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1

Site Map  

Cancer.gov

Site Map Programs & Resources Research Groups Foundations of Prevention Biometry Publications Statistical Software About the Research Group Cancer Biomarkers Funding Opportunities Key Programs Meetings and Events Publications About

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

Site Map  

Cancer.gov

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

4

Human migrations map, interactive 2D animationSite: DNA Interactive (www.dnai.org)  

NSDL National Science Digital Library

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

2008-10-06

5

Importance of genetic maps, Mary-Claire KingSite: DNA Interactive (www.dnai.org)  

NSDL National Science Digital Library

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

2008-03-26

6

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

7

Montana Maps Interactive  

NSDL National Science Digital Library

Montana Maps Interactive is a new tool provided by the state's Natural Resource Information System (NRIS). The program shows a variety of geographic information layers for the state of Montana. Users can view cities, natural and political features, national parks and forests, and various types of land use, among other features. Maps can be zoomed in or out. The feature query allows users to locate features from a layer (e.g. streams or land use) by selecting the layer and then identifying the feature on the map or by letting the program find the feature given its name. The map is then redrawn with the selected feature highlighted in yellow and its attributes listed above the map.

8

NCI: SBIR & STTR - Site Map  

Cancer.gov

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

9

Mapping polyamide-DNA interactions in human cells reveals a new design strategy for effective targeting of genomic sites.  

PubMed

Targeting the genome with sequence-specific synthetic molecules is a major goal at the interface of chemistry, biology, and personalized medicine. Pyrrole/imidazole-based polyamides can be rationally designed to target specific DNA sequences with exquisite precision in?vitro; yet, the biological outcomes are often difficult to interpret using current models of binding energetics. To directly identify the binding sites of polyamides across the genome, we designed, synthesized, and tested polyamide derivatives that enabled covalent crosslinking and localization of polyamide-DNA interaction sites in live human cells. Bioinformatic analysis of the data reveals that clustered binding sites, spanning a broad range of affinities, best predict occupancy in cells. In contrast to the prevailing paradigm of targeting single high-affinity sites, our results point to a new design principle to deploy polyamides and perhaps other synthetic molecules to effectively target desired genomic sites in?vivo. PMID:25066383

Erwin, Graham S; Bhimsaria, Devesh; Eguchi, Asuka; Ansari, Aseem Z

2014-09-15

10

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. PMID:23572591

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

2013-01-01

11

Mapping the interaction site of Rpb4 and Rpb7 subunits of RNA polymerase II in Saccharomyces cerevisiae.  

PubMed

Rpb4 and Rpb7, the fourth and the seventh largest subunits of RNA polymerase II, form a heterodimer in Saccharomyces cerevisiae. To identify the site of interaction between these subunits, we constructed truncation mutants of both these proteins and carried out yeast two hybrid analysis. Deletions in the amino and carboxyl terminal domains of Rpb7 abolished its interaction with Rpb4. In comparison, deletion of up to 49 N-terminal amino acids of Rpb4 reduced its interaction with Rpb7. Complete abolishment of interaction between Rpb4 and Rpb7 occurred by truncation of 1-106, 1-142, 108-221, 172-221 or 198-221 amino acids of Rpb4. Use of the yeast two-hybrid analysis in conjunction with computational analysis of the recently reported crystal structure of Rpb4/Rpb7 sub-complex allowed us to identify regions previously not suspected to be involved in the functional interaction of these proteins. Taken together, our results have identified the regions that are involved in interaction between the Rpb4 and Rpb7 subunits of S. cerevisiae RNA polymerase II in vivo. PMID:15913559

Sareen, Archana; Choudhry, Priya; Mehta, Surbhi; Sharma, Nimisha

2005-07-01

12

Accurately mapping the location of the binding site for the interaction between hepatitis B virus X protein and cytochrome c oxidase III.  

PubMed

The hepatitis B virus (HBV) X protein (HBx) plays an important pathogenetic role in hepatocarcinoma tumorigenesis. As HBx does not have the ability to bind to double-stranded DNA (dsDNA), protein-protein interaction is crucial for HBx functions. In a previous study, we screened a novel HBx-interacting protein, the cytochrome c oxidase subunit III (COXIII). In the present study, we aimed to accurately map the location of the binding site for the interaction of HBx with COXIII. Two fragments of HBx mutants (X1 aa1-72 and X2 aa1-117) were amplified by polymerase chain reaction (PCR) and separately inserted into the pAS2-1 plasmid. PCR and gene sequencing confirmed the correct insertion of the mutant fragments in the plasmid. The tanscription of the mutant fragments in yeast cells was demonstrated by RT-PCR and western blot analysis confirmed that they were accurately translated into fusion proteins. Hybridization on solid medium and the detection of ?-galactosidase (?-gal) activity indicated that the binding site for the interaction between HBx and COXIII was located between aa72 and aa117. Specific interactions between the HBxX2 protein and COXIII were verified by co-immunoprecipitation. To the best of our knowledge, this is the first study showing to demonstrate that aa72-117 in HBx is the key region for binding with COXIII. PMID:25483779

Li, Dan; Ding, Jian; Chen, Zhixin; Chen, Yun; Lin, Na; Chen, Fenglin; Wang, Xiaozhong

2015-02-01

13

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

14

Site Map | Clinical Assay Development Program (CADP)  

Cancer.gov

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

15

Site Map | Radiation Research Program (RRP)  

Cancer.gov

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

16

Mapping the interaction sites between AMPA receptors and TARPs reveals a role for the receptor N-terminal domain in channel gating.  

PubMed

AMPA-type glutamate receptors (AMPARs) mediate fast neurotransmission at excitatory synapses. The extent and fidelity of postsynaptic depolarization triggered by AMPAR activation are shaped by AMPAR auxiliary subunits, including the transmembrane AMPAR regulatory proteins (TARPs). TARPs profoundly influence gating, an effect thought to be mediated by an interaction with the AMPAR ion channel and ligand binding domain (LBD). Here, we show that the distal N-terminal domain (NTD) contributes to TARP modulation. Alterations in the NTD-LBD linker result in TARP-dependent and TARP-selective changes in AMPAR gating. Using peptide arrays, we identify a TARP interaction region on the NTD and define the path of TARP contacts along the LBD surface. Moreover, we map key binding sites on the TARP itself and show that mutation of these residues mediates gating modulation. Our data reveal a TARP-dependent allosteric role for the AMPAR NTD and suggest that TARP binding triggers a drastic reorganization of the AMPAR complex. PMID:25373908

Cais, Ondrej; Herguedas, Beatriz; Krol, Karolina; Cull-Candy, Stuart G; Farrant, Mark; Greger, Ingo H

2014-10-23

17

Digital Soil Mapping: Interactions with  

E-print Network

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

Grunwald, Sabine

18

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

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

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

19

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

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

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

20

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

21

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".

22

Protein-surface interaction maps for ion-exchange chromatography.  

PubMed

In this paper, protein-surface interaction maps were generated by performing coarse-grained protein-surface calculations. This approach allowed for the rapid determination of the protein-surface interaction energies at a range of orientations and distances. Interaction maps of lysozyme indicated that there was a contiguous series of orientations corresponding to several adjacent preferred binding regions on the protein surface. Examination of these orientations provided insight into the residues involved in surface interactions, which qualitatively agreed with the retention data for single-site mutants. Interaction maps of lysozyme single-site mutants were also generated and provided significant insight into why these variants exhibited significant differences in their chromatographic behavior. This approach was also employed to study the binding behavior of CspB and related mutants. The results indicated that, in addition to describing general trends in the data, these maps provided significant insight into retention data of the single-site mutants. In particular, subtle retention trends observed with the K12 and K13 mutants were well-described using this interaction map approach. Finally, the number of interaction points with energies stronger than -2 kcal/mol was shown to be able to semi-quantitatively predict the behavior of most of the mutants. This rapid approach for calculating protein-surface interaction maps is expected to facilitate future method development for separating closely related protein variants in ion-exchange systems. PMID:21375221

Freed, Alexander S; Cramer, Steven M

2011-04-01

23

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

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

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. PMID:22761417

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

2012-01-01

26

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

27

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

28

Interactive Geophysical Mapping on the Web  

Microsoft Academic Search

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,

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

2002-01-01

29

Mapping of sites in forest stands.  

PubMed

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

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

2014-12-01

30

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

31

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

32

An improved map of conserved regulatory sites for Saccharomyces cerevisiae  

PubMed Central

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

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

2006-01-01

33

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.

34

3D interactive pictorial maps  

E-print Network

with landmarks, city icons and mountain ranges. Later on, I created more examples of countries such as, France, the United Kingdom, and the entire continent of Europe. While building the pictorial map of Europe, I had to be selective and choose only some major... . . . . . . . . . . . . . . . 16 IV.2.1. Applying the Process of Caricature . . . . . . . . 16 IV.2.2. Caricature of Land and Choosing Major Elements 17 IV.2.3. Modeling Mountain Ranges . . . . . . . . . . . . 18 IV.2.4. Creating Rivers, Road Networks and Vegetation . 19 IV.2...

Naz, Asma

2005-02-17

35

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.

36

Soil Survey and Ecological Sites: Integrated Map Unit Design and  

E-print Network

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

37

47 CFR 73.4108 - FM transmitter site map submissions.  

Code of Federal Regulations, 2010 CFR

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

2010-10-01

38

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. PMID:9832519

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

1998-01-01

39

eSales Interactive Mapping -Viewing and Printing Introduction  

E-print Network

eSales Interactive Mapping - Viewing and Printing Introduction Our eSales system includes an integrated interactive map facility. This allows you to view and print maps for all lots on offer. Various in the opposite direction, e.g. move mouse to right for westerly direction. Printing of Maps Printing of maps can

40

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

41

University of Tennessee Solar Pathfinder Site Analysis Map.................................................................................................................................................2  

E-print Network

University of Tennessee Solar Pathfinder Site Analysis July 2010 #12;1 Map, mainly parking lots and garages, for solar energy potential. The analysis was performed using a solar sites. All readings, except for UC plaza, were taken with the solar pathfinder at a height of eight feet

Wang, Xiaorui "Ray"

42

Fast binding site mapping using GPUs and CUDA  

Microsoft Academic Search

Binding site mapping refers to the computational prediction of the regions on a protein surface that are likely to bind a small molecule with high affinity. The process involves flexibly docking a variety of small molecule probes and finding a consensus site that binds most of those probes. Due to the computational complexity of flexible docking, the process is often

Bharat Sukhwani; Martin C. Herbordt

2010-01-01

43

24 CFR 3285.103 - Site suitability with design zone maps.  

Code of Federal Regulations, 2010 CFR

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

2010-04-01

44

Geologic mapping as a prerequisite to hazardous waste facility siting  

SciTech Connect

The nation's welfare is based on its capability to develop the mineral, water, and energy resources of the land. In addition, these resources must be developed with adequate consideration of environmental impact and the future welfare of the country. Geologic maps are an absolute necessity in the discovery and development of natural resources; for managing radioactive, toxic, and hazardous wastes; and for the assessment of hazards and risks such as those associated with volcanic action, earthquakes, landslides, and subsidence. Geologic maps are the basis for depicting rocks and rock materials, minerals, coal, oil, and water at or near the earth's surface. Hazardous waste facility projects require the preparation of detailed geologic maps. Throughout most of the USA, this type of mapping detail is not available. If these maps were available, it is estimated that the duration of an individual project could be reduced by at least one-fourth (1/4). Therefore, adequate site-specific mapping is required if one is to eliminate environmental problems associated with hazardous, toxic, radioactive, and municipal waste sites.

