Identification of the Gbetagamma coiled-coil in Ste5p binding may set a precedent for Gbetagamma-effector interactions in more complex organisms.

Dowell, S J; Bishop, A L; Dyos, S L; Brown, A J; Whiteway, M S

1998-01-01

47

Site-City Interaction through Modifications of Site Effects  

Microsoft Academic Search

The analysis of seismic site effects generally disregards the influence of surface structures on the free field motion in densely urbanized areas. This paper aims at investigating this particular problem called site-city interaction especially by comparison to the \\

Jean-François Semblat; Marc Kham; Philippe Guéguen; Pierre-Yves Bard; Anne Marie Duval

2009-01-01

48

Protein interaction mapping: a Drosophila case study.  

PubMed

The Drosophila (fruit fly) model system has been instrumental in our current understanding of human biology, development, and diseases. Here, we used a high-throughput yeast two-hybrid (Y2H)-based technology to screen 102 bait proteins from Drosophila melanogaster, most of them orthologous to human cancer-related and/or signaling proteins, against high-complexity fly cDNA libraries. More than 2300 protein-protein interactions (PPI) were identified, of which 710 are of high confidence. The computation of a reliability score for each protein-protein interaction and the systematic identification of the interacting domain combined with a prediction of structural/functional motifs allow the elaboration of known complexes and the identification of new ones. The full data set can be visualized using a graphical Web interface, the PIMRider (http://pim.hybrigenics.com), and is also accessible in the PSI standard Molecular Interaction data format. Our fly Protein Interaction Map (PIM) is surprisingly different from the one recently proposed by Giot et al. with little overlap between the two data sets. Analysis of the differences in data sets and methods suggests alternative strategies to enhance the accuracy and comprehensiveness of the post-genomic generation of broad-scale protein interaction maps. PMID:15710747

Formstecher, Etienne; Aresta, Sandra; Collura, Vincent; Hamburger, Alexandre; Meil, Alain; Trehin, Alexandra; Reverdy, Céline; Betin, Virginie; Maire, Sophie; Brun, Christine; Jacq, Bernard; Arpin, Monique; Bellaiche, Yohanns; Bellusci, Saverio; Benaroch, Philippe; Bornens, Michel; Chanet, Roland; Chavrier, Philippe; Delattre, Olivier; Doye, Valérie; Fehon, Richard; Faye, Gérard; Galli, Thierry; Girault, Jean-Antoine; Goud, Bruno; de Gunzburg, Jean; Johannes, Ludger; Junier, Marie-Pierre; Mirouse, Vincent; Mukherjee, Ashim; Papadopoulo, Dora; Perez, Franck; Plessis, Anne; Rossé, Carine; Saule, Simon; Stoppa-Lyonnet, Dominique; Vincent, Alain; White, Michael; Legrain, Pierre; Wojcik, Jérôme; Camonis, Jacques; Daviet, Laurent

2005-03-01

49

Protein interaction mapping: A Drosophila case study  

PubMed Central

The Drosophila (fruit fly) model system has been instrumental in our current understanding of human biology, development, and diseases. Here, we used a high-throughput yeast two-hybrid (Y2H)-based technology to screen 102 bait proteins from Drosophila melanogaster, most of them orthologous to human cancer-related and/or signaling proteins, against high-complexity fly cDNA libraries. More than 2300 protein-protein interactions (PPI) were identified, of which 710 are of high confidence. The computation of a reliability score for each protein-protein interaction and the systematic identification of the interacting domain combined with a prediction of structural/functional motifs allow the elaboration of known complexes and the identification of new ones. The full data set can be visualized using a graphical Web interface, the PIMRider (http://pim.hybrigenics.com), and is also accessible in the PSI standard Molecular Interaction data format. Our fly Protein Interaction Map (PIM) is surprisingly different from the one recently proposed by Giot et al. with little overlap between the two data sets. Analysis of the differences in data sets and methods suggests alternative strategies to enhance the accuracy and comprehensiveness of the post-genomic generation of broad-scale protein interaction maps.

Formstecher, Etienne; Aresta, Sandra; Collura, Vincent; Hamburger, Alexandre; Meil, Alain; Trehin, Alexandra; Reverdy, Celine; Betin, Virginie; Maire, Sophie; Brun, Christine; Jacq, Bernard; Arpin, Monique; Bellaiche, Yohanns; Bellusci, Saverio; Benaroch, Philippe; Bornens, Michel; Chanet, Roland; Chavrier, Philippe; Delattre, Olivier; Doye, Valerie; Fehon, Richard; Faye, Gerard; Galli, Thierry; Girault, Jean-Antoine; Goud, Bruno; de Gunzburg, Jean; Johannes, Ludger; Junier, Marie-Pierre; Mirouse, Vincent; Mukherjee, Ashim; Papadopoulo, Dora; Perez, Franck; Plessis, Anne; Rosse, Carine; Saule, Simon; Stoppa-Lyonnet, Dominique; Vincent, Alain; White, Michael; Legrain, Pierre; Wojcik, Jerome; Camonis, Jacques; Daviet, Laurent

2005-01-01

50

47 CFR 73.4108 - FM transmitter site map submissions.  

Code of Federal Regulations, 2013 CFR

...2013-10-01 2013-10-01 false FM transmitter site map submissions. 73.4108 Section 73.4108 Telecommunication...to All Broadcast Stations § 73.4108 FM transmitter site map submissions. See Memorandum Opinion and Order and...

2013-10-01

51

Wetlands proximity mapping of 86 waste sites on the Savannah River Plant  

SciTech Connect

This project developed wetlands proximity maps and provided wetlands information by means of a Geographic Environmental Data Base (GEDB) for each of 11 interaction zones identified in DPST-84-684. It includes an analysis of 86 hazardous waste sites at the Savannah River Plant (SRP). The map of each interaction zone is intended to indicate major wetland and land cover types, with emphasis on locations of hazardous waste sites with wetland areas identified within a 1000 meter radius. Statistics of aerial extent for wetland and land cover for each interaction zone are provided. 80 figs., 93 tabs.

Jensen, J.R. (South Carolina Univ., Columbia, SC (USA). Dept. of Geography)

1985-09-16

52

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.

53

National Site Classification Map for Australia  

NASA Astrophysics Data System (ADS)

Historic earthquakes have demonstrated that the properties of geological materials beneath a site have a major influence on the amplitude and frequency content of ground shaking. Consideration of site conditions is therefore an important part of seismic hazard and risk assessment. This study presents a national scale site classification for Australia, for use in regional scale seismic hazard and risk assessment. Site classes are assigned based on the methodology developed by Wills et al. (2000) for California, which uses the relationship between rock type and the shear wave velocity of the upper 30 m (Vs30). The application of this methodology to Australia is tested successfully using bore hole data from a variety of Quaternary sedimentary sequences in the Newcastle, Sydney and Perth urban areas. Adjustments to the classification scheme are suggested to better account for the deep cover of highly weathered Mesozoic (and older) regolith found in the generally stable continental setting.

Hall, L. S.; McPherson, A. A.

2005-12-01

54

National Cancer Institute - Cancer Prevention Fellowship Program - Site Map  

Cancer.gov

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

55

A NEHRP Site Class Map for the Island of Hawaii  

NASA Astrophysics Data System (ADS)

As demonstrated in the 2006 M 6.7 Kiholo Bay earthquake, where some strong motion stations recorded peak horizontal accelerations close to 1g, site response effects can be significant on the Big Island. As part of FEMA-supported studies following the earthquake, we have produced a new 1:100,000-scale map of site conditions for the Big Island of Hawaii. The mapping makes use of about 25 new SASW measurements (Wong et al., 2008) and 1:100,000-scale geologic mapping by Sherrod et al. (2007). An earlier 2006 site class map portrayed nearly all of the island as NEHRP site class B; however, based on about 20 SASW measurements in areas mapped as basalt, we believe that most of the island should be mapped as NEHRP C or D. Vs30 estimates for these basalt sites ranged from 844 to 1,812 ft/sec, spanning NEHRP classes C and D. The median value for these Vs30 estimates is 1,304 ft/sec, with a log mean of 1,274 ft/sec and a standard deviation of 274 ft/sec. The sites cover a range of basaltic rock conditions as depicted on the geologic map, including lava flows, scoria cones, littoral deposits, spatter or tuff cones, cinder cones, and lava domes. Other geologic map unit groups for which only a few Vs30 estimates were made from SASW data include alluvium, ash/tephra, and artificial fill. We assign to these map units NEHRP site class D?, C to E, and C to E, respectively. Geologic deposits for which we do not have quantitative velocity data and have made preliminary site class assignments are sand dunes (D?), landslide deposits (D?), and glacial deposits (D?). We also attempted to relate Vs30 estimates to mapped pedogenic soil units, ages of mapped basalt units, and source volcanoes for basalt units, but found little basis for making these correlations. This new map will be incorporated into ShakeMap and HAZUS, which are operational on the Big Island.

Knudsen, K. L.; Wong, I. G.; Terra, F.

2008-12-01

56

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. Its goals are to stress the basic principles of physics, engage students in modeling, and include 20th century applications. The web site provides extensive resources for instructors using the texts, including software, discussion forums, instructional activities, and lecture notes.

Chabay, Ruth W.; Sherwood, Bruce A.

2009-03-17

57

Interactive Mapping on Virtual Terrain Models Using RIMS (Real-time, Interactive Mapping System)  

NASA Astrophysics Data System (ADS)

Recent and ongoing space missions are yielding new multispectral data for the surfaces of Earth and other planets at unprecedented rates and spatial resolution. With their high spatial resolution and widespread coverage, these data have opened new frontiers in observational Earth and planetary science. But they have also precipitated an acute need for new analytical techniques. To address this problem, we have developed RIMS, a Real-time, Interactive Mapping System that allows scientists to visualize, interact with, and map directly on, three-dimensional (3D) displays of georeferenced texture data, such as multispectral satellite imagery, that is draped over a surface representation derived from digital elevation data. The system uses a quadtree-based multiresolution method to render in real time high-resolution (3 to 10 m/pixel) data over large (800 km by 800 km) spatial areas. It allows users to map inside this interactive environment by generating georeferenced and attributed vector-based elements that are draped over the topography. We explain the technique using 15 m ASTER stereo-data from Iraq, P.R. China, and other remote locations because our particular motivation is to develop a technique that permits the detailed (10 m to 1000 m) neotectonic mapping over large (100 km to 1000 km long) active fault systems that is needed to better understand active continental deformation on Earth. RIMS also includes a virtual geologic compass that allows users to fit a plane to geologic surfaces and thereby measure their orientations. It also includes tools that allow 3D surface reconstruction of deformed and partially eroded surfaces such as folded bedding planes. These georeferenced map and measurement data can be exported to, or imported from, a standard GIS (geographic information systems) file format. Our interactive, 3D visualization and analysis system is designed for those who study planetary surfaces, including neotectonic geologists, geomorphologists, marine geophysicists, and planetary scientists. The strength of our system is that it combines interactive rendering with interactive mapping and measurement of features observed in topographic and texture data. Comparison with commercially available software indicates that our system improves mapping accuracy and efficiency. More importantly, it enables Earth scientists to rapidly achieve a deeper level of understanding of remotely sensed data, as observations can be made that are not possible with existing systems.

Bernardin, T.; Cowgill, E.; Gold, R. D.; Hamann, B.; Kreylos, O.; Schmitt, A.

2006-12-01

58

Groundwater Maps of the Hanford Site, December 1991.  

National Technical Information Service (NTIS)

The Groundwater Maps of the Hanford Site, December 1991 is the latest update to a series of semiannual reports providing the results of the water level measurement activity at the Hanford Site (Figure 1). These reports present a compilation of the ground ...

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

1992-01-01

59

INTERACTIVE NAME PLACEMENT FOR PROVISIONAL MAPS.  

USGS Publications Warehouse

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

Goldberg, Jeffrey, L.; Miller, Thomas, C.

1983-01-01

60

Comprehensive interaction map of the Arabidopsis MADS box transcription factors  

Microsoft Academic Search

Interactions between proteins are essential for their functioning and the biological processes they control. The elucidation of interaction maps based on yeast studies is a first step toward the understanding of molecular networks and provides a framework of proteins that possess the capacity and specificity to interact. Here, we present a comprehensive plant protein–protein interactome map of nearly all members

Stefan de Folter; Richard G. H. Immink; Martin Kieffer; L. Parenicová; Stefan R. Henz; Detlef Weigel; Marco Busscher; K. Kooiker; Lucia Colombo; Martin M. Kater; B. Davis; G. C. Angenent

2005-01-01

61

Design Issues for Pen-Centric Interactive Maps  

Microsoft Academic Search

\\u000a Recent advances in interactive pen-aware systems, pattern recognition technologies, and human–computer interaction have provided\\u000a new opportunities for pen-based communication between human users and intelligent computer systems. Using interactive maps,\\u000a users can annotate pictorial or cartographic information by means of pen gestures and handwriting. Interactive maps may provide\\u000a an efficient means of communication, in particular in the envisaged contexts of crisis

Louis Vuurpijl; Don Willems; Ralph Niels; Marcel van Gerven

2010-01-01

62

Quantitative Genetic Interaction Mapping Using the E-MAP Approach  

PubMed Central

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

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

2010-01-01

63

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

PubMed

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

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

2014-01-01

64

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

PubMed Central

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

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

2014-01-01

65

Groundwater Maps of the Hanford Site, December 1992  

SciTech Connect

The Groundwater maps of the Hanford Site, December 1992 is the semiannual update of the series of reports that document the configuration of the uppermost unconfined aquifer beneath the Hanford Site (Figure 1). This series is based on water level measurements collected from site groundwater monitoring wells each June and December. These reports document the changes in the groundwater level at Hanford as the site transitions from a nuclear material production role to environmental restoration and remediation. In addition, these reports provide water level data to support the various site characterization and groundwater monitoring programs currently in progress on the Hanford Site. Groundwater Maps of the Hanford Site are prepared for the US Department of Energy, Office of Environmental Restoration and Waste Management, by the Hanford Site Operations and Engineering Contractor, Westinghouse Hanford Company (WHC). This document fulfills reporting requirements specified by WHC (1988a) Section 8.0, ``Water Quality`` and also described in the environmental monitoring plan for the Hanford Site (DOE-RL 1991).

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

1993-09-01

66

Hanford site Computer Automated Mapping Information System (CAMIS)  

SciTech Connect

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

Rush, S.F. [ICF Kaiser Hanford Co., Richland, WA (United States)

1995-09-01

67

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.

1975-01-01

68

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

2004-01-01

69

Groundwater maps of the Hanford Site, December 1995.  

National Technical Information Service (NTIS)

This the latest in a series of reports that document the configuration of the water table aquifer beneath the Hanford Site. This series presents the results of the semiannual water level measurement program and the water table maps generated from these me...

M. D. Sweeney

1996-01-01

70

Interactive Journey Through the Innerbody Web Site  

Microsoft Academic Search

Innerbody.com is a commercial, educational Web site designed for anyone interested in learning the intricacies of the human anatomy. It provides an interactive journey through the ten systems of the human body using tutorials, animations, diagrams, and descriptive links.

2008-01-01

71

Mapping glycoconjugate-mediated interactions of marine Bacteroidetes with diatoms.  

PubMed

The degradation of diatoms is mainly catalyzed by Bacteroidetes and this process is of global relevance for the carbon cycle. In this study, a combination of catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) and fluorescent lectin binding analysis (FLBA) was used to identify and map glycoconjugates involved in the specific interactions of Bacteroidetes and diatoms, as well as detritus, at the coastal marine site Helgoland Roads (German Bight, North Sea). The study probed both the presence of lectin-specific extracellular polymeric substances (EPS) of Bacteroidetes for cell attachment and that of glycoconjugates on diatoms with respect to binding sites for Bacteroidetes. Members of the clades Polaribacter and Ulvibacter were shown to form microcolonies within aggregates for which FLBA indicated the presence of galactose containing slime. Polaribacter spp. was shown to bind specifically to the setae of the abundant diatom Chaetoceros spp., and the setae were stained with fucose-specific lectins. In contrast, Ulvibacter spp. attached to diatoms of the genus Asterionella which bound, among others, the mannose-specific lectin PSA. The newly developed CARD-FISH/FLBA protocol was limited to the glycoconjugates that persisted after the initial CARD-FISH procedure. The differential attachment of bacteroidetal clades to diatoms and their discrete staining by FLBA provided evidence for the essential role that formation and recognition of glycoconjugates play in the interaction of bacteria with phytoplankton. PMID:23809997

Bennke, Christin M; Neu, Thomas R; Fuchs, Bernhard M; Amann, Rudolf

2013-09-01

72

Global Land Survey Impervious Mapping Project Web Site  

NASA Technical Reports Server (NTRS)

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

DeColstoun, Eric Brown; Phillips, Jacqueline

2014-01-01

73

CRISM mapping of surface photometric parameters at MER landing sites  

NASA Astrophysics Data System (ADS)

CRISM (Compact Reconnaissance Imaging Spectrometer for Mars) on-board MRO (Mars Reconnaissance Orbiter) acquires observations under varied geometry conditions in visible/near infrared which can provide constraints on the surface physical properties. The study consists on the estimation of the surface photometric parameters by inverting Hapke's photometric model in a Bayesian framework at Mars Exploration Rover (MER) landing sites (Gusev Crater and Meridiani Planum). We present here one of the 6 photometric parameter map, the single scattering albedo ?, which is related to the composition and the particle size. The map of the parameter ? is estimated at 750 nm with a spatial resolution of 180m/pxl.

Fernando, J.; Schmidt, F.; Pinet, P.; Ceamanos, X.; Douté, S.; Daydou, Y.

2013-09-01

74

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

PubMed

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 http://mupit.icm.jhu.edu . PMID:23793516

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

2013-11-01

75

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.

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

2012-01-01

76

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.

2007-01-01

77

The measurement of molecular diversity by receptor site interaction simulation.  

PubMed

The assembly of large compound libraries for the purpose of screening against various receptor targets to identify chemical leads for drug discovery programs has created a need for methods to measure the molecular diversity of such libraries. The method described here, for which we propose the acronym RESIS (for Receptor Site Interaction Simulation), relates directly to this use. A database is built of three-dimensional representations of the compounds in the library and a set of three-point three-dimensional theoretical receptor sites is generated based on putative hydrophobic and polar interactions. A series of flexible, three-dimensional searches is then performed over the database, using each of the theoretical sites as the basis for one such search. The resulting pattern of hits across the grid of theoretical receptor sites provides a measure of the molecular diversity of the compound library. This can be conveniently displayed as a density map which provides a readily comprehensible visual impression of the library diversity characteristics. A library of 7500 drug compounds derived from the CIPSLINEPC databases was characterized with respect to molecular diversity using the RESIS method. Some specific uses for the information obtained from application of the method are discussed. A comparison was made of the results from the RESIS method with those from a recently published two-dimensional approach for assessing molecular diversity using sets of compounds from the Maybridge database (MAY). PMID:9834906

Parks, C A; Crippen, G M; Topliss, J G

1998-09-01

78

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

2009-01-01

79

Mapping Genetically Compensatory Pathways from Synthetic Lethal Interactions in Yeast  

PubMed Central

Background Synthetic lethal genetic interaction analysis has been successfully applied to predicting the functions of genes and their pathway identities. In the context of synthetic lethal interaction data alone, the global similarity of synthetic lethal interaction patterns between two genes is used to predict gene function. With physical interaction data, such as protein-protein interactions, the enrichment of physical interactions within subsets of genes and the enrichment of synthetic lethal interactions between those subsets of genes are used as an indication of compensatory pathways. Result In this paper, we propose a method of mapping genetically compensatory pathways from synthetic lethal interactions. Our method is designed to discover pairs of gene-sets in which synthetic lethal interactions are depleted among the genes in an individual set and where such gene-set pairs are connected by many synthetic lethal interactions. By its nature, our method could select compensatory pathway pairs that buffer the deleterious effect of the failure of either one, without the need of physical interaction data. By focusing on compensatory pathway pairs where genes in each individual pathway have a highly homogenous cellular function, we show that many cellular functions have genetically compensatory properties. Conclusion We conclude that synthetic lethal interaction data are a powerful source to map genetically compensatory pathways, especially in systems lacking physical interaction information, and that the cellular function network contains abundant compensatory properties.

Ma, Xiaotu; Tarone, Aaron M.; Li, Wenyuan

2008-01-01

80

Interaction of kinesin motors, microtubules, and MAPs  

Microsoft Academic Search

Kinesins are a family of microtubule-dependent motor proteins that carry cargoes such as vesicles, organelles, or protein complexes along microtubules. Here we summarize structural studies of the “conventional” motor protein kinesin-1 and its interactions with microtubules, as determined by X-ray crystallography and cryo-electron microscopy. In particular, we consider the docking between the kinesin motor domain and tubulin subunits and summarize

A. MARX; J. MÜLLER; E.-M. MANDELKOW; A. HOENGER

2006-01-01

81

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.

1980-01-01

82

A geostatistical approach to mapping site response spectral amplifications  

USGS Publications Warehouse

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

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

2010-01-01

83

Perry-Castaneda Library Map Collection: Country and Regional Map Sites  

NSDL National Science Digital Library

This map collection covers nearly every country and region from the Adriatic Sea to Zimbabwe. There are also cartographic reference resources (gazetteers, distance calculators, time zone maps, sun and moon rise/set calculators, tidal information, map projections, bibliographies, glossaries and guides), outline maps, city maps, state maps, historic maps, and weather maps.

84

Where Have All the Interactions Gone? Estimating the Coverage of Two-Hybrid Protein Interaction Maps  

PubMed Central

Yeast two-hybrid screens are an important method for mapping pairwise physical interactions between proteins. The fraction of interactions detected in independent screens can be very small, and an outstanding challenge is to determine the reason for the low overlap. Low overlap can arise from either a high false-discovery rate (interaction sets have low overlap because each set is contaminated by a large number of stochastic false-positive interactions) or a high false-negative rate (interaction sets have low overlap because each misses many true interactions). We extend capture–recapture theory to provide the first unified model for false-positive and false-negative rates for two-hybrid screens. Analysis of yeast, worm, and fly data indicates that 25% to 45% of the reported interactions are likely false positives. Membrane proteins have higher false-discovery rates on average, and signal transduction proteins have lower rates. The overall false-negative rate ranges from 75% for worm to 90% for fly, which arises from a roughly 50% false-negative rate due to statistical undersampling and a 55% to 85% false-negative rate due to proteins that appear to be systematically lost from the assays. Finally, statistical model selection conclusively rejects the Erdös-Rényi network model in favor of the power law model for yeast and the truncated power law for worm and fly degree distributions. Much as genome sequencing coverage estimates were essential for planning the human genome sequencing project, the coverage estimates developed here will be valuable for guiding future proteomic screens. All software and datasets are available in Datasets S1 and S2, Figures S1–S5, and Tables S1?S6, and are also available from our Web site, http://www.baderzone.org.

Huang, Hailiang; Jedynak, Bruno M; Bader, Joel S

2007-01-01

85

Auto-FACE: An NMR Based Binding Site Mapping Program for Fast Chemical Exchange Protein-Ligand Systems  

PubMed Central

Background Nuclear Magnetic Resonance (NMR) spectroscopy offers a variety of experiments to study protein-ligand interactions at atomic resolution. Among these experiments, N Heteronuclear Single Quantum Correlation (HSQC) experiment is simple, less time consuming and highly informative in mapping the binding site of the ligand. The interpretation of N HSQC becomes ambiguous when the chemical shift perturbations are caused by non-specific interactions like allosteric changes and local structural rearrangement. Under such cases, detailed chemical exchange analysis based on chemical shift perturbation will assist in locating the binding site accurately. Methodology/Principal Findings We have automated the mapping of binding sites for fast chemical exchange systems using information obtained from N HSQC spectra of protein serially titrated with ligand of increasing concentrations. The automated program Auto-FACE (Auto-FAst Chemical Exchange analyzer) determines the parameters, e.g. rate of change of perturbation, binding equilibrium constant and magnitude of chemical shift perturbation to map the binding site residues. Interestingly, the rate of change of perturbation at lower ligand concentration is highly sensitive in differentiating the binding site residues from the non-binding site residues. To validate this program, the interaction between the protein and the ligand BH3I-1 was studied. Residues in the hydrophobic BH3 binding groove of were easily identified to be crucial for interaction with BH3I-1 from other residues that also exhibited perturbation. The geometrically averaged equilibrium constant () calculated for the residues present at the identified binding site is consistent with the values obtained by other techniques like isothermal calorimetry and fluorescence polarization assays (). Adjacent to the primary site, an additional binding site was identified which had an affinity of 3.8 times weaker than the former one. Further NMR based model fitting for individual residues suggest single site model for residues present at these binding sites and two site model for residues present between these sites. This implies that chemical shift perturbation can represent the local binding event much more accurately than the global binding event. Conclusion/Significance Detail NMR chemical shift perturbation analysis enabled binding site residues to be distinguished from non-binding site residues for accurate mapping of interaction site in complex fast exchange system between small molecule and protein. The methodology is automated and implemented in a program called “Auto-FACE”, which also allowed quantitative information of each interaction site and elucidation of binding mechanism.

Krishnamoorthy, Janarthanan; Yu, Victor C. K.; Mok, Yu-Keung

2010-01-01

86

Seismic site classification and site period mapping of Chennai City using geophysical and geotechnical data  

NASA Astrophysics Data System (ADS)

Subsurface conditions play a major role in the damage potential of earthquakes and the seismic soil amplification of a site which is a critical factor affecting the level of ground shaking. Shear wave velocity ( Vs) of the soil layer is an important parameter influencing the amplification behaviour of the site. Site characterization in calculating seismic hazards is usually based on the near-surface shear wave velocity values. The average shear wave velocity of the top 30 m of the soil, referred to as ( Vs) 30 is commonly adopted by competent building codes to classify the sites for earthquake resistant design of structures and in general it is widely used in microzonation studies. In the present study, the shear wave velocity of soil layers was measured at 30 locations in Chennai City by Multichannel Analysis of Surface Waves (MASW) test. In addition, nearly 300 borehole data were used to estimate Vs based on the correlations between Vs and SPT-N values for Chennai developed by authors earlier. Merging of MASW test results with borehole data yields sufficient coverage of Vs to develop a new site classification map for Chennai based on the NEHRP standard. It is found that part of the city belong to site D category (stiff soil). The developed site period map reveals that the fundamental site period varies in the range of 0.03 to 0.6 s, thus the soil conditions in Chennai pose a potential threat during earthquakes to low rise buildings (less than 6 storeys) which are densely distributed throughout the city.

Maheswari, R. Uma; Boominathan, A.; Dodagoudar, G. R.

2010-11-01

87

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)

2011-04-01

88

Facilitating participatory multilevel decision-making by using interactive mental maps.  

PubMed

Participation of citizens in political, economic or social decisions is increasingly recognized as a precondition to foster sustainable development processes. Since spatial information is often important during planning and decision making, participatory mapping gains in popularity. However, little attention has been paid to the fact that information must be presented in a useful way to reach city planners and policy makers. Above all, the importance of visualisation tools to support collaboration, analytical reasoning, problem solving and decision-making in analysing and planning processes has been underestimated. In this paper, we describe how an interactive mental map tool has been developed in a highly interdisciplinary disaster management project in Chennai, India. We moved from a hand drawn mental maps approach to an interactive mental map tool. This was achieved by merging socio-economic and geospatial data on infrastructure, local perceptions, coping and adaptation strategies with remote sensing data and modern technology of map making. This newly developed interactive mapping tool allowed for insights into different locally-constructed realities and facilitated the communication of results to the wider public and respective policy makers. It proved to be useful in visualising information and promoting participatory decision-making processes. We argue that the tool bears potential also for health research projects. The interactive mental map can be used to spatially and temporally assess key health themes such as availability of, and accessibility to, existing health care services, breeding sites of disease vectors, collection and storage of water, waste disposal, location of public toilets or defecation sites. PMID:19021113

Pfeiffer, Constanze; Glaser, Stephanie; Vencatesan, Jayshree; Schliermann-Kraus, Elke; Drescher, Axel; Glaser, Rüdiger

2008-11-01

89

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.

90

Context modeling with Evolutionary Fuzzy Cognitive Map in interactive storytelling  

Microsoft Academic Search

To generate a believable and dynamic virtual world is a great challenge in interactive storytelling. In this paper, we propose a model, namely evolutionary fuzzy cognitive map (E-FCM), to model the dynamic causal relationships among different context variables. As an extension to conventional FCM, E-FCM models not only the fuzzy causal relationships among the variables, but also the probabilistic property

Yundong Cai; Chunyan Miao; Ah-Hwee Tan; Zhiqi Shen

2008-01-01

91

Multimodal Interaction with a Map-Based Simulation System  

Microsoft Academic Search

LACE was originally developed for the Symbolics Lisp machine, where it had a graphical interface con- sisting of an interactive Map Display System and two tools, the Hierarchy and Rack Systems, for viewing object hierarchies and monitoring the simulation run. We acquired a Common LISP port of LACE (minus the graphical interface) distributed as a testbed application with the TEXPLAN

Kenneth Wauchope

1996-01-01

92

Mapping of Vps21 and HOPS binding sites in Vps8 and effect of binding site mutants on endocytic trafficking.  