LaMoreaux, P.E. (P.E. LaMoreaux and Associates, Inc., Tuscaloosa, AL (United States))

1993-03-01

45

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

46

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

47

Site of fasciculin interaction with acetylcholinesterase.  

PubMed

Fasciculin, a 6750-Da peptide from the venom of Dendroaspis, is known to inhibit reversibly mammalian and fish acetylcholinesterases at picomolar concentrations, but is a relatively weak inhibitor of avian, reptile, and insect acetylcholinesterases and mammalian butyryl-cholinesterases. An examination of fasciculin association with several mutant forms of recombinant DNA-derived acetylcholinesterase from mouse shows that it interacts with a cluster of residues near the rim of the gorge on the enzyme. The aromatic residues, Trp286, Tyr72, and Tyr124, have the most marked influence on fasciculin binding, whereas Asp74, a charged residue in the vicinity of the binding site that affects the binding of low molecular weight inhibitors, has little influence on fasciculin binding. The 3 aromatic residues are unique to the susceptible acetylcholinesterases and, along with Asp74, constitute part of the peripheral anionic site. Fasciculin falls in the family of three-loop toxins that include the receptor blocking alpha-toxins and cardiotoxins. From this basic structural motif, a binding site has evolved on fasciculin to be highly specific for the peripheral site on acetylcholinesterase. Acetylthiocholine affects rates of fasciculin binding at concentrations causing substrate inhibition. In the case of the mutant cholinesterases where rates of fasciculin dissociation are more rapid, steady state kinetic parameters also show acetylthiocholine-fasciculin competition to be consistent with occupation at a peripheral or substrate inhibition site rather than the active center. PMID:8157652

Radi?, Z; Duran, R; Vellom, D C; Li, Y; Cervenansky, C; Taylor, P

1994-04-15

48

An in-depth map of polyadenylation sites in cancer  

PubMed Central

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

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

2012-01-01

49

Access to Space Interactive Design Web Site  

NASA Technical Reports Server (NTRS)

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

Leon, John; Cutlip, William; Hametz, Mark

2000-01-01

50

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

51

Visualising interactive flood risk maps in a dynamic Geobrowser  

NASA Astrophysics Data System (ADS)

Communicating flood forecast products effectively to end-users is the final step in the flood event simulation process. A prototype of the Novel Flood Early Warning System (NEWS) based on the TIGGE (THORPEX Interactive Grand Global Ensemble) database explores new avenues to visualise flood forecast products in a dynamic and interactive manner. One of the possibilities NEWS is currently assessing is Google Maps. Google Maps is a basic web mapping service application and technology provided by Google, free (for non-commercial use). It powers many map-based services including maps embedded on third-party websites via the Google Maps API. Creating a customized map interface requires adding the Google JavaScript code to a page, and then using Javascript functions to add points to the map. Flood maps allow end-users to visualise and navigate a world that is too large and complex to be seen directly. The NEWS software will attempt to deal with the following issues: • Uncertainty visualization in hazards maps • Visualizing uncertainty for sector specific risk managers • Uncertainty representation of point and linear data The objective is improve the information content of flood risk maps making them more useful to specific end-users.

Yaw Manful, Desmond; He, Yi; Cloke, Hannah; Pappenberger, Florian; Li, Zhijia; Wetterhall, Fredrik; Huang, Yingchun; Hu, Yuzhong

2010-05-01

52

Site classification map for Tbilisi using seismic prospecting methods  

NASA Astrophysics Data System (ADS)

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

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

2013-04-01

53

Molecular interaction maps as information organizers and simulation guides  

Microsoft Academic Search

A graphical method for mapping bioregulatory networks is presented that is suited for the representation of multimolecular complexes, protein modifications, as well as actions at cell membranes and between protein domains. The symbol conventions defined for these molecular interaction maps are designed to accommodate multiprotein assemblies and protein modifications that can generate combinatorially large numbers of molecular species. Diagrams can

Kurt W. Kohn

2001-01-01

54

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. PMID:20174626

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

2010-01-01

55

Tools for Glycomics: Mapping Interactions of Carbohydrates in Biological Systems  

E-print Network

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

Ratner, Daniel M.

56

Molecular interaction maps as information organizers and simulation guides  

NASA Astrophysics Data System (ADS)

A graphical method for mapping bioregulatory networks is presented that is suited for the representation of multimolecular complexes, protein modifications, as well as actions at cell membranes and between protein domains. The symbol conventions defined for these molecular interaction maps are designed to accommodate multiprotein assemblies and protein modifications that can generate combinatorially large numbers of molecular species. Diagrams can either be "heuristic," meaning that detailed knowledge of all possible reaction paths is not required, or "explicit," meaning that the diagrams are totally unambiguous and suitable for simulation. Interaction maps are linked to annotation lists and indexes that provide ready access to pertinent data and references, and that allow any molecular species to be easily located. Illustrative interaction maps are included on the domain interactions of Src, transcription control of E2F-regulated genes, and signaling from receptor tyrosine kinase through phosphoinositides to Akt/PKB. A simple method of going from an explicit interaction diagram to an input file for a simulation program is outlined, in which the differential equations need not be written out. The role of interaction maps in selecting and defining systems for modeling is discussed.

Kohn, Kurt W.

2001-03-01

57

R/qtlcharts: Interactive Graphics for Quantitative Trait Locus Mapping.  

PubMed

Every data visualization can be improved with some level of interactivity. Interactive graphics hold particular promise for the exploration of high-dimensional data. R/qtlcharts is an R package to create interactive graphics for experiments to map quantitative trait loci (QTL) (genetic loci that influence quantitative traits). R/qtlcharts serves as a companion to the R/qtl package, providing interactive versions of R/qtl's static graphs, as well as additional interactive graphs for the exploration of high-dimensional genotype and phenotype data. PMID:25527287

Broman, Karl W

2015-02-01

58

R/qtlcharts: Interactive Graphics for Quantitative Trait Locus Mapping  

PubMed Central

Every data visualization can be improved with some level of interactivity. Interactive graphics hold particular promise for the exploration of high-dimensional data. R/qtlcharts is an R package to create interactive graphics for experiments to map quantitative trait loci (QTL) (genetic loci that influence quantitative traits). R/qtlcharts serves as a companion to the R/qtl package, providing interactive versions of R/qtl’s static graphs, as well as additional interactive graphs for the exploration of high-dimensional genotype and phenotype data. PMID:25527287

Broman, Karl W.

2015-01-01

59

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. PMID:18039026

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

2007-01-01

60

Mapping the interaction site for the tarantula toxin hainantoxin-IV (?-TRTX-Hn2a) in the voltage sensor module of domain II of voltage-gated sodium channels.  

PubMed

Peptide toxins often have pharmacological applications and are powerful tools for investigating the structure-function relationships of voltage-gated sodium channels (VGSCs). Although a group of potential VGSC inhibitors have been reported from tarantula venoms, little is known about the mechanism of their interaction with VGSCs. In this study, we showed that hainantoxin-IV (?-TRTX-Hn2a, HNTX-IV in brief), a 35-residue peptide from Ornithoctonus hainana venom, preferentially inhibited rNav1.2, rNav1.3 and hNav1.7 compared with rNav1.4 and hNav1.5. hNav1.7 was the most sensitive to HNTX-IV (IC50?21nM). In contrast to many other tarantula toxins that affect VGSCs, HNTX-IV at subsaturating concentrations did not alter activation and inactivation kinetics in the physiological range of voltages, while very large depolarization above +70mV could partially activate toxin-bound hNav1.7 channel, indicating that HNTX-IV acts as a gating modifier rather than a pore blocker. Site-directed mutagenesis indicated that the toxin bound to site 4, which was located on the extracellular S3-S4 linker of hNav1.7 domain II. Mutants E753Q, D816N and E818Q of hNav1.7 decreased toxin affinity for hNav1.7 by 2.0-, 3.3- and 130-fold, respectively. In silico docking indicated that a three-toed claw substructure formed by residues with close contacts in the interface between HNTX-IV and hNav1.7 domain II stabilized the toxin-channel complex, impeding movement of the domain II voltage sensor and inhibiting hNav1.7 activation. Our data provide structural details for structure-based drug design and a useful template for the design of highly selective inhibitors of a specific subtype of VGSCs. PMID:25218973

Cai, Tianfu; Luo, Ji; Meng, Er; Ding, Jiuping; Liang, Songping; Wang, Sheng; Liu, Zhonghua

2014-09-10

61

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

Microsoft Academic Search

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

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

2007-01-01

62

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

63

Picture Browsing and Map Interaction using a Projector Phone  

E-print Network

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

64

Integrating physical and genetic maps: from genomes to interaction networks  

Microsoft Academic Search

Physical and genetic mapping data have become as important to network biology as they once were to the Human Genome Project. Integrating physical and genetic networks currently faces several challenges: increasing the coverage of each type of network; establishing methods to assemble individual interaction measurements into contiguous pathway models; and annotating these pathways with detailed functional information. A particular challenge

Andreas Beyer; Sourav Bandyopadhyay; Trey Ideker

2007-01-01

65

Remote Sensing Interactive: Land Cover Map / Image Comparison  

NSDL National Science Digital Library

The Land Cover Map/Image Comparison is one of a number of interactive tools being developed to illustrate basic remote-sensing concepts. Here, the user is able to examine a portion of the Cricahua Mountains in southern Arizona by viewing two sets of images from TM and Modis sensors, and selecting areas within them for closer examination at three magnification levels.

Ned Horning

66

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.

67

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

PubMed Central

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 regulators focused on the JNK family of MAP kinases. Predictions were tested by peptide array followed by rigorous biochemical verification with in vitro binding and kinase assays on wild-type and mutant proteins. Using this procedure, we found new ‘D-site’ class docking sites in previously known JNK substrates (hnRNP-K, PPM1J/PP2Czeta), as well as new JNK-interacting proteins (MLL4, NEIL1). Finally, we identified new D-site-dependent MAPK substrates, including the hedgehog-regulated transcription factors Gli1 and Gli3, suggesting that a direct connection between MAP kinase and hedgehog signaling may occur at the level of these key regulators. These results demonstrate that a genome-wide search for MAP kinase docking sites can be used to find new docking sites and substrates. PMID:20865152

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

2010-01-01

68

LRR conservation mapping to predict functional sites within protein leucine-rich repeat domains.  

PubMed

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. PMID:21789174

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

2011-01-01

69

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. PMID:21789174

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

2011-01-01

70

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

Microsoft Academic Search

In site-specific crop management, treatments (e.g., fertilizer and herbicides) are applied precisely where they are needed. Global positioning system receivers allow accurate navigation of field implements and creation of crop yield maps. Remote sensing products help producers explain the wide range of yields shown on these maps and become the basis for digitized field management maps. Previous sources of remote

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

1996-01-01

71

(2007). Proceedings of SITE 2007. Is Interactivity Important in Information Literacy Tutorial Sites?  

E-print Network

(2007). Proceedings of SITE 2007. Is Interactivity Important in Information Literacy Tutorial Sites,herring}@indiana.edu Abstract: Online information literacy tutorials are potentially useful tools to facilitate the learning of information literacy skills. Interactivity has been identified as a key element in Web-based learning (Chou

Herring, Susan

72

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

73

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

74

Maps  

NSDL National Science Digital Library

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

Griffith, Christopher

75

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

PubMed Central

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

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

2013-01-01

76

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. PMID:24571656

Yun, Jonghyun; Wang, Tao; Xiao, Guanghua

2014-01-01

77

RNA Antisense Purification (RAP) for Mapping RNA Interactions with Chromatin.  

PubMed

RNA-centric biochemical purification is a general approach for studying the functions and mechanisms of noncoding RNAs. Here, we describe the experimental procedures for RNA antisense purification (RAP), a method for selective purification of endogenous RNA complexes from cell extracts that enables mapping of RNA interactions with chromatin. In RAP, the user cross-links cells to fix endogenous RNA complexes and purifies these complexes through hybrid capture with biotinylated antisense oligos. DNA loci that interact with the target RNA are identified using high-throughput DNA sequencing. PMID:25555582

Engreitz, Jesse; Lander, Eric S; Guttman, Mitchell

2015-01-01

78

Online Maps and Data  

NSDL National Science Digital Library

From the California Geological Survey, the Online Maps and Data site contains information focused on natural hazards. Topics include minerals, earthquakes, and landslide and erosion hazards. The site also includes the General Location Guide for Ultramafic Rocks in California. The site also has links to a publications page and a new interactive mapping program called the Seismic Hazards Mapping Web page.

2000-01-01

79

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

E-print Network

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

Skorobogatiy, Maksim

80

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

PubMed Central

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

2014-01-01

81

Mapping the interactions of the p53 transactivation domain with the KIX domain of CBP.  

PubMed

Molecular interactions between the tumor suppressor p53 and the transcriptional coactivators CBP/p300 are critical for the regulation of p53 transactivation and stability. The transactivation domain (TAD) of p53 binds directly to several CBP/p300 domains (TAZ1, TAZ2, NCBD, and KIX). Here we map the interaction between the p53 TAD and the CBP KIX domain using isothermal titration calorimetry and NMR spectroscopy. KIX is a structural domain in CBP/p300 that can simultaneously bind two polypeptide ligands, such as the activation domain of MLL and the kinase-inducible activation domain (pKID) of CREB, using distinct interaction surfaces. The p53 TAD consists of two subdomains (AD1 and AD2); peptides corresponding to the isolated AD1 and AD2 subdomains interact with KIX with relatively low affinity, but a longer peptide containing both subdomains binds KIX tightly. In the context of the full-length p53 TAD, AD1 and AD2 bind synergistically to KIX. Mapping of the chemical shift perturbations onto the structure of KIX shows that isolated AD1 and AD2 peptides bind to both the MLL and pKID sites. Spin-labeling experiments show that the complex of the full-length p53 TAD with KIX is disordered, with the AD1 and AD2 subdomains each interacting with both the MLL and pKID binding surfaces. Phosphorylation of the p53 TAD at Thr18 or Ser20 increases the KIX binding affinity. The affinity is further enhanced by simultaneous phosphorylation of Thr18 and Ser20, and the specificity of the interaction is increased. The p53 TAD simultaneously occupies the two distinct sites that have been identified on the CBP KIX domain and efficiently competes for these sites with other known KIX-binding transcription factors. PMID:19220000

Lee, Chul Won; Arai, Munehito; Martinez-Yamout, Maria A; Dyson, H Jane; Wright, Peter E

2009-03-17

82

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

PubMed

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

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

2014-12-01

83

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. PMID:23672344

2013-01-01

84

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

DOE Data Explorer

Newberry project drill site location map 2010. Once the exploration mythology is validated, it can be applied throughout the Cascade Range and elsewhere to locate and develop “blind” geothermal resources.

Jaffe, Todd

85

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

E-print Network

Resource A Global Map of p53 Transcription-Factor Binding Sites in the Human Genome Chia-Lin Wei,1,1,6, * and Yijun Ruan1, * 1 Genome Institute of Singapore, Singapore 138672 2 Bioinformatics 10.1016/j.cell.2005.10.043 SUMMARY The ability to derivea whole-genome map of transcription

Weng, Zhiping

86

Ecoregions of North Dakota and South Dakota: Interactive Map  

NSDL National Science Digital Library

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

87

Interactive Linked Micromap Plots And Dynamically Conditioned Choropleth Maps  

Microsoft Academic Search

as of the writing of this abstract. A Java applet showing trial interactive extensions to LM plots is available http:\\/\\/www.netgraphi.com\\/cancer4\\/index.html. (Contact jchen@cs.gmu.edu if the site is down.) The displays are of test data, not of official cancer statistics. The full paper will address many changes emerging from ongoing usability evaluations. CCmaps is a java application and available as shareware from

Daniel B. Carr; Jim Chen; Sue Bell; Linda Pickle

88

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

89

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

90

Mapping epitopes and antigenicity by site-directed masking  

NASA Astrophysics Data System (ADS)

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

Paus, Didrik; Winter, Greg

2006-06-01

91

Mapping epitopes and antigenicity by site-directed masking  

PubMed Central

Here we describe a method for mapping the binding of antibodies to the surface of a folded antigen. We first created a panel of mutant antigens (?-lactamase) in which single surface-exposed residues were mutated to cysteine. We then chemically tethered the cysteine residues to a solid phase, thereby masking a surface patch centered on each cysteine residue and blocking the binding of antibodies to this region of the surface. By these means we mapped the epitopes of several mAbs directed to ?-lactamase. Furthermore, by depleting samples of polyclonal antisera to the masked antigens and measuring the binding of each depleted sample of antisera to unmasked antigen, we mapped the antigenicity of 23 different epitopes. After immunization of mice and rabbits with ?-lactamase in Freund’s adjuvant, we found that the antisera reacted with both native and denatured antigen and that the antibody response was mainly directed to an exposed and flexible loop region of the native antigen. By contrast, after immunization in PBS, we found that the antisera reacted only weakly with denatured antigen and that the antibody response was more evenly distributed over the antigenic surface. We suggest that denatured antigen (created during emulsification in Freund’s adjuvant) elicits antibodies that bind mainly to the flexible regions of the native protein and that this explains the correlation between antigenicity and backbone flexibility. Denaturation of antigen during vaccination or natural infections would therefore be expected to focus the antibody response to the flexible loops. PMID:16754878

Paus, Didrik; Winter, Greg

2006-01-01

92

Cartographic Perspectives, Number 64, Fall 2009 Cartography 2.0: For People Who Make Interactive Maps -Harrower | 41 Cartography 2.0: For people who make interactive maps  

E-print Network

Cartographic Perspectives, Number 64, Fall 2009 Cartography 2.0: For People Who Make Interactive Maps - Harrower | 41 Cartography 2.0: For people who make interactive maps Prof. Mark Harrower 1 Sheesely 2 | ben@axismaps.com Cartography 2.0 (http://Cartography2.org) is a free online knowledge base

Klippel, Alexander

93

Mapping the interactions between the Alzheimer's A?-peptide and human serum albumin beyond domain resolution.  

PubMed

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

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

2013-10-01

94

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

NASA Technical Reports Server (NTRS)

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

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

1975-01-01

95

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

96

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

E-print Network

GEO 599 Web Mapping & Human Computer Interaction (Credits 4) soon to be GEO 568 Interactive in interactive cartographic visualization drawing from research and practice on human-computer interaction an overview of methods and applications in interactive, dynamic cartographic visualization and teaches

Jenny, Bernhard

97

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

98

Location map showing sites MAT1-3 to be drilled in summer 07. The Redbeds  

E-print Network

. Previous drilling offshore the New Jersey coastline has met with limited success: drill sites no closer-1- Location map showing sites MAT1-3 to be drilled in summer 07. The Redbeds The Annual Newsletter. Integrated Ocean Drilling Program Expedition 313 Invades New Jersey Contributed by Gregory S. Mountain

99

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

100

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

E-print Network

Constraint-based simulation of biological systems described by Molecular Interaction Maps Luca of biochemical networks de- scribed by the graphical notation of Molecular Interaction Maps. Such maps generating the full list of reactions. 1 Introduction The aim of this work is the simulation of biological

Bortolussi, Luca

101

BAX Activation is Initiated at a Novel Interaction Site  

PubMed Central

BAX is a pro-apoptotic protein of the BCL-2 family stationed in the cytosol until activated by a diversity of stress stimuli to induce cell death. Anti-apoptotic proteins such as BCL-2 counteract BAX-mediated cell death. Although an interaction site that confers survival functionality has been defined for anti-apoptotic proteins, an activation site has not been identified for BAX, rendering its explicit trigger mechanism unknown. We previously developed Stabilized Alpha-Helix of BCL-2 domains (SAHBs) that directly initiate BAX-mediated mitochondrial apoptosis. Here we demonstrate by NMR analysis that BIM SAHB binds BAX at an interaction site that is distinct from the canonical binding groove characterized for anti-apoptotic proteins. The specificity of the BIM SAHB-BAX interaction is highlighted by point mutagenesis that abrogates functional activity, confirming that BAX activation is initiated at this novel structural location. Thus, we have now defined a BAX interaction site for direct activation, establishing a new target for therapeutic modulation of apoptosis. PMID:18948948

Gavathiotis, Evripidis; Suzuki, Motoshi; Davis, Marguerite L.; Pitter, Kenneth; Bird, Gregory H.; Katz, Samuel G.; Tu, Ho-Chou; Kim, Hyungjin; Cheng, Emily H.-Y.; Tjandra, Nico; Walensky, Loren D.

2008-01-01

102

Mapping substance P binding sites on the neurokinin-1 receptor using genetic incorporation of a photoreactive amino acid.  