PubMed

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

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

2010-04-01

93

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

PubMed Central

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

Pawelec, Agnes; Arsic, Janja; Kolling, Ralf

2010-01-01

94

Instant visitation maps for interactive visualization of uncertain particle trajectories  

NASA Astrophysics Data System (ADS)

Visitation maps are an effective means to analyze the frequency of similar occurrences in large sets of uncertain particle trajectories. A visitation map counts for every cell the number of trajectories passing through this cell, and it can then be used to visualize pathways of a certain visitation percentage. In this paper, we introduce an interactive method for the construction and visualization of high-resolution 3D visitation maps for large numbers of trajectories. To achieve this we employ functionality on recent GPUs to efficiently voxelize particle trajectories into a 3D texture map. In this map we visualize envelopes enclosing particle pathways that are followed by a certain percentage of particles using direct volume rendering techniques. By combining visitation map construction with GPU-based Monte-Carlo particle tracing we can even demonstrate the instant construction of a visitation map from a given vector field. To facilitate the visualization of safety regions around possible trajectories, we further generate Euclidean distance transform volumes to these trajectories on the fly. We demonstrate the application of our approach for visualizing the variation of stream lines in 3D flows due to different numerical integration schemes or errors introduced through data transformation operations, as well as for visualizing envelopes of probabilistic fiber bundles in DTI tractography.

Bürger, Kai; Fraedrich, Roland; Merhof, Dorit; Westermann, Rüdiger

2012-01-01

95

Gate Map Tunneling Spectroscopy of Interactions in Graphene  

NASA Astrophysics Data System (ADS)

The local electron density of states (LDOS) in semiconductors and semimetals like graphene can be adjusted with respect to the Fermi energy by using an electric field applied by a nearby gate electrode. In this way interaction physics can be turned on and off as the electron density is modulated at the Fermi level in an applied magnetic field. Interaction physics in graphene has been an interesting subject since the first isolation of single layer graphene, due the singular nature of the Dirac point in the graphene spectrum. The electronic density of states at the Dirac point vanishes and the long-range Coulomb interactions are not effectively screened, which gives rise to a rich spectrum of interaction-driven physics in magnetic fields at low temperatures. In this talk, I will present recent experimental results in graphene on boron nitride substrates using gate mapping tunneling spectroscopy [1]. Gate map tunneling spectroscopy consists of series of single tunneling spectra obtained as a back gate voltage is varied to change the carrier density at the Fermi level. The gate maps show clear variations of the tunneling spectrum as a function of carrier density. The formation of Landau levels (LLs) in magnetic fields up to 8 T is observed to form a staircase pattern in maps of the tunneling conductance in the 2-dimensional tunneling bias voltage-gate voltage plane. LLs modulate the LDOS at the Fermi level as the carrier density is varied with the gate potential. An analysis of the LL peak positions shows that the graphene energy-momentum remains linear at low energies, but that the dispersion velocity is enhanced due to interactions as the density is lowered approaching the Dirac point. Interaction effects are also strongly seen near zero density by the opening of large Coulomb gaps in the tunneling spectra, which will be discussed in terms of the competing effects of residual substrate induced disorder and interactions. [4pt] [1] J. Chae et. al., PRL 197, 116802 (2012)

Chae, Jungseok

2013-03-01

96

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

Microsoft Academic Search

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

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

1997-01-01

97

In silico mapping of polymorphic miRNA-mRNA interactions in autoimmune thyroid diseases.  

PubMed

Abstract MicroRNAs (miRNAs) are important regulators of gene expression and translation. The genetic variants altering miRNA targets have been associated with many diseases. Here we systematically mapped the human genetic polymorphisms that may affect miRNA-mRNA interactions in the autoimmune thyroid disease (AITD) pathway. We also mapped the polymorphic miRNA target sites in the genes that have been linked to AITDs or other thyroid-related diseases/phenotypes in genome-wide association studies (GWAS). These genetic polymorphisms may potentially contribute to the pathogenesis of AITDs and other thyroid diseases. The polymorphic miRNA-mRNA interactions we mapped in the AITD pathway and the GWAS-informed thyroid disease loci may provide insights into the possible miRNA-mediated molecular mechanisms through which genetic variants assert their influences on thyroid diseases and phenotypes. PMID:24611733

Cui, Yan

2014-08-01

98

Phylogeny-guided interaction mapping in seven eukaryotes  

PubMed Central

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 accurate predictions. We apply our framework to reconcile seven eukaryotic interactomes: H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, S. cerevisiae and A. thaliana. Comprehensive GO-based quality assessment indicates a 5% to 44% score increase in predicted interactomes compared to the input data. Further support is provided by gold-standard MIPS, CYC2008 and HPRD datasets. We demonstrate the ability to recover known PPIs in well-characterized yeast and human complexes (26S proteasome, endosome and exosome) and suggest possible new partners interacting with the putative SWI/SNF chromatin remodeling complex in A. thaliana. Conclusion Our phylogeny-guided approach compares favorably to two standard methods for mapping PPIs across species. Detailed analysis of predictions in selected functional modules uncovers specific PPI profiles among homologous proteins, establishing interaction-based partitioning of protein families. Provided evidence also suggests that interactions within core complex subunits are in general more conserved and easier to transfer accurately to other organisms, than interactions between these subunits.

2009-01-01

99

Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data  

PubMed Central

Recently, a number of advanced screening technologies have allowed for the comprehensive quantification of aggravating and alleviating genetic interactions among gene pairs. In parallel, TAP-MS studies (tandem affinity purification followed by mass spectroscopy) have been successful at identifying physical protein interactions that can indicate proteins participating in the same molecular complex. Here, we propose a method for the joint learning of protein complexes and their functional relationships by integration of quantitative genetic interactions and TAP-MS data. Using 3 independent benchmark datasets, we demonstrate that this method is >50% more accurate at identifying functionally related protein pairs than previous approaches. Application to genes involved in yeast chromosome organization identifies a functional map of 91 multimeric complexes, a number of which are novel or have been substantially expanded by addition of new subunits. Interestingly, we find that complexes that are enriched for aggravating genetic interactions (i.e., synthetic lethality) are more likely to contain essential genes, linking each of these interactions to an underlying mechanism. These results demonstrate the importance of both large-scale genetic and physical interaction data in mapping pathway architecture and function.

Bandyopadhyay, Sourav; Kelley, Ryan; Krogan, Nevan J.; Ideker, Trey

2008-01-01

100

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

2014-05-01

101

USGS Topographic Maps  

NSDL National Science Digital Library

The United States Geological Survey (USGS) is the primary civilian mapping agency of the United States. Materials available at this site include general information about topographic mapping, and information about USGS map products and how to obtain them. There is also information on digital raster graphics (DRG), scanned images of U.S. Geological Survey (USGS) standard series topographic maps. Other links provide access to data on map revisions, map symbols, mapping standards, and the National Map, a new interactive online mapping application.

2010-10-26

102

Methods for Mapping of Interaction Networks Involving Membrane Proteins  

SciTech Connect

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

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

2007-11-23

103

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

2013-05-01

104

Microarray Profiling of Phage-Display Selections for Rapid Mapping of Transcription Factor-DNA Interactions  

PubMed Central

Modern computational methods are revealing putative transcription-factor (TF) binding sites at an extraordinary rate. However, the major challenge in studying transcriptional networks is to map these regulatory element predictions to the protein transcription factors that bind them. We have developed a microarray-based profiling of phage-display selection (MaPS) strategy that allows rapid and global survey of an organism's proteome for sequence-specific interactions with such putative DNA regulatory elements. Application to a variety of known yeast TF binding sites successfully identified the cognate TF from the background of a complex whole-proteome library. These factors contain DNA-binding domains from diverse families, including Myb, TEA, MADS box, and C2H2 zinc-finger. Using MaPS, we identified Dot6 as a trans-active partner of the long-predicted orphan yeast element Polymerase A & C (PAC). MaPS technology should enable rapid and proteome-scale study of bi-molecular interactions within transcriptional networks.

Freckleton, Gordon; Lippman, Soyeon I.; Broach, James R.; Tavazoie, Saeed

2009-01-01

105

A Site Response Map of the Continental U.S  

NASA Astrophysics Data System (ADS)

We create a site response map of the continental U.S. using the topographic slope methodology, which uses correlations between slope and Vs30 (Wald and Allen, 2007). We determine new regional correlations for the central and eastern U.S. (CEUS) and western U.S. (WUS) calibrated to the Vs30 observation database of Pacific Engineering and Analysis, and introduce a novel correlation for areas of the WUS that hosted Pleistocene and younger lakes. In the WUS we develop a new correlation by first removing Vs30 observations from Utah basins and the Imperial Valley, California, from the database, and second using a stochastic simulation to choose slope and Vs30 bins and calculate standard deviation and bias. We select the best model based on three criteria: (i) bias and standard deviation is among the smallest; (ii) the correlations will not change dramatically for neighboring bins; and (iii) the Vs30 bin boundaries can be matched to NEHRP categories. Relative to WUS, the Utah and Imperial Valley Vs30 values are low for a given slope. We fit a separate correlation in the manner described above. We attribute the low values to the occupation of these areas by Pleistocene and younger lakes. We posit that when sediment-laden streams entered these lakes, the flow velocity was reduced so that all coarse sediments were deposited at the lake margin, and only very fine grained (and seismically slow) material was distributed over the lake bed. This model is confirmed by: (i) relatively high Vs30 values in the geologically similar Las Vegas Valley that was not occupied by a lake; (ii) ordinary Vs30 values in Utah and Imperial Valley locations above the high lake stands; and (iii) a consistent pattern of Vs30 values in the Reno, Nevada, basin across a paleo-lake boundary. In the CEUS, we use the recent correlation of Silva et al. (2011) that includes better constraints on the correlation at rock sites. In all regions the slopes are determined from SRTM digital elevation data (Jarvis et al., 2008). The CEUS correlation is appropriate for tectonically stable regions, and the WUS correlation for tectonically active regions. We merge the two by an east-west linear weighting over the Rocky Mountain physiographic province. The Rocky Mountains were formed 40 to 80 million years ago and have subsequently experienced only epeirogenic activity since, so represent a tectonic condition intermediate between the CEUS and WUS.

Magistrale, H.; Rong, Y.; Thompson, E.; Silva, W. J.

2012-12-01

106

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

NASA Astrophysics Data System (ADS)

A team of multi-disciplinary geoscientists was tasked to characterize and evaluate a legacy nuclear detonation site in order to develop research locations with the long-term goal of improving treaty monitoring, verification, and other national security applications. There was a test at the site of interest that was detonated on June 12, 1985 in a vertical emplacement borehole at a depth of 608m below the surface in rhyolites. With announced yield of 20-150 kt, the event did not collapse to the surface and form a crater, but rather experienced a subsurface collapse with more subtle surface expressions of deformation. This result provides the team with an opportunity to evaluate a number of surface and subsurface inspection technologies in a broad context. The team collected ground-based visual observation, ground penetrating radar, electromagnetic, ground-based and airborne LiDAR, ground-based and airborne hyperspectral, gravity and magnetics, dc and induction electrical methods, and active seismic data during field campaigns in the summers of 2012 and 2013. Detection of features was performed using various approaches that were assessed for accuracy, efficiency and diversity of target features. For example, whereas the primary target of the ground-based visual observation survey was to map the surface features, the target of the gravity survey was to attempt the detection of a possible subsurface collapse zone which might be located as little as 200 meters below the surface. The datasets from surveys described above are integrated into a geographical information system (GIS) database for analysis and visualization. Other presentations during this session provide further details as to some of the work conducted. Work by Los Alamos National Laboratory and Lawrence Livermore National Laboratory was sponsored by the National Nuclear Security Administration Award No. DE-AC52-06NA25946/NST10-NCNS-PD00. Work by National Security Technologies, LLC, was performed under Contract No. DE AC52 06NA25946 with the U.S. Department of Energy. Sandia National Laboratories, is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

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

2013-12-01

107

View All Sites on a Map - National Cancer Institute  

Cancer.gov

JavaScript must be enabled in order for you to use Google Maps. However, it seems JavaScript is either disabled or not supported by your browser. To view Google Maps, enable JavaScript by changing your browser options, and then try again.

108

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

2010-01-01

109

Divalent cation sites in tomato bushy stunt virus. Difference maps at 2-9 A resolution.  

PubMed

Difference electron density maps, using as few as four 1/2 degrees oscillation photographs, have been computed for tomato bushy stunt virus crystals soaked in EDTA. GdCl3 and silicotungstate. The maps define a double divalent cation site, responsible for regulating expansion of the virus particle, as well as sites for binding tungstate anions. PMID:6417343

Hogle, J; Kirchhausen, T; Harrison, S C

1983-11-25

110

LRR Conservation Mapping to Predict Functional Sites within Protein Leucine-Rich Repeat Domains  

PubMed Central

Computational prediction of protein functional sites can be a critical first step for analysis of large or complex proteins. Contemporary methods often require several homologous sequences and/or a known protein structure, but these resources are not available for many proteins. Leucine-rich repeats (LRRs) are ligand interaction domains found in numerous proteins across all taxonomic kingdoms, including immune system receptors in plants and animals. We devised Repeat Conservation Mapping (RCM), a computational method that predicts functional sites of LRR domains. RCM utilizes two or more homologous sequences and a generic representation of the LRR structure to identify conserved or diversified patches of amino acids on the predicted surface of the LRR. RCM was validated using solved LRR+ligand structures from multiple taxa, identifying ligand interaction sites. RCM was then used for de novo dissection of two plant microbe-associated molecular pattern (MAMP) receptors, EF-TU RECEPTOR (EFR) and FLAGELLIN-SENSING 2 (FLS2). In vivo testing of Arabidopsis thaliana EFR and FLS2 receptors mutagenized at sites identified by RCM demonstrated previously unknown functional sites. The RCM predictions for EFR, FLS2 and a third plant LRR protein, PGIP, compared favorably to predictions from ODA (optimal docking area), Consurf, and PAML (positive selection) analyses, but RCM also made valid functional site predictions not available from these other bioinformatic approaches. RCM analyses can be conducted with any LRR-containing proteins at www.plantpath.wisc.edu/RCM, and the approach should be modifiable for use with other types of repeat protein domains.

Helft, Laura; Reddy, Vignyan; Chen, Xiyang; Koller, Teresa; Federici, Luca; Fernandez-Recio, Juan; Gupta, Rishabh; Bent, Andrew

2011-01-01

111

Interactive Data Map from JGI's Microbial Earth Project  

DOE Data Explorer

The Microbial Earth Project's interactive data map is a graphical representation of the NCBI taxonomy tree for 7623 type strains from DSMZ culture collection. Each leaf represents a type strain. Colors denote stains with or without genome projects (red vs green). Internal nodes (transparent) denote higher taxonomic ranks. Branch lengths are not meaningful. A selection of named taxonomic groups are shown in yellow. Note the highly uneven coverage of the type strain material by genome sequencing projects. For example, groups such as the families Halobacteriaceae and Coriobacteriaceae are well represented by sequencing projects whereas other groups such as the genera Streptomyces and Pseudomonas are largely untouched. The figure was generated by mapping NCBI taxonomic information to DSMZ type strains. Information about genome projects was obtained from the GOLD database. The Guess visualization program was used for rendering with the 'gem' layout. [Copied from http://genome.jgi-psf.org/programs/bacteria-archaea/MEP/index.jsf

112

Map Maker  

NSDL National Science Digital Library

This interactive mapping site allows users to build maps of any portion of the United States including overlays of many different kinds of data. Some of the categories of data available include agriculture, biology, climate, environment, geology, and water. The maps are printable and savable and can be shared with others via email.

Interior, United S.

113

MIMO: an efficient tool for molecular interaction maps overlap  

PubMed Central

Background Molecular pathways represent an ensemble of interactions occurring among molecules within the cell and between cells. The identification of similarities between molecular pathways across organisms and functions has a critical role in understanding complex biological processes. For the inference of such novel information, the comparison of molecular pathways requires to account for imperfect matches (flexibility) and to efficiently handle complex network topologies. To date, these characteristics are only partially available in tools designed to compare molecular interaction maps. Results Our approach MIMO (Molecular Interaction Maps Overlap) addresses the first problem by allowing the introduction of gaps and mismatches between query and template pathways and permits -when necessary- supervised queries incorporating a priori biological information. It then addresses the second issue by relying directly on the rich graph topology described in the Systems Biology Markup Language (SBML) standard, and uses multidigraphs to efficiently handle multiple queries on biological graph databases. The algorithm has been here successfully used to highlight the contact point between various human pathways in the Reactome database. Conclusions MIMO offers a flexible and efficient graph-matching tool for comparing complex biological pathways.

2013-01-01

114

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

PubMed

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

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

2012-10-01

115

Mapping the FEN1 interaction domain with hTERT  

PubMed Central

The activity of telomerase in cancer cells is tightly regulated by numerous proteins including DNA replication factors. However, it is unclear how replication proteins regulate telomerase action in higher eukaryotic cells. Previously we have demonstrated that the multifunctional DNA replication and repair protein flap endonuclease 1 (FEN1) is in complex with telomerase and may regulate telomerase activity in mammalian cells. In this study, we further analyzed the nature of this association. Our results show that FEN1 and telomerase association occurs throughout the S phase, with the maximum association in the mid S phase. We further mapped the physical domains in FEN1 required for this association and found that the C terminus and the nuclease domain of FEN1 are involved in this interaction, whereas the PCNA binding ability of FEN1 is dispensable for the interaction. These results provide insights into the nature of possible protein-protein associations that telomerase participates in for maintaining functional telomeres.

Sampathi, Shilpa; Chai, Weihang

2011-01-01

116

Progress Toward More Detailed Site-Conditions Maps for California  

NASA Astrophysics Data System (ADS)

We have developed a map of geologic units that can be distinguished by their shear-wave velocity. In developing this map we build upon earlier work to determine the shear-wave velocity characteristics of geologic units in California (Wills and Silva, 1998) and grouping geologic units with similar Vs into NEHRP categories (Wills and others, 2000). We have further refined those categories and prepared a map showing geologic units with distinct Vs characteristics (Wills and Clahan, 2006). We are testing potential refinements of the existing statewide map based on: 1. Improving the precision of locations the geologically-defined units and 2. Improving the definition of shear-wave velocity classes. For a test area in southern California, we have compiled the available high resolution geologic mapping. We have simplified the hundreds of individual geologic units shown on those maps to simplified units based on shear- wave velocity defined units of Wills and Clahan (2006). The result is a map showing geologic units with defined Vs30 values based on the most detailed available geologic mapping. Most of the simplified geologic units have well-defined ranges of shear-wave velocity, with the very important exception of younger alluvial deposits. These deposits may be thin - and profiles to 30 m include other, higher velocity materials, and the grain size and density may vary substantially. As a result there is a wide range of measured Vs30 values in younger alluvium. To sub-divide the young alluvium Wills and Clahan (2006) attempted to use very simple geographic criteria. We developed classes called thin alluvium, deep alluvium, fine alluvium and coarse alluvium based on geographic criteria. These categories appear to have differing shear-wave velocity characteristics, but the criteria for distinguishing them was not explicitly defined, nor were options for defining these classes explored. In order to make the mapping more consistent, and more applicable to other areas, we are exploring the use of two simplified rules for sub-dividing young alluvium. Preliminary results suggest that distance from bedrock and slope may both correlate with shear-wave velocity in young alluvium. Further work will define the relations between these factors and shear-wave velocity, and result in methods for producing improved maps of Vs30 for estimating seismic amplification in southern California and elsewhere.

Wills, C. J.; Gutierrez, C. I.; Silva, M. A.

2007-12-01

117

A hierarchical map of regulatory genetic interactions in membrane trafficking.  

PubMed

Endocytosis is critical for cellular physiology and thus is highly regulated. To identify regulatory interactions controlling the endocytic membrane system, we conducted 13 RNAi screens on multiple endocytic activities and their downstream organelles. Combined with image analysis of thousands of single cells per perturbation and their cell-to-cell variability, this created a high-quality and cross-comparable quantitative data set. Unbiased analysis revealed emergent properties of the endocytic membrane system and how its complexity evolved and distinct programs of regulatory control that coregulate specific subsets of endocytic uptake routes and organelle abundances. We show that these subset effects allow the mapping of functional regulatory interactions and their interaction motifs between kinases, membrane-trafficking machinery, and the cytoskeleton at a large scale, some of which we further characterize. Our work presents a powerful approach to identify regulatory interactions in complex cellular systems from parallel single-gene or double-gene perturbation screens in human cells and yeast. PMID:24906158

Liberali, Prisca; Snijder, Berend; Pelkmans, Lucas

2014-06-01

118

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 ftp://ftp.ccrs.nrcan.gc.ca/ad/CCRS_ARM/ and ARM IOP data archive under “PI data Trishchenko”. II) Surface albedo properties over the ARM SGP area have been described for 10-year period. Comparison with ECMWF data product showed some deficiencies in the ECMWF surface scheme, such as missing some seasonal variability and no dependence on sky-conditions which biases surface energy budget and has some influence of the diurnal cycle of upward radiation and atmospheric absorption. III) Four surface albedo Intensive Observation Period (IOP) Field Campaigns have been conducted for every season (August, 2002, May 2003, February 2004 and October 2004). Data have been prepared, documented and transferred to ARM IOP archive. Nine peer-reviewed journal papers and 26 conference papers have been published.

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

2008-11-28

119

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

USGS Publications Warehouse

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

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

2006-01-01

120

Bayesian Hidden Markov Models to Identify RNA-Protein Interaction Sites in PAR-CLIP  

PubMed Central

Summary The photoactivatable ribonucleoside enhanced cross-linking immunoprecipitation (PAR-CLIP) has been increasingly used for the global mapping of RNA-protein interaction sites. There are two key features of the PAR-CLIP experiments: The sequence read tags are likely to form an enriched peak around each RNA-protein interaction site; and the cross-linking procedure is likely to introduce a specific mutation in each sequence read tag at the interaction site. Several ad hoc methods have been developed to identify the RNA-protein interaction sites using either sequence read counts or mutation counts alone; however, rigorous statistical methods for analyzing PAR-CLIP are still lacking. In this study, we propose an integrative model to establish a joint distribution of observed read and mutation counts. To pinpoint the interaction sites at single base-pair resolution, we developed a novel modeling approach that adopts non-homogeneous hidden Markov models to incorporate the nucleotide sequence at each genomic location. Both simulation studies and data application showed that our method outperforms the ad hoc methods, and provides reliable inferences for the RNA-protein binding sites from PAR-CLIP data.

Yun, Jonghyun; Wang, Tao; Xiao, Guanghua

2014-01-01

121

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.

1988-01-01

122

AUTOMATION IN MARS LANDING-SITE MAPPING AND ROVER LOCALIZATION  

Microsoft Academic Search

Our project aims to automate Mars mapping and localization using robotic stereo and descent imagery. Stereo vision is a well- studied domain. However, most efforts aim only at a general scene; little work has been done toward a natural, extraterrestrial environment through consideration of its special geometry and features. Our methodology utilized the properties of piece-wise continuity of natural scene

Fengliang Xu

123

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

2005-01-01

124

Interactive Multi Objective Inverse Groundwater Modeling for the WIPP Site  

Microsoft Academic Search

This paper presents ongoing research on building an interactive and multi - objective framework to solve the groundwater inverse problem. Our research has shown that the inherent instability and non -uniqueness of this problem can be improved by incorporating expert knowledge about the hydro -geology of the site. The interactive multi -objective genetic algorithm (IMOGA) considers user preference (for different

Abhishek Singh; Barbara S. Minsker; Albert Valocchi; Douglas D. Walker

125

Mapping the energy surface of transmembrane helix-helix interactions.  

PubMed Central

Transmembrane helices are no longer believed to be just hydrophobic segments that exist solely to anchor proteins to a lipid bilayer, but rather they appear to have the capacity to specify function and structure. Specific interactions take place between hydrophobic segments within the lipid bilayer whereby subtle mutations that normally would be considered innocuous can result in dramatic structural differences. That such specificity takes place within the lipid bilayer implies that it may be possible to identify the most favorable interaction surface of transmembrane alpha-helices based on computational methods alone, as shown in this study. Herein, an attempt is made to map the energy surface of several transmembrane helix-helix interactions for several homo-oligomerizing proteins, where experimental data regarding their structure exist (glycophorin A, phospholamban, Influenza virus A M2, Influenza virus C CM2, and HIV vpu). It is shown that due to symmetry constraints in homo-oligomers the computational problem can be simplified. The results obtained are mostly consistent with known structural data and may additionally provide a view of possible alternate and intermediate configurations.

Torres, J; Kukol, A; Arkin, I T

2001-01-01

126

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

2012-05-01

127

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

Microsoft Academic Search

Summary • The provision of sequence-tagged site (STS) anchor points allows meaningful comparisons between mapping studies but can be a time-consuming process for nonmodel species or orphan crops.  Here, the first use of high-resolution melt analysis (HRM) to generate STS markers for use in linkage mapping is described. This strategy is rapid and low-cost, and circumvents the need for

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

2008-01-01

128

Current approaches to fine mapping of antigen-antibody interactions.  

PubMed

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

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

2014-08-01

129

Structural mapping of nucleotide binding sites on chloroplast coupling factor  

SciTech Connect

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

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

1982-02-16

130

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

1998-01-01

131

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

SciTech Connect

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

Bechtel Nevada

2005-08-01

132

Unambiguous Identification of miRNA:Target Site Interactions by Different Types of Ligation Reactions.  

PubMed

To exert regulatory function, miRNAs guide Argonaute (AGO) proteins to partially complementary sites on target RNAs. Crosslinking and immunoprecipitation (CLIP) assays are state-of-the-art to map AGO binding sites, but assigning the targeting miRNA to these sites relies on bioinformatics predictions and is therefore indirect. To directly and unambiguously identify miRNA:target site interactions, we modified our CLIP methodology in C. elegans to experimentally ligate miRNAs to their target sites. Unexpectedly, ligation reactions also occurred in the absence of the exogenous ligase. Our in vivo data set and reanalysis of published mammalian AGO-CLIP data for miRNA-chimeras yielded ?17,000 miRNA:target site interactions. Analysis of interactions and extensive experimental validation of chimera-discovered targets of viral miRNAs suggest that our strategy identifies canonical, noncanonical, and nonconserved miRNA:targets. About 80% of miRNA interactions have perfect or partial seed complementarity. In summary, analysis of miRNA:target chimeras enables the systematic, context-specific, in vivo discovery of miRNA binding. PMID:24857550

Grosswendt, Stefanie; Filipchyk, Andrei; Manzano, Mark; Klironomos, Filippos; Schilling, Marcel; Herzog, Margareta; Gottwein, Eva; Rajewsky, Nikolaus

2014-06-19

133

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

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

134

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

1972-01-01

135

Delineating the functional map of the interaction between nimotuzumab and the epidermal growth factor receptor.  

PubMed

Molecular details of epidermal growth factor receptor (EGFR) targeting by nimotuzumab, a therapeutic anti-cancer antibody, have been largely unknown. The current study delineated a functional map of their interface, based on phage display and extensive mutagenesis of both the target antigen and the Fv antibody fragment. Five residues in EGFR domain III (R353, S356, F357, T358, and H359T) and the third hypervariable region of nimotuzumab heavy chain were shown to be major functional contributors to the interaction. Fine specificity differences between nimotuzumab and other anti-EGFR antibodies were revealed. Mapping information guided the generation of a plausible in silico binding model. Knowledge about the epitope/paratope interface opens new avenues for the study of tumor sensitivity/resistance to nimotuzumab and for further engineering of its binding site. The developed mapping platform, also validated with the well-known cetuximab epitope, allows a comprehensive exploration of antigenic regions and could be expanded to map other anti-EGFR antibodies. PMID:24759767

Tundidor, Yaima; García-Hernández, Claudia Patricia; Pupo, Amaury; Cabrera Infante, Yanelys; Rojas, Gertrudis

2014-01-01

136

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.

1997-01-01

137

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

SciTech Connect

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

1997-09-09

138

Halogenated naphthyl methoxy piperidines for mapping serotonin transporter sites  

DOEpatents

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.

1999-07-06

139

Halogenated naphthyl methoxy piperidines for mapping serotonin transporter sites  

DOEpatents

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

1999-01-01

140

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

National Technical Information Service (NTIS)

Physical mapping of DNA can be accomplished by direct AFM imaging of site specific proteins bound to DNA molecules. Using Gln-111, a mutant of EcoRI endonuclease with a specific affinity for EcoRI sites 1,000 times greater than wild type enzyme but with c...

D. P. Allison T. Thundat M. J. Doktycz P. S. Kerper R. J. Warmack

1995-01-01

141

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.