PubMed

Substance P (SP) is a neuropeptide that mediates numerous physiological responses, including transmission of pain and inflammation through the neurokinin-1 (NK1) receptor, a G protein-coupled receptor. Previous mutagenesis studies and photoaffinity labeling using ligand analogues suggested that the binding site for SP includes multiple domains in the N-terminal (Nt) segment and the second extracellular loop (ECLII) of NK1. To map precisely the NK1 residues that interact with SP, we applied a novel receptor-based targeted photocross-linking approach. We used amber codon suppression to introduce the photoreactive unnatural amino acid p-benzoyl-l-phenylalanine (BzF) at 11 selected individual positions in the Nt tail (residues 11-21) and 23 positions in the ECLII (residues 170(C-10)-193(C+13)) of NK1. The 34 NK1 variants were expressed in mammalian HEK293 cells and retained the ability to interact with a fluorescently labeled SP analog. Notably, 10 of the receptor variants with BzF in the Nt tail and 4 of those with BzF in ECLII cross-linked efficiently to SP, indicating that these 14 sites are juxtaposed to SP in the ligand-bound receptor. These results show that two distinct regions of the NK1 receptor possess multiple determinants for SP binding and demonstrate the utility of genetically encoded photocross-linking to map complex multitopic binding sites on G protein-coupled receptors in a cell-based assay format. PMID:24831006

Valentin-Hansen, Louise; Park, Minyoung; Huber, Thomas; Grunbeck, Amy; Naganathan, Saranga; Schwartz, Thue W; Sakmar, Thomas P

2014-06-27

103

A subunit interaction site in human luteinizing hormone: identification by photoaffinity cross-linking.  

PubMed

The sites of noncovalent association between the alpha- (common) and beta- (hormone-specific) subunits in the glycoprotein hormones [LH, human CG (hCG), FSH, and TSH] remain to be completely defined. This information is essential to efforts to map the three-dimensional structure of the hormones and to help explain the stability of the hormone heterodimer in the circulation. Among numerous approaches that have been employed to identify these sites of subunit interaction, chemical or photoaffinity cross-linking has the advantage of identifying the complementary sites of contact on the respective subunits. We have used the stable photoaffinity ligand, L-benzoylphenylalanine (Bpa), to evaluate subunit interaction by the hLH beta sequence (1-15). A peptide from this region of hCG beta has been shown previously to inhibit subunit association. The 3H-labeled Bpa was incorporated into the peptide at position 8 (Trp) during solid-phase synthesis. After incubation with alpha under long-wavelength (366 nm) ultraviolet light, a Bpa- (1-15)-labeled-alpha-fraction was isolated. Control experiments showed the binding to be covalent and specific to (1-15). Two other Bpa-labeled beta-fragments, the receptor-binding loop (38-57) and the (30-43) peptide containing the highly conserved CAGY sequence, did not cross-link. The site of contact in alpha was localized by peptide mapping and sequence analysis to the N-terminal fragment (18-33), most likely at Met-29 or Gly-30. Both the alpha- and beta-sites are adjacent to or overlapping receptor-binding regions. Subunit contact sites and receptor-binding segments may thus be oriented in close proximity to provide a multicomponent receptor-binding domain imparting full activity to the native hormone. PMID:7679977

Keutmann, H T; Rubin, D A

1993-03-01

104

Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces  

NASA Astrophysics Data System (ADS)

Polar residue hot spots have been observed at protein-protein binding sites. Here we show that hot spots occur predominantly at the interfaces of macromolecular complexes, distinguishing binding sites from the remainder of the surface. Consequently, hot spots can be used to define binding epitopes. We further show a correspondence between energy hot spots and structurally conserved residues. The number of structurally conserved residues, particularly of high ranking energy hot spots, increases with the binding site contact size. This finding may suggest that effectively dispersing hot spots within a large contact area, rather than compactly clustering them, may be a strategy to sustain essential key interactions while still allowing certain protein flexibility at the interface. Thus, most conserved polar residues at the binding interfaces confer rigidity to minimize the entropic cost on binding, whereas surrounding residues form a flexible cushion. Furthermore, our finding that similar residue hot spots occur across different protein families suggests that affinity and specificity are not necessarily coupled: higher affinity does not directly imply greater specificity. Conservation of Trp on the protein surface indicates a highly likely binding site. To a lesser extent, conservation of Phe and Met also imply a binding site. For all three residues, there is a significant conservation in binding sites, whereas there is no conservation on the exposed surface. A hybrid strategy, mapping sequence alignment onto a single structure illustrates the possibility of binding site identification around these three residues.

Ma, Buyong; Elkayam, Tal; Wolfson, Haim; Nussinov, Ruth

2003-05-01

105

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

106

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

PubMed Central

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

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

1992-01-01

107

Sequestration of Polo kinase to microtubules by phosphopriming-independent binding to Map205 is relieved by phosphorylation at a CDK site in mitosis  

PubMed Central

The conserved Polo kinase controls multiple events in mitosis and cytokinesis. Although Polo-like kinases are regulated by phosphorylation and proteolysis, control of subcellular localization plays a major role in coordinating their mitotic functions. This is achieved largely by the Polo-Box Domain, which binds prephosphorylated targets. However, it remains unclear whether and how Polo might interact with partner proteins when priming mitotic kinases are inactive. Here we show that Polo associates with microtubules in interphase and cytokinesis, through a strong interaction with the microtubule-associated protein Map205. Surprisingly, this interaction does not require priming phosphorylation of Map205, and the Polo-Box Domain of Polo is required but not sufficient for this interaction. Moreover, phosphorylation of Map205 at a CDK site relieves this interaction. Map205 can stabilize Polo and inhibit its cellular activity in vivo. In syncytial embryos, the centrosome defects observed in polo hypomorphs are enhanced by overexpression of Map205 and suppressed by its deletion. We propose that Map205-dependent targeting of Polo to microtubules provides a stable reservoir of Polo that can be rapidly mobilized by the activity of Cdk1 at mitotic entry. PMID:18832073

Archambault, Vincent; D’Avino, Pier Paolo; Deery, Michael J.; Lilley, Kathryn S.; Glover, David M.

2008-01-01

108

Common Hydrogen Bond Interactions in Diverse Phosphoryl Transfer Active Sites  

PubMed Central

Phosphoryl transfer reactions figure prominently in energy metabolism, signaling, transport and motility. Prior detailed studies of selected systems have highlighted mechanistic features that distinguish different phosphoryl transfer enzymes. Here, a top-down approach is developed for comparing statistically the active site configurations between populations of diverse structures in the Protein Data Bank, and it reveals patterns of hydrogen bonding that transcend enzyme families. Through analysis of large samples of structures, insights are drawn at a level of detail exceeding the experimental precision of an individual structure. In phosphagen kinases, for example, hydrogen bonds with the O3? of the nucleotide substrate are revealed as analogous to those in unrelated G proteins. In G proteins and other enzymes, interactions with O3? have been understood in terms of electrostatic favoring of the transition state. Ground state quantum mechanical calculations on model compounds show that the active site interactions highlighted in our database analysis can affect substrate phosphate charge and bond length, in ways that are consistent with prior experimental observations, by modulating hyperconjugative orbital interactions that weaken the scissile bond. Testing experimentally the inference about the importance of O3? interactions in phosphagen kinases, mutation of arginine kinase Arg280 decreases kcat, as predicted, with little impact upon KM. PMID:25238155

Summerton, Jean C.; Martin, Gregory M.; Evanseck, Jeffrey D.; Chapman, Michael S.

2014-01-01

109

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

E-print Network

iGMT: Interactive Mapping of Geoscientific Datasets. User manual for version 1.0 Thorsten W. Becker of geoscientific datasets that is built around the GMT mapping tools. iGMT is intended to assist in the creation of GMT scripts for mapping raster or polygon datasets and has built­in support for topography, sea

Taylor, Mark A J

110

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

E-print Network

iGMT: Interactive Mapping of Geoscienti c Datasets. User manual for version 1.0 Thorsten W. Becker datasets that is built around the GMT mapping tools. iGMT is intended to assist in the creation of GMT scripts for mapping raster or polygon datasets and has built-in support for topography, sea- oor age, free

Taylor, Mark A J

111

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

PubMed Central

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

Koller, Teresa; Bent, Andrew F

2014-01-01

112

Interaction of anions with the active site of carboxypeptidase A.  

PubMed

Studies of azide inhibition of peptide hydrolysis catalyzed by cobalt(II) carboxypeptidase A identify two anion binding sites. Azide binding to the first site (KI = 35 mM) inhibits peptide hydrolysis in a partial competitive mode while binding at the second site (KI = 1.5 M) results in competitive inhibition. The cobalt electronic absorption spectrum is insensitive to azide binding at the first site but shows marked changes upon azide binding to the second site. Thus, azide elicits a spectral change with new lambda max (epsilon M) values of 590 (330) and 540 nm (190) and a KD of 1.4 M, equal to the second kinetic KI value for the cobalt enzyme, indicating that anion binding at the weaker site involves an interaction with the active-site metal. Remarkably, in the presence of the C-terminal products of peptide or ester hydrolysis or carboxylate inhibitor analogues, anion (e.g., azide, cyanate, and thiocyanate) binding is strongly synergistic; thus, KD for azide decreases to 4 mM in the presence of L-phenylalanine. These ternary complexes have characteristic absorption, CD, MCD, and EPR spectra. The absorption spectra of azide/carboxylate inhibitor ternary complexes with Co(II)CPD display a near-UV band between 305 and 310 nm with epsilon M values around 900-1250 M-1 cm-1. The lambda max values are close to the those of the charge-transfer band of an aquo Co(II)-azide complex (310 nm), consistent with the presence of a metal azide bond in the enzyme complex.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:2835074

Bicknell, R; Schäffer, A; Bertini, I; Luchinat, C; Vallee, B L; Auld, D S

1988-02-01

113

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

NASA Astrophysics Data System (ADS)

Developed by the Terrain Sciences Division (TSD) of the Geological Survey of Canada (GSC), an interactive map viewer, called GEOSERV (www.geoserv.org), is now available on the Internet. The purpose of this viewer is to provide engineers, planners, decision makers, and the general public with the geoscience information required for sound regional planning in densely populated areas, such as Canada's national capital, Ottawa (Ontario). Urban geology studies rely on diverse branches of earth sciences such as hydrology, engineering geology, geochemistry, stratigraphy, and geomorphology in order to build a three-dimensional model of the character of the land and to explain the geological processes involved in the dynamic equilibrium of the local environment. Over the past few years, TSD has compiled geoscientific information derived from various sources such as borehole logs, geological maps, hydrological reports and digital elevation models, compiled it in digital format and stored it in georeferenced databases in the form of point, linear, and polygonal data. This information constitutes the geoscience knowledge base which is then processed by Geographic Information Systems (GIS) to integrate the various sources of information and produce derived graphics, maps and models describing the geological infrastructure and response of the geological environment to human activities. Urban Geology of Canada's National Capital Area is a pilot project aiming at developing approaches, methodologies and standards that can be applied to other major urban centres of the country, while providing the geoscience knowledge required for sound regional planning and environmental protection of the National Capital Area. Based on an application developed by ESRI (Environmental System Research Institute), namely ArcIMS, the TSD has customized this web application to give free access to geoscience information of the Ottawa/Outaouais (Ontario/Québec) area including geological history, subsurface database, stratigraphy, bedrock, surficial and hydrogeology maps, and a few others. At present, each layer of geospatial information in TSD's interactive map viewer is connected to simple independent flat files (i.e. shapefiles), but it is also possible to connect GEOSERV to other types of (relational) databases (e.g. Microsoft SQL Server, Oracle). Frequent updating of shapefiles could be a cumbersome task, when new records are added, since we have to completely rebuild the updated shapefiles. However, new attributes can be added to existing shapefiles easily. At present, the updating process can not be done on-the-fly; we must stop and restart the updated MapService if one of its shapefiles is changed. The public can access seventeen MapServices that provide interactive tools that users can use to query, zoom, pan, select, and so on, or print the map displayed on their monitor. The map viewer is light-weight as it uses HTML and Javascript, so end users do not have to download and install any plug-ins. A free CD and a companion web site were also developed to give access to complementary information, like high resolution raster maps and reports. Some of the datasets are available free of charge, on-line.