1987-12-31

142

Rover Localization and Landing Site Mapping Technology for the 2003 Mars Exploration Rover Mission  

Microsoft Academic Search

The technology and experiments planned for rover localiza- tion and landing site mapping in the 2003 Mars Exploration Rover (MER) mission are described. We introduce the Mars global and landing site local reference systems. For global rover localization in the Mars body-fixed reference system, a triangulation can be performed using observations of common landmarks on satellite images and the very

Rongxing Li; Kaichang Di; Larry H. Matthies; Raymond E. Arvidson; William M. Folkner; Brent A. Archinal

2003-01-01

143

Prediction of protein-protein interaction sites using electrostatic desolvation profiles.  

PubMed

Protein-protein complex formation involves removal of water from the interface region. Surface regions with a small free energy penalty for water removal or desolvation may correspond to preferred interaction sites. A method to calculate the electrostatic free energy of placing a neutral low-dielectric probe at various protein surface positions has been designed and applied to characterize putative interaction sites. Based on solutions of the finite-difference Poisson equation, this method also includes long-range electrostatic contributions and the protein solvent boundary shape in contrast to accessible-surface-area-based solvation energies. Calculations on a large set of proteins indicate that in many cases (>90%), the known binding site overlaps with one of the six regions of lowest electrostatic desolvation penalty (overlap with the lowest desolvation region for 48% of proteins). Since the onset of electrostatic desolvation occurs even before direct protein-protein contact formation, it may help guide proteins toward the binding region in the final stage of complex formation. It is interesting that the probe desolvation properties associated with residue types were found to depend to some degree on whether the residue was outside of or part of a binding site. The probe desolvation penalty was on average smaller if the residue was part of a binding site compared to other surface locations. Applications to several antigen-antibody complexes demonstrated that the approach might be useful not only to predict protein interaction sites in general but to map potential antigenic epitopes on protein surfaces. PMID:20441756

Fiorucci, Sébastien; Zacharias, Martin

2010-05-19

144

EnSite Velocity cardiac mapping system: a new platform for 3D mapping of cardiac arrhythmias.  

PubMed

Accurate understanding and visualization of the mechanisms of cardiac arrhythmias originating from a complex 3D substrate are a prerequisite for successful treatment of such disorders. Nonfluoroscopic cardiac mapping systems are designed to provide the required spatial anatomical information in combination with local electrical information. During recent years, the EnSite system, with its EnSite NavX navigation and visualization technology, and CARTO have evolved as the main representatives. EnSite Velocity is the latest released platform of the EnSite NavX technology. It represents an open system enabling 3D visualization of multiple intracardiac catheters from different manufacturers. Fusion algorithms and respiratory compensation allow for model-guided therapy with real-time nonfluoroscopic visualization of intracardiac catheters within registered 3D CT/MRI images. PMID:20214424

Eitel, Charlotte; Hindricks, Gerhard; Dagres, Nikolaos; Sommer, Philipp; Piorkowski, Christopher

2010-03-01

145

Identifying ultrasonic scattering sites from three-dimensional impedance maps  

NASA Astrophysics Data System (ADS)

Ultrasonic backscattered signals contain frequency-dependent information that is usually discarded to produce conventional B-mode images. It is hypothesized that parametrization of the quantitative ultrasound frequency-dependent information (i.e., estimating scatterer size and acoustic concentration) may be related to discrete scattering anatomic structures in tissues. Thus, an estimation technique is proposed to extract scatterer size and acoustic concentration from the power spectrum derived from a three-dimensional impedance map (3DZM) of a tissue volume. The 3DZM can be viewed as a computational phantom and is produced from a 3D histologic data set. The 3D histologic data set is constructed from tissue sections that have been appropriately stained to highlight specific tissue features. These tissue features are assigned acoustic impedance values to yield a 3DZM. From the power spectrum, scatterer size and acoustic concentration estimates were obtained by optimization. The 3DZM technique was validated by simulations that showed relative errors of less than 3% for all estimated parameters. Estimates using the 3DZM technique were obtained and compared against published ultrasonically derived estimates for two mammary tumors, a rat fibroadenoma and a 4T1 mouse mammary carcinoma. For both tumors, the relative difference between ultrasonic and 3DZM estimates was less than 10% for the average scatterer size. .

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

2005-01-01

146

An interactive graphical system for automated mapping and display of cardiac rhythms  

Microsoft Academic Search

Electrical cardiac mapping has been used to study the mechanisms of cardiac arrhythmias, to assist in clinical diagnosis of rhythm disorders, to guide interventional procedures, or to evaluate the effects of antiarrhythmic drugs. Manual determination of local activation times, the first step in constructing activation maps, is a time-consuming process that precludes the possibility of on-line interactive mapping during an

Ye H He; Raja N Ghanem; Albert L Waldo; Yoram Rudy

1999-01-01

147

Evaluating web-based static, animated and interactive maps for injury prevention  

Microsoft Academic Search

Public health planning can benefit from visual exploration and analysis of geospatial data. Maps and geo- visualization tools must be developed with the user-group in mind. User-needs assessment and usability testing are cru- cial elements in the iterative process of map design and implementation. This study presents the results of a usability test of static, animated and interactive maps of

Jonathan Cinnamon; Claus Rinner; Michael D. Cusimano; Sean Marshall; Tony Hernandez; Richard H. Glazier; Mary L. Chipman

2009-01-01

148

Mapping Tidal Interactions in the M51 System  

NASA Astrophysics Data System (ADS)

We present deep R-band imaging of the NGC 5194/94 (M51) galaxy pair obtained with the WIYN 0.9-m telescope. Dithered R-band images are mosaicked to provide a wider field of view covering the main body of the interacting system. We estimate stellar densities in the outer features from surface photometry and look for small structures to locate possible outer sites of recent star formation. We interpret our data in the context of simulations of the interactions in the M51 system. The northern region in particular contains several unusual features around NGC 5195, such as sharp stellar density gradients, multiple debris streams, stellar shell candidates, and radial dust streamers which are not reproduced by models. We also note differences between the northern and southern tidal streams in terms of gas content, star formation and which galaxy appears to be the source of the stars. This work was supported by the National Science Foundation's REU program and the Department of Defense's ASSURE program through NSF Award AST-0453442.

Noble, Allison G.; Gallagher, J. S.; Dellenbusch, K. E.

2006-12-01

149

Protein Interaction Mapping in C. elegans Using Proteins Involved in Vulval Development  

Microsoft Academic Search

Protein interaction mapping using large-scale two-hybrid analysis has been proposed as a way to functionally annotate large numbers of uncharacterized proteins predicted by complete genome sequences. This approach was examined in Caenorhabditis elegans, starting with 27 proteins involved in vulval development. The resulting map reveals both known and new potential interactions and provides a functional annotation for approximately 100 uncharacterized

Albertha J. M. Walhout; Raffaella Sordella; Xiaowei Lu; James L. Hartley; Gary F. Temple; Michael A. Brasch; Nicolas Thierry-Mieg; Marc Vidal

2000-01-01

150

Fine mapping of the amyloid ?-protein binding site on myelin basic protein  

PubMed Central

The assembly and deposition of amyloid ?-protein (A?) in brain is a key pathological feature of Alzheimer’s disease and related disorders. Factors have been identified that can either promote or inhibit A? assembly in brain. We previously reported that myelin basic protein (MBP) is a potent inhibitor of A? fibrillar assembly [Hoos et al. 2007 J. Biol. Chem. 282:9952–9961; Hoos et al. 2009 Biochemistry 48:4720–4727]. Moreover, the region on MBP responsible for this activity was localized to the N-terminal 64 amino acids (MBP1-64) [Liao et al. 2010 J. Biol. Chem. 285:35590–35598]. In the present study we sought to further define the site on MBP1-64 involved in this activity. Deletion mapping studies showed that the C-terminal region (residues 54–64) is required for the ability of MBP1-64 to bind A? and inhibit fibril assembly. Alanine scanning mutagenesis revealed that amino acids K54, R55, G56 and K59 within MBP1-64 are important for both A? binding and inhibition of fibril assembly as assessed by solid phase binding, thioflavin T binding and fluorescence, and transmission electron microscopy studies. Strong spectral shifts are observed by solution NMR spectroscopy of specific N-terminal residues (E3, R5, D7, E11 and Q15) of A?42 upon the interaction with MBP1-64. Although the C-terminal region of MBP1-64 is required for interactions with A?, a synthetic MBP50-64 peptide was itself devoid of activity. These studies identify key residues in MBP and A? involved in their interactions and provide structural insight into how MBP regulates A? fibrillar assembly.

Kotarba, AnnMarie E.; Aucoin, Darryl; Hoos, Michael D.; Smith, Steven O.; Van Nostrand, William E.

2013-01-01

151

Derivation of elastic stiffness from site-matched mineral density and acoustic impedance maps  

Microsoft Academic Search

200 MHz acoustic impedance maps and site-matched synchrotron radiation micro computed tomography (SR-muCT) maps of tissue degree of mineralization of bone (DMB) were used to derive the elastic coefficient c33 in cross sections of human cortical bone. To accomplish this goal, a model was developed to relate the DMB accessible with SR-muCT to mass density. The formulation incorporates the volume

Kay Raum; Robin O. Cleveland; Françoise Peyrin; Pascal Laugier

2006-01-01

152

Measuring and mapping team interaction : A cross-cultural comparison of US and Spanish MBA teams  

Microsoft Academic Search

Purpose – The purpose of this paper is four-fold: to highlight the emerging stream of team interaction in research; to present a methodology to measure and map out team interaction; to compare team interaction between US and Spanish MBA teams so as to identify any differences between the two cultures; and to propose team interaction focused programs in educational institutions

Tony Lingham; Bonnie A. Richley; Ricard S. Serlavos

2009-01-01

153

Mapping the architecture of the ATP-binding site of the KATP channel subunit Kir6.2.  

PubMed

ATP-sensitive potassium (K(ATP)) channels comprise Kir6.2 and SUR subunits. The site at which ATP binds to mediate K(ATP) channel inhibition lies on Kir6.2, but the potency of block is enhanced by coexpression with SUR1. To assess the structure of the ATP-binding site on Kir6.2, we used a range of adenine nucleotides as molecular measuring sticks to map the internal dimensions of the binding site. We compared their efficacy on Kir6.2-SUR1, and on a truncated Kir6.2 (Kir6.2DeltaC) that expresses in the absence of SUR. We show here that SUR1 modifies the ATP-binding pocket of Kir6.2, by increasing the width of the groove that binds the phosphate tail of ATP, without changing the length of the groove, and by enhancing interaction with the adenine ring. PMID:15004210

Dabrowski, Michael; Tarasov, Andrei; Ashcroft, Frances M

2004-06-01

154

Site-specific mapping of transition metal oxygen coordination in complex oxides  

NASA Astrophysics Data System (ADS)

We demonstrate site-specific mapping of the oxygen coordination number for transition metals in complex oxides using atomically resolved electron energy-loss spectroscopy in an aberration-corrected scanning transmission electron microscope. Pb2Sr2Bi2Fe6O16 contains iron with a constant Fe3+ valency in both octahedral and tetragonal pyramidal coordination and is selected to demonstrate the principle of site-specific coordination mapping. Analysis of the site-specific Fe-L2,3 data reveals distinct variations in the fine structure that are attributed to Fe in a six-fold (octahedron) or five-fold (distorted tetragonal pyramid) oxygen coordination. Using these variations, atomic resolution coordination maps are generated that are in excellent agreement with simulations.

Turner, S.; Egoavil, R.; Batuk, M.; Abakumov, A. A.; Hadermann, J.; Verbeeck, J.; Van Tendeloo, G.

2012-12-01

155

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

2005-08-01

156

Mapping Hfq-RNA interaction surfaces using tryptophan fluorescence quenching  

PubMed Central

Hfq is a posttranscriptional riboregulator and RNA chaperone that binds small RNAs and target mRNAs to effect their annealing and message-specific regulation in response to environmental stressors. Structures of Hfq-RNA complexes indicate that U-rich sequences prefer the proximal face and A-rich sequences the distal face; however, the Hfq-binding sites of most RNAs are unknown. Here, we present an Hfq-RNA mapping approach that uses single tryptophan-substituted Hfq proteins, all of which retain the wild-type Hfq structure, and tryptophan fluorescence quenching (TFQ) by proximal RNA binding. TFQ properly identified the respective distal and proximal binding of A15 and U6 RNA to Gram-negative Escherichia coli (Ec) Hfq and the distal face binding of (AA)3A, (AU)3A and (AC)3A to Gram-positive Staphylococcus aureus (Sa) Hfq. The inability of (GU)3G to bind the distal face of Sa Hfq reveals the (R-L)n binding motif is a more restrictive (A-L)n binding motif. Remarkably Hfq from Gram-positive Listeria monocytogenes (Lm) binds (GU)3G on its proximal face. TFQ experiments also revealed the Ec Hfq (A-R-N)n distal face-binding motif should be redefined as an (A-A-N)n binding motif. TFQ data also demonstrated that the 5?-untranslated region of hfq mRNA binds both the proximal and distal faces of Ec Hfq and the unstructured C-terminus.

Robinson, Kirsten E.; Orans, Jillian; Kovach, Alexander R.; Link, Todd M.; Brennan, Richard G.

2014-01-01

157

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.

1978-01-01

158

Comparative receptor mapping of serotoninergic 5-HT3 and 5-HT4 binding sites.  

PubMed

The clinical use of currently available drugs acting at the 5-HT4 receptor has been hampered by their lack of selectivity over 5-HT3 binding sites. For this reason, there is considerable interest in the medicinal chemistry of these serotonin receptor subtypes, and significant effort has been made towards the discovery of potent and selective ligands. Computer-aided conformational analysis was used to characterize serotoninergic 5-HT3 and 5-HT4 receptor recognition. On the basis of the generally accepted model of the 5-HT3 antagonist pharmacophore, we have performed a receptor mapping of this receptor binding site, following the active analog approach (AAA) defined by Marshall. The receptor excluded volume was calculated as the union of the van der Waals density maps of nine active ligands (pKi > or = 8.9), superimposed in pharmacophoric conformations. Six inactive analogs (pKi < 7.0) were subsequently used to define the essential volume, which in its turn can be used to define the regions of steric intolerance of the 5-HT3 receptor. Five active ligands (pKi > or = 9.3) at 5-HT4 receptors were used to construct an antagonist pharmacophore for this receptor, and to determine its excluded volume by superimposition of pharmacophoric conformations. The volume defined by the superimposition of five inactive 5-HT4 receptor analogs that possess the pharmacophoric elements (pKi < or = 6.6) did not exceed the excluded volume calculated for this receptor. In this case, the inactivity may be due to the lack of positive interaction of the amino moiety with a hypothetical hydrophobic pocket, which would interact with the voluminous substituents of the basic nitrogen of active ligands. The difference between the excluded volumes of both receptors has confirmed that the main difference is indeed in the basic moiety. Thus, the 5-HT3 receptor can only accommodate small substituents in the position of the nitrogen atom, whereas the 5-HT4 receptor requires more voluminous groups. Also, the basic nitrogen is located at ca. 8.0 A from the aromatic moiety in the 5-HT4 antagonist pharmacophore, whereas this distance is ca. 7.5 A in the 5-HT3 antagonist model. The comparative mapping of both serotoninergic receptors has allowed us to confirm the three-component pharmacophore accepted for the 5-HT3 receptor, as well as to propose a steric model for the 5-HT4 receptor binding site. This study offers structural insights to aid the design of new selective ligands, and the resulting models have received some support from the synthesis of two new active and selective ligands: 24 (Ki(5-HT3) = 3.7 nM; Ki(5-HT4) > 1000 nM) and 25 (Ki(5-HT4) = 13.7 nM; Ki(5-HT3) > 10,000 nM). PMID:9491351

López-Rodríguez, M L; Morcillo, M J; Benhamú, B; Rosado, M L

1997-11-01

159

Groundwater vulnerability: Interactions of chemical and site properties  

USGS Publications Warehouse

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

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

2002-01-01

160

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.

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

2011-01-01

161

Developing Exhibit-based, Interactive Web Sites to Communicate Science  

NASA Astrophysics Data System (ADS)

New technologies are transforming the Web from a static medium to an interactive environment with tremendous potential for informal education and inquiry-based investigations. ASTC, the trade association of science museums, gave its 2000 innovation award to the Exploratorium's Web page rather than a physical exhibit. The increased power of the Web as an informal learning tool is partly the result of technologies (such as Java, Flash and Shockwave) that allow the development of inquiry-based, interactive experiences. Web site visitors can now "learn science by doing science." This report features two online projects funded by NSF and NASA: MarsQuest Online and the Space Weather Center. TERC, the Space Science Institute, and NASA's Jet Propulsion Laboratory are developing MarsQuest Online, an interactive, exploration-based Web site that extends the reach and scope of the MarsQuest exhibit. The Space Weather Center Web site is based on the Space Weather Center exhibit that was developed in partnership with scientists and educators at NASA/GSFC. Both exhibits represent a tremendous, collaborative effort by scientists, educators, and designers to communicate the essentials of Mars science and space weather to the public. As such, the graphics, text, and story developed for the exhibits represent a valuable resource that will provide the framework and base content for the public site. Given that framework, the Web sites can then expand both the content and audience of the exhibits in key ways. In particular, the sites will 1) extend the reach of the exhibit by making it available online, 2) extend the scope of the exhibit, linking to the latest imagery and results from ground and space-based missions, and 3) provide support and follow-up for the exhibit education programs, while making materials available to more teachers, parents, and museum educators and docents.

Dusenbery, P. B.; Harold, J.

2003-12-01

162

Development of Rapid & Low Cost Archaeological Site Mapping Using Photogrammetric Technique  

NASA Astrophysics Data System (ADS)

In digital photogrammetry, unmanned aerial vehicle (UAV) platform is a new technology that can be used to capture digital images for large scale mapping with accuracy down to centimeter level from various waypoints for archaeological site documentation. UAV is one of the great alternatives to replace piloted aircraft and with combination of non -metric camera, thus it can be applied for small area such as cultural heritage building/ archeological site area. With the recent technology of non-metric cameras, this camera is capable of producing high resolution digital images. This study investigates the application of UAV images for documentation and mapping of a simulated archaeological sites. An archaeological site simulation modelwith dimension of 2.4 m × 3.5 m is used in this study. The accuracy for mapping the archeological sites based on the UAV system is evaluated and analyzed by performing the Root Mean Square Error (RMSE) derived from the differences of coordinates between reference value and the coordinates observed from photogrammetric output such as digital terrain model and orthophoto. In this application, a simulation model was used to simulate the archaeological site excavation. The results clearly demonstrate the potential and the capability of UAV and non-metric camera in providing the accuracy of centimetre level for this application. From this study, it can be concluded that the UAV and the photogrammetric technique procedure satisfied the needs of archaeological sites survey and documentation.

Mohd Azhar, N. A.; Ahmad, Anuar

2014-02-01

163

Three Site Magnetic Interactions and the Transition Metal Spin Glass.  

NASA Astrophysics Data System (ADS)

We present a general study of three site interactions in transition metal spin glass alloys. The Fert-Levy model of microscopic anisotropy, when extended, is found to account for various properties of these systems. The hysteresis loop data of Prejean et al for CuMnAu can be explained by the additional assumption of a d-vacancy in the gold ions of about 1/6 an electron. Although this assumption runs counter to the conventional belief that the 5d level of gold impurities is filled, it is supported by chemical valence and residual resistivity data. Integral forms of the Rayleigh-Schrodinger perturbation series through fifth order are developed to enable us to determine the form of the anisotropic interaction in the binary spin glass. We present both a rotationally invariant calculation and one based on the Hartree-Fock approximation in order to provide a framework for discussion of the data for CuMn and AuFe. The treatment of three site anisotropic interactions together with a somewhat simplified discussion of both two and three site isotropic interactions provides the beginnings of a general theory of transition metal spin glass alloys which sheds some light on the questions of the concentration dependence of the scaling temperature, the numerical discrepancy between the theoretical and experimental values of the anisotropy constant, and the apparent success of the mean field theories. In particular, we demonstrate that virtual bound state contributions to both the Dzyaloshinsky -Moriya and isotropic interactions are of short range. The theory is in conflict with the widely accepted viewpoint that the dominant interaction in these systems is that of Ruderman and Kittel.

Goldberg, Stephen M.

164

Mapping the tRNA binding site on the surface of human DNMT2 methyltransferase.  

PubMed

The DNMT2 enzyme methylates tRNA-Asp at position C38. Because there is no tRNA-Dnmt2 cocrystal structure available, we have mapped the tRNA binding site of DNMT2 by systematically mutating surface-exposed lysine and arginine residues to alanine and studying the tRNA methylation activity and binding of the corresponding variants. After mutating 20 lysine and arginine residues, we identified eight of them that caused large (>4-fold) decreases in catalytic activity. These residues cluster within and next to a surface cleft in the protein, which is large enough to accommodate the tRNA anticodon loop and stem. This cleft is located next to the binding pocket for the cofactor S-adenosyl-L-methionine, and the catalytic residues of DNMT2 are positioned at its walls or bottom. Many of the variants with strongly reduced catalytic activity showed only a weak loss of tRNA binding or even bound better to tRNA than wild-type DNMT2, which suggests that the enzyme induces some conformational changes in the tRNA in the transition state of the methyl group transfer reaction. Manual placement of tRNA into the structure suggests that DNMT2 mainly interacts with the anticodon stem and loop. PMID:22591353

Jurkowski, Tomasz P; Shanmugam, Raghuvaran; Helm, Mark; Jeltsch, Albert

2012-06-01

165

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

PubMed

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

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

2011-01-01

166

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

PubMed Central

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

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

2010-01-01

167

Mass spectrometry reveals modularity and a complete subunit interaction map of the eukaryotic translation factor eIF3  

PubMed Central

The eukaryotic initiation factor 3 (eIF3) plays an important role in translation initiation, acting as a docking site for several eIFs that assemble on the 40S ribosomal subunit. Here, we use mass spectrometry to probe the subunit interactions within the human eIF3 complex. Our results show that the 13-subunit complex can be maintained intact in the gas phase, enabling us to establish unambiguously its stoichiometry and its overall subunit architecture via tandem mass spectrometry and solution disruption experiments. Dissociation takes place as a function of ionic strength to form three stable modules eIF3(c:d:e:l:k), eIF3(f:h:m), and eIF3(a:b:i:g). These modules are linked by interactions between subunits eIF3b:c and eIF3c:h. We confirmed our interaction map with the homologous yeast eIF3 complex that contains the five core subunits found in the human eIF3 and supplemented our data with results from immunoprecipitation. These results, together with the 27 subcomplexes identified with increasing ionic strength, enable us to define a comprehensive interaction map for this 800-kDa species. Our interaction map allows comparison of free eIF3 with that bound to the hepatitis C virus internal ribosome entry site (HCV-IRES) RNA. We also compare our eIF3 interaction map with related complexes, containing evolutionarily conserved protein domains, and reveal the location of subunits containing RNA recognition motifs proximal to the decoding center of the 40S subunit of the ribosome.

Zhou, Min; Sandercock, Alan M.; Fraser, Christopher S.; Ridlova, Gabriela; Stephens, Elaine; Schenauer, Matthew R.; Yokoi-Fong, Theresa; Barsky, Daniel; Leary, Julie A.; Hershey, John W.; Doudna, Jennifer A.; Robinson, Carol V.

2008-01-01

168

Mass spectrometry reveals modularity and a complete subunit interaction map of the eukaryotic translation factor eIF3.  

PubMed

The eukaryotic initiation factor 3 (eIF3) plays an important role in translation initiation, acting as a docking site for several eIFs that assemble on the 40S ribosomal subunit. Here, we use mass spectrometry to probe the subunit interactions within the human eIF3 complex. Our results show that the 13-subunit complex can be maintained intact in the gas phase, enabling us to establish unambiguously its stoichiometry and its overall subunit architecture via tandem mass spectrometry and solution disruption experiments. Dissociation takes place as a function of ionic strength to form three stable modules eIF3(c:d:e:l:k), eIF3(f:h:m), and eIF3(a:b:i:g). These modules are linked by interactions between subunits eIF3b:c and eIF3c:h. We confirmed our interaction map with the homologous yeast eIF3 complex that contains the five core subunits found in the human eIF3 and supplemented our data with results from immunoprecipitation. These results, together with the 27 subcomplexes identified with increasing ionic strength, enable us to define a comprehensive interaction map for this 800-kDa species. Our interaction map allows comparison of free eIF3 with that bound to the hepatitis C virus internal ribosome entry site (HCV-IRES) RNA. We also compare our eIF3 interaction map with related complexes, containing evolutionarily conserved protein domains, and reveal the location of subunits containing RNA recognition motifs proximal to the decoding center of the 40S subunit of the ribosome. PMID:18599441

Zhou, Min; Sandercock, Alan M; Fraser, Christopher S; Ridlova, Gabriela; Stephens, Elaine; Schenauer, Matthew R; Yokoi-Fong, Theresa; Barsky, Daniel; Leary, Julie A; Hershey, John W; Doudna, Jennifer A; Robinson, Carol V

2008-11-25

169

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.

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

2012-01-01

170

Evaluating web-based static, animated and interactive maps for injury prevention.  

PubMed

Public health planning can benefit from visual exploration and analysis of geospatial data. Maps and geovisualization tools must be developed with the user-group in mind. User-needs assessment and usability testing are crucial elements in the iterative process of map design and implementation. This study presents the results of a usability test of static, animated and interactive maps of injury rates and socio-demographic determinants of injury by a sample of potential end-users in Toronto, Canada. The results of the user-testing suggest that different map types are useful for different purposes and for satisfying the varying skill level of the individual user. The static maps were deemed to be easy to use and versatile, while the animated maps could be made more useful if animation controls were provided. The split-screen concept of the interactive maps was highlighted as particularly effective for map comparison. Overall, interactive maps were identified as the preferred map type for comparing patterns of injury and related socio-demographic risk factors. Information collected from the user-tests is being used to expand and refine the injury web maps for Toronto, and could inform other public health-related geo-visualization projects. PMID:19908186

Cinnamon, Jonathan; Rinner, Claus; Cusimano, Michael D; Marshall, Sean; Bakele, Tsegaye; Hernandez, Tony; Glazier, Richard H; Chipman, Mary L

2009-11-01

171

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.

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

2012-01-01

172

Paclitaxel-HSA interaction. Binding sites on HSA molecule.  

PubMed

Paclitaxel (trade name Taxol) is one of the world's most effective anticancer drugs. It is used to treat several cancers including tumours of the breast, ovary and lung. In the present work the interaction of paclitaxel with human serum albumin (HSA) in aqueous solution at physiological pH has been investigated through CD, fluorescence spectroscopy and by the antibody precipitate test. Binding of paclitaxel to albumin impact on protein structure and it influences considerably albumin binding of other molecules like warfarin, heme or bilirubin. The paclitaxel-HSA interaction causes the conformational changes with the loss of helical stability of protein and local perturbation in the domain IIA binding pocket. The relative fluorescence intensity of the paclitaxel-bound HSA decreased, suggesting that perturbation around the Trp 214 residue took place. This was confirmed by the destabilization of the warfarin binding site, which includes Trp 214, and high affinity bilirubin binding site located in subdomain IIA. PMID:15158795

Trynda-Lemiesz, Lilianna

2004-06-15

173

Interaction-site representation of polar mixtures and electrolyte solutions  

NASA Astrophysics Data System (ADS)

In this work we present an interaction-site theory for mixture electrolyte solutions. The theory is semi theoretically adjusted for dielectrical properties. The theory preserves the correct asymptotic limits of the dielectric constant when the solution approaches the limit of any of its pure component. In the intermediate concentration range it interpolates the dielectric constants according to a quadratic mixing rule in relative dipole densities. For the simplified interaction-site models applied here, the excess energies of water/methanol at 293.15 K and experimentally measured densities are in fair agreement with experimental values. The estimated average number of hydrogen bonds for a mole fraction of water equal to 0.75 also compares well with published simulations. Estimated energies with and without the dielectric correction indicate that the dielectric constant may have a significant impact on the energy for this molecule. Excess energies for mixtures of water and ethanol are estimated to be too low.

Kvamme, B.

1995-05-01

174

The potential for signal integration and processing in interacting MAP kinase cascades.  

PubMed

The cellular response to environmental stimuli requires biochemical information processing through which sensory inputs and cellular status are integrated and translated into appropriate responses by way of interacting networks of enzymes. One such network, the mitogen-activated protein (MAP) kinase cascade is a highly conserved signal transduction module that propagates signals from cell surface receptors to various cytosolic and nuclear targets by way of a phosphorylation cascade. We have investigated the potential for signal processing within a network of interacting feed-forward kinase cascades typified by the MAP kinase cascade. A genetic algorithm was used to search for sets of kinetic parameters demonstrating representative key input-output patterns of interest. We discuss two of the networks identified in our study, one implementing the exclusive-or function (XOR) and another implementing what we refer to as an in-band detector (IBD) or two-sided threshold. These examples confirm the potential for logic and amplitude-dependent signal processing in interacting MAP kinase cascades demonstrating limited cross-talk. Specifically, the XOR function allows the network to respond to either one, but not both signals simultaneously, while the IBD permits the network to respond exclusively to signals within a given range of strength, and to suppress signals below as well as above this range. The solution to the XOR problem is interesting in that it requires only two interacting pathways, crosstalk at only one layer, and no feedback or explicit inhibition. These types of responses are not only biologically relevant but constitute signal processing modules that can be combined to create other logical functions and that, in contrast to amplification, cannot be achieved with a single cascade or with two non-interacting cascades. Our computational results revealed surprising similarities between experimental data describing the JNK/MKK4/MKK7 pathway and the solution for the IBD that evolved from the genetic algorithm. The evolved IBD not only exhibited the required non-monotonic signal strength-response, but also demonstrated transient and sustained responses that properly reflected the input signal strength, dependence on both of the MAPKKs for signaling, phosphorylation site preferences by each of the MAPKKs, and both activation and inhibition resulting from the overexpression of one of the MAPKKs. PMID:17337011

Schwacke, John H; Voit, Eberhard O

2007-06-21

175

Computer-based Approaches for Training Interactive Digital Map Displays.  

National Technical Information Service (NTIS)

Five variations of computer-based training (CBT) for learning to use functions underlying a digital map interface were compared using 85 Infantry One-Station-Unit Training (OSUT) Soldiers and 67 Infantry Officer Basic Course (IOBC) Soldiers. The variation...

J. L. Dyer H. Singh T. L. Clark

2005-01-01

176

Mapping the binding site of thiopeptide antibiotics by proximity-induced covalent capture.  

PubMed

Proximity-induced covalent capture (PICC) has been established for the investigation of ligand binding to composite protein/oligonucleotide target complexes. The RNA-induced attachment of the thiopeptides Thiostrepton and Nosiheptide to engineered Cys mutants of the ribosomal protein L11 was highly position selective and allowed mapping of their binding site at amino acid resolution. PMID:18380436

Baumann, Sascha; Schoof, Sebastian; Harkal, Surendra D; Arndt, Hans-Dieter

2008-04-30

177

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

Microsoft Academic Search

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

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

1978-01-01

178

Eisenhower National Historic Site: Historic Resource Study and Historical Base Map, Eisenhower Farm, 1762-1967.  

National Technical Information Service (NTIS)

This report was prepared to satisfy research needs for the Eisenhower National Historic Site. Included in the subject study is a history of the Eisenhower Farm from the mid-eighteenth century until 1970. The Historical Base Maps reflect the physical condi...

E. C. Bearss

1970-01-01

179

Matrix model maps and reconstruction of AdS supergravity interactions  

NASA Astrophysics Data System (ADS)

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; de Mello Koch, Robert; Jevicki, Antal

2008-05-01

180

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

2012-01-01

181

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.

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

2008-01-01

182

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

SciTech Connect

New techniques for mapping mammalian DNA replication origins are needed. We have modified the existing nascent-strand size analysis technique to provide an independent means of studying replication initiation sites. We call the new method nascent-strand abundance analysis. We confirmed the validity of this method with replicating simian virus 40 DNA as a model. We then applied nascent-strand abundance and nascent-strand size analyses to mapping of initiation sites in human (HeLa) ribosomal DNA (rDNA), a region previously examined exclusively by two-dimensional gel electrophoresis methods. Our results partly confirm those obtained by two-dimensional gel electrophoresis techniques. Both studies suggest that replication initiates at relatively high frequency a few kilobase pairs upstream of the transcribed region and that many additional low-frequency initiation sites are distributed through most of the remainder of the ribosomal DNA repeat unit. 51 refs., 5 figs.

Yoon, Y.; Sanchez, J.A.; Brun, C. [Roswell Park Cancer Institute, Buffalo, NY (United States)] [and others

1995-05-01

183

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

NASA Astrophysics Data System (ADS)

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

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

1995-01-01

184

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.

2014-04-01

185

Interactive Query Processing in Big Data Systems: A Cross Industry Study of MapReduce Workloads.  

National Technical Information Service (NTIS)

Within the past few years, organizations in diverse industries have adopted MapReduce-based systems for large-scale data processing. Along with these new users, important new workloads have emerged which feature many small, short and increasingly interact...

R. H. Katz S. Alspaugh Y. Chen

2012-01-01

186

Mobile Map Interaction - Evaluation in an indoor scenario  

Microsoft Academic Search

Providing indoor navigation within a building is usually associated with large investments in infrastructure. We present and evaluate an approach to provide indoor navigation with minimal infrastructure investments. In our approach people use a mobile camera device like a mobile phone as a magic lens. When the device is sweeped over a map of the building, the way is augmented

Hans Jorg

187

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.

1994-01-01

188

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.

2014-07-01

189

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

PubMed

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

2009-11-01

190

A Drosophila protein-interaction map centered on cell-cycle regulators  

Microsoft Academic Search

Background  Maps depicting binary interactions between proteins can be powerful starting points for understanding biological systems.\\u000a A proven technology for generating such maps is high-throughput yeast two-hybrid screening. In the most extensive screen to\\u000a date, a Gal4-based two-hybrid system was used recently to detect over 20,000 interactions among Drosophila proteins. Although these data are a valuable resource for insights into protein

Clement A Stanyon; Guozhen Liu; Bernardo A Mangiola; Nishi Patel; Loic Giot; Bing Kuang; Huamei Zhang; Jinhui Zhong; Russell L Finley Jr

2004-01-01

191

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

DOE Data Explorer

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

192

High Quality Binary Protein Interaction Map of the Yeast Interactome Network  

Microsoft Academic Search

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 datasets, demonstrating that high-throughput yeast two-hybrid (Y2H) provides high-quality binary interaction information. As a large fraction of the yeast binary interactome remains to be mapped, we developed an empirically-controlled

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

2009-01-01

193

High-Quality Binary Protein Interaction Map of the Yeast Interactome Network  

Microsoft Academic Search

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

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

2008-01-01

194

Genome-Wide Mapping of in Vivo Protein-DNA Interactions  

Microsoft Academic Search

In vivo protein-DNA interactions connect each transcription factor with its direct targets to form a gene network scaffold. To map these protein-DNA interactions comprehensively across entire mammalian genomes, we developed a large-scale chromatin immunoprecipitation assay (ChIPSeq) based on direct ultrahigh-throughput DNA sequencing. This sequence census method was then used to map in vivo binding of the neuron-restrictive silencer factor (NRSF;

J. Knop; R. Stremmer; C. Neumann; E. De Maeyer; David S. Johnson; Ali Mortazavi; Richard M. Myers; Barbara Wold

2007-01-01

195

Topoisomerase I tyrosine phosphorylation site and the DNA-interactive site  

SciTech Connect

Phosphorylation of topoisomerase I (topo I) at serine by NII kinase is accompanied by stimulation of enzymatic activity. In contrast, phosphorylation at tyrosine by tyrosine kinase seems to inhibit enzymatic activity. This inhibition may be caused by interference of the phosphorylated tyrosine residue with the interaction of topo I with DNA. To test this, topo I was labeled with crude membrane fraction enriched for EGF-receptor kinase in presence of ..gamma..-P32-ATP and electrophoresed on SDS-polyacrylamide gels. Stained topo I bands were excised, dried, digested with trypsin and analyzed on a C18 reverse-phase HPLC column. One major peak of radioactivity eluted at fraction 23 with 20% acetonitrile. To obtain the DNA-interactive site, topo I was incubated with pBR322 DNA labeled by nick-translation followed by DNase I treatment, and electrophoresis on SDS-polyacrylamide gels. Tryptic peptides were generated and analyzed by reverse-phase HPLC. A major peak of radioactivity eluted at fraction 16-18 with 15.5-17% acetonitrile. Studies are in progress to resolve whether (a) the two peptides are different, i.e. the tyrosine-P site and DNA-tyrosine interactive site are localized at different regions of the topo I or (b) the peptide sequences are identical but the covalent attachment of deoxynucleotides altered the peptide's elution from the HPLC column.

Roll, D.; Durban, E.

1986-05-01

196

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.

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

2004-01-01

197

Mapping Haplotype-haplotype Interactions with Adaptive LASSO  

PubMed Central

Background The genetic etiology of complex diseases in human has been commonly viewed as a complex process involving both genetic and environmental factors functioning in a complicated manner. Quite often the interactions among genetic variants play major roles in determining the susceptibility of an individual to a particular disease. Statistical methods for modeling interactions underlying complex diseases between single genetic variants (e.g. single nucleotide polymorphisms or SNPs) have been extensively studied. Recently, haplotype-based analysis has gained its popularity among genetic association studies. When multiple sequence or haplotype interactions are involved in determining an individual's susceptibility to a disease, it presents daunting challenges in statistical modeling and testing of the interaction effects, largely due to the complicated higher order epistatic complexity. Results In this article, we propose a new strategy in modeling haplotype-haplotype interactions under the penalized logistic regression framework with adaptive L1-penalty. We consider interactions of sequence variants between haplotype blocks. The adaptive L1-penalty allows simultaneous effect estimation and variable selection in a single model. We propose a new parameter estimation method which estimates and selects parameters by the modified Gauss-Seidel method nested within the EM algorithm. Simulation studies show that it has low false positive rate and reasonable power in detecting haplotype interactions. The method is applied to test haplotype interactions involved in mother and offspring genome in a small for gestational age (SGA) neonates data set, and significant interactions between different genomes are detected. Conclusions As demonstrated by the simulation studies and real data analysis, the approach developed provides an efficient tool for the modeling and testing of haplotype interactions. The implementation of the method in R codes can be freely downloaded from http://www.stt.msu.edu/~cui/software.html.

2010-01-01

198

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

SciTech Connect

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

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

1988-07-01

199

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.

2006-01-01

200

Mapping the interactions of selected antibiotics and their Cu2+ complexes with the antigenomic ? ribozyme.  

PubMed

The interactions of selected antibiotics with the trans-acting antigenomic delta ribozyme were mapped. Ribozyme with two oligonucleotide substrates was used, one uncleavable with deoxycytidine at the cleavage site, mimicking the initial state of ribozyme, and the other with an all-RNA substrate mimicking, after cleavage, the product state. Mapping was performed with a set of RNA structural probing methods: Pb(2+) -induced cleavage, nuclease digestion, and the selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) approach. The experimental results combined with molecular modeling revealed different binding sites for neomycin B, amikacin and actinomycin D inside the ribozyme structure. Neomycin B, an aminoglycoside antibiotic, which strongly inhibited the catalytic properties of delta ribozyme, was bound to the pocket formed by the P1 stem, the P1.1 pseudoknot, and the J4/2 junction. Amikacin showed less effective binding to the ribozyme catalytic core, resulting in weak inhibition. Complexes of these aminoglycosides with Cu(2+) ions were bound to the same ribozyme regions, but more effectively, showing lower Kd values. On the other hand, the Cu(2+) complex of the cyclopeptide antibiotic actinonomycin D was preferentially intercalated into the P2 and the P4 double-stranded region, and was three times more potent in ribozyme inhibition than the free antibiotic. In addition, some differences in SHAPE reactivities between the ribozyme forms containing all-RNA and deoxycytidine-modified substrates in the J4/2 region were detected, pointing to different ribozyme conformations before and after the cleavage event. PMID:23527582

Wrzesinski, Jan; B?aszczyk, Leszek; Wro?ska, Magdalena; Kasprowicz, Aleksandra; Stokowa-So?tys, Kamila; Nagaj, Justyna; Szafraniec, Milena; Kulinski, Tadeusz; Je?owska-Bojczuk, Ma?gorzata; Ciesio?ka, Jerzy

2013-06-01

201

A proteome-wide protein interaction map for Campylobacter jejuni  

Microsoft Academic Search

Background  Data from large-scale protein interaction screens for humans and model eukaryotes have been invaluable for developing systems-level\\u000a models of biological processes. Despite this value, only a limited amount of interaction data is available for prokaryotes.\\u000a Here we report the systematic identification of protein interactions for the bacterium Campylobacter jejuni, a food-borne pathogen and a major cause of gastroenteritis worldwide.\\u000a \\u000a \\u000a \\u000a \\u000a Results  Using

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

2007-01-01

202

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

NASA Technical Reports Server (NTRS)

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

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

1992-01-01

203

A Case Study of Earthquake Loss Estimation with Detailed Site Classification Map in Korea  

NASA Astrophysics Data System (ADS)

Earthquake loss estimation system help to obtain reliable estimates of seismic hazard and losses soon after occurrence of major earthquakes, to simulate earthquake scenarios, to provide useful estimates for local/federal officials and public services to propose their earthquake hazard mitigation plan, and to provide catastrophic risk management tool. Site classification map, one of inventory data for an earthquake loss estimation system, is crucial for reliable results. We constructed a site classification map of the Gyeongju, Pohang, Ulsan area in the southeastern Korea. Study area is characterized by complex site condition. It is then incorporated to the loss estimation system. We observe large differences between the results of loss estimation with and without detailed site information. Without the detail information, the estimated losses decrease with increased epicentral distances. With the detailed information, it is noted that Gyeongju area will experience large damage due to the short epicentral distance. It is also noticed that Pohang-nam-gu areas will experience greater loss than other areas. Located at an equivalent epicentral distance, Ulsan-dong-gu is expected to experience much smaller loss due to the site condition.

Kang, S.; Kim, K.; Suk, B.

2011-12-01

204

New results for geologic units mapping of Utah test sites using Landsat TM data  

NASA Technical Reports Server (NTRS)

This paper continues a study on the accuracy of geological mapping using Landsat Thematic Mapper data (Short, 1984). In June 1976, both the White Mountain alteration zone and the Waterpocket Fold sedimentary rock sites in Utah were surveyed by the Bendix 24-band scanner on a NASA NC-130B aircraft. Mid-June 1984 TM data for these two sites have been processed like the 1976 data to test the quality of simulation of TM data. Principal-components (PC) color composite images for White Mountain show close correspondence to the Bendix PC images. At this site carbonate strata are uniquely discriminated in both Bendix and TM composites that use an inverted PC 3 image. Alunite/kaolinite and hematite/limonite alteration zones developed on volcanic flows are also sharply separated, but iron oxide and silicified zones are less so. The accuracy of rock-units mapping at the Waterpocket Fold site by supervised classification of the June TM data is significantly better, reaching 70 percent in the best case, than for January 1983 data for that site.

Short, N. M.; Marcell, R.

1986-01-01

205

WebCutter: A System for Dynamic and Tailorable Site Mapping  

Microsoft Academic Search

Conventional information discovery tools can be classified as being either search oriented or browse oriented. In the context of the Web, search-oriented tools employ text-analysis techniques to find Web documents based on user-specified queries, whereas browse-oriented ones employ site mapping and visualization techniques to allow users to navigate through the Web. This paper presents a unique approach that tightly integrates

Yoëlle S. Maarek; Michal Jacovi; Menachem Shtalhaim; Ur Sigalit; Dror Zernik; Israel Z. Ben-Shaul

1997-01-01

206

Identification of in Vivo Phosphorylation Sites of MLK3 by Mass Spectrometry and Phosphopeptide Mapping †  

Microsoft Academic Search

MLK3 is a serine\\/threonine protein kinase that functions as an upstream activator of the JNK pathway. Previous work has suggested that MLK3 is a multiphosphorylated protein. In this study, mass spectrometry coupled with comparative phosphopeptide mapping was used to directly characterize MLK3 in vivo phosphorylation sites. Various types of mass spectrometry were used to analyze MLK3 tryptic peptides separated by

Panayiotis O. Vacratsis; Brett S. Phinney; Douglas A. Gage; Kathleen A. Gallo

2002-01-01

207

Comparison of canine parvovirus with mink enteritis virus by restriction site mapping.  

PubMed Central

The genomes of canine parvovirus and mink enteritis virus were compared by restriction enzyme analysis of their replicative-form DNAs. Of 79 mapped sites, 68, or 86%, were found to be common for both types of DNA, indicating that canine parvovirus and mink enteritis virus are closely related viruses. Whether they evolved from a common precursor or whether canine parvovirus is derived from mink enteritis virus, however, cannot be deduced from our present data. Images

McMaster, G K; Tratschin, J D; Siegl, G

1981-01-01

208

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.

2011-01-01

209

The Documentation of Historic Maps of World Heritage Site City Suzhou  

NASA Astrophysics Data System (ADS)

Documentation and analysis of historic maps enhance understanding of temporal and spatial interactions between events and the evolution of physical canals upon which they occurred. And the challenge of this work lies on carefully sifting of information through the maps drawn with relative accuracy by traditional cartographical principles before the emergence of scientific survey. This research project focuses on sorting out the evolution of historic city Suzhou in a spatio-temporal view. The investigation was conducted through an in-depth analysis of historic maps. Re-projection of the geographical elements of the city to one single georeference, that is to say a standard map BASE, help acquiring an actual sense of the scale and facilitate the recognition of the city's evolution in clear details. It is an important contribution of this thesis in coordination of variously distorted geographical information contained in nineteen periods span from 1229 to 2013 into a single research resource. Through the work both quantitative and qualitative, a clear vision of the evolution and characteristics of the urban structure of ancient Suzhou is achieved. Meanwhile, in the process of projecting the historical geometrical information onto the topographic map, historical bibliographic and cartographic records is key to the data coordination and readjustment, this inspire as well on the cautious utilization of historical materials from ancient time in the recording, documentation work.

Guangwei, Z.

2013-07-01

210

High-resolution physical and functional mapping of the template adjacent DNA binding site in catalytically active telomerase  

PubMed Central

Telomerase is a cellular reverse transcriptase, which utilizes an integral RNA template to extend single-stranded telomeric DNA. We used site-specific photocrosslinking to map interactions between DNA primers and the catalytic protein subunit (tTERT) of Tetrahymena thermophila telomerase in functional enzyme complexes. Our assays reveal contact of the single-stranded DNA adjacent to the primer-template hybrid and tTERT residue W187 at the periphery of the N-terminal domain. This contact was detected in complexes with three different registers of template in the active site, suggesting that it is maintained throughout synthesis of a complete telomeric repeat. Substitution of nearby residue Q168, but not W187, alters the Km for primer elongation, implying that it plays a role in the DNA recognition. These findings are the first to directly demonstrate the physical location of TERT-DNA contacts in catalytically active telomerase and to identify amino acid determinants of DNA binding affinity. Our data also suggest a movement of the TERT active site relative to the template-adjacent single-stranded DNA binding site within a cycle of repeat synthesis.

Romi, Erez; Baran, Nava; Gantman, Marina; Shmoish, Michael; Min, Bosun; Collins, Kathleen; Manor, Haim

2007-01-01

211

Picture browsing and map interaction using a projector phone  

Microsoft Academic Search

It is expected that projector phones (mobile phones with built-in pico projectors) will hit the market by 2010. Such phones provide a completely new way to display information and interaction techniques. The system presented in this paper allows the simulation of these projector phones as the real devices are not yet available. Through this, we demonstrate that it is currently

Andrew Greaves; Alina Hang; Enrico Rukzio

2008-01-01

212

Protein–protein interaction maps: a lead towards cellular functions  

Microsoft Academic Search

The availability of complete genome sequences now permits the development of tools for functional biology on a proteomic scale. Several experimental approaches or in silico algorithms aim at clustering proteins into networks with biological significance. Among those, the yeast two-hybrid system is the technology of choice to detect protein–protein interactions. Recently, optimized versions were applied at a genomic scale, leading

Pierre Legrain; Jérôme Wojcik; Jean-Michel Gauthier

2001-01-01

213

Operation and research at the Ithaca MAP3S regional precipitation chemistry site  

SciTech Connect

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

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

1991-07-01

214

Tetragonal Lysozyme Interactions Studied by Site Directed Mutagenesis  

NASA Technical Reports Server (NTRS)

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

Crawford, Lisa; Karr, Laurel; Pusey, Marc

1998-01-01

215

Tetragonal Lysozyme Interactions Studied by Site Directed Mutagenesis  

NASA Technical Reports Server (NTRS)

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

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

1999-01-01

216

Dissecting chromatin interactions in living cells from protein mobility maps  

Microsoft Academic Search

The genome of eukaryotes is organized into a dynamic nucleoprotein complex referred to as chromatin, which can adopt different\\u000a functional states. Both the DNA and the protein component of chromatin are subject to various post-translational modifications\\u000a that define the cell’s gene expression program. Their readout and establishment occurs in a spatio-temporally coordinated\\u000a manner that is controlled by numerous chromatin-interacting proteins.

Fabian Erdel; Katharina Müller-Ott; Michael Baum; Malte Wachsmuth; Karsten Rippe

2011-01-01

217

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.

2004-03-23

218

The 3D rRNA modification maps database: with interactive tools for ribosome analysis  

Microsoft Academic Search

The 3D rRNA modification maps database is the first general resource of information about the locations of modified nucleotides within the 3D structure of the full ribosome, with mRNA and tRNAs in the A-, P- and E-sites. The database supports analyses for several model organisms, including higher eukar- yotes, and enables users to construct 3D maps for other organisms. Data

Dorota Piekna-przybylska; Wayne A. Decatur; Maurille J. Fournier

2008-01-01

219

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

NASA Technical Reports Server (NTRS)

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

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

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

This map and its interpretation are in a May 3, 2007, report in the journal Nature by Joshua Bandfield of Arizona State University, Tempe. The Thermal Emission Imaging System camera on NASA's Mars Odyssey orbiter collected the data presented in the map. The site is centered near 67.5 degrees north latitude, 132 degrees east longitude, in the Martian arctic plains called Vastitas Borealis. It was formerly a candidate landing site for NASA's Phoenix Mars Lander mission. This site is within the portion of the planet where, in 2002, the Gamma Ray Spectrometer suite of instruments on Mars Odyssey found evidence for water ice lying just below the surface. The information from the Gamma Ray Spectrometer is averaged over patches of ground hundreds of kilometers or miles wide. The information from the Thermal Emission Imaging System allows more than 100-fold higher resolution in mapping variations in the depth to ice.

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

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

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

2007-01-01

220

Molecular mapping of general anesthetic sites in a voltage-gated ion channel.  

PubMed

Several voltage-gated ion channels are modulated by clinically relevant doses of general anesthetics. However, the structural basis of this modulation is not well understood. Previous work suggested that n-alcohols and inhaled anesthetics stabilize the closed state of the Shaw2 voltage-gated (Kv) channel (K-Shaw2) by directly interacting with a discrete channel site. We hypothesize that the inhibition of K-Shaw2 channels by general anesthetics is governed by interactions between binding and effector sites involving components of the channel's activation gate. To investigate this hypothesis, we applied Ala/Val scanning mutagenesis to the S4-S5 linker and the post-PVP S6 segment, and conducted electrophysiological analysis to evaluate the energetic impact of the mutations on the inhibition of the K-Shaw2 channel by 1-butanol and halothane. These analyses identified residues that determine an apparent binding cooperativity and residue pairs that act in concert to modulate gating upon anesthetic binding. In some instances, due to their critical location, key residues also influence channel gating. Complementing these results, molecular dynamics simulations and in silico docking experiments helped us visualize possible anesthetic sites and interactions. We conclude that the inhibition of K-Shaw2 by general anesthetics results from allosteric interactions between distinct but contiguous binding and effector sites involving inter- and intrasubunit interfaces. PMID:21961587

Barber, Annika F; Liang, Qiansheng; Amaral, Cristiano; Treptow, Werner; Covarrubias, Manuel

2011-10-01

221

Molecular Mapping of General Anesthetic Sites in a Voltage-Gated Ion Channel  

PubMed Central

Several voltage-gated ion channels are modulated by clinically relevant doses of general anesthetics. However, the structural basis of this modulation is not well understood. Previous work suggested that n-alcohols and inhaled anesthetics stabilize the closed state of the Shaw2 voltage-gated (Kv) channel (K-Shaw2) by directly interacting with a discrete channel site. We hypothesize that the inhibition of K-Shaw2 channels by general anesthetics is governed by interactions between binding and effector sites involving components of the channel's activation gate. To investigate this hypothesis, we applied Ala/Val scanning mutagenesis to the S4-S5 linker and the post-PVP S6 segment, and conducted electrophysiological analysis to evaluate the energetic impact of the mutations on the inhibition of the K-Shaw2 channel by 1-butanol and halothane. These analyses identified residues that determine an apparent binding cooperativity and residue pairs that act in concert to modulate gating upon anesthetic binding. In some instances, due to their critical location, key residues also influence channel gating. Complementing these results, molecular dynamics simulations and in silico docking experiments helped us visualize possible anesthetic sites and interactions. We conclude that the inhibition of K-Shaw2 by general anesthetics results from allosteric interactions between distinct but contiguous binding and effector sites involving inter- and intrasubunit interfaces.

Barber, Annika F.; Liang, Qiansheng; Amaral, Cristiano; Treptow, Werner; Covarrubias, Manuel

2011-01-01

222

Uncertainty in North America wet deposition isopleth maps: Effect of site selection and valid sample criteria  

SciTech Connect

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, kriging, is presented and it's derivation in terms of generalized least squares regression is given. Four different annual summaries for pH, sulfate concentration, and sulfate deposition in 1986 are prepared using either the Unified Deposition Database Committee (UDDC) definition of valid sample criteria or a relaxed valid sample criteria and the UDDC data completeness rating or a relaxed data completeness rating. The kriged estimates for the different annual summaries and the differences between these estimates are contoured. The effects of relaxing the valid sample criteria and data completeness rating are discussed. Conclusions are drawn about network operation, network design and the uncertainty of contour maps. It is recommended that in the case where the objective is contour maps to show regional patterns, the emphasis in most regions needs to be on the number of valid samples per site and the regional representativeness of the sites. 4 refs., 14 figs., 7 tabs.

Simpson, J.C.; Olsen, A.R.

1990-04-01

223

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

PubMed

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

2014-07-01

224

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

2013-01-01

225

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

1995-04-01

226

Evolutionary Interactions between N-Linked Glycosylation Sites in the HIV-1 Envelope  

PubMed Central

The addition of asparagine (N)-linked polysaccharide chains (i.e., glycans) to the gp120 and gp41 glycoproteins of human immunodeficiency virus type 1 (HIV-1) envelope is not only required for correct protein folding, but also may provide protection against neutralizing antibodies as a “glycan shield.” As a result, strong host-specific selection is frequently associated with codon positions where nonsynonymous substitutions can create or disrupt potential N-linked glycosylation sites (PNGSs). Moreover, empirical data suggest that the individual contribution of PNGSs to the neutralization sensitivity or infectivity of HIV-1 may be critically dependent on the presence or absence of other PNGSs in the envelope sequence. Here we evaluate how glycan–glycan interactions have shaped the evolution of HIV-1 envelope sequences by analyzing the distribution of PNGSs in a large-sequence alignment. Using a “covarion”-type phylogenetic model, we find that the rates at which individual PNGSs are gained or lost vary significantly over time, suggesting that the selective advantage of having a PNGS may depend on the presence or absence of other PNGSs in the sequence. Consequently, we identify specific interactions between PNGSs in the alignment using a new paired-character phylogenetic model of evolution, and a Bayesian graphical model. Despite the fundamental differences between these two methods, several interactions are jointly identified by both. Mapping these interactions onto a structural model of HIV-1 gp120 reveals that negative (exclusive) interactions occur significantly more often between colocalized glycans, while positive (inclusive) interactions are restricted to more distant glycans. Our results imply that the adaptive repertoire of alternative configurations in the HIV-1 glycan shield is limited by functional interactions between the N-linked glycans. This represents a potential vulnerability of rapidly evolving HIV-1 populations that may provide useful glycan-based targets for neutralizing antibodies.

Poon, Art F. Y; Lewis, Fraser I; Pond, Sergei L. Kosakovsky; Frost, Simon D. W

2007-01-01

227

Accurate mapping of cleavage and polyadenylation sites by 3' region extraction and deep sequencing.  

PubMed

Deep sequencing of RNA (RNA-seq) is becoming a standard method to study gene expression. While RNA-seq reads cover most regions of an mRNA sequence, they are often depleted in the 3' end region, making them less amenable for mapping the cleavage and polyadenylation site (pA). A major problem in identification of pA is mispriming at internal A-rich regions and oligo(A) tails when an oligo(dT) primer is used for reverse transcription or sequencing. We recently developed a method named 3' region extraction and deep sequencing (3'READS), which completely addresses mispriming issues and is straightforward to use. The method accurately maps pAs and allows quantitative analysis of alternative cleavage and polyadenylation (APA) isoforms and gene expression. PMID:24590784

Hoque, Mainul; Li, Wencheng; Tian, Bin

2014-01-01

228

Reassembly of JIP1 Scaffold Complex in JNK MAP Kinase Pathway Using Heterologous Protein Interactions  

PubMed Central

Formation of signaling protein complexes is crucial for proper signal transduction. Scaffold proteins in MAP kinase pathways are thought to facilitate complex assembly, thereby promoting efficient and specific signaling. To elucidate the assembly mechanism of scaffold complexes in mammals, we attempted to rationally rewire JIP1-dependent JNK MAP kinase pathway via alternative assembly of JIP1 complex. When JIP1-JNK docking interaction in the complex was replaced with heterologous protein interaction domains, such as PDZ domains and JNK-binding domains, a functional scaffold complex was reconstituted, and JNK signaling was rescued. Reassembly of JIP1 complex using heterologous protein interactions was sufficient for restoring of JNK MAP kinase pathway to induce signaling responses, including JNK activation and cell death. These results suggest a simple yet modular mechanism for JIP1 scaffold assembly in mammals.