Giroux, D.; Bélanger, R.

2003-04-01

114

Home Contact Us Help Site Map Index Search Combating Illegal Logging in Africa  

E-print Network

Home · Contact Us · Help · Site Map · Index · Search Combating Illegal Logging in Africa, and corruption in the forest sector at the Africa Forest Law Enforcement and Governance (AFLEG) conference held in Africa "Forest law enforcement and governance are the foundation upon which all real forest conservation

115

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

Microsoft Academic Search

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

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

2010-01-01

116

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

USGS Publications Warehouse

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

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

2008-01-01

117

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

PubMed

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

Boulos, Maged N Kamel

2005-09-21

118

Available online at www.sciencedirect.com Charting the genetic interaction map of a cell  

E-print Network

in higher organisms [6,7 ,8 ,9 ,10 ,11 ]. Thus, mapping genetic interaction networks in simple systems of organisms. We are now faced with the formidable challenge of assigning functions to thousands of genes the mapping of genetic interaction networks in genetically tractable model organ- isms amenable to large

Boone, Charlie

119

Interactive System of Real-world Video Based on Maps Tomoyuki Yatabe  

E-print Network

Interactive System of Real-world Video Based on Maps Tomoyuki Yatabe , Hiroshi Kawasaki- scription", "Question and Answer", and "Retrieval" regarding real-world video based on digital maps Interactive TV service, called ADTV. In our method, users not only get information about specific video

Tokyo, University of

120

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

E-print Network

Constraint-based simulation of biological systems described by Molecular Interaction Maps Luca to simulate biochemical networks de- scribed by the graphical notation of Molecular Interaction Maps within The aim of this work is the simulation of biological regulatory networks described by the graphical

Bortolussi, Luca

121

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

NSDL National Science Digital Library

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

Gregg, Tracy

122

An approach to mapping haplotype-specific recombination sites in human MHC class III  

SciTech Connect

Studies of the major histocompatibility complex (MHC) in mouse indicate that the recombination sites are not randomly distributed and their occurrence is haplotype-dependent. No data concerning haplotype-specific recombination sites in human are available due to the low number of informative families. To investigate haplotype-specific recombination sites in human MHC, we describe an approach based on identification of recombinant haplotypes derived from one conserved haplotype at the population level. The recombination sites were mapped by comparing polymorphic markers between the recombinant and assumed original haplotypes. We tested this approach on the extended haplotype HLA A3; B47; Bf{sup *}F; C4A{sup *}1; C4B{sup *}Q0; DR7, which is most suitable for this analysis. First, it carries a number of rare markers, and second, the haplotype, albeit rare in the general population, is frequent in patients with 21-hydroxylase (21OH) defect. We observed recombinants derived from this haplotype in patients with 21OH defect. All these haplotypes had the centromeric part (from Bf to DR) identical to the original haplotype, but they differed in HLA A and B. We therefore assumed that they underwent recombinations in the segment that separates the Bf and HLA B genes. Polymorphic markers indicated that all break points mapped to two segments near the TNF locus. This approach makes possible the mapping of preferential recombination sites in different haplotypes. 20 refs., 1 fig., 1 tab.

Levo, A.; Westman, P.; Partanen, J. [Finnish Red Cross Blood Transfusion Service, Helsinki (Finland)

1996-12-31

123

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

NASA Astrophysics Data System (ADS)

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

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

2015-01-01

124

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

PubMed Central

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

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

2014-01-01

125

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

PubMed

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

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

2014-07-01

126

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

USGS Publications Warehouse

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

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

2012-01-01

127

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

128

RRHP: a tag-based approach for 5-hydroxymethylcytosine mapping at single-site resolution.  

PubMed

Current methods for genomic mapping of 5-hydroxymethylcytosine (5hmC) have been limited by either costly sequencing depth, high DNA input, or lack of single-base resolution. We present an approach called Reduced Representation 5-Hydroxymethylcytosine Profiling (RRHP) to map 5hmC sites at single-base resolution by exploiting the use of beta-glucosyltransferase to inhibit enzymatic digestion at the junction where adapters are ligated to a genomic library. Therefore, only library fragments presenting glucosylated 5hmC residues at the junction are sequenced. RRHP can detect sites with low 5hmC abundance, and when combined with RRBS data, 5-methylcytosine and 5-hydroxymethylcytosine can be compared at a specific site. PMID:25248841

Petterson, Adam; Chung, Tzu; Tan, Darany; Sun, Xueguang; Jia, Xi-Yu

2014-09-24

129

Preliminary Site Classification using the Geologic Map of the Korean Peninsula  

NASA Astrophysics Data System (ADS)

Studies of the earthquake ground motion consider the soil properties or the bed rock properties in the upper 30 m. The average shear wave velocity in the upper 30 m defined from borehole data is routinely used for classifying the site conditions. However, it is difficult to classify the site condition using the limited borehole data to cover the whole Korean Peninsula. In the study of Lee et al. (2001), site classification of Taiwan was refined using surface geology from the geologic map, geomorphologic data, and borehole data following the guidelines of National Earthquake Reduction Program (NEHRP). Wald and Allen (2007) defined shear wave velocity using slope of topography or gradient in global scale. They also compared their results in the Taiwan region to those proposed by Lee et al. (2001). In this study, we used geologic map, geomorphologic data, estimated average shear wave velocity from slope of topography, and borehole data to define the site conditions of the Korean Peninsula. We compared our results to the borehole data or seismic site condition data which include seismometer locations and ground conditions. There are some differences between our results and seismic site condition data. The discrepancy is attributed to the relatively large scale geologic map (1:250000) which may not include accurate site condition of the regions. Estimated site conditions of the study, however, agree with those from borehole data when a 1-mile buffering distance is applied to geologic condition boundaries. These results provide useful information for the further study of regional hazard estimation, risk management, and other seismological and geotechnical applications.

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

2008-12-01

130

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. PMID:24288369

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

2014-01-01

131

Mapping Hfq-RNA interaction surfaces using tryptophan fluorescence quenching.  

PubMed

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. PMID:24288369

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

2014-02-01

132

Mapping the initiation sites of in vitro transcripts of bacteriophage S13.  

PubMed

Analysis of in vitro run-off transcripts synthesized by Escherichia coli RNA polymerase holoenzyme on linearized bacteriophage S13 DNA templates revealed five major transcription initiation sites. The sites, located at positions 45, 982, 1823 (1827), 4876 and 5211, are each within the boundaries of promoters or putative promoters previously mapped by footprinting and RNA polymerase binding analyses. They correspond to initiations at promoters upstream of the A, B, and D genes, and at a medium-affinity and a high-affinity RNA polymerase binding site P5211, respectively. Sequence analysis of the 5'-ends of two transcripts confirmed their initiation with pppA at nt 982 and nt 5211, the B gene and high-affinity binding site P5211, respectively. Some of the transcripts initiated at nt 4876 and nt 5211 terminated at nt 64, providing direct evidence of the functionality of a p-independent termination site at nt 64. PMID:8049259

Ringuette, M J; Spencer, J H

1994-08-01

133

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

PubMed Central

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

Boulos, Maged N Kamel

2005-01-01

134

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

NASA Astrophysics Data System (ADS)

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

Yordkayhun, Sawasdee; Sujitapan, Chedtaporn; Chalermyanont, Tanit

2015-02-01

135

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

PubMed

Four different methods of epiphytic lichen mapping were used for the assessment of air quality in the region under the influence of the Sostanj Thermal Power Plant (Salek Valley, Slovenia). Three methods were based on the presence of different lichen species (VDI, EU and ICP-Forest), the fourth on a frequency and coverage assessment of different growth forms of epiphytic lichens, e.g. crustose, foliose and fruticose (SI). A comparison of the results from the assessment of air quality between forest sites (ICP-Forest, SI) and open areas (VDI, EU and SI), obtained by the different methods of epiphytic lichen mapping, is presented in the contribution. Data showed that lichen species richness is worse in forest sites in comparison with open areas. From the data obtained it can be concluded that epiphytic lichen mapping in open areas is a better method for the assessment of air pollution in a given area than mapping in forest sites. The species-based methods in open areas are more powerful and useful for air quality assessment in polluted research areas than the SI and ICP-Forest methods. PMID:17683836

Policnik, Helena; Simoncic, Primoz; Batic, Franc

2008-01-01

136

Packaging effects on site-specific DNA-protein interactions.  

PubMed

We show that the rate of site-specific association of a protein molecule of interest with the DNA chain can be approximately 10(2) times higher than that of the three-dimensional diffusion-controlled collision rate limit approximately 10(8) mol(-1) s(-1) only when the protein molecule of interest searches for its specific site on the DNA chain in a reduced dimensional space with a dimensionality dr of dr<1. Upon considering the concurrent dynamics of the linear DNA chain that is embedded in a d-dimensional space along with the one-dimensional diffusion dynamics of the nonspecifically bound protein molecule on the DNA chain, we derive the generalized scaling law epsilon approximately 2(3(2-d)+3), where epsilon is the number of times by which the rate of site-specific association of the protein molecule with the DNA chain can be enhanced over the three-dimensional diffusion-controlled collision rate limit and d is the dimensionality of the reduced search space. Using the analogy between the self-intersection loop length in the theory of random walks and the ring-closure events in the theory of site specific interactions of a protein molecule with the DNA chain, we further show that the extent of packaging and volume compression of the genomic DNA inside the living cell is designed in such a way that the efficiency of the protein molecule in the process of searching for its specific site on the genomic DNA is a maximum. Our simulation results suggest that the volume compression factor theta which is the ratio between the total volume of the living cell and the volume occupied by the DNA chain along with all the other bound protein molecules should be such that theta>or=100 for an efficient site specific interaction of a protein molecule of interest with the linear DNA chain that is embedded in a three-dimensional space. Our theoretical and simulation results agree well with the E. coli cellular system. PMID:19658537

Murugan, Rajamanickam

2009-06-01

137

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

138

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

139

High-Throughput Yeast Two-Hybrid Assays for Large-Scale Protein Interaction Mapping  

Microsoft Academic Search

Protein-protein interactions play fundamental roles in many biological processes. Hence, protein interaction mapping is becoming a well-established functional genomics approach to generate functional annotations for predicted proteins that so far have remained uncharacterized. The yeast two-hybrid system is currently one of the most standardized protein interaction mapping techniques. Here, we describe the protocols for a semiautomated, high-throughput, Gal4-based yeast two-hybrid