Moon, Jiyoung; Park, Sang-Hyun

2014-01-01

229

Microscopic structure of an interacting boson model in terms of the Dyson boson mapping  

NASA Astrophysics Data System (ADS)

In an application of the generalized Dyson boson mapping to a shell model Hamiltonian acting in a single j shell, a clear distinction emerges between pair bosons and kinematically determined seniority bosons. As in the Otsuka-Arima-Iachello method it is found that the latter type of boson determines the structure of an interactive boson-model-like Hamiltonian for the single j-shell model. It is furthermore shown that the Dyson boson mapping formalism is equally well suited for investigating possible interactive boson-model-like structures in a multishell case, where dynamical considerations are expected to play a much more important role in determining the structure of physical bosons. NUCLEAR STRUCTURE Boson mapping, interacting boson model, shell model.

Geyer, H. B.; Lee, S. Y.

1982-08-01

230

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

NASA Technical Reports Server (NTRS)

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

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

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

This map and its interpretation are in a May 3, 2007, report in the journal Nature by Joshua Bandfield of Arizona State University, Tempe. The Thermal Emission Imaging System camera on NASA's Mars Odyssey orbiter collected the data presented in the map. The site is centered near 67 degrees south latitude, 36.5 degrees east longitude, near a plain named Melea Planum. This site is within the portion of the planet where, in 2002, the Gamma Ray Spectrometer suite of instruments on Mars Odyssey found evidence for water ice lying just below the surface. The information from the Gamma Ray Spectrometer is averaged over patches of ground hundreds of kilometers or miles wide. The information from the Thermal Emission Imaging System allows more than 100-fold higher resolution in mapping variations in the depth to ice.

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

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

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

2007-01-01

231

MicroCT analysis of calcium/phosphorus ratio maps at different bone sites  

NASA Astrophysics Data System (ADS)

The Ca/P ratio was measured in cortical bone samples from the femoral neck, front and rear tibia of rats, rabbits and lambs using synchrotron microCT. Use of a monoenergetic X-ray beam, as provided by the synchrotron facility, generates accurate 3-D maps of the linear attenuation coefficient within the sample and hence gives the ability to map different chemical components. Data were taken at 20 keV for each bone sample and calibration phantoms. From the 3-D data sets, multiple 2-D slices were reconstructed with a slice thickness of ˜28 ?m and converted to Ca/P ratios using the calibration phantom results. Average values for each animal and bone site were estimated. Differences between the same bone sites from different animals are not significant (0.3< p<0.5) while those between different bone sites and different animals are highly significant ( p<10-3) demonstrating a dependence upon lifestyle and bone use. The spatial distribution of Ca/P was found to be non-uniform for some bones and some animals possibly indicating the structural mechanism for obtaining bone strength.

Speller, R.; Pani, S.; Tzaphlidou, M.; Horrocks, J.

2005-08-01

232

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

USGS Publications Warehouse

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

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

2007-01-01

233

Mapping and analysis of HPV16 integration sites in a head and neck cancer cell line.  

PubMed

Human papillomavirus (HPV) is a circular double-stranded DNA virus implicated in at least 90% of cervical and anogenital cancers and has been observed in approximately 20% of squamous cell carcinomas of the head and neck (SCCHN). Transcription of the viral oncogenes E6 and E7 is regulated by expression of the E2 protein. Disruption of the E2 gene sequence due to viral integration results in upregulation of E6 and E7, which promote tumorigenesis by abrogating p53 and pRb functions. HPV integration sites in cervical and anogenital cancers have been mapped primarily to chromosomal fragile sites and in some cases have been shown to integrate within tumor suppressor genes or other cancer-related genes. To study viral integration sites in SCCHN, we examined an HPV16-infected SCCHN cell line cultured from a tongue-base tumor. HPV fluorescence in situ hybridization (FISH) revealed multiple integrated viral DNA copies in blocks throughout the genome. Sequential FISH and spectral karyotyping identified integration sites on chromosomes 3, 6, 9q, 13q and t(1;8)(q;?). Restriction site-polymerase chain reaction (RS-PCR) was performed to identify the viral-cellular junctions. Sequence analyses confirmed integration sites at 9q31.1 and 6p21 and revealed a novel junction at 16p12.3. Subsequent chromosome breakage studies suggested that the observed viral-cellular integration sites may have occurred within common fragile sites. Additional studies using RT-PCR for E6--E7 viral transcripts showed oncoprotein expression from episomal and integrated viral sequences. Our results suggest that viral integration of HPV in SCCHN appears to occur nonrandomly through targeting specific chromosomal sequences prone to breakage. PMID:15146560

Ragin, Camille C Rose; Reshmi, Shalini C; Gollin, Susanne M

2004-07-10

234

A map for the thick beam-beam interaction  

SciTech Connect

The authors give a closed-form expression for the thick beam-beam interaction for a small disruption parameter, as typical in electron-positron storage rings. The dependence on transverse angle and position of the particle trajectory as well as the longitudinal position of collision and the waist-modified shape of the beam distribution are included. Large incident angles, as are present for beam-halo particles or for large crossing-angle geometry, are accurately represented. The closed-form expression is well approximated by polynomials times the complex error function. Comparisons with multi-slice representations show even the first order terms are more accurate than a five slice representation, saving a factor of 5 in computation time.

Irwin, J.; Chen, T.

1995-06-01

235

The FIRST experiment: interaction region and MAPS vertex detector  

NASA Astrophysics Data System (ADS)

The improvement of the precision of the measurement of the nuclear cross-section, in order to fulfill the requirements of the actual Monte Carlo simulations for hadrontherapy and space radioprotection, is the main goal of the FIRST experiment. After a brief introduction on the treatment planning in hadrontherapy, this paper describes main characteristics and components of the experiment. The features of the interaction region detectors and their main needs (low material budget, high angular coverage, two tracks resolution and large trigger rate) are discussed. Special emphasis is devoted in discussing the new silicon pixel vertex detector, in particular its new developed data acquisition and its characterization with the first test results obtained with a prototype of the detector.

Spiriti, E.; de Napoli, M.; Romano, F.; FIRST Collaboration

236

Mapping of mosquito breeding sites in malaria endemic areas in Pos Lenjang, Kuala Lipis, Pahang, Malaysia  

PubMed Central

Background The application of the Geographic Information Systems (GIS) to the study of vector transmitted diseases considerably improves the management of the information obtained from the field survey and facilitates the study of the distribution patterns of the vector species. Methods As part of a study to assess remote sensing data as a tool for vector mapping, geographical features like rivers, small streams, forest, roads and residential area were digitized from the satellite images and overlaid with entomological data. Map of larval breeding habitats distribution and map of malaria transmission risk area were developed using a combination of field data, satellite image analysis and GIS technique. All digital data in the GIS were displayed in the WGS 1984 coordinate system. Six occasions of larval surveillance were also conducted to determine the species of mosquitoes, their characteristics and the abundance of habitats. Results Larval survey studies showed that anopheline and culicine larvae were collected and mapped from 79 and 67 breeding sites respectively. Breeding habitats were located at 100-400 m from human settlement. Map of villages with 400 m buffer zone visualizes that more than 80% of Anopheles maculatus s.s. immature habitats were found within the buffer zone. Conclusions This study amplifies the need for a broadening of the GIS approach which is emphasized with the aim of rejuvenating the dynamic aspect of entomological studies in Malaysia. In fact, the use of such basic GIS platforms promote a more rational basis for strategic planning and management in the control of endemic diseases at the national level.

2011-01-01

237

Value of epicardial potential maps in localizing pre-excitation sites for radiofrequency ablation. A simulation study  

NASA Astrophysics Data System (ADS)

Using computer simulations, we systematically investigated the limitations of an inverse solution that employs the potential distribution on the epicardial surface as an equivalent source model in localizing pre-excitation sites in Wolff-Parkinson-White syndrome. A model of the human ventricular myocardium that features an anatomically accurate geometry, an intramural rotating anisotropy and a computational implementation of the excitation process based on electrotonic interactions among cells, was used to simulate body surface potential maps (BSPMs) for 35 pre-excitation sites positioned along the atrioventricular ring. Two individualized torso models were used to account for variations in torso boundaries. Epicardial potential maps (EPMs) were computed using the L-curve inverse solution. The measure for accuracy of the localization was the distance between a position of the minimum in the inverse EPMs and the actual site of pre-excitation in the ventricular model. When the volume conductor properties and lead positions of the torso were precisely known and the measurement noise was added to the simulated BSPMs, the minimum in the inverse EPMs was at 12 ms after the onset on average within cm of the pre-excitation site. When the standard torso model was used to localize the sites of onset of the pre-excitation sequence initiated in individualized male and female torso models, the mean distance between the minimum and the pre-excitation site was cm for the male torso and cm for the female torso. The findings of our study indicate that a location of the minimum in EPMs computed using the inverse solution can offer non-invasive means for pre-interventional planning of the ablative treatment.

Hren, Rok

1998-06-01

238

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.

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

2002-01-01

239

Vegetation Analysis and Mapping of the R and D Research Site. Progress Report, July 1, 1984-December 31, 1985.  

National Technical Information Service (NTIS)

The project goals are to map and document the natural vegetation and environmental gradients within the R4D research site and develop methods of extrapolating the information from the Uyamitquaq watershed experiments to the entire North Slope. Progress is...

P. J. Webber D. A. Walker

1985-01-01

240

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.

2006-09-15

241

Demonstration of REBASE-assisted restriction mapping to determine the recognition site of unknown restriction endonucleases.  

PubMed

An important step in the characterization of a new restriction enzyme involves determination of its recognition site. Comparison of its DNA substrate digestion fragment patterns with those obtained using enzymes of known specificity indicates whether the enzyme recognizes a novel sequence or is an isoschizomer of already existing prototype. REBASE (Restriction Enzyme dataBASE: http://www.neb.com/rebase)-assisted restriction mapping is described in this paper for a rare cutter [TspMI (REBASE No. 7191)] and a frequent cutter [BflI (REBASE No. 4910)] as a practical exercise for undergraduate students to understand how to determine recognition sequence of a REase. PMID:21591120

Parashar, Vijay; Capalash, Neena; Sharma, Prince

2007-09-01

242

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

243

Atlas of paced body surface QRS integral maps for localization of the site of origin of postinfarction ventricular tachycardia.  

PubMed

Current mapping during radiofrequency (RF) catheter ablation of postinfarction ventricular tachycardia (VT) is based primarily on the use of single-site mapping techniques. Although such techniques are highly suitable for distinguishing the ultimate site where RF energy is delivered by enabling detailed localization of the exit site or critical component of the VT reentrant circuit, they are time-consuming and inefficient for initial rapid identification of the arrhythmogenic target area. This study features the design and preliminary clinical application of a new noninvasive method that is aimed at speeding up the initial phase of the VT mapping procedure. This method is based on the use of an atlas of 62-lead body surface QRS integral map patterns that was previously developed using left ventricular pace mapping in patients with remote anterior or inferior myocardial infarction. The atlas contains 18 and 22 different paced QRS integral map patterns obtained in patients with previous anterior or inferior myocardial infarction, respectively. Each specific QRS pattern in the atlas provides a unique infarct-specific spatial electrocardiographic representation of the onset of ectopic ventricular activation in a circumscribed endocardial segment of the left ventricle. Localization of the segment of VT origin is obtained by visually or mathematically comparing the QRS integral map recorded during VT with one of the two sets of paced QRS integral maps contained within the atlas with the purpose of selecting the best matching paced QRS integral map pattern.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7884343

SippensGroenewegen, A; Hauer, R N; van Hemel, N M; Janse, M J; Robles de Medina, E O

1994-01-01

244

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

PubMed

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

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

2010-12-10

245

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.

2003-12-01

246

Mapping antibody binding sites on cytochrome c with synthetic peptides: are results representative of the antigenic structure of proteins?  

PubMed Central

Crystallographic work on antigen-antibody complexes has revealed that extensive surface areas of proteins may interact with antibodies. On the other hand, most experimental approaches to locate and define antigenic determinants of protein antigens rely on the linear sequence of the polypeptide chain. Hence the question arises whether mapping of antibody binding sites by analysis of the reactivity of anti-protein antibodies with synthetic peptides can provide a representative picture of the antigenic structure of a protein antigen. We have addressed this question using yeast iso-1 cytochrome c as a protein antigen against which antisera were raised in rabbits. The reaction of the antisera with 103 synthetic hexapeptides covering the entire sequence of cytochrome c was tested by the pepscan procedure in which peptides are coupled to polyethylene rods and tested by ELISA. For the assay, anti-cytochrome c antibodies were fractionated by affinity chromatography on native yeast iso-1 cytochrome c and on apo-cytochrome c; the latter is a random coil. It was found that only antibodies retained by the apo-cytochrome c affinity column react with synthetic peptides. These antibodies comprise a small fraction, probably less than 2%, of all cytochrome c-specific antibodies. The majority of antigenic determinants, which seem to consist of strongly conformation-dependent topographic epitopes, could not be uncovered by the peptide approach. Epitope mapping with short peptides seems of limited usefulness in the case of small, globular, and conformationally stable proteins like cytochrome c.

Schwab, C.; Twardek, A.; Lo, T. P.; Brayer, G. D.; Bosshard, H. R.

1993-01-01

247

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

PubMed

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

2007-01-01

248

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

PubMed

Identification and mapping of natural vegetation are major issues for biodiversity management and conservation. Remotely sensed data with very high spatial resolution are currently used to study vegetation, but most satellite sensors are limited to four spectral bands, which is insufficient to identify some natural vegetation formations. The study objectives are to discriminate natural vegetation and identify natural vegetation formations using a Worldview-2 satellite image. The classification of the Worldview-2 image and ancillary thematic data was performed using a hybrid pixel-based and object-oriented approach. A hierarchical scheme using three levels was implemented, from land cover at a field scale to vegetation formation. This method was applied on a 48 km² site located on the French Atlantic coast which includes a classified NATURA 2000 dune and marsh system. The classification accuracy was very high, the Kappa index varying between 0.90 and 0.74 at land cover and vegetation formation levels respectively. These results show that Wordlview-2 images are suitable to identify natural vegetation. Vegetation maps derived from Worldview-2 images are more detailed than existing ones. They provide a useful medium for environmental management of vulnerable areas. The approach used to map natural vegetation is reproducible for a wider application by environmental managers. PMID:24973612

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

2014-11-01

249

Interfering with Protein-Protein Contact: Molecular Interaction Maps and Peptide Modulators  

Microsoft Academic Search

Protein-protein interactions (PPIs) can be useful targets for different pathologies. In fact controlling a function or attempting to repair an anomaly often means interfering with the cross-talk among different proteins. In order to have a general view of these cross-talks, Molecular Interaction Maps (MIMs) are used, organizing the enormous available information that is added every day and trying to understand

Erika Nieddu; Stefania Pasa

2007-01-01

250

Interactive High Resolution Texture Mapping for the 3D Models of Cultural Heritages  

Microsoft Academic Search

Virtual reconstruction of cultural heritage is not only the basis but also one of important contents of its digitized research.\\u000a The techniques of interactive texture reconstruction researched in this article are of great significance to heighten the\\u000a effect of virtual reconstruction of cultural heritage. Firstly, interactive and precise texture mapping is aiming at establishing\\u000a the relationship between texture images and

Changyu Diao; Dongming Lu

2007-01-01

251

MAP2-MEDIATED IN VITRO INTERACTIONS OF BRAIN MICROTUBULES AND THEIR MODULATION BY CAMP  

PubMed Central

Microtubule-associated proteins (MAPs) are involved in microtubule (MT) bundling and in crossbridges between MTs and other organelles. Previous studies have assigned the MT bundling function of MAPs to their MT-binding domain and its modulation by the projection domain. In the present work, we analyse the viscoelastic properties of MT suspensions in the presence or the absence of cAMP. The experimental data reveal the occurrence of interactions between MT polymers involving MAP2 and modulated by cAMP. Two distinct mechanisms of action of cAMP are identified, which involve on one hand the phosphorylation of MT proteins by the cAMP-dependent protein kinase A (PKA) bound to the end of the N-terminal projection of MAP2, and on the other hand the binding of cAMP to the RII subunit of the PKA affecting interactions between MTs in a phosphorylation-independent manner. These findings imply a role for the complex of PKA with the projection domain of MAP2 in MT-MT interactions and suggest that cAMP may influence directly the density and bundling of MT arrays in dendrites of neurons.

Leterrier, J.F.; Kurachi, M.; Tashiro, T.; Janmey, P. A.

2010-01-01

252

The gross architecture of an antibody-combining site as determined by spin-label mapping  

PubMed Central

1. A series of Dnp (dinitrophenyl) nitroxide spin labels was used to map the dimensions of the combining site of the Dnp-binding immunoglobulin A myeloma protein MOPC 315. The method compares the observed e.s.r. (electron-spin-resonance) hyperfine splittings with those calculated on the basis of different postulated motions for the spin label. The analysis is complicated by the sensitivity of the e.s.r. hyperfine splitting to the overall `tumbling' time of the antibody–hapten complex and the polarity of the spin-label's environment. When these effects are considered quantitatively, it is then possible to determine the degree of mobility of each hapten which is allowed by the shape of the combining site. 2. The dinitrophenyl ring is rigidly held, and the depth of the site is 1.1–1.2nm and has lateral dimensions at the entrance to the site ?0.6nm×0.9nm. The analysis of the results for spin-labelled haptens with chiral centres allows these lateral dimensions to be refined to 0.8nm and 1.1nm, and it is shown that the site is asymmetric with respect to the plane of the dinitrophenyl ring. 3. A polarity profile of the combining site was also obtained and a positively charged amino acid residue, possibly arginine-95L (light chain), was located at the entrance to the site. 4. The binding of Gd(III) to the antibody–hapten complexes results in quenching of the e.s.r. signal of the nitroxide. By using La(III) as a control, the paramagnetic contribution to the quenching is measured. 5. Analysis of the differential quenchings of the enantiomers of two five-membered nitroxide ring spin labels gives two possible locations of the metal-binding site. One of these is equidistant (0.7nm) from each of the three dinitrophenyl aromatic protons, and nuclear-magnetic-resonance relaxation studies, at 270MHz, on solutions of dinitrobenzene, Gd(III) and the Fv fragment (variable region of heavy and light chain) from protein MOPC 315 support this location for the metal site. 6. The e.s.r. and metal-binding data were then compared with the results of a model of the combining site constructed on the basis of framework invariance in immunoglobulins [Padlan, Davies, Pecht, Givol & Wright (1976) Cold Spring Harbor Symp. Quant. Biol. 41, in the press]. The overall agreement is very good. Assignments of possible chelating groups for the metal can be made.

Sutton, Brian J.; Gettins, Peter; Givol, David; Marsh, Derek; Wain-Hobson, Simon; Willan, Keith J.; Dwek, Raymond A.

1977-01-01

253

MAPPING MOLECULAR FLEXIBILITY OF PROTEINS WITH SITE DIRECTED SPIN LABELING: A CASE STUDY OF MYOGLOBIN‡  

PubMed Central

Site directed spin labeling (SDSL) has potential for mapping protein flexibility under physiological conditions. The purpose of the present study was to explore this potential using 38 singly spin-labeled mutants of myoglobin distributed throughout the sequence. Correlation of the EPR spectra with protein structure provides new evidence that the site dependent variation in lineshape, and hence motion of the spin label, is due largely to differences in mobility of the helical backbone in the ns time range. Fluctuations between conformational substates, typically in the ?s-ms time range, are slow on the EPR time scale and the spectra provide a snapshot of conformational equilibria frozen in time as revealed by multiple components in the spectra. A recent study showed that osmolyte perturbation can positively identify conformational exchange as the origin of multicomponent spectra (Lopez et al. (2009), Protein Sci. 18, 1637). In the present study this new strategy is employed in combination with lineshape analysis and pulsed-EPR interspin distance measurements to investigate the conformation and flexibility of myoglobin in three folded and partially folded states. The regions identified to be in conformational exchange in the three forms agree remarkably well with those assigned by NMR, but the faster time scale of EPR allows characterization of localized states not detected in NMR. Collectively, the results suggest that SDSL-EPR and osmolyte perturbation provide a facile means for mapping the amplitude of fast backbone fluctuations and for detecting sequences in slow conformational exchange in folded and partially folded protein sequences.

Lopez, Carlos J.; Oga, Shirley; Hubbell, Wayne L.

2012-01-01

254

Genome-wide high-resolution mapping of chromosome fragile sites in Saccharomyces cerevisiae  

PubMed Central

In mammalian cells, perturbations in DNA replication result in chromosome breaks in regions termed “fragile sites.” Using DNA microarrays, we mapped recombination events and chromosome rearrangements induced by reduced levels of the replicative DNA polymerase-? in the yeast Saccharomyces cerevisiae. We found that the recombination events were nonrandomly associated with a number of structural/sequence motifs that correlate with paused DNA replication forks, including replication-termination sites (TER sites) and binding sites for the helicase Rrm3p. The pattern of gene-conversion events associated with cross-overs suggests that most of the DNA lesions that initiate recombination between homologs are double-stranded DNA breaks induced during S or G2 of the cell cycle, in contrast to spontaneous recombination events that are initiated by double-stranded DNA breaks formed prior to replication. Low levels of DNA polymerase-? also induced very high rates of aneuploidy, as well as chromosome deletions and duplications. Most of the deletions and duplications had Ty retrotransposons at their breakpoints.

Song, Wei; Dominska, Margaret; Greenwell, Patricia W.; Petes, Thomas D.

2014-01-01

255

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

PubMed

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

2008-10-01

256

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.

257

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.

258

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

PubMed Central

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

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

2013-01-01

259

Does an Interactive WebCT Site Help Students Learn?  

ERIC Educational Resources Information Center

We examined whether students with access to a supplemental course Web site enhanced with e-mail, discussion boards, and chat room capability reacted to it more positively than students who used a Web site with the same content but no communication features. Students used the Web sites on a voluntary basis. At the end of the semester, students…

Elicker, Joelle D.; O'Malley, Alison L.; Williams, Christine M.

2008-01-01

260

InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale  

PubMed Central

We propose InSite, a computational method that integrates high-throughput protein and sequence data to infer the specific binding regions of interacting protein pairs. We compared our predictions with binding sites in Protein Data Bank and found significantly more binding events occur at sites we predicted. Several regions containing disease-causing mutations or cancer polymorphisms in human are predicted to be binding for protein pairs related to the disease, which suggests novel mechanistic hypotheses for several diseases.

Wang, Haidong; Segal, Eran; Ben-Hur, Asa; Li, Qian-Ru; Vidal, Marc; Koller, Daphne

2007-01-01

261

Toward an Integrated Linkage Map of Common Bean. III. Mapping Genetic Factors Controlling Host-Bacteria Interactions  

PubMed Central

Restriction fragment length polymorphism (RFLP)-based genetic linkage maps allow us to dissect the genetic control of quantitative traits (QT) by locating individual quantitative trait loci (QTLs) on the linkage map and determining their type of gene action and the magnitude of their contribution to the phenotype of the QT. We have performed such an analysis for two traits in common bean, involving interactions between the plant host and bacteria, namely Rhizobium nodule number (NN) and resistance to common bacterial blight (CBB) caused by Xanthomonas campestris pv. phaseoli. Analyses were conducted in the progeny of a cross between BAT93 (fewer nodules; moderately resistant to CBB) and Jalo EEP558 (more nodules; susceptible to CBB). An RFLP-based linkage map for common bean based on 152 markers had previously been derived in the F(2) of this cross. Seventy F(2)-derived F(3) families were inoculated in separate greenhouse experiments with Rhizobium tropici strain UMR1899 or X. c. pv. phaseoli isolate isolate W18. Regression and interval mapping analyses were used to identify genomic regions involved in the genetic control of these traits. These two methods identified the same genomic regions for each trait, with a few exceptions. For each trait, at least four putative QTLs were identified, which accounted for approximately 50% and 75% of the phenotypic variation in NN and CBB resistance, respectively. A chromosome region on linkage group D7 carried factor(s) influencing both traits. In all other cases, the putative QTLs affecting NN and CBB were located in different linkage groups or in the same linkage group, but far apart (more than 50 cM). Both BAT93 and Jalo EEP558 contributed alleles associated with higher NN, whereas CBB resistance was always associated with BAT93 alleles. Further investigations are needed to determine whether the QTLs for NN and CBB on linkage group D7 represent linked genes or the same gene with pleiotropic effects. Identification of the QTLs raises the possibility of initiating map-based cloning and marker-assisted selection for these traits.

Nodari, R. O.; Tsai, S. M.; Guzman, P.; Gilbertson, R. L.; Gepts, P.

1993-01-01

262

Mapping genetic loci that interact with myostatin to affect growth traits  

PubMed Central

Myostatin, or GDF8, is an inhibitor of skeletal muscle growth. A non-functional myostatin mutation leads to a double muscling phenotype in some species, for example, mice, cattle and humans. Previous studies have indicated that there are loci in the genome that interact with myostatin to control backfat depth and other complex traits. We now report a quantitative trait loci (QTL) mapping study designed to identify loci that interact with myostatin to impact growth traits in mice. Body weight and average daily gain traits were collected on F2 progeny derived from a myostatin-null C57BL/6 strain by M16i cross. In all, 44 main effect QTL were detected above a 5% genome-wide significance threshold when an interval mapping method was used. An additional 37 QTL were identified to significantly interact with myostatin, sex or reciprocal cross. A total of 12 of these QTL interacted with myostatin genotype. These results provide a foundation for the further fine mapping of genome regions that harbor loci that interact with myostatin.

Cheng, Y; Rachagani, S; Dekkers, J C M; Mayes, M S; Tait, R; Reecy, J M

2011-01-01

263

Allelic Association under Map Error and Recombinational Heterogeneity: A Tale of Two Sites  

Microsoft Academic Search

Recombination acts on the genetic map, not on the physical map. On the other hand, the physical map is usually more accurate. Choice of the genetic or physical map for positional cloning by allelic association depends on the goodness of fit of data to each map under an established model. Huntington disease illustrates the usual case in which the greater

Christine Lonjou; Andrew Collins; Richard S. Ajioka; Lynn B. Jorde; James P. Kushner; Newton E. Morton

1998-01-01

264

Web Mapping for Promoting Interaction and Collaboration in Community Land Planning  

NASA Astrophysics Data System (ADS)

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

Veenendaal, B.; Dhliwayo, M.

2013-10-01

265

Concept Mapping as a Support for Mars Landing-Site Selection  

NASA Technical Reports Server (NTRS)

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

Cabrol, Nathalie A.; Briggs, Geoffrey A.

1999-01-01

266

Genotype Matrix Mapping: Searching for Quantitative Trait Loci Interactions in Genetic Variation in Complex Traits  

PubMed Central

Abstract In order to reveal quantitative trait loci (QTL) interactions and the relationship between various interactions in complex traits, we have developed a new QTL mapping approach, named genotype matrix mapping (GMM), which searches for QTL interactions in genetic variation. The central approach in GMM is the following. (1) Each tested marker is given a virtual matrix, named a genotype matrix (GM), containing intersecting lines and rows equal to the total allele number for that marker in the population analyzed. (2) QTL interactions are then estimated and compared through virtual networks among the GMs. To evaluate the contribution of marker combinations to a quantitative phenotype, the GMM method divides the samples into two non-overlapping subclasses, S0 and S1; the former contains the samples that have a specific genotype pattern to be evaluated, and the latter contains samples that do not. Based on this division, the F-measure is calculated as an index of significance. With the GMM method, we extracted significant marker combinations consisting of one to three interacting markers. The results indicated there were multiple QTL interactions affecting the phenotype (flowering date). GMM will be a valuable approach to identify QTL interactions in genetic variation of a complex trait within a variety of organisms.

Isobe, Sachiko; Nakaya, Akihiro; Tabata, Satoshi

2007-01-01

267

A Gaussian Evolutionary Method for Predicting Protein-Protein Interaction Sites  

Microsoft Academic Search

Protein-protein interactions play a pivotal role in modern molecular biology. Identifying the protein-protein interaction\\u000a sites is great scientific and practical interest for predicting protein-protein interactions. In this study, we proposed a\\u000a Gaussian Evolutionary Method (GEM) to optimize 18 features, including ten atomic solvent and eight protein 2\\u000a nd\\u000a structure features, for predicting protein-protein interaction sites. The training set consists of

Kang-ping Liu; Jinn-moon Yang

2007-01-01

268

The light chains of microtubule-associated proteins MAP1A and MAP1B interact with ?1-syntrophin in the central and peripheral nervous system.  

PubMed

Microtubule-associated proteins of the MAP1 family (MAP1A, MAP1B, and MAP1S) share, among other features, a highly conserved COOH-terminal domain approximately 125 amino acids in length. We conducted a yeast 2-hybrid screen to search for proteins interacting with this domain and identified ?1-syntrophin, a member of a multigene family of adapter proteins involved in signal transduction. We further demonstrate that the interaction between the conserved COOH-terminal 125-amino acid domain (which is located in the light chains of MAP1A, MAP1B, and MAP1S) and ?1-syntrophin is direct and occurs through the pleckstrin homology domain 2 (PH2) and the postsynaptic density protein 95/disk large/zonula occludens-1 protein homology domain (PDZ) of ?1-syntrophin. We confirmed the interaction of MAP1B and ?1-syntrophin by co-localization of the two proteins in transfected cells and by co-immunoprecipitation experiments from mouse brain. In addition, we show that MAP1B and ?1-syntrophin partially co-localize in Schwann cells of the murine sciatic nerve during postnatal development and in the adult. However, intracellular localization of ?1-syntrophin and other Schwann cell proteins such as ezrin and dystrophin-related protein 2 (DRP2) and the localization of the axonal node of Ranvier-associated protein Caspr1/paranodin were not affected in MAP1B null mice. Our findings add to a growing body of evidence that classical MAPs are likely to be involved in signal transduction not only by directly modulating microtubule function, but also through their interaction with signal transduction proteins. PMID:23152929

Fuhrmann-Stroissnigg, Heike; Noiges, Rainer; Descovich, Luise; Fischer, Irmgard; Albrecht, Douglas E; Nothias, Fatiha; Froehner, Stanley C; Propst, Friedrich

2012-01-01

269

The Light Chains of Microtubule-Associated Proteins MAP1A and MAP1B Interact with ?1-Syntrophin in the Central and Peripheral Nervous System  

PubMed Central

Microtubule-associated proteins of the MAP1 family (MAP1A, MAP1B, and MAP1S) share, among other features, a highly conserved COOH-terminal domain approximately 125 amino acids in length. We conducted a yeast 2-hybrid screen to search for proteins interacting with this domain and identified ?1-syntrophin, a member of a multigene family of adapter proteins involved in signal transduction. We further demonstrate that the interaction between the conserved COOH-terminal 125-amino acid domain (which is located in the light chains of MAP1A, MAP1B, and MAP1S) and ?1-syntrophin is direct and occurs through the pleckstrin homology domain 2 (PH2) and the postsynaptic density protein 95/disk large/zonula occludens-1 protein homology domain (PDZ) of ?1-syntrophin. We confirmed the interaction of MAP1B and ?1-syntrophin by co-localization of the two proteins in transfected cells and by co-immunoprecipitation experiments from mouse brain. In addition, we show that MAP1B and ?1-syntrophin partially co-localize in Schwann cells of the murine sciatic nerve during postnatal development and in the adult. However, intracellular localization of ?1-syntrophin and other Schwann cell proteins such as ezrin and dystrophin-related protein 2 (DRP2) and the localization of the axonal node of Ranvier-associated protein Caspr1/paranodin were not affected in MAP1B null mice. Our findings add to a growing body of evidence that classical MAPs are likely to be involved in signal transduction not only by directly modulating microtubule function, but also through their interaction with signal transduction proteins.

Descovich, Luise; Fischer, Irmgard; Albrecht, Douglas E.; Nothias, Fatiha; Froehner, Stanley C.; Propst, Friedrich

2012-01-01

270

Protein-protein interaction map is a key gateway into liver regeneration  

PubMed Central

Recent studies indicate that the process of liver regeneration involves multiple signaling pathways and a variety of genes, cytokines and growth factors. Protein-protein interactions (PPIs) play a role in nearly all events that take place within the cell and PPI maps should be helpful in further understanding the process of liver regeneration. In this review, we discuss recent progress in understanding the PPIs that occur during liver regeneration especially those in the transforming growth factor ? signaling pathways. We believe the use of large-scale PPI maps for integrating the information already known about the liver regeneration is a useful approach in understanding liver regeneration from the standpoint of systems biology.

Xie, Chao; Gao, Jin; Zhu, Run-Zhi; Yuan, Yun-Sheng; He, Hong-Lin; Huang, Qiu-Shi; Han, Wei; Yu, Yan

2010-01-01

271

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.

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

2013-01-01

272

Mapping of scorpion toxin receptor sites at voltage-gated sodium channels.  

PubMed

Scorpion alpha and beta toxins interact with voltage-gated sodium channels (Na(v)s) at two pharmacologically distinct sites. Alpha toxins bind at receptor site-3 and inhibit channel inactivation, whereas beta toxins bind at receptor site-4 and shift the voltage-dependent activation toward more hyperpolarizing potentials. The two toxin classes are subdivided to distinct pharmacological groups according to their binding preferences and ability to compete for the receptor sites at Na(v) subtypes. To elucidate the toxin-channel surface of interaction at both receptor sites and clarify the molecular basis of varying toxin preferences, an efficient bacterial system for their expression in recombinant form was established. Mutagenesis accompanied by toxicity, binding and electrophysiological assays, in parallel to determination of the three-dimensional structure using NMR and X-ray crystallography uncovered a bipartite bioactive surface in toxin representatives of all pharmacological groups. Exchange of external loops between the mammalian brain channel rNa(v)1.2a and the insect channel DmNa(v)1 highlighted channel regions involved in the varying sensitivity to assorted toxins. In parallel, thorough mutagenesis of channel external loops illuminated points of putative interaction with the toxins. Amino acid substitutions at external loops S1-S2 and S3-S4 of the voltage sensor module in domain II of rNa(v)1.2a had prominent impact on the activity of the beta-toxin Css4 (from Centruroides suffusus suffusus), and substitutions at external loops S1-S2 and S3-S4 of the voltage sensor module in domain IV affected the activity of the alpha-toxin Lqh2 (from Leiurus quinquestriatus hebraeus). Rosetta modeling of toxin-Na(v) interaction using the voltage sensor module of the potassium channel as template raises commonalities in the way alpha and beta toxins interact with the channel. Css4 interacts with rNa(v)1.2a at a crevice between S1-S2 and S3-S4 transmembrane segments in domain II, while Lqh2 interacts with rNa(v)1.2a at a crevice between S1-S2 and S3-S4 transmembrane segments in domain IV. Double-mutant cycle analysis and dissociation assays employing a battery of Lqh2 mutants against rNa(v)1.2a mutants identified the docking orientation of alpha toxins at the channel external surface of the Gating-module in domain IV. The other point of interaction between the toxin and the channel has not yet been defined and may involve channel residues of either the Pore-module or the Gating-module. PMID:22694883

Gurevitz, Michael

2012-09-15

273

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

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

274

An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803  

PubMed Central

There has been an increasing interest in cyanobacteria because these photosynthetic organisms convert solar energy into biomass and because of their potential for the production of biofuels. However, the exploitation of cyanobacteria for bioengineering requires knowledge of their transcriptional organization. Using differential RNA sequencing, we have established a genome-wide map of 3,527 transcriptional start sites (TSS) of the model organism Synechocystis sp. PCC6803. One-third of all TSS were located upstream of an annotated gene; another third were on the reverse complementary strand of 866 genes, suggesting massive antisense transcription. Orphan TSS located in intergenic regions led us to predict 314 noncoding RNAs (ncRNAs). Complementary microarray-based RNA profiling verified a high number of noncoding transcripts and identified strong ncRNA regulations. Thus, ?64% of all TSS give rise to antisense or ncRNAs in a genome that is to 87% protein coding. Our data enhance the information on promoters by a factor of 40, suggest the existence of additional small peptide-encoding mRNAs, and provide corrected 5? annotations for many genes of this cyanobacterium. The global TSS map will facilitate the use of Synechocystis sp. PCC6803 as a model organism for further research on photosynthesis and energy research.

Mitschke, Jan; Georg, Jens; Scholz, Ingeborg; Sharma, Cynthia M.; Dienst, Dennis; Bantscheff, Jens; Voss, Bjorn; Steglich, Claudia; Wilde, Annegret; Vogel, Jorg; Hess, Wolfgang R.

2011-01-01

275

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.

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

2011-01-01

276

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.

2013-08-01

277

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.

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

2012-01-01

278

Interactive marine spatial planning: siting tidal energy arrays around the Mull of Kintyre.  

PubMed

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

2012-01-01

279

Mapping of the Regions Involved in Homotypic Interactions of Tula Hantavirus N Protein  

PubMed Central

Hantavirus nucleocapsid (N) protein has been suggested to form homodimers and homotrimers that are further integrated into the nucleocapsid filaments around the viral RNA. Here we report detailed mapping of the regions involved in the homotypic N protein interactions in Tula hantavirus (TULV). Peptide scan screening was used to define the interaction regions, and the mammalian two-hybrid assay was used for the functional analysis of N protein mutants. To study linear regions responsible for N protein interaction(s), we used peptide scanning in which N peptides synthesized on membranes recognize recombinant TULV N protein. The data showed that the N protein bound to membrane-bound peptides comprising amino acids 13 to 30 and 41 to 57 in the N-terminal part and 340 to 379, 391 to 407, and 410 to 419 in the C-terminal part of the molecule. Further mapping of the interaction regions by alanine scanning indicated the importance of basic amino acids along the N protein and especially asparagine-394, histidine-395, and phenyalanine-396 in forming the binding interface. Analysis of truncated mutants in the mammalian two-hybrid assay showed that N-terminal amino acids 1 to 43 are involved in and C-terminal amino acids 393 to 398 (VNHFHL) are absolutely crucial for the homotypic interactions. Furthermore, our data suggested a tail-to-tail and head-to-head binding scheme for the N proteins.

Kaukinen, Pasi; Vaheri, Antti; Plyusnin, Alexander

2003-01-01

280

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

PubMed

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

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

2013-07-30

281

Improving the Apollo 12 landing site mapping with Chandrayaan M3 data  

NASA Astrophysics Data System (ADS)

The geology of the Apollo 12 landing site has been the subject of many studies, including recently by Korotev et al. (2011) and Snape et al. (2013). This research attempts to bring additional understanding from a remote sensing perspective using the Moon Mineralogy Mapper (M3) sensor data, onboard the Chandrayaan lunar orbiter. This has a higher spatial-spectral resolution sensor than the Clementine UV-Vis sensor and provides the opportunity to study the lunar surface with detailed spectral signatures. Mapping of FeO (wt%) and TiO2 (wt%) is done using the methods of Lucey et al. (2000) and Wilcox et al. (2005). A FeO & TiO2 processing module (i.feotio2) is made specifically for this research within the Free & Open Source Software GRASS GIS. Attempts will be made to estimate the lava flow thickness using the method of Bugiolacchi et al. (2006) and individual lava layers thicknesses (Weider et al., 2010). Integration of this new information will be put in perspective and integrated with previous work. Analysis from the combined higher spatial and spectral resolutions will improve the accuracy of the geological mapping at the Apollo 12 landing site. References Bugiolacchi, R., Spudis, P.D., Guest, J.E., 2006. Stratigraphy and composition of lava flows in Mare Nubium and Mare Cognitum. Meteoritics & Planetary Science. 41(2):285-304. Korotev, R.L., Jolliff, B.L., Zeigler, R.A., Seddio, S.M., Haskin, L.A., 2011. Apollo 12 revisited. Geochimica et Cosmochimica Acta. 75(6):1540-1573. Lucey, P.G., Blewett, D.T., Jolliff, B.L., 2000. Lunar iron and titanium abundance algorithms based on final processing of Clementine ultraviolet-visible images. J. Geophys. Res. 105(E8): 20297-20305. Snape, J.F., Alexander, L., Crawford, I.A., Joy, K.H., 2013. Basaltic Regolith Sample 12003,314: A New Member of the Apollo 12 Feldspathic Basalt Suite? Lunar and Planetary Institute Science Conference Abstracts 44:1044. Weider, S.Z., Crawford, I.A. and Joy, K.H., "Individual lava flow thicknesses in Oceanus Procellarum and Mare Serenitatis determined from Clementine multi-spectral data," Icarus, 209, 323-336, (2010). Wilcox, B.B., Lucey, P.G., Gillis, J.J., 2005. Mapping iron in the lunar mare: An improved approach. J. Geophys. Res. 110(E11):2156-2202.

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

2014-05-01

282

HeatMapViewer: interactive display of 2D data in biology  

PubMed Central

Summary: The HeatMapViewer is a BioJS component that lays-out and renders two-dimensional (2D) plots or heat maps that are ideally suited to visualize matrix formatted data in biology such as for the display of microarray experiments or the outcome of mutational studies and the study of SNP-like sequence variants. It can be easily integrated into documents and provides a powerful, interactive way to visualize heat maps in web applications. The software uses a scalable graphics technology that adapts the visualization component to any required resolution, a useful feature for a presentation with many different data-points. The component can be applied to present various biological data types. Here, we present two such cases – showing gene expression data and visualizing mutability landscape analysis. Availability: https://github.com/biojs/biojs; http://dx.doi.org/10.5281/zenodo.7706.

Yachdav, Guy

2014-01-01

283

HeatMapViewer: interactive display of 2D data in biology.  

PubMed

Summary: The HeatMapViewer is a BioJS component that lays-out and renders two-dimensional (2D) plots or heat maps that are ideally suited to visualize matrix formatted data in biology such as for the display of microarray experiments or the outcome of mutational studies and the study of SNP-like sequence variants. It can be easily integrated into documents and provides a powerful, interactive way to visualize heat maps in web applications. The software uses a scalable graphics technology that adapts the visualization component to any required resolution, a useful feature for a presentation with many different data-points. The component can be applied to present various biological data types. Here, we present two such cases - showing gene expression data and visualizing mutability landscape analysis. Availability:https://github.com/biojs/biojs; http://dx.doi.org/10.5281/zenodo.7706. PMID:24860644

Yachdav, Guy; Hecht, Maximilian; Pasmanik-Chor, Metsada; Yeheskel, Adva; Rost, Burkhard

2014-01-01

284

Comprehensive Binary Interaction Mapping of SH2 Domains via Fluorescence Polarization Reveals Novel Functional Diversification of ErbB Receptors  

PubMed Central

First-generation interaction maps of Src homology 2 (SH2) domains with receptor tyrosine kinase (RTK) phosphosites have previously been generated using protein microarray (PM) technologies. Here, we developed a large-scale fluorescence polarization (FP) methodology that was able to characterize interactions between SH2 domains and ErbB receptor phosphosites with higher fidelity and sensitivity than was previously achieved with PMs. We used the FP assay to query the interaction of synthetic phosphopeptides corresponding to 89 ErbB receptor intracellular tyrosine sites against 93 human SH2 domains and 2 phosphotyrosine binding (PTB) domains. From 358,944 polarization measurements, the affinities for 1,405 unique biological interactions were determined, 83% of which are novel. In contrast to data from previous reports, our analyses suggested that ErbB2 was not more promiscuous than the other ErbB receptors. Our results showed that each receptor displays unique preferences in the affinity and location of recruited SH2 domains that may contribute to differences in downstream signaling potential. ErbB1 was enriched versus the other receptors for recruitment of domains from RAS GEFs whereas ErbB2 was enriched for recruitment of domains from tyrosine and phosphatidyl inositol phosphatases. ErbB3, the kinase inactive ErbB receptor family member, was predictably enriched for recruitment of domains from phosphatidyl inositol kinases and surprisingly, was enriched for recruitment of domains from tyrosine kinases, cytoskeletal regulatory proteins, and RHO GEFs but depleted for recruitment of domains from phosphatidyl inositol phosphatases. Many novel interactions were also observed with phosphopeptides corresponding to ErbB receptor tyrosines not previously reported to be phosphorylated by mass spectrometry, suggesting the existence of many biologically relevant RTK sites that may be phosphorylated but below the detection threshold of standard mass spectrometry procedures. This dataset represents a rich source of testable hypotheses regarding the biological mechanisms of ErbB receptors.

Ciaccio, Mark F.; Chuu, Chih-pin; Jones, Richard B.

2012-01-01

285

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 cpsxoutreach@uwo.ca if you are interested.

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

2013-12-01

286

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

2011-01-01

287

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

2010-07-01

288

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.

1998-01-01

289

Research Resource: Genome-Wide Mapping of in Vivo Androgen Receptor Binding Sites in Mouse Epididymis  

PubMed Central

Epididymal function depends on androgen signaling through the androgen receptor (AR), although most of the direct AR target genes in epididymis remain unknown. Here we globally mapped the AR binding regions in mouse caput epididymis in which AR is highly expressed. Chromatin immunoprecipitation sequencing indicated that AR bound selectively to 19,377 DNA regions, the majority of which were intergenic and intronic. Motif analysis showed that 94% of the AR binding regions harbored consensus androgen response elements enriched with multiple binding motifs that included nuclear factor 1 and activator protein 2 sites consistent with combinatorial regulation. Unexpectedly, AR binding regions showed limited conservation across species, regardless of whether the metric for conservation was based on local sequence similarity or the presence of consensus androgen response elements. Further analysis suggested the AR target genes are involved in diverse biological themes that include lipid metabolism and sperm maturation. Potential novel mechanisms of AR regulation were revealed at individual genes such as cysteine-rich secretory protein 1. The composite studies provide new insights into AR regulation under physiological conditions and a global resource of AR binding sites in a normal androgen-responsive tissue.

Hu, Shuanggang; Yao, Guangxin; Guan, Xiaojun; Ni, Zimei; Ma, Wubin; Wilson, Elizabeth M.; French, Frank S.; Liu, Qiang; Zhang, Yonglian

2010-01-01

290

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

SciTech Connect

Adenovirus early region 1A (E1A) encodes two acidic phosphoproteins which are required for transactivation of viral transcription, efficient viral DNA replication in phase G/sub 0/-arrested human cells, and oncogenic transformation of rodent cells. Biochemical analysis of in vivo /sup 32/P-labeled adenovirus type 2 E1A proteins purified with monoclonal antibodies demonstrated that these proteins were phosphorylated at multiple serine residues. Two-dimensional phosphotryptic peptide maps of wild-type and mutant E1A proteins were used to locate a major site of E1A protein phosphorylation at serine-219 of the large E1A protein. Although this serine fell within a consensus sequence for phosphorylation by the cyclic AMP-dependent protein kinases, experiments with mutant CHO cells defective in these enzymes indicated that it was not. Oligonucleotide-directed mutagenesis was used to substitute an alanine for serine-219. This mutation prevented phosphorylation at this site. Nonetheless, the mutant was indistinguishable from the wild type for early gene transactivation, replication on G/sub 0/-arrested WI-38 cells, and transformation of cloned rat embryo fibroblast cells.

Tsukamotot, A.S.; Ponticelli, A.; Berk, A.J.; Gaynor, R.B.

1986-07-01

291

Barbara WeberSite: DNA Interactive (www.dnai.org)  

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.

2008-10-06

292

High resolution seismic mapping at a groundwater contamination site: 3-D reflection data  

NASA Astrophysics Data System (ADS)

We conducted a near-surface, 3-D seismic reflection survey at a groundwater contamination site. Part of a month-long experiment that included tomography and downhole seismic studies, the experiments were designed to image the near surface (<20m) at a high level of detail (< 0.5m laterally and vertically) to enhance ongoing remediation activities at the site. The site, Operable Unit 2 (OU2), located at Hill Air Force Base in Ogden, Utah has been subject to continuing efforts to remove dense, nonaqueous-phase liquids (DNAPLs) released at the site. Subsurface mapping of the near-surface geology, based on more than 200 monitoring wells drilled at the site, is not sufficiently detailed to allow effective remediation. The near-surface geology of OU2 includes unconsolidated sands, silts and gravels overlying a thick clay aquiclude. Incised in the clay is a paleochannel about 15m deep trapping both groundwater and at its deepest points DNAPL. The 3-D reflection survey, covering an area of 95 by 37m centered over the channel, used RefTek “Texans”, a single-channel, non-cabled recording system. Approximately 610 receivers were spaced in a six line swath at 0.35m intervals across the channel profile (east west) with a 2.1m separation along the channel strike (north south). The source, a .223 caliber rifle, was fired in a rotated brick shooting pattern between the receiver lines producing a data set of over 1.8B traces with .175 x .175m CMP bin size. Over 3,700 useable shot records were taken, forming a data volume of 3.6 Gbytes. After data preprocessing, filtering (90-440Hz passband), spectral whitening, velocity analysis and DMO, the 3-D stack shows coherent shallow reflections from the stratigraphy within the channel and the top of the clay layer from 30 to 90ms. Inline sections show the changing channel profile, steeply dipping along the western wall, with a gentle slope along the east wall. Consistent with depth-to-clay values from the well data, the depth to the base of the channel, the likely collection points for DNAPL, varies from 55ms to 75ms at different points within the stack. The sections also correlate with our results from the initial 2-D survey at OU2. Comparison of the seismic data with maps made from well data show excellent correlation between the separate data sets with the seismic data successfully imaging the varying depth-to-clay at the site from 3 to 15m. The reflection images also agree well with the travel time tomography images of the channel made from the complementary tomography experiment. The velocity model from the tomography experiment will be used for depth migration of the reflection data.

Dana, D.; Levander, A.; Danbom, S.; Zelt, C.

2003-04-01

293

Molecular Interaction Maps--A Diagrammatic Graphical Language for Bioregulatory Networks  

NSDL National Science Digital Library

Molecular interaction maps (MIMs) use a clear, accurate, and versatile graphical language to depict complex biological processes. Here, we discuss the main features of the MIM language and its potential uses. MIMs can be used as database resources and simulation guides, and can serve to generate new hypotheses regarding the roles of specific molecules in the bioregulatory networks that control progression through the cell cycle, differentiation, and cell death.

Yves Pommier (National Cancer Institute;Center for Cancer Research REV); Kurt W. Kohn (National Cancer Institute;Center for Cancer Research REV); Mirit I. Aladjem (National Cancer Institute;Center for Cancer Research REV); Stefania Pasa (National Institute of Cancer Research and University of Genoa;Laboratory of Experimental Oncology REV); Silvio Parodi (National Institute of Cancer Research and University of Genoa;Laboratory of Experimental Oncology REV); John N. Weinstein (National Cancer Institute;Center for Cancer Research REV)

2004-03-02

294

Human-Robot Interactive Guiding System's Application in Sonar Quick Mapping  

Microsoft Academic Search

This study introduces the sonar quick mapping method using tethered-robot guiding system, Navi-guider, that is one of the human and robot interactive devices. Basic function of the Navi-guider is to actively control the robot through the tension length and an orientation of the cable. This is able to easily control the mobile robot, is applied to robot controller for quick

Yu-cheol Lee; Sangik Na; Hyo-sung Ahn; Wonpil Yu

2007-01-01

295

Mapping Dynamic Protein Interactions to Insulin Secretory Granule Behavior with TIRF-FRET  

PubMed Central

Biological processes are governed by extensive networks of dynamic molecular interactions. Yet, establishing a spatial and temporal map of these interactions and their direct relationship to specific cell functions has remained a challenge. Here, we implement sensitized emission Förster resonance energy transfer (FRET) stoichiometry under total internal reflection fluorescence (TIRF) microscopy. We demonstrate through quantitative analysis and modeling that evanescent fields must be precisely matched between FRET excitation wavelengths to isolate dynamic interactions between bimolecular FRET pairs that are not entirely membrane-delimited. We then use TIRF-FRET to monitor the behavior of individual insulin-containing secretory granules at the plasma membrane of living cells, while simultaneously tracking the dynamic interaction between the GTPase Rab27A and its effector Slp4A, on those same granules. Notably, insulin granules that underwent exocytosis demonstrated a specific increase in Rab27A-GTP/Slp4A FRET in the 5 s before membrane fusion, which coincided temporally with an increase in granule displacement and mobility. These results demonstrate an initial spatiotemporal mapping of a dynamic protein-protein interaction on individual secretory granules that is linked to a specific granule behavior in living cells.

Lam, Alice D.; Ismail, Sahar; Wu, Ray; Yizhar, Ofer; Passmore, Daniel R.; Ernst, Stephen A.; Stuenkel, Edward L.

2010-01-01

296

Protein interaction mapping on a functional shotgun sequence of Rickettsia sibirica  

PubMed Central

Protein interaction maps can reveal novel pathways and functional complexes, allowing ‘guilt by association’ annotation of uncharacterized proteins. To address the need for large-scale protein interaction analyses, a bacterial two-hybrid system was coupled with a whole genome shotgun sequencing approach for microbial genome analysis. We report the first large-scale proteomics study using this system, integrating de novo genome sequencing with functional interaction mapping and annotation in a high-throughput format. We apply the approach by shotgun sequencing and annotating the genome of Rickettsia sibirica strain 246, an obligate intracellular human pathogen among the Spotted Fever Group rickettsiae. The bacteria invade endothelial cells and cause lysis after large amounts of progeny have accumulated. Little is known about specific Rickettsial virulence factors and their mode of pathogenicity. Analysis of the combined genomic sequence and protein–protein interaction data for a set of virulence related Type IV secretion system (T4SS) proteins revealed over 250 interactions and will provide insight into the mechanism of Rickettsial pathogenicity.

Malek, Joel A.; Wierzbowski, Jamey M.; Tao, Wei; Bosak, Stephanie A.; Saranga, David J.; Doucette-Stamm, Lynn; Smith, Douglas R.; McEwan, Paul J.; McKernan, Kevin J.

2004-01-01

297

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

PubMed

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

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

2014-08-01

298

Mapping of the plasminogen binding site of streptokinase with short synthetic peptides.  

PubMed Central

Although several recent studies employing various truncated fragments of streptokinase (SK) have demonstrated that the high-affinity interactions of this protein with human plasminogen (HPG) to form activator complex (SK-HPG) are located in the central region of SK, the exact location and nature of such HPG interacting site(s) is still unclear. In order to locate the "core" HPG binding ability in SK, we focused on the primary structure of a tryptic fragment of SK derived from the central region (SK143-293) that could bind as well as activate HPG, albeit at reduced levels in comparison to the activity of the native, full-length protein. Because this fragment was refractory to further controlled proteolysis, we took recourse to a synthetic peptide approach wherein the HPG interacting properties of 16 overlapping 20-mer peptides derived from this region of SK were examined systematically. Only four peptides from this set, viz., SK234-253, SK254-273, SK274-293, and SK263-282, together representing the contiguous sequence SK234-293, displayed HPG binding ability. This was established by a specific HPG-binding ELISA as well as by dot blot assay using 125I-labeled HPG. These results showed that the minimal sequence with HPG binding function resided between residues 234 and 293. None of the synthetic SK peptides was found to activate HPG, either individually or in combination, but, in competition experiments where each of the peptides was added prior to complex formation between SK and HPG, three of the HPG binding peptides (SK234-253, SK254-273, and SK274-293) inhibited strongly the generation of a functional activator complex by SK and HPG. This indicated that residues 234-293 in SK participate directly in intermolecular contact formation with HPG during the formation of the 1:1 SK-HPG complex. Two of the three peptides (SK234-253 and SK274-293), apart from interfering in SK-HPG complex formation, also showed inhibition of the amidolytic activity of free HPN by increasing the K(m) by approximately fivefold. A similar increase in K(m) for amidolysis by HPN as a result of complexation with SK has been interpreted previously to arise from the steric hinderance at or near the active site due to the binding of SK in this region. Thus, our results suggest that SK234-253 and SK274-293 also, like SK, bound close to the active site of HPN, an event that was reflected in the observed alteration in its substrate accessibility. By contrast, whereas the intervening peptide (SK254-273) could not inhibit amidolysis by free HPN, it showed a marked inhibition of the activation of "substrate" PG (human or bovine plasminogen) by activator complex, indicating that this particular region is intimately involved in interaction of the SK-HPG activator complex with substrate plasminogen during the catalytic cycle. This finding provides a rational explanation for one of the most intriguing aspects of SK action, i.e., the ability of the SK-HPG complex to catalyze selectively the activation of substrate molecules of PG to PN, whereas free HPN alone cannot do so. Taken together, the results presented in this paper strongly support a model of SK action in which the segment 234-293 of SK, by virtue of the epitopes present in residues 234-253 and 274-293, binds close to the active center of HPN (or, a cryptic active site, in the case of HPG) during the intermolecular association of the two proteins to form the equimolar activator complex; the segment SK254-273 present in the center of the core region then imparts an ability to the activator complex to interact selectively with substrate PG molecules during each PG activation cycle.

Nihalani, D.; Raghava, G. P.; Sahni, G.

1997-01-01

299

Antiferromagnetic interaction between A'-site Mn spins in A-site-ordered perovskite YMn3Al4O12.  