Albertha J. M. Walhout; Marc Vidal

2001-01-01

140

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

Microsoft Academic Search

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

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

2007-01-01

141

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

Microsoft Academic Search

MAP kinases phosphorylate specific groups of substrate proteins. Here we show that the amino acid sequence FXFP is an evolutionarily conserved docking site that mediates ERK MAP kinase binding to substrates in multiple protein families. FXFP and the D box, a different docking site, form a modular recognition system, as they can function independently or in combination. FXFP is specific

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

1999-01-01

142

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

143

Do Electrostatic Interactions with Positively Charged Active Site Groups Tighten the Transition State for Enzymatic  

E-print Network

Do Electrostatic Interactions with Positively Charged Active Site Groups Tighten the Transition-mail: herschla@cmgm.stanford.edu Abstract: The effect of electrostatic interactions on the transition reactions at the AP active site and, thus, negligible effects of active site electrostatic interactions

Herschlag, Dan

144

Interactive flare sites within an active region complex  

NASA Technical Reports Server (NTRS)

We examine here a set of images of an active region complex, acquired on June 24-25, 1980, by the Hard X-ray Imaging Spectrometer on SMM, with the purpose of establishing whether there was any interplay between the frequent activity observed at different sites in the activity center and, in such a case, how the interaction was established. By analyzing both quiet and active orbits we show that, as a rule, activity originating in one region triggers the other region's activity. However, we find little unambiguous evidence for the presence of large-scale interconnecting loops. A comparison of X-ray images with magnetic field observations suggested that we interpret the active region behavior in terms of the interaction between different loop systems, in a scenario quite analogous to the interacting bipole representation of individual flares. We conclude that active region interplay provides an easily observable case to study the time-dependent topology and the mechanisms for the spreading of activity in transient events over all energy scales.

Poletto, G.; Gary, G. A.; Machado, M. E.

1993-01-01

145

Matrix model maps and reconstruction of AdS supergravity interactions  

SciTech Connect

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

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

2008-05-15

146

Using ¹?N-ammonium to characterise and map potassium binding sites in proteins by NMR spectroscopy.  

PubMed

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

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

2014-03-01

147

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

148

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

149

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

150

GEO 499/599 Web Mapping and Human Computer Interaction Spring 2013  

E-print Network

GEO 499/599 Web Mapping and Human Computer Interaction Spring 2013 Instructor Dr. Helen Jenny Burt access OSU Libraries #12;Haklay, Muki (2010): Interacting with Geospatial Technologies (selected and applications in interactive cartographic visualization and teaches the skills of building customized web

Jenny, Bernhard

151

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

E-print Network

Genetic Mapping of Specific Interactions between Aedes aegypti Mosquitoes and Dengue Viruses. In this study, we aimed to determine whether G6G interactions observed between dengue viruses and their Aedes that G6G interactions between dengue viruses and mosquito vectors can be assigned to physical regions

Paris-Sud XI, Université de

152

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

PubMed Central

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

Singh, Durg Vijay; Misra, Krishna

2009-01-01

153

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. PMID:17494734

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

2007-01-01

154

Mapping of Antigenic Sites on the Nucleocapsid Protein of the Severe Acute Respiratory Syndrome Coronavirus  

Microsoft Academic Search

Received 9 June 2004\\/Returned for modification 18 July 2004\\/Accepted 27 July 2004 Antigenic sites on the nucleocapsid (N) protein of severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) were mapped by Pepscan analysis with overlapping peptides that span the N protein sequence. Two major immunodominant epitopes located in the C-terminal region (amino acids (aa) 362 to 412) and middle region (aa

Yuxian He; Yusen Zhou; Hao Wu; Zhihua Kou; Shuwen Liu; Shibo Jiang

2004-01-01

155

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

PubMed

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

Nosrati, Geoffrey R; Houk, K N

2012-09-18

156

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

157

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

NASA Astrophysics Data System (ADS)

With current research efforts shifting towards the 4d and 5d transition metal oxides, understanding the evolution of the electronic and magnetic structure as one moves away from 3d materials is of critical importance. Here we perform X-ray spectroscopy and electronic structure calculations on A-site-ordered perovskites with Cu in the A-site and the B-sites descending along the ninth group of the periodic table to elucidate the emerging properties as d-orbitals change from partially filled 3d to 4d to 5d. The results show that when descending from Co to Ir, the charge transfers from the cuprate-like Zhang-Rice state on Cu to the t2g orbital of the B site. As the Cu d-orbital occupation approaches the Cu2+ limit, a mixed valence state in CaCu3Rh4O12 and heavy fermion state in CaCu3Ir4O12 are obtained. The investigated d-electron compounds are mapped onto the Doniach phase diagram of the competing RKKY and Kondo interactions developed for the f-electron systems.

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

2014-12-01

158

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

PubMed

With current research efforts shifting towards the 4d and 5d transition metal oxides, understanding the evolution of the electronic and magnetic structure as one moves away from 3d materials is of critical importance. Here we perform X-ray spectroscopy and electronic structure calculations on A-site-ordered perovskites with Cu in the A-site and the B-sites descending along the ninth group of the periodic table to elucidate the emerging properties as d-orbitals change from partially filled 3d to 4d to 5d. The results show that when descending from Co to Ir, the charge transfers from the cuprate-like Zhang-Rice state on Cu to the t2g orbital of the B site. As the Cu d-orbital occupation approaches the Cu(2+) limit, a mixed valence state in CaCu3Rh4O12 and heavy fermion state in CaCu3Ir4O12 are obtained. The investigated d-electron compounds are mapped onto the Doniach phase diagram of the competing RKKY and Kondo interactions developed for the f-electron systems. PMID:25517129

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

2014-01-01

159

Phosphorylation of the kinase interaction motif in mitogen-activated protein (MAP) kinase phosphatase-4 mediates cross-talk between protein kinase A and MAP kinase signaling pathways.  

PubMed

MAP kinase phosphatase 4 (DUSP9/MKP-4) plays an essential role during placental development and is one of a subfamily of three closely related cytoplasmic dual-specificity MAPK phosphatases, which includes the ERK-specific enzymes DUSP6/MKP-3 and DUSP7/MKP-X. However, unlike DUSP6/MKP-3, DUSP9/MKP-4 also inactivates the p38? MAP kinase both in vitro and in vivo. Here we demonstrate that inactivation of both ERK1/2 and p38? by DUSP9/MKP-4 is mediated by a conserved arginine-rich kinase interaction motif located within the amino-terminal non-catalytic domain of the protein. Furthermore, DUSP9/MKP-4 is unique among these cytoplasmic MKPs in containing a conserved PKA consensus phosphorylation site (55)RRXSer-58 immediately adjacent to the kinase interaction motif. DUSP9/MKP-4 is phosphorylated on Ser-58 by PKA in vitro, and phosphorylation abrogates the binding of DUSP9/MKP-4 to both ERK2 and p38? MAP kinases. In addition, although mutation of Ser-58 to either alanine or glutamic acid does not affect the intrinsic catalytic activity of DUSP9/MKP-4, phospho-mimetic (Ser-58 to Glu) substitution inhibits both the interaction of DUSP9/MKP-4 with ERK2 and p38? in vivo and its ability to dephosphorylate and inactivate these MAP kinases. Finally, the use of a phospho-specific antibody demonstrates that endogenous DUSP9/MKP-4 is phosphorylated on Ser-58 in response to the PKA agonist forskolin and is also modified in placental tissue. We conclude that DUSP9/MKP-4 is a bona fide target of PKA signaling and that attenuation of DUSP9/MKP-4 function can mediate cross-talk between the PKA pathway and MAPK signaling through both ERK1/2 and p38? in vivo. PMID:21908610

Dickinson, Robin J; Delavaine, Laurent; Cejudo-Marín, Rocío; Stewart, Graeme; Staples, Christopher J; Didmon, Mark P; Trinidad, Antonio Garcia; Alonso, Andrés; Pulido, Rafael; Keyse, Stephen M

2011-11-01

160

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

NASA Astrophysics Data System (ADS)

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

Kang, S.; Kim, K.

2013-12-01

161

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

162

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

163

Mapping  

ERIC Educational Resources Information Center

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

Kinney, Douglas M.; McIntosh, Willard L.

1978-01-01

164

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

E-print Network

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

Bortolussi, Luca

165

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

166

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

E-print Network

HABITAT AND BIODIVERSITY MAPPING, FOR THE DETERMINATION OF ALGAL BIOMASS AQUACULTURE SITES for Puerto Rico. Two models were developed to analyze possible aquaculture sites. The first model evaluates conflict areas and the second model incorporates optimal areas for aquaculture sites. The union

Gilbes, Fernando

167

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

168

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

USGS Publications Warehouse

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

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

1996-01-01

169

Cave detection and mapping in a construction site in Israel: a case study  

NASA Astrophysics Data System (ADS)

The Geophysical Institute of Israel (G.I.I.) carried out a Ground Penetrating Radar -- GPR -- survey at the construction site for the administration building of the I.E.C. (The Israel Electricity Company) in the town of Ariel in the Samaria mountains of Israel. The construction workers at the site found a void in one of the pile boreholes and the GPR crew carried out a survey to detect and map the cave. The GPR data show a very clear 'cave shape' with an area of about 81m2, the roof of the cave was at a depth of 5m - 7m, while the floor of the cave was at a depth of 8m - 11m. The volume estimations of the target were incorrect and the construction workers did not find any indication of the existence of the cave under the pile sites except the one prior to the GPR survey.

Ronen, Amit

2000-04-01

170

Regulatory and essential light-chain-binding sites in myosin heavy chain subfragment-1 mapped by site-directed mutagenesis.  

PubMed

Site-directed mutagenesis of the cloned subfragment-1 (S-1) region of the unc-54 gene, encoding the myosin heavy chain B (MHC B) from Caenorhabditis elegans, has been used to locate binding sites for the regulatory and essential light chains. MHC B S-1 synthesized in Escherichia coli co-migrated with rabbit skeletal muscle myosin S-1 (Mr 90,000), was recognized by anti-nematode myosin antiserum on immunoblots, and specifically bound to 125I-labelled regulatory and essential light chains in a gel overlay assay. Deletion of 102 residues from the C terminus (mutant 655) reduced regulatory and essential light-chain binding to about 30% and 20% of wild-type levels, respectively. Similar reductions in relative binding of the two light chains were seen with mutant 534, in which 38 residues were deleted from the C terminus. Potential binding sites within 75 residues of the C terminus of S-1 were mapped by construction of five other mutant S-1 clones (398, 399, 400, 409 and 411) containing internal deletions of ten to 12 amino acid residues. These showed up to 30% reductions in their ability to bind essential light chains, but did not differ significantly from wild-type in their ability to bind regulatory light chains. Another mutant, 415, containing a deletion of a conserved acidic hexapeptide, E-D-I-R-D-E, showed enhancement of binding of regulatory and essential light chains to 150% and 165% of wild-type levels. Hence, the major binding sites for both light chains are within 38 amino acid residues of the C terminus. PMID:2769753

Mitchell, E J; Karn, J; Brown, D M; Newman, A; Jakes, R; Kendrick-Jones, J

1989-07-01

171

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

172

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

173

The Potential for Mapping Nematode Distributions for Site-specific Management  

PubMed Central

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

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

2002-01-01

174

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

NASA Astrophysics Data System (ADS)

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

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

1996-11-01

175

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

PubMed Central

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

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

1994-01-01

176

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

NASA Astrophysics Data System (ADS)

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

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

2014-01-01

177

Predicting Protein-Protein Interaction Sites Using Radial Basis Function Neural Networks  

E-print Network

as well as protein synthesis [1]. In general, understanding the characteristic of interfacial sitesPredicting Protein-Protein Interaction Sites Using Radial Basis Function Neural Networks Bing Wang--Identifying protein-protein interaction sites is crucial for understanding of the principles of biological systems

Hefei Institute of Intelligent Machines

178

Self-organizing maps of document collections: A new approach to interactive exploration  

SciTech Connect

Powerful methods for interactive exploration and search from collections of free-form textual documents axe needed to manage the ever-increasing flood of digital information. In this article we present a method, WEBSOM, for automatic organization of full-text document collections using the self-organizing map (SOM) algorithm. The document collection is ordered onto a map in an unsupervised manner utilizing statistical information of short word contexts. The resulting ordered map where similar documents lie near each other thus presents a general view of the document space. With the aid of a suitable (WWW-based) interface, documents in interesting areas of the map can be browsed. The browsing can also be interactively extended to related topics, which appear in nearby areas on the map. Along with the method we present a case study of its use.

Lagus, K.; Honkela, T.; Kaski, S.; Kohonen, T. [Helsinki Univ. of Technology (Finland)

1996-12-31

179

Detection of peptide-binding sites on protein surfaces: The first step towards the modeling and targeting of peptide-mediated interactions  

PubMed Central

Peptide-mediated interactions, in which a short linear motif binds to a globular domain, play major roles in cellular regulation. An accurate structural model of this type of interaction is an excellent starting point for the characterization of the binding specificity of a given peptide-binding domain. A number of different protocols have recently been proposed for the accurate modeling of peptide-protein complex structures, given the structure of the protein receptor and the binding site on its surface. When no information about the peptide binding site(s) is a priori available, there is a need for new approaches to locate peptide-binding sites on the protein surface. While several approaches have been proposed for the general identification of ligand binding sites, peptides show very specific binding characteristics, and therefore, there is a need for robust and accurate approaches that are optimized for the prediction of peptide-binding sites. Here we present PeptiMap, a protocol for the accurate mapping of peptide binding sites on protein structures. Our method is based on experimental evidence that peptide-binding sites also bind small organic molecules of various shapes and polarity. Using an adaptation of ab initio ligand binding site prediction based on fragment mapping (FTmap), we optimize a protocol that specifically takes into account peptide binding site characteristics. In a high-quality curated set of peptide-protein complex structures PeptiMap identifies for most the accurate site of peptide binding among the top ranked predictions. We anticipate that this protocol will significantly increase the number of accurate structural models of peptide-mediated interactions. PMID:24123488

Lavi, Assaf; Ngan, Chi Ho; Movshovitz-Attias, Dana; Bohnuud, Tanggis; Yueh, Christine; Beglov, Dmitri; Schueler-Furman, Ora; Kozakov, Dima

2013-01-01

180

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

181

Mapping the Protein Interaction Network for TFIIB-Related Factor Brf1 in the RNA Polymerase III Preinitiation Complex  

PubMed Central

TFIIB-related factor Brf1 is essential for RNA polymerase (Pol) III recruitment and open-promoter formation in transcription initiation. We site specifically incorporated a nonnatural amino acid cross-linker into Brf1 to map its protein interaction targets in the preinitiation complex (PIC). Our cross-linking analysis in the N-terminal domain of Brf1 indicated a pattern of multiple protein interactions reminiscent of TFIIB in the Pol active-site cleft. In addition to the TFIIB-like protein interactions, the Brf1 cyclin repeat subdomain is in contact with the Pol III-specific C34 subunit. With site-directed hydroxyl radical probing, we further revealed the binding between Brf1 cyclin repeats and the highly conserved region connecting C34 winged-helix domains 2 and 3. In contrast to the N-terminal domain of Brf1, the C-terminal domain contains extensive binding sites for TBP and Bdp1 to hold together the TFIIIB complex on the promoter. Overall, the domain architecture of the PIC derived from our cross-linking data explains how individual structural subdomains of Brf1 integrate the protein network from the Pol III active center to the promoter for transcription initiation. PMID:24277937

Khoo, Seok-Kooi; Wu, Chih-Chien; Lin, Yu-Chun; Lee, Jin-Cheng

2014-01-01

182

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

NASA Astrophysics Data System (ADS)

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

Chirasatitsin, Somyot; Engler, Adam J.

2010-05-01

183

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

PubMed Central

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

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

1995-01-01

184

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

PubMed

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 electrophysiologic experiment or a clinical procedure. This report describes an interactive graphic user interface application that (1) automatically determines the activation sequences with good accuracy, (2) displays graphical presentations of activation maps within seconds, and (3) allows manual interactive adjustments. Five automated activation time detection algorithms, one for bipolar electrograms and four for unipolar electrograms, were evaluated and compared. High-density canine recordings were used to evaluate the accuracy of the system. Data included normal atrial activation (sinus rhythm) and abnormal reentrant atrial activation (atrial flutter). PMID:10465566

He, Y H; Ghanem, R N; Waldo, A L; Rudy, Y

1999-07-01

185

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

186

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

187

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

188

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

PubMed Central

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

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

2013-01-01

189

Comparison of reproductive parameters in male yellow-blotched map turtles ( Graptemys flavimaculata) from a historically contaminated site and a reference site  

Microsoft Academic Search

From May to September of 1998, we collected monthly plasma samples from male yellow-blotched map turtles captured at two sites in the Pascagoula River drainage, Mississippi. One site (Vancleave) has a documented history of pollution from industrial sources (principally 2,3,7,8-tetrachlorodibenzo-p-dioxin, TCDD). Fish consumption advisories at the Vancleave site were lifted in 1996 and current impacts appear minimal. However, the yellow-blotched

J. A. Shelby; M. T. Mendonça

2001-01-01

190

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

PubMed

The high and persistent radioactivity at the injection site hinders the accuracy and expansion of sentinel lymph node (SLN) mapping. We investigated the mechanism underlying the undesirable radioactivity after subcutaneous injection of (99m)Tc-labeled mannosylated dextran ((99m)Tc(CO)3-DCM20), a SLN mapping agent targeting mannose receptors on macrophages and dendritic cells, in a mouse model. Biodistribution studies were performed 1 h after subcutaneous injection of (99m)Tc(CO)3-DCM20 from the rear footpad of mice in the presence of varying molar amounts of DCM20 or DC15, a modified dextran without mannose. Biodistribution studies were also conducted after subcutaneous injection of [(125)I]radioiodinated mannosyl-neoglycoalbumin ((125)I-NMA) from the rear footpad. The distribution of fluorescence-labeled DCM20 and DC15 at the injection site was also compared 1 h after subcutaneous injection by immunofluorescent histochemistry. The radioactivity levels of (99m)Tc(CO)3-DCM20 at the injection site and popliteal lymph node, a SLN in this model, decreased with an increase in the molar amounts of DCM20, whereas no significant changes in biodistribution were observed after injection of (99m)Tc(CO)3-DCM20 with varying molar amounts of DC15. (125)I-NMA exhibited rapid elimination of radioactivity from both the popliteal lymph node and the injection site. The fluorescence-labeled DCM20 colocalized well with CD68-positive cells such as macrophages and dendritic cells at the injection site. While partial colocalization was observed between DC15 and CD68-positive cells, the signal intensity was very weak. These findings suggest that specific binding of (99m)Tc(CO)3-DCM20 to the mannose receptor on macrophages and dendritic cells would be responsible for the sustained radioactivity levels at the injection site. These results also imply that discriminated blockage of (99m)Tc(CO)3-DCM20 binding to mannose receptors at the injection sites would reduce the radioactivity at the injection site. PMID:25423619

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

2015-02-01

191

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

Microsoft Academic Search

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

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

2007-01-01

192

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

PubMed Central

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

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

2014-01-01

193

Mapping the heparin-binding sites on type I collagen monomers and fibrils  

PubMed Central

The glycosaminoglycan chains of cell surface heparan sulfate proteoglycans are believed to regulate cell adhesion, proliferation, and extracellular matrix assembly, through their interactions with heparin-binding proteins (for review see Ruoslahti, E. 1988. Annu. Rev. Cell Biol. 4:229-255; and Bernfield, M., R. Kokenyesi, M. Kato, M. T. Hinkes, J. Spring, R. L. Gallo, and E. J. Lose. 1992. Annu. Rev. Cell Biol. 8:365-393). Heparin-binding sites on many extracellular matrix proteins have been described; however, the heparin-binding site on type I collagen, a ubiquitous heparin-binding protein of the extracellular matrix, remains undescribed. Here we used heparin, a structural and functional analogue of heparan sulfate, as a probe to study the nature of the heparan sulfate proteoglycan-binding site on type I collagen. We used affinity coelectrophoresis to study the binding of heparin to various forms of type I collagen, and electron microscopy to visualize the site(s) of interaction of heparin with type I collagen monomers and fibrils. Using affinity coelectrophoresis it was found that heparin has similar affinities for both procollagen and collagen fibrils (Kd's approximately 60-80 nM), suggesting that functionally similar heparin- binding sites exist in type I collagen independent of its aggregation state. Complexes of heparin-albumin-gold particles and procollagen were visualized by rotary shadowing and electron microscopy, and a preferred site of heparin binding was observed near the NH2 terminus of procollagen. Native or reconstituted type I collagen fibrils showed one region of significant heparin-gold binding within each 67-nm period, present near the division between the overlap and gap zones, within the "a" bands region. According to an accepted model of collagen fibril structure, our data are consistent with the presence of a single preferred heparin-binding site near the NH2 terminus of the collagen monomer. Correlating these data with known type I collagen sequences, we suggest that the heparin-binding site in type I collagen may consist of a highly basic triple helical domain, including several amino acids known sometimes to function as disaccharide acceptor sites. We propose that the heparin-binding site of type I collagen may play a key role in cell adhesion and migration within connective tissues, or in the cell- directed assembly or restructuring of the collagenous extracellular matrix. PMID:8195298

1994-01-01

194

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

PubMed Central

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

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

2014-01-01

195

Getting the Picture: Examining How Feedback and Layout Impact Mobile Device Interaction with Maps on Physical Media  

Microsoft Academic Search

We present results from a study examining how visual selection feedback and map layout impact interaction when expressing spatial queries on paper maps using handheld devices. A sequence analysis of gaze patterns indicates that efficient queries involved a progression of visual attention from the paper map to the handheld device for a city street map with a grid layout, and

Derek F. Reilly; Kori M. Inkpen; Carolyn R. Watters

2009-01-01

196

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

SciTech Connect

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

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

2012-03-02

197

Noninvasive Localization of Maximal Frequency Sites of Atrial Fibrillation by Body Surface Potential Mapping  

PubMed Central

Background Ablation of high-frequency sources in patients with atrial fibrillation (AF) is an effective therapy to restore sinus rhythm. However, this strategy may be ineffective in patients without a significant dominant frequency (DF) gradient. The aim of this study was to investigate whether sites with high-frequency activity in human AF can be identified noninvasively, which should help intervention planning and therapy. Methods and Results In 14 patients with a history of AF, 67-lead body surface recordings were simultaneously registered with 15 endocardial electrograms from both atria including the highest DF site, which was predetermined by atrial-wide real-time frequency electroanatomical mapping. Power spectra of surface leads and the body surface location of the highest DF site were compared with intracardiac information. Highest DFs found on specific sites of the torso showed a significant correlation with DFs found in the nearest atrium (?=0.96 for right atrium and ?=0.92 for left atrium) and the DF gradient between them (?=0.93). The spatial distribution of power on the surface showed an inverse relationship between the frequencies versus the power spread area, consistent with localized fast sources as the AF mechanism with fibrillatory conduction elsewhere. Conclusions Spectral analysis of body surface recordings during AF allows a noninvasive characterization of the global distribution of the atrial DFs and the identification of the atrium with the highest frequency, opening the possibility for improved noninvasive personalized diagnosis and treatment. PMID:23443619

Guillem, Maria S.; Climent, Andreu M.; Millet, Jose; Arenal, Ángel; Fernández-Avilés, Francisco; Jalife, José; Atienza, Felipe; Berenfeld, Omer

2014-01-01

198

Mapping of Antigenic Sites on the Nucleocapsid Protein of the Severe Acute Respiratory Syndrome Coronavirus  

PubMed Central

Antigenic sites on the nucleocapsid (N) protein of severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) were mapped by Pepscan analysis with overlapping peptides that span the N protein sequence. Two major immunodominant epitopes located in the C-terminal region (amino acids [aa] 362 to 412) and middle region (aa 153 to 178) reacted with more than 75% of sera from SARS patients. Several minor immunodominant epitopes were reactive with about 50% of the SARS sera. Antisera from mice immunized with inactivated SARS-CoV recognized the two major immunodominant epitopes and one antigenic site located adjacent to the N-terminal region (aa 76 to 101), which did not react with the sera from SARS patients. Several monoclonal antibodies against SARS-CoV bound to the N- or C-terminal antigenic sites. These results suggest that the above antigenic sites on the N protein are important in eliciting humoral immune response against SARS-CoV in humans and animals and can be used as antigens for developing diagnostic tests. PMID:15528730

He, Yuxian; Zhou, Yusen; Wu, Hao; Kou, Zhihua; Liu, Shuwen; Jiang, Shibo

2004-01-01

199

A Comprehensive Molecular Interaction Map for Rheumatoid Arthritis  

Microsoft Academic Search

BackgroundComputational biology contributes to a variety of areas related to life sciences and, due to the growing impact of translational medicine - the scientific approach to medicine in tight relation with basic science -, it is becoming an important player in clinical-related areas. In this study, we use computation methods in order to improve our understanding of the complex interactions

Gang Wu; Lisha Zhu; Jennifer E. Dent; Christine Nardini; Frank Beier

2010-01-01

200

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

201

Mapping of impediments to contamination flow using multicomponent reflection seismology at the Savannah River Site  

SciTech Connect

A major obstacle to the remediation of contaminated aquifers at the Savannah River Site in Aiken, South Carolina is the presence of discontinuous sand and clay lenses that are difficult to map effectively using geologic and geophysical well logs. In order to map these discontinuous sand and clay lenses we acquire two perpendicular nine-component (9C) seismic lines, a 9C Vertical Seismic Profile, (VSP) and p-wave and s-wave sonic logs in a borehole south of the Old Burial Ground at the Savannah River Site within which were available natural gamma ray and interpreted geology logs. P-wave reflections are interpreted as originating from water table, the Tan Clay, the Green Clay, the top of the Ellenton Clay, and a calcareous sediment layer within the Barnwell/McBean aquifer. Along the east-west trending line, reflectors are generally continuous except for the occurrence of a discontinuity in the upper reflectors near the east end of the line. This discontinuity could be interpreted as a sediment slump feature possibly related to the dissolution of the calcareous sediment layer, or as the eastern terminus of a large scour feature. Along the north-south trending line, reflectors are spatially less continuous and are interpreted as being cut by several channel/scour features.

Dickenson, O.A.; Steensma, G.J.; Boyd, T.M. [Colorado School of Mines, Golden, CO (United States)

1996-11-01

202

Multiple-sited interaction of caldesmon with Ca(2+)-calmodulin.  

PubMed Central

The binding of Ca(2+)- and Ba(2+)-calmodulin to caldesmon and its functional consequence was investigated with three different calmodulin mutants. Two calmodulin mutants have pairs of cysteine residues substituted and oxidized to a disulphide bond in either the N- or C-terminal lobe (C41/75 and C85/112). The third mutant has phenylalanine-92 replaced by alanine (F92A). Binding measurements in the presence of Ca2+ by separation on native gels and by carbodiimide-induced cross-linking showed a lower affinity for caldesmon in all the mutants. When Ca2+ was replaced by Ba2+ the affinity of calmodulin for caldesmon was further reduced. The ability of Ca(2+)-calmodulin to release caldesmon's inhibition of the actin-tropomyosin-activated myosin ATPase was virtually abolished by mutation of phenylalanine-92 to alanine or by replacing Ba2+ for Ca2+ in native calmodulin. Both cysteine mutants retained their functional ability, but the increased concentration needed for 50% release of caldesmon inhibition reflected their decreased affinity. Ca2+ -calmodulin produced a broadening in the signals of the NMR spectrum of the 10 kDa Ca(2+)-calmodulin-binding C-terminal fragment of caldesmon arising from tryptophans -749 and -779 and caused an enhancement of maximum tryptophan fluorescence of 49% and a 16 nm blue shift of the maximum. Ca(2+)-calmodulin F92A produced a change in wavelength of 4 nm but no change in maximum, whereas Ca(2+)-calmodulin C41/75 binding produced a decrease in fluorescence with no shift of the maximum. We conclude that functional binding of Ca(2+)-calmodulin to caldesmon requires multiple interaction sites on both molecules. However, some structural modification in calmodulin does not abolish the caldesmon-related functionality. This suggests that various EF hand proteins can substitute for the calmodulin molecule. PMID:8687382

Huber, P A; El-Mezgueldi, M; Grabarek, Z; Slatter, D A; Levine, B A; Marston, S B

1996-01-01

203

High resolution dynamical mapping of social interactions with active RFID  

E-print Network

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

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

2008-01-01

204

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

USGS Publications Warehouse

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

Torresan, Michael E.; Gardner, James V.

2000-01-01

205

Mapping shallow underground features that influence site-specific agricultural production  

NASA Astrophysics Data System (ADS)

Modern agricultural production practices are rapidly evolving in the United States of America (USA). These new production practices present significant applications for nonintrusive subsurface imaging. One such imaging technology is GPR, and it is now being incorporated within site-specific agriculture in the detection of soil horizons, perched water (episaturation), fragipans, hydrological preferential flow paths, and soil compaction. These features traditionally have been mapped by soil scientists using intrusive measurements (e.g., soil augers, soil pits, coring tools). Rather than developing a tool for soil mapping, our studies are targeting the identification, dimensioning, and position of subsurface features that directly influence agricultural productivity. It is foreseen that this information will allow for an increase in agricultural efficiency through infield machinery automation, and it will also greatly enhance development of highly efficient crop production strategies. The field sensing methodologies that we have developed using existing geophysical technologies are highly dependent upon both the soil and site characteristics due to seasonal variations. The GPR applications presented herein were conducted primarily in a region of loess soil that extends east of the Mississippi River into western Tennessee. GPR studies were also conducted in central Tennessee on the Cumberland Plateau within a region of shallow, sandy loam soils. Additional studies were conducted on the karst area of central Kentucky. Although targeting site-specific agriculture, our results and procedures may benefit the traditional users of GPR technology. We suggest that large-scale agricultural applications of the technology would be enhanced by integrating global positioning (GPS) technology in future hardware and software products.

Freeland, Robert S.; Yoder, Ronald E.; Ammons, John T.

1998-10-01

206

Interaction Techniques for Exploring Historic Sites through Situated Media  

Microsoft Academic Search

We present a set of augmented reality and virtual reality interaction techniques that enable mobile users to visualize and interact virtually with representations of past events. These approaches use historic photographic imagery registered with real and virtual 3D objects to depict events in situ, and to provide interactive timelines. We demonstrate our techniques through examples developed for an important landmark,

Sinem Güven; Steven Feiner

2006-01-01

207

Allosteric sites can be identified based on the residue-residue interaction energy difference.  

PubMed

Allosteric drugs act at a distance to regulate protein functions. They have several advantages over conventional orthosteric drugs, including diverse regulation types and fewer side effects. However, the rational design of allosteric ligands remains a challenge, especially when it comes to the identification allosteric binding sites. As the binding of allosteric ligands may induce changes in the pattern of residue-residue interactions, we calculated the residue-residue interaction energies within the allosteric site based on the molecular mechanics generalized Born surface area energy decomposition scheme. Using a dataset of 17 allosteric proteins with structural data for both the apo and the ligand-bound state available, we used conformational ensembles generated by molecular dynamics simulations to compute the differences in the residue-residue interaction energies in known allosteric sites from both states. For all the known sites, distinct interaction energy differences (>25%) were observed. We then used CAVITY, a binding site detection program to identify novel putative allosteric sites in the same proteins. This yielded a total of 31 "druggable binding sites", of which 21 exhibited >25% difference in residue interaction energies, and were hence predicted as novel allosteric sites. Three of the predicted allosteric sites were supported by recent experimental studies. All the predicted sites may serve as novel allosteric sites for allosteric ligand design. Our study provides a computational method for identifying novel allosteric sites for allosteric drug design. © Proteins 2014;. © 2014 Wiley Periodicals, Inc. PMID:25185787

Ma, Xiaomin; Qi, Yifei; Lai, Luhua

2014-09-01

208

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

PubMed Central

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

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

2012-01-01

209

Genetic Mapping in the Major Histocompatibility Complex by Restriction Enzyme Site Polymorphisms: Most Mouse Class I Genes Map to the Tla Complex  

Microsoft Academic Search

From a genomic library constructed from sperm DNA of the inbred BALB\\/c mouse, we previously isolated 54 cosmid clones that contain 36 class I genes and can be divided by restriction map analyses