PubMed

The A-site-ordered perovskite YMn(3)Al(4)O(12) was prepared by high-pressure synthesis. Structural analysis with synchrotron powder X-ray diffraction data and the Mn L-edges X-ray absorption spectrum revealed that the compound has a chemical composition Y(3+)Mn(3+)(3)Al(3+)(4)O(2-)(12) with magnetic Mn(3+) at the A' site and non-magnetic Al(3+) at the B site. An antiferromagnetic interaction between the A'-site Mn(3+) spins is induced by the nearest neighboring Mn-Mn direct exchange interaction and causes an antiferromagnetic transition at 34.3 K. PMID:20108915

Tohyama, Takenori; Saito, Takashi; Mizumaki, Masaichiro; Agui, Akane; Shimakawa, Yuichi

2010-03-01

300

Mapping the receptor site for ?-scorpion toxins on a Na+ channel voltage sensor  

PubMed Central

The ?-scorpions toxins bind to the resting state of Na+ channels and inhibit fast inactivation by interaction with a receptor site formed by domains I and IV. Mutants T1560A, F1610A, and E1613A in domain IV had lower affinities for Leiurus quinquestriatus hebraeus toxin II (LqhII), and mutant E1613R had ?73-fold lower affinity. Toxin dissociation was accelerated by depolarization and increased by these mutations, whereas association rates at negative membrane potentials were not changed. These results indicate that Thr1560 in the S1-S2 loop, Phe1610 in the S3 segment, and Glu1613 in the S3-S4 loop in domain IV participate in toxin binding. T393A in the SS2-S6 loop in domain I also had lower affinity for LqhII, indicating that this extracellular loop may form a secondary component of the receptor site. Analysis with the Rosetta-Membrane algorithm resulted in a model of LqhII binding to the voltage sensor in a resting state, in which amino acid residues in an extracellular cleft formed by the S1-S2 and S3-S4 loops in domain IV interact with two faces of the wedge-shaped LqhII molecule. The conserved gating charges in the S4 segment are in an inward position and form ion pairs with negatively charged amino acid residues in the S2 and S3 segments of the voltage sensor. This model defines the structure of the resting state of a voltage sensor of Na+ channels and reveals its mode of interaction with a gating modifier toxin.

Wang, Jinti; Yarov-Yarovoy, Vladimir; Kahn, Roy; Gordon, Dalia; Gurevitz, Michael; Scheuer, Todd; Catterall, William A.

2011-01-01

301

Jules Map Server  

NSDL National Science Digital Library

This site offers map tools to better visualize geophysical and geological processes and structures. Jules Verne Voyager is an interactive map tool for virtual exploration of Earth and other worlds (e.g. Mars, Jupiter and their moons); with custom map creation and fully interactive pan and zoom and extensive image selection. An ILP Global Strain Rate Map displays the latest global model of strain in the Earth's crust. Voyager Junior is designed for more casual browsing of Earth. It is usually faster, with pre-set pan and zoom using pre-made Voyager images.

Estey, Lou

2004-05-18

302

M sub 1 muscarinic antagonists interact with. sigma. recognition sites  

SciTech Connect

The M{sub 1}-selective muscarinic antagonists aprophen, caramiphen, carbetapentane, 2-DAEX, dicyclomine, hexahydrosiladifenidol, iodocaramiphen, nitrocaramiphen, oxybutynin and trihexyphenidyl potently inhibited binding to {sigma} sites in brain. Both basic ester and non-ester structural type compounds which exhibit affinity for the muscarinic receptor also demonstrated affinity for the {sigma} site, while the classical antimuscarinic agents atropine and QNB, and the tricyclic pirenzepine, were ineffective in binding to this site. The authors also observed a significant correlation between the K{sub i} values for {sigma}compounds to inhibit ({sup 3}H)pirenzepine binding and their IC{sub 50} values to inhibit carbachol-stimulated phosphoinositide turnover. These observations may aid in elucidating the relationship of {sigma} binding to inhibition of phosphoinositide turnover stimulated by cholinergic agonists.

Hudkins, R.L. (Virginia Commonwealth Univ., Richmond (United States)); DeHaven-Hudkins, D.L. (Sterling Research Group, Malvern, PA (United States))

1991-01-01

303

Mapping intended spinal site of care from the upright to prone position: an interexaminer reliability study  

PubMed Central

Background Upright examination procedures like radiology, thermography, manual muscle testing, and spinal motion palpation may lead to spinal interventions with the patient prone. The reliability and accuracy of mapping upright examination findings to the prone position is unknown. This study had 2 primary goals: (1) investigate how erroneous spine-scapular landmark associations may lead to errors in treating and charting spine levels; and (2) study the interexaminer reliability of a novel method for mapping upright spinal sites to the prone position. Methods Experiment 1 was a thought experiment exploring the consequences of depending on the erroneous landmark association of the inferior scapular tip with the T7 spinous process upright and T6 spinous process prone (relatively recent studies suggest these levels are T8 and T9, respectively). This allowed deduction of targeting and charting errors. In experiment 2, 10 examiners (2 experienced, 8 novice) used an index finger to maintain contact with a mid-thoracic spinous process as each of 2 participants slowly moved from the upright to the prone position. Interexaminer reliability was assessed by computing Intraclass Correlation Coefficient, standard error of the mean, root mean squared error, and the absolute value of the mean difference for each examiner from the 10 examiner mean for each of the 2 participants. Results The thought experiment suggesting that using the (inaccurate) scapular tip landmark rule would result in a 3 level targeting and charting error when radiological findings are mapped to the prone position. Physical upright exam procedures like motion palpation would result in a 2 level targeting error for intervention, and a 3 level error for charting. The reliability experiment showed examiners accurately maintained contact with the same thoracic spinous process as the participant went from upright to prone, ICC (2,1)?=?0.83. Conclusions As manual therapists, the authors have emphasized how targeting errors may impact upon manual care of the spine. Practitioners in other fields that need to accurately locate spinal levels, such as acupuncture and anesthesiology, would also be expected to draw important conclusions from these findings.

2014-01-01

304

Mapping, genetic effects, and epistatic interaction of two bacterial canker resistance QTLs from Lycopersicon hirsutum.  

PubMed

Two quantitative trait loci (QTL) from Lycopersicon hirsutum, Rcm 2.0 and Rcm 5.1, control resistance to Clavibacter michiganensis subsp. michiganensis ( Cmm). To precisely map both loci, we applied interval mapping techniques to 1,056 individuals in three populations exhibiting F(2) segregation. Based on a 1-LOD confidence interval, Rcm 2.0 mapped to a 14.9-cM interval on chromosome 2 and accounted for 25.7-34.0% of the phenotypic variation in disease severity. Rcm 5.1 mapped to a 4.3-cM interval on chromosome 5 and accounted for 25.8-27.9% of the phenotypic variation. Progeny testing of recombinant plants narrowed the QTL location for Rcm 2.0 to a 4.4-cM interval between TG537-TG091 and to a 2.2-cM interval between CT202-TG358 for Rcm 5.1. A population of 750 individuals exhibiting F(2) segregation was used to detect epistasis between both loci using ANOVA and orthogonal contrasts ( P=0.027), suggesting that resistance was determined by additive gene action and an additive-by-additive epistatic interaction. A partial diallel mating design was used to confirm epistasis, advance superior genotypes, randomize genetic backgrounds, and create recombination opportunities. This crossing scheme created a more balanced population ( n=112) containing the nine F(2) genotypic classes. Parents in the diallel were selected from the previous population based on resistance, genotype at the Rcm 2.0 and Rcm 5.1 loci, and horticultural traits. A replicated trial using the diallel population confirmed additive-by-additive epistasis ( P<0.0001). These results validate the gene action, intra -locus interaction, and map position of two loci controlling resistance to Cmm. PMID:15067391

Coaker, G L; Francis, D M

2004-04-01

305

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

PubMed

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

2013-06-15

306

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.

2012-01-01

307

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

2004-01-01

308

Mapping the Genetic Basis of Symbiotic Variation in Legume-Rhizobium Interactions in Medicago truncatula  

PubMed Central

Mutualisms are known to be genetically variable, where the genotypes differ in the fitness benefits they gain from the interaction. To date, little is known about the loci that underlie such genetic variation in fitness or whether the loci influencing fitness are partner specific, and depend on the genotype of the interaction partner. In the legume-rhizobium mutualism, one set of potential candidate genes that may influence the fitness benefits of the symbiosis are the plant genes involved in the initiation of the signaling pathway between the two partners. Here we performed quantitative trait loci (QTL) mapping in Medicago truncatula in two different rhizobium strain treatments to locate regions of the genome influencing plant traits, assess whether such regions are dependent on the genotype of the rhizobial mutualist (QTL × rhizobium strain), and evaluate the contribution of sequence variation at known symbiosis signaling genes. Two of the symbiotic signaling genes, NFP and DMI3, colocalized with two QTL affecting average fruit weight and leaf number, suggesting that natural variation in nodulation genes may potentially influence plant fitness. In both rhizobium strain treatments, there were QTL that influenced multiple traits, indicative of either tight linkage between loci or pleiotropy, including one QTL with opposing effects on growth and reproduction. There was no evidence for QTL × rhizobium strain or genotype × genotype interactions, suggesting either that such interactions are due to small-effect loci or that more genotype-genotype combinations need to be tested in future mapping studies.

Gorton, Amanda J.; Heath, Katy D.; Pilet-Nayel, Marie-Laure; Baranger, Alain

2012-01-01

309

Geologic Maps  

NSDL National Science Digital Library

This web site provides an introduction to geologic maps. Topics covered include what is a geologic map, unique features of geologic maps, letter symbols, faults, and strike and dip. Users may click to view colored geologic maps, the geologic map of the United States and the geologic relief map of the United States.

Graymer, Russell

310

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

PubMed

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

2012-09-15

311

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

Wirkus, Lars; Strunck, Alexander

2013-04-01

312

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.

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

2012-01-01

313

CYCLOSTREPTIN DERIVATIVES SPECIFICALLY TARGET CELLULAR TUBULIN AND FURTHER MAP THE PACLITAXEL SITE†  

PubMed Central

Cyclostreptin is the first microtubule stabilizing agent whose mechanism of action was discovered to involve formation of a covalent bond with tubulin. Treatment of cells with cyclostreptin irreversibly stabilizes their microtubules because cyclostreptin forms a covalent bond to ?-tubulin at either the T220 or the N228 residue, located, respectively, at the microtubule pore and luminal taxoid binding sites. Due to its unique mechanism of action, cyclostreptin overcomes P-glycoprotein-mediated multidrug resistance in tumor cells. We used a series of reactive cyclostreptin analogues, 6-chloroacetyl-cyclostreptin, 8-chloroacetyl-cyclostreptin, and [14C-acetyl]-8-acetyl-cyclostreptin, to characterize the cellular target of the compound and to map the binding site. The three analogues were cytotoxic and stabilized microtubules in both sensitive and multidrug resistant tumor cells. In both types of cells, we identified ?-tubulin as the only or the predominantly labeled cellular protein, indicating that a covalent binding to microtubules is sufficient to prevent drug efflux mediated by P-glycoprotein. 6-chloroacetyl-cyclostreptin, 8-chloroacetyl-cyclostreptin, and 8-acetyl-cyclostreptin labeled both microtubules and unassembled tubulin at a single residue of the same tryptic peptide of ?-tubulin as was labeled by cyclostreptin (219-LTTPTYGDLNHLVSATMSGVTTCLR-243), but labeling with the analogues occurred at different positions of the peptide. 8-Acetyl-cyclostreptin reacted either with T220 or N228, as did the natural product, while 8-chloroacetyl-cyclostreptin formed a cross link to C241. Finally 6-chloroacetyl-cyclostreptin reacted with any one of the three residues, thus labeling the pathway for cyclostreptin-like compounds, leading from the pore where these compounds enter the microtubule to the luminal binding pocket.

Calvo, Enrique; Barasoain, Isabel; Matesanz, Ruth; Pera, Benet; Camafeita, Emilio; Pineda, Oriol; Hamel, Ernest; Vanderwal, Christopher D.; Andreu, Jose Manuel; Lopez, Juan A.; Diaz, Jose Fernando

2012-01-01

314

Examination of molecular interaction sites of acetanilides with organic matter surrogates using nuclear magnetic resonance techniques.  

PubMed

The dynamics of acetanilide pesticide interactions with organic matter (OM) surrogates were examined using nuclear magnetic resonance (NMR) spectroscopy. Differences in the relative changes in (13)C and (1)H spin-lattice relaxation times (T(1)) were measured at multiple molecular sites of metolachlor and the probe compound acetanilide to identify interaction sites and/or surfaces between the molecules and dissolved and colloidal OM surrogates. The decrease in T(1) at specific sites of acetanilide molecules was a function of the OM used and its concentration. High-affinity interactions at nonaromatic sites of metolachlor and acetanilide were observed with cellulose, chitin, and collagen, but interactions with lignin occurred with less site specificity and involved both aromatic and nonaromatic sites of the molecules. Changes in relaxation were compared to calculated and experimentally determined binding coefficients (K(oc)). The T(1) relaxation of the aromatic sites of acetanilides showed better relations with K(oc) than the nonaromatic sites. This study shows that NMR relaxation measurements can identify the high-affinity molecular interaction sites of acetanilides to OM surrogates. PMID:12797751

Jayasundera, Shalini; Schmidt, Walter F; Hapeman, Cathleen J; Torrents, Alba

2003-06-18

315

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.

2011-01-01

316

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

USGS Publications Warehouse

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

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

2001-01-01

317

Computational Prediction and Experimental Verification of New MAP Kinase Docking Sites and Substrates Including Gli Transcription Factors  

Microsoft Academic Search

In order to fully understand protein kinase networks, new methods are needed to identify regulators and substrates of kinases, especially for weakly expressed proteins. Here we have developed a hybrid computational search algorithm that combines machine learning and expert knowledge to identify kinase docking sites, and used this algorithm to search the human genome for novel MAP kinase substrates and

Thomas C. Whisenant; David T. Ho; Ryan W. Benz; Jeffrey S. Rogers; Robyn M. Kaake; Elizabeth A. Gordon; Lan Huang; Pierre Baldi; Lee Bardwell

2010-01-01

318

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

Microsoft Academic Search

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

R. L. Kirk; E. Howington-Kraus; T. Hare; E. Dorrer; D. Cook; K. Becker; K. Thompson; B. Redding; J. Blue; D. Galuszka; E. M. Lee; L. R. Gaddis; J. R. Johnson; L. A. Soderblom; A. W. Ward; P. H. Smith; D. T. Britt

1999-01-01

319

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

NASA Astrophysics Data System (ADS)

Introduction. Luna-17 landed on November 17, 1970 and deployed Lunokhod-1, the first remotely operated roving vehicle ever to explore a planetary surface. Within 332 days, the vehicle conquered a traverse of approx. 10 km. The rover was equipped with a navigation camera system as well as a scanner camera with which panoramic images were obtained. From separated stations, stereoscopic views were obtained. The history of the Lunokhods came back into focus recently, when the Lunar Reconnaissance Orbiter [1] obtained images from orbit at highest resolutions of 0.5-0.25 m/pixel. The Luna-17 landing platform as well as the roving vehicles at their final resting positions can clearly be identified. In addition, the rover tracks are clearly visible in most areas. From LRO stereo images, digital elevation model (DEM) of the Lunokhod-1 landing site areas have been derived [2]. These are useful to study the topographic profile and slopes of the traverse. The data are also useful to study the 3-D morphology of craters in the surroundings. Methodology. Lunokhod-1 area mapping have been done using GIS techniques. With CraterTools [3] we digitized craters in the Lunokhod-1 traverse area and created a geodatabase, which consists at this moment of about 45,000 craters including their diameters and depths, obtained from the DEM [4]. The LRO DEM also was used to measure traverse. We used automatic GIS functions for calculating various surface parameters of the Lunokhod-1 area surface including slopes, roughness, crater cumulative and spatial densities, and prepared respective thematic maps. We also measured relative depth (ratio D/H) and inner slopes of craters and classified craters by their morphological type using automatic and visual methods. Vertical profiles through several craters using the high resolution DEM have been done, and the results show good agreement with the topographic models with contours in 10cm that have been obtained from the Lunokhod-1 stereo images [5]. The preliminary results of crater morphology show that highest H/D for studied craters of the Lunokhod 1 area is ~0.14, that is noticeably smaller than that for very fresh well studied small craters, for example, in the Apollo 14 [6]. At present more detailed geomorphology analyses using orthoimages with different illumination is in progress and will be shown at the conference. Conclusions and future works. While new missions to the Lunar surface are being planned, it is of utmost importance to identify and make available for access all Lunar surface data. We show that these data can be used for large-scale mapping and surface studies of landing sites for future lunar missions, for example LUNA-GLOB and LUNA-RESOURCE. Acknowledgments: This research was partly funded by the Ministry of Education and Science of the Russian Federation (MEGA-GRANT, Project name: "Geodesy, cartography and the study of planets and satellites", contract No. 11.G34.31.0021).

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

2012-04-01

320

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

PubMed

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

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

2013-02-14

321

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.

2013-12-01

322

A Systematic Mammalian Genetic Interaction Map Reveals Pathways Underlying Ricin Susceptibility  

PubMed Central

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

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

2013-01-01

323

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

PubMed

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

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

2014-04-01

324

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.

2006-01-01

325

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.

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

2012-01-01

326

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.

1992-10-01

327

Using mutagenesis and structural biology to map the binding site for the Plasmodium falciparum merozoite protein PfRh4 on the human immune adherence receptor.  

PubMed

To survive and replicate within the human host, malaria parasites must invade erythrocytes. Invasion can be mediated by the P. falciparum reticulocyte-binding homologue protein 4 (PfRh4) on the merozoite surface interacting with complement receptor type 1 (CR1, CD35) on the erythrocyte membrane. The PfRh4 attachment site lies within the three N-terminal complement control protein modules (CCPs 1-3) of CR1, which intriguingly also accommodate binding and regulatory sites for the key complement activation-specific proteolytic products, C3b and C4b. One of these regulatory activities is decay-accelerating activity. Although PfRh4 does not impact C3b/C4b binding, it does inhibit this convertase disassociating capability. Here, we have employed ELISA, co-immunoprecipitation, and surface plasmon resonance to demonstrate that CCP 1 contains all the critical residues for PfRh4 interaction. We fine mapped by homologous substitution mutagenesis the PfRh4-binding site on CCP 1 and visualized it with a solution structure of CCPs 1-3 derived by NMR and small angle x-ray scattering. We cross-validated these results by creating an artificial PfRh4-binding site through substitution of putative PfRh4-interacting residues from CCP 1 into their homologous positions within CCP 8; strikingly, this engineered binding site had an ?30-fold higher affinity for PfRh4 than the native one in CCP 1. These experiments define a candidate site on CR1 by which P. falciparum merozoites gain access to human erythrocytes in a non-sialic acid-dependent pathway of merozoite invasion. PMID:24214979

Park, Hyon Ju; Guariento, Mara; Maciejewski, Mateusz; Hauhart, Richard; Tham, Wai-Hong; Cowman, Alan F; Schmidt, Christoph Q; Mertens, Haydyn D T; Liszewski, M Kathryn; Hourcade, Dennis E; Barlow, Paul N; Atkinson, John P

2014-01-01

328

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

PubMed Central

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

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

2012-01-01

329

PLASMAP: an interactive computational tool for storage, retrieval and device-independent graphic display of conventional restriction maps.  

PubMed Central

We describe an interactive computational tool, PLASMAP, which allows the user to electronically store, retrieve, and display circular restriction maps. PLASMAP permits users to construct libraries of plasmid restriction maps as a set of files which may be edited in the laboratory at any time. The display feature of PLASMAP quickly generates device-independent, artist-quality, full-color or monochrome, hard copies or CRT screens of complex, conventional circular restriction maps.

Stone, B N; Griesinger, G L; Modelevsky, J L

1984-01-01

330

Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues  

PubMed Central

Deregulated cellular signalling is a common hallmark of disease, and delineating tissue phosphoproteomes is key to unravelling the underlying mechanisms. Here we present the broadest tissue catalogue of phosphoproteins to date, covering 31,480 phosphorylation sites on 7,280 proteins quantified across 14 rat organs and tissues. We provide the data set as an easily accessible resource via a web-based database, the CPR PTM Resource. A major fraction of the presented phosphorylation sites are tissue-specific and modulate protein interaction networks that are essential for the function of individual organs. For skeletal muscle, we find that phosphotyrosines are over-represented, which is mainly due to proteins involved in glycogenolysis and muscle contraction, a finding we validate in human skeletal muscle biopsies. Tyrosine phosphorylation is involved in both skeletal and cardiac muscle contraction, whereas glycogenolytic enzymes are tyrosine phosphorylated in skeletal muscle but not in the liver. The presented phosphoproteomic method is simple and rapid, making it applicable for screening of diseased tissue samples.

Lundby, Alicia; Secher, Anna; Lage, Kasper; Nordsborg, Nikolai B.; Dmytriyev, Anatoliy; Lundby, Carsten; Olsen, Jesper V.

2012-01-01

331

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

PubMed

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] (), 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 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

2014-07-23

332

MAP Kinase Pathway-dependent Phosphorylation of the L1-CAM Ankyrin Binding Site Regulates Neuronal Growth  

PubMed Central

The growth of neuronal processes depends critically on the function of adhesion proteins that link extracellular ligands to the cytoskeleton. The neuronal adhesion protein L1-CAM serves as a receptor for nerve growth–promoting proteins, a process that is inhibited by the interaction between L1-CAM and the cytoskeleton adaptor ankyrin. Using a novel reporter based on intramolecular bioluminescence resonance energy transfer, we have determined that the MAP kinase pathway regulates the phosphorylation of the FIGQY motif in the adhesion protein L1-CAM and its interaction with ankyrin B. MAP kinase pathway inhibitors block L1-CAM–mediated neuronal growth. However, this blockade is partially rescued by inhibitors of L1-CAM–ankyrin binding. These results demonstrate that the MAP kinase pathway regulates L1-CAM–mediated nerve growth by modulating ankyrin binding, suggesting that nerve growth can be regulated at the level of individual receptors.

Whittard, John D.; Sakurai, Takeshi; Cassella, Melanie R.; Gazdoiu, Mihaela

2006-01-01

333

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

ERIC Educational Resources Information Center

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

Zheng, Lanqin; Yang, Kaicheng; Huang, Ronghuai

2012-01-01

334

Epitope mapping in cell surface proteins by site-directed masking: defining the structural elements of NTPDase3 inhibition by a monoclonal antibody.  

PubMed

We adapted the method of epitope mapping by site-directed masking, which was described for purified soluble antigens [Paus,D. and Winter,G. (2006) Proc. Natl Acad. Sci. USA, 103, 9172-9177.], to map the binding site of an inhibitory monoclonal antibody on the cell surface protein ecto-nucleotidase NTPDase3. Using homology modeling, we built a 3D structure of NTPDase3 and designed 21 single cysteine mutations distributed over the surface of the enzyme. The mutant proteins were expressed in cells, biotinylated with a cysteine-specific reagent, and then extracted with detergent and immobilized on streptavidin-coated plates. Tethering NTPDase3 via cysteine residues located in a surface patch near the active site cleft masked the epitope and blocked antibody binding, as evaluated by enzyme inhibition assay and by ELISA. We then constructed 18 single alanine substitution mutations within the defined patch and found that W403A, D414A, E415A and R419A decreased the inhibitory effect of the antibody, whereas the double mutation W403A/R419A abolished both antibody binding and enzyme inhibition, suggesting the critical role of these residues for interaction with the antibody. Lack of competition between the antibody and a non-hydrolyzable substrate analog AMPPCP, as well as location of the epitope adjacent to the active site, suggest a noncompetitive mechanism of inhibition by steric hindrance. The described technique should be useful for systematic epitope mapping in cell membrane proteins for which either a 3D structure is available, or a sufficiently accurate 3D model can be obtained by homology modeling. PMID:20511214

Ivanenkov, Vasily V; Crawford, Patrick A; Toyama, Aimi; Sévigny, Jean; Kirley, Terence L

2010-07-01

335

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.

2010-12-01

336

Mapping subsurface pathways for contaminant migration at a proposed low level waste disposal site using electromagnetic methods  

SciTech Connect

Electromagnetic methods have been used to measure apparent terrain conductivity in the downstream portion of a watershed in which a waste disposal site is proposed. At that site, the pathways for waste migration in ground water are controlled by subsurface channels. The channels are identified using isocurves of measured apparent conductivity. Two upstream channel branches are found to merge into a single downstream channel which constitutes the main drainage path out of the watershed. The identification and mapping of the ground water pathways is an important contribution to the site characterization study and the pathways analysis. The direct applications of terrain conductivity mapping to the planning of the monitoring program, the hydrogeological testing, and the modeling study are demonstrated. 7 references, 4 figures.

Pin, F.G.; Ketelle, R.H.

1984-01-01

337

Interactive learning tool: site-specific schema crossword puzzles.  

PubMed

Staying abreast of the TNM and Collaborative Staging updates can be overwhelming. Reading voluminous amounts of study material may be the last task on a to-do list for the busy cancer registrar. Crossword puzzles can provide an alternative, interesting learning tool to support continuing education. Researching puzzle clue answers serves as an interactive approach. Puzzles included in this article are considered "informal" as their layout is not symmetrical, but the learning value is not adversely affected. Try them out and see what you know, or don't know. It can be fun! PMID:22096883

Berryhill, Tammy Lynn

2011-01-01

338

Mapping of the Auto-Inhibitory Interactions of Protein Kinase R by Nuclear Magnetic Resonance  

PubMed Central

Summary The dsRNA-dependent protein kinase (PKR) is a key mediator of the anti-viral and anti-proliferative effects of interferon. Unphosphorylated PKR is characterized by inhibitory interactions between the kinase and RNA binding domains (RBDs), but the structural details of the latent state and its unraveling during activation are not well understood. To study PKR regulation by NMR we assigned a large portion of the backbone resonances of the catalytically inactive K296R kinase domain, and performed 15N-HSQC titrations of this kinase domain with the RBDs. Chemical shift perturbations in the kinase indicate that RBD2 binds to the substrate eIF2? docking site in the kinase C-lobe. Consistent with these results, a mutation in the eIF2? docking site, F495A displays weaker interactions with the RBD. The full-length RBD1+2 binds more strongly to the kinase domain than RBD2 alone. The observed chemical shift changes extend from the eIF2? binding site into the kinase N-lobe and inside the active site, consistent with weak interactions between the N-terminal part of the RBD and the kinase.

Gelev, Vladimir; Aktas, Husseyin; Marintchev, Assen; Ito, Takuhiro; Frueh, Dominique; Hemond, Michael; Rovnyak, David; Debus, Miriam; Hyberts, Sven; Usheva, Anny; Halperin, Jose; Wagner, Gerhard

2007-01-01

339

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

PubMed

Government and private sector organizations are increasingly turning to the use of maps and other visual models to provide a depiction of environmental hazards and the potential risks they represent to humans and ecosystems. Frequently, the graphic presentation is tailored to address a specific contaminant, its location and possible exposure pathways, and potential receptors. Its format is usually driven by the data available, choice of graphics technology, and the audience being served. A format that is effective for displaying one contaminant at one scale at one site, however, may be ineffective in accurately portraying the circumstances surrounding a different contaminant at the same site, or the same contaminant at a different site, because of limitations in available data or the graphics technology being used. This is the daunting challenge facing the U.S. Department of Energy (DOE), which is responsible for the nation's legacy wastes from nuclear weapons research, testing, and production at over 100 sites in the United States. In this article, we discuss the development and use of integrated geospatial mapping and conceptual site models to identify hazards and evaluate alternative long-term environmental clean-up strategies at DOE sites located across the United States. While the DOE probably has the greatest need for such information, the Department of Defense and other public and private responsible parties for many large and controversial National Priority List or Superfund sites would benefit from a similar approach. PMID:15876215

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

2005-04-01

340

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

SciTech Connect

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

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

2000-03-08

341

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

SciTech Connect

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

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

2005-04-11

342

A comprehensive Plasmodium falciparum protein interaction map reveals a distinct architecture of a core interactome  

PubMed Central

We derive a map of protein interactions in the parasite P. falciparum from conserved interactions in S. cerevisiae, C. elegans, D. melanogaster and E. coli and pool them with experimental interaction data. The application of a clique-percolation algorithm allows us to find overlapping clusters, strongly correlated with yeast specific conserved protein complexes. Such clusters contain core activities that govern gene expression, largely dominated by components of protein production and degradation processes as well as RNA metabolism. A critical role of protein hubs in the interactome of P. falciparum is supported by their appearance in multiple clusters and the tendencies of their interactions to reach into many distinct protein clusters. Parasite proteins with a human ortholog tend to appear in single complexes. Annotating each protein with the stage where it is maximally expressed we observe a high level of cluster integrity in the ring stage. While we find no signal in the trophozoite phase, expression patterns are reversed in the schizont phase, implying a preponderance of parasite specific functions in this late, invasive schizont stage. As such, the inference of potential protein interactions and their analysis contributes to our understanding of the parasite, indicating basic pathways and processes as unique targets for therapeutic intervention.

Wuchty, Stefan; Adams, John H.; Ferdig, Michael T.

2011-01-01

343

Exactly solvable models through the empty interval method, for more-than-two-site interactions  

Microsoft Academic Search

Single-species reaction-diffusion systems on a one-dimensional lattice are considered, in which more than two neighbouring sites interact. Constraints on the interaction rates are obtained, that guarantee the closedness of the time evolution equation for En(t), the probability that n consecutive sites are empty at time t. The general method of solving the time evolution equation is discussed. As an example,

M. Khorrami; A. Aghamohammadi; M. Alimohammadi

2003-01-01

344

Density functional study the interaction of oxygen molecule with defect sites of graphene  

NASA Astrophysics Data System (ADS)

The present article reports a theoretical study of oxygen interacted with graphene surface containing defect sites on the atomic level by employing the density functional theory combined with the graphene cluster model. It was founded that oxygen molecule prefers to be chemisorbed on the graphene surface containing defect sites compared to the perfect surface. The adsorption energy of O2 on the double defect site is about 2.5 times as large as that on the perfect graphene surface. Moreover, the oxygen molecule interacts with S-W defect site gives rise to stable epoxy structure, which pulling the carbon atom outward from the original site in the direction perpendicular to the surface. If the oxygen molecule is adsorbed on the single vacancy site, two Csbnd O bonds are formed on the graphene surface. However, when the oxygen molecule is chemisorbed on the double vacancy site, the oxygen atoms substitute the missing carbon atom's position in the carbon plane and form a hexagonal structure on the graphene network. The results indicate that single active oxygen atom approaches the defect site, it's completely adsorbed in the plane and high energy is released. In all cases, the interaction of an oxygen atom with defect surface involves an exothermic process. The defect site creates active sites on the surface of graphene and produces catalytic effects during the process of oxidation of carbonaceous materials.

Qi, Xuejun; Guo, Xin; Zheng, Chuguang

2012-10-01

345

Toward an Integrated Linkage Map of Common Bean. 111. Mapping Genetic Factors Controlling Host-Bacteria Interactions  

Microsoft Academic Search

Restriction fragment length polymorphism (RFLP)-based genetic linkage maps allow us to dissect the genetic control of quantitative traits (QT) by locating individual quantitative trait loci (QTLs) on the linkage map and determining their type of gene action and the magnitude of their contribution to the phenotype of the QT. We have performed such an analysis for two traits in common

S. M. Tsai; P. Guzman; R. L. Gilbertsont; P. Gepts; Calqornia Davis

346

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

SciTech Connect

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

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

1988-12-31

347

A new map of glycosaminoglycan and C3b binding sites on factor H.  

PubMed

Human complement factor H, consisting of 20 complement control protein (CCP) modules, is an abundant plasma glycoprotein. It prevents C3b amplification on self surfaces bearing certain polyanionic carbohydrates, while complement activation progresses on most other, mainly foreign, surfaces. Herein, locations of binding sites for polyanions and C3b are reexamined rigorously by overexpressing factor H segments, structural validation, and binding assays. As anticipated, constructs corresponding to CCPs 7-8 and 19-20 bind well in heparin-affinity chromatography. However, CCPs 8-9, previously reported to bind glycosaminoglycans, bind neither to heparin resin nor to heparin fragments in gel-mobility shift assays. Introduction of nonnative residues N-terminal to a construct containing CCPs 8-9, identical to those in proteins used in the previous report, converted this module pair to an artificially heparin-binding one. The module pair CCPs 12-13 does not bind heparin appreciably, notwithstanding previous suggestions to the contrary. We further checked CCPs 10-12, 11-14, 13-15, 10-15, and 8-15 for ability to bind heparin but found very low affinity or none. As expected, constructs corresponding to CCPs 1-4 and 19-20 bind C3b amine coupled to a CM5 chip (K(d)s of 14 and 3.5 microM, respectively) or a C1 chip (K(d)s of 10 and 4.5 microM, respectively). Constructs CCPs 7-8 and 6-8 exhibit measurable affinities for C3b according to surface plasmon resonance, although they are weak compared with CCPs 19-20. Contrary to expectations, none of several constructs encompassing modules from CCP 9 to 15 exhibited significant C3b binding in this assay. Thus, we propose a new functional map of factor H. PMID:18684951

Schmidt, Christoph Q; Herbert, Andrew P; Kavanagh, David; Gandy, Carina; Fenton, Christopher J; Blaum, Bärbel S; Lyon, Malcolm; Uhrín, Dusan; Barlow, Paul N

2008-08-15

348

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.

1998-01-01

349

Integrative features of the yeast phosphoproteome and protein-protein interaction map.  

PubMed

Following recent advances in high-throughput mass spectrometry (MS)-based proteomics, the numbers of identified phosphoproteins and their phosphosites have greatly increased in a wide variety of organisms. Although a critical role of phosphorylation is control of protein signaling, our understanding of the phosphoproteome remains limited. Here, we report unexpected, large-scale connections revealed between the phosphoproteome and protein interactome by integrative data-mining of yeast multi-omics data. First, new phosphoproteome data on yeast cells were obtained by MS-based proteomics and unified with publicly available yeast phosphoproteome data. This revealed that nearly 60% of ?6,000 yeast genes encode phosphoproteins. We mapped these unified phosphoproteome data on a yeast protein-protein interaction (PPI) network with other yeast multi-omics datasets containing information about proteome abundance, proteome disorders, literature-derived signaling reactomes, and in vitro substratomes of kinases. In the phospho-PPI, phosphoproteins had more interacting partners than nonphosphoproteins, implying that a large fraction of intracellular protein interaction patterns (including those of protein complex formation) is affected by reversible and alternative phosphorylation reactions. Although highly abundant or unstructured proteins have a high chance of both interacting with other proteins and being phosphorylated within cells, the difference between the number counts of interacting partners of phosphoproteins and nonphosphoproteins was significant independently of protein abundance and disorder level. Moreover, analysis of the phospho-PPI and yeast signaling reactome data suggested that co-phosphorylation of interacting proteins by single kinases is common within cells. These multi-omics analyses illuminate how wide-ranging intracellular phosphorylation events and the diversity of physical protein interactions are largely affected by each other. PMID:21298081

Yachie, Nozomu; Saito, Rintaro; Sugiyama, Naoyuki; Tomita, Masaru; Ishihama, Yasushi

2011-01-01

350

Mapping the Nucleotide Binding Site of Uncoupling Protein 1 Using Atomic Force Microscopy  

PubMed Central

A tight regulation of proton transport in the inner mitochondrial membrane is crucial for physiological processes such as ATP synthesis, heat production, or regulation of the reactive oxygen species as proposed for the uncoupling protein family members (UCP). Specific regulation of proton transport is thus becoming increasingly important in the therapy of obesity and inflammatory, neurodegenerative, and ischemic diseases. We and other research groups have shown previously that UCP1- and UCP2-mediated proton transport is inhibited by purine nucleotides. Several hypotheses have been proposed to explain the inhibitory effect of ATP, although structural details are still lacking. Moreover, the unresolved mystery is how UCP operates in vivo despite the permanent presence of high (millimolar) concentrations of ATP in mitochondria. Here we use the topographic and recognition (TREC) mode of an atomic force microscope to visualize UCP1 reconstituted into lipid bilayers and to analyze the ATP–protein interaction at a single molecule level. The comparison of recognition patterns obtained with anti-UCP1 antibody and ATP led to the conclusion that the ATP binding site can be accessed from both sides of the membrane. Using cantilever tips with different cross-linker lengths, we determined the location of the nucleotide binding site inside the membrane with 1 Å precision. Together with the recently published NMR structure of a UCP family member (Berardi et al. Nature, 2011, 476, 109–113), our data provide a valuable insight into the mechanism of the nucleotide binding and pave the way for new pharmacological approaches against the diseases mentioned above.

2013-01-01

351

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.

352

Stochastic signalling rewires the interaction map of a multiple feedback network during yeast evolution.  

PubMed

During evolution, genetic networks are rewired through strengthening or weakening their interactions to develop new regulatory schemes. In the galactose network, the GAL1/GAL3 paralogues and the GAL2 gene enhance their own expression mediated by the Gal4p transcriptional activator. The wiring strength in these feedback loops is set by the number of Gal4p binding sites. Here we show using synthetic circuits that multiplying the binding sites increases the expression of a gene under the direct control of an activator, but this enhancement is not fed back in the circuit. The feedback loops are rather activated by genes that have frequent stochastic bursts and fast RNA decay rates. In this way, rapid adaptation to galactose can be triggered even by weakly expressed genes. Our results indicate that nonlinear stochastic transcriptional responses enable feedback loops to function autonomously, or contrary to what is dictated by the strength of interactions enclosing the circuit. PMID:22353713

Hsu, Chieh; Scherrer, Simone; Buetti-Dinh, Antoine; Ratna, Prasuna; Pizzolato, Julia; Jaquet, Vincent; Becskei, Attila

2012-01-01

353

Stochastic signalling rewires the interaction map of a multiple feedback network during yeast evolution  

PubMed Central

During evolution, genetic networks are rewired through strengthening or weakening their interactions to develop new regulatory schemes. In the galactose network, the GAL1/GAL3 paralogues and the GAL2 gene enhance their own expression mediated by the Gal4p transcriptional activator. The wiring strength in these feedback loops is set by the number of Gal4p binding sites. Here we show using synthetic circuits that multiplying the binding sites increases the expression of a gene under the direct control of an activator, but this enhancement is not fed back in the circuit. The feedback loops are rather activated by genes that have frequent stochastic bursts and fast RNA decay rates. In this way, rapid adaptation to galactose can be triggered even by weakly expressed genes. Our results indicate that nonlinear stochastic transcriptional responses enable feedback loops to function autonomously, or contrary to what is dictated by the strength of interactions enclosing the circuit.

Hsu, Chieh; Scherrer, Simone; Buetti-Dinh, Antoine; Ratna, Prasuna; Pizzolato, Julia; Jaquet, Vincent; Becskei, Attila

2012-01-01

354

A Comprehensive Rice Transcript Map Containing 6591 Expressed Sequence Tag Sites  

Microsoft Academic Search

To determine the chromosomal positions of expressed rice genes, we have performed an expressed sequence tag (EST) mapping project by polymerase chain reaction-based yeast artificial chromosome (YAC) screening. Specific primers designed from 6713 unique EST sequences derived from 19 cDNA libraries were screened on 4387 YAC clones and used for map construction in combination with genetic analysis. Here, we describe

Jianzhong Wu; Tomoko Maehara; Takanori Shimokawa; Shinichi Yamamoto; Chizuko Harada; Yuka Takazaki; Nozomi Ono; Yoshiyuki Mukai; Kazuhiro Koike; Jyunshi Yazaki; Fumiko Fujii; Ayahiko Shomura; Tsuyu Ando; Izumi Kono; Kazunori Waki; Kimiko Yamamoto; Masahiro Yano; Takashi Matsumoto; Takuji Sasaki

2002-01-01

355

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.

1984-12-04

356

Fine mapping and epistatic interactions of the vernalization gene VRN-D4 in hexaploid wheat.  

PubMed

Wheat vernalization requirement is mainly controlled by the VRN1, VRN2, VRN3, and VRN4 genes. The first three have been cloned and have homoeologs in all three genomes. VRN4 has been found only in the D genome (VRN-D4) and has not been cloned. We constructed a high-density genetic map of the VRN-D4 region and mapped VRN-D4 within a 0.09 cM interval in the centromeric region of chromosome 5D. Using telocentric 5D chromosomes generated from the VRN-D4 donor Triple Dirk F, we determined that VRN-D4 is located on the short arm. The VRN-D4 candidate region is colinear with a 2.24 Mb region on Brachypodium distachyon chromosome 4, which includes 127 predicted genes. Ten of these genes have predicted roles in development but we detected no functional polymorphisms associated to VRN-D4. Two recombination events separated VRN-D4 from TaVIL-D1, the wheat homolog of Arabidopsis vernalization gene VIL1, confirming that this gene is not a candidate for VRN-D4. We detected significant interactions between VRN-D4 and other four genes controlling vernalization requirement (Vrn-A1, Vrn-B1, Vrn-D1, and Vrn-B3), which confirmed that VRN-D4 is part of the vernalization pathway and that it is either upstream or is part of the regulatory feedback loop involving VRN1, VRN2 and VRN3 genes. The precise mapping of VRN-D4 and the characterization of its interactions with other vernalization genes provide valuable information for the utilization of VRN-D4 in wheat improvement and for our current efforts to clone this vernalization gene. PMID:24213553

Kippes, Nestor; Zhu, Jie; Chen, Andrew; Vanzetti, Leonardo; Lukaszewski, Adam; Nishida, Hidetaka; Kato, Kenji; Dvorak, Jan; Dubcovsky, Jorge

2014-02-01

357

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

PubMed

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

2013-01-01

358

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.

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

2013-01-01

359

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.

1972-01-01

360

Female site-specific transposase-induced recombination: a high-efficiency method for fine mapping mutations on the X chromosome in Drosophila.  

PubMed Central

P-element transposons in the Drosophila germline mobilize only in the presence of the appropriate transposase enzyme. Sometimes, instead of mobilizing completely, P elements will undergo site-specific recombination with the homologous chromosome. Site-specific recombination is the basis for male recombination mapping, since the male germline does not normally undergo recombination. Site-specific recombination also takes place in females, but this has been difficult to study because of the obscuring effects of meiotic recombination. Using map functions, I demonstrate that it is possible to employ female site-specific transposase-induced recombination (FaSSTIR) to map loci on the X chromosome and predict that FaSSTIR mapping should be more efficient than meiotic mapping over short genetic intervals. Both FaSSTIR mapping and meiotic mapping were used to fine map the crossveinless locus on the X chromosome. Both techniques identified the same 10-kb interval as the probable location of the crossveinless mutation. Over short intervals (< approximately 7.6 cM), FaSSTIR produces more informative recombination events than does meiotic recombination. Over longer intervals, FaSSTIR is not always more efficient than meiotic mapping, but it produces the correct gene order. FaSSTIR matches the expectations suggested by the map functions and promises to be a useful technique, particularly for mapping X-linked loci.

Marcus, Jeffrey M

2003-01-01

361

Interaction site prediction by structural similarity to neighboring clusters in protein-protein interaction networks  

Microsoft Academic Search

BACKGROUND: Recently, revealing the function of proteins with protein-protein interaction (PPI) networks is regarded as one of important issues in bioinformatics. With the development of experimental methods such as the yeast two-hybrid method, the data of protein interaction have been increasing extremely. Many databases dealing with these data comprehensively have been constructed and applied to analyzing PPI networks. However, few

Hiroyuki Monji; Satoshi Koizumi; Tomonobu Ozaki; Takenao Ohkawa

2011-01-01

362

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

PubMed

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

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

2014-02-01

363

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

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

364

Efficient Bayesian approach for multilocus association mapping including gene-gene interactions  

PubMed Central

Background Since the introduction of large-scale genotyping methods that can be utilized in genome-wide association (GWA) studies for deciphering complex diseases, statistical genetics has been posed with a tremendous challenge of how to most appropriately analyze such data. A plethora of advanced model-based methods for genetic mapping of traits has been available for more than 10 years in animal and plant breeding. However, most such methods are computationally intractable in the context of genome-wide studies. Therefore, it is hardly surprising that GWA analyses have in practice been dominated by simple statistical tests concerned with a single marker locus at a time, while the more advanced approaches have appeared only relatively recently in the biomedical and statistical literature. Results We introduce a novel Bayesian modeling framework for association mapping which enables the detection of multiple loci and their interactions that influence a dichotomous phenotype of interest. The method is shown to perform well in a simulation study when compared to widely used standard alternatives and its computational complexity is typically considerably smaller than that of a maximum likelihood based approach. We also discuss in detail the sensitivity of the Bayesian inferences with respect to the choice of prior distributions in the GWA context. Conclusions Our results show that the Bayesian model averaging approach which explicitly considers gene-gene interactions may improve the detection of disease associated genetic markers in two respects: first, by providing better estimates of the locations of the causal loci; second, by reducing the number of false positives. The benefits are most apparent when the interacting genes exhibit no main effects. However, our findings also illustrate that such an approach is somewhat sensitive to the prior distribution assigned on the model structure.

2010-01-01

365

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.

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

2014-01-01

366

Use of stratigraphic and lithofacies maps in hydrogeologic studies: Examples from the General Separations Area, Savannah River Site, S. C  

Microsoft Academic Search

Stratigraphic and lithofacies maps are effective tools for assessing hydrologic properties of Tertiary aquifer and confining units in the 15mi[sup 2] General Separations Area (GSA) at the Savannah River Site, S.C. Pumping tests and laboratory permeability data indicate that the type, geometry, and spatial distribution of lithofacies are important factors controlling the lateral and vertical variability of hydraulic conductivity in

P. A. Thayer; A. D. Smits; M. K. Harris

1993-01-01

367

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

USGS Publications Warehouse

An aeromagnetic map of the Nevada Test Site area was prepared from publicly available aeromagnetic data described by McCafferty and Grauch (1997). Magnetic surveys were processed using standard techniques. Southwest Nevada is characterized by magnetic anomalies that reflect the distribution of thick sequences of volcanic rocks, magnetic sedimentary rocks, and the occurrence of granitic rocks. In addition, aeromagnetic data reveal the presence of linear features that reflect faulting at both regional and local scales.

Ponce, David A.

2000-01-01

368

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

2001-05-21

369

Subcortical pathways serving cortical language sites: initial experience with diffusion tensor imaging fiber tracking combined with intraoperative language mapping  

PubMed Central

The combination of mapping functional cortical neurons by intraoperative cortical stimulation and axonal architecture by diffusion tensor MRI fiber tracking can be used to delineate the pathways between functional regions. In this study the authors investigated the feasibility of combining these techniques to yield connectivity associated with motor speech and naming. Diffusion tensor MRI fiber tracking provides maps of axonal bundles and was combined with intraoperative mapping of eloquent cortex for a patient undergoing brain tumor surgery. Tracks from eight stimulated sites in the inferior frontal cortex including mouth motor, speech arrest, and anomia were generated from the diffusion tensor MRI data. The regions connected by the fiber tracking were compared to foci from previous functional imaging reports on language tasks. Connections were found between speech arrest, mouth motor, and anomia sites and the SMA proper and cerebral peduncle. The speech arrest and a mouth motor site were also seen to connect to the putamen via the external capsule. This is the first demonstration of delineation of subcortical pathways using diffusion tensor MRI fiber tracking with intraoperative cortical stimulation. The combined techniques may provide improved preservation of eloquent regions during neurological surgery, and may provide access to direct connectivity information between functional regions of the brain.

Henry, Roland G.; Berman, Jeffrey I.; Nagarajan, Srikantan S.; Mukherjee, Pratik; Berger, Mitchel S.

2014-01-01

370

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

PubMed

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

2014-03-01

371

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.

2012-12-01

372

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

PubMed

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

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

2011-12-01

373

Tracing the path of DNA substrates in active Tetrahymena telomerase holoenzyme complexes: mapping of DNA contact sites in the RNA subunit  

PubMed Central

Telomerase, the enzyme that extends single-stranded telomeric DNA, consists of an RNA subunit (TER) including a short template sequence, a catalytic protein (TERT) and accessory proteins. We used site-specific UV cross-linking to map the binding sites for DNA primers in TER within active Tetrahymena telomerase holoenzyme complexes. The mapping was performed at single-nucleotide resolution by a novel technique based on RNase H digestion of RNA–DNA hybrids made with overlapping complementary oligodeoxynucleotides. These data allowed tracing of the DNA path through the telomerase complexes from the template to the TERT binding element (TBE) region of TER. TBE is known to bind TERT and to be involved in the template 5?-boundary definition. Based on these findings, we propose that upstream sequences of each growing telomeric DNA chain are involved in regulation of its growth arrest at the 5?-end of the RNA template. The upstream DNA–TBE interaction may also function as an anchor for the subsequent realignment of the 3?-end of the DNA with the 3?-end of the template to enable initiation of synthesis of a new telomeric repeat.

Goldin, Svetlana; Kertesz Rosenfeld, Karin; Manor, Haim

2012-01-01

374

Monte Carlo Simulations with reference interaction site model theory for simulating peptide molecules in aqueous solution  

NASA Astrophysics Data System (ADS)

We have developed Monte Carlo simulations with reference interaction site model theory for simulating proteins in aqueous solution. The reference interaction site model theory based on the liquid theory of statistical mechanics can treat solvent effect with solvent molecular shape and estimate solvation free energy around proteins. We have developed simulation algorithms which combine with generalized-ensemble algorithms and reference interaction site model theory. We showed results of a simulated annealing Monte Carlo simulation, a multicanonical Monte Carlo simulation, and a replica-exchange Monte Carlo simulation with one dimensional reference interaction site model theory for Met-Enkephalin, a penta-peptide [1,2,3]. Recently we have performed a Monte Carlo simulation with three-dimensional reference interaction site model theory for simulating C-peptide in aqueous solution. We will describe these attempts and discuss results of these simulations. [1] M. Kinoshita, Y. Okamoto, and F. Hirata, J. Am. Chem. Soc. 120, 1855 (1998) [2] A. Mitsutake, M. Kinoshita, Y. Okamoto, and F. Hirata, Chem. Phys. Lett. 329, 295 (2000) [3] A. Mitsutake, M. Kinoshita, Y. Okamoto, and F. Hirata, J. Phys. Chem. B 108, 19002 (2004)

Mitsutake, Ayori; Maruyama, Yutaka; Imai, Takashi; Kinoshita, Masahiro; Okamoto, Yuko; Hirata, Fumio

2008-03-01

375

Mapping Networks of Protein-mediated Physical Interactions between Chromatin Elements  

PubMed Central

Recent decade has witnessed an extensive advancement in our understanding of transcriptional regulation, in part due to a rapid progress in technologies which allow studying physical proximities between various chromatin regions at a resolution beyond that offered by conventional microscopy techniques. However, these methods do not specifically identify the protein component(s) that might mediate such interactions. Here we discusses the detailed protocol for Combined 3C-ChIP-Cloning (6C) technology which combines multiple techniques to simultaneously identify physical proximities between chromatin elements as well as the proteins that mediate these interactions. We further explore how the 6C assay can be incorporated with other techniques for a complete, cell-type-specific mapping of all inter and intrachromosomal interactions mediated by specific proteins. Thus, 6C assay provides an indispensable tool to address the role of specific proteins in nuclear organization and advances our understanding about the relation of chromatin higher order organization with transcriptional regulation to the next level.

Tiwari, Vijay K.; Baylin, Stephen B.

2010-01-01

376

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

NASA Astrophysics Data System (ADS)

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

Ghrenassia, Sarah; Ménard, Lucie; Laporte, Catherine

2014-03-01

377

LISE: a server using ligand-interacting and site-enriched protein triangles for prediction of ligand-binding sites  

PubMed Central

LISE is a web server for a novel method for predicting small molecule binding sites on proteins. It differs from a number of servers currently available for such predictions in two aspects. First, rather than relying on knowledge of similar protein structures, identification of surface cavities or estimation of binding energy, LISE computes a score by counting geometric motifs extracted from sub-structures of interaction networks connecting protein and ligand atoms. These network motifs take into account spatial and physicochemical properties of ligand-interacting protein surface atoms. Second, LISE has now been more thoroughly tested, as, in addition to the evaluation we previously reported using two commonly used small benchmark test sets and targets of two community-based experiments on ligand-binding site predictions, we now report an evaluation using a large non-redundant data set containing >2000 protein–ligand complexes. This unprecedented test, the largest ever reported to our knowledge, demonstrates LISE’s overall accuracy and robustness. Furthermore, we have identified some hard to predict protein classes and provided an estimate of the performance that can be expected from a state-of-the-art binding site prediction server, such as LISE, on a proteome scale. The server is freely available at http://lise.ibms.sinica.edu.tw.

Xie, Zhong-Ru; Liu, Chuan-Kun; Hsiao, Fang-Chih; Yao, Adam; Hwang, Ming-Jing

2013-01-01

378

Genetic Interaction Maps in Escherichia coli Reveal Functional Crosstalk among Cell Envelope Biogenesis Pathways  

PubMed Central

As the interface between a microbe and its environment, the bacterial cell envelope has broad biological and clinical significance. While numerous biosynthesis genes and pathways have been identified and studied in isolation, how these intersect functionally to ensure envelope integrity during adaptive responses to environmental challenge remains unclear. To this end, we performed high-density synthetic genetic screens to generate quantitative functional association maps encompassing virtually the entire cell envelope biosynthetic machinery of Escherichia coli under both auxotrophic (rich medium) and prototrophic (minimal medium) culture conditions. The differential patterns of genetic interactions detected among >235,000 digenic mutant combinations tested reveal unexpected condition-specific functional crosstalk and genetic backup mechanisms that ensure stress-resistant envelope assembly and maintenance. These networks also provide insights into the global systems connectivity and dynamic functional reorganization of a universal bacterial structure that is both broadly conserved among eubacteria (including pathogens) and an important target.

Vlasblom, James; Gagarinova, Alla; Phanse, Sadhna; Graham, Chris; Yousif, Fouad; Ding, Huiming; Xiong, Xuejian; Nazarians-Armavil, Anaies; Alamgir, Md; Ali, Mehrab; Pogoutse, Oxana; Pe'er, Asaf; Arnold, Roland; Michaut, Magali; Parkinson, John; Golshani, Ashkan; Whitfield, Chris; Wodak, Shoshana J.; Moreno-Hagelsieb, Gabriel; Greenblatt, Jack F.; Emili, Andrew

2011-01-01

379

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

NASA Technical Reports Server (NTRS)

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

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

1983-01-01

380

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

2012-11-01

381

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.

1997-01-01

382

Interactive Web-Mapping System for Satellite Based Agricultural Applications in Bulgaria and Romania  

NASA Astrophysics Data System (ADS)

The interactive web-mapping system for satellite based agricultural application in Bulgaria and Romania was developed in the frame if the PROA GROB URO project. To achieve the project objectives a large amount of geospatial data was collected in the form of satellite images, maps and vector layers. Furthermore, the field measurements and descriptions were linked with the exact location where they have been made. There was a strong need to be able to analyse the data in an integrated way. Thus, a geodatabase was necessary with corresponding web-interface and applications providing data access to each of the partners. Using the newest Internet technologies a set of tools for creating and online publishing of geospatial data was successfully implemented The system components were developed entirely with standard compliant free and open source software like GDAL/OGR. GeoServer, OpenLayers and PostgreSQL+PostGIS. GMES recommendations and INSPIRE directive were taken into account when designing and implementing the system.

Craciunescu, Vasile; Stancalie, Gheorghe; Roumenina, Eugenia; Kazandjiev, Valentin; Jelev, Georgi; Filchev, Lachezar; Savin, Elena; Catana, Simona; Mihailescu, Denis

2012-06-01

383

Feedback control of Hopf-Hopf interaction bifurcation with development of torus solutions in high-dimensional maps  

NASA Astrophysics Data System (ADS)

This Letter reports a feedback control method to create a Hopf-Hopf interaction bifurcation that could lead to a torus solution of maps. The implicit forms of the eigenvalue assignment and the transversality condition of the bifurcation are proposed for designing control gains. With the aid of a washout-filter feedback controller, we show the application of the technique in four- and five-dimensional maps.

Wen, Gui-Lin; Xu, Daolin

2004-01-01

384

CANCER MORTALITY MAPS AND GRAPHS  

EPA Science Inventory

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

385

A Method for Place Name Display Considering User Locating Habits in Map Sites  

NASA Astrophysics Data System (ADS)

The traditional researches for cartographic lettering and display focus on conflict among labels and overlap between labels and features. But these two issues are not significant in web maps. It is worthwhile to concern about how to improve labels' readability considering user locating habits for enhancing user experience. This paper has established a new method for place name display called "the gravitational field". This method is appropriate for the display of dotted place names from the national level (approximately 1:20 million) to city level (approximately 1:250 thousand) in web maps. We have conducted a usability test which used all nationwide provincial capitals, autonomous regions, municipalities, prefecture-level cities, municipal districts, countries and part of the townships dotted names. The results show that this rule improves web map's legibility, and can significantly enhance the user experience.

Liu, X. C.; Li, X.; Wang, L.; Wang, P.

2013-11-01

386

Elucidation of IP6 and Heparin Interaction Sites and Conformational Changes in Arrestin-1 by Solution NMR†  

PubMed Central

Arrestins specifically bind activated and phosphorylated G protein-coupled receptors, and orchestrate both receptor trafficking, and channel signaling to G protein-independent pathways via direct interactions with numerous non-receptor partners. Here we report the first successful use of solution NMR to map the binding sites in arrestin-1 (visual arrestin) for two polyanionic compounds that mimic phosphorylated light-activated rhodopsin: inositol hexaphosphate (IP6) and heparin. This yielded a more complete identification of residues involved in the binding with these ligands than has previously been feasible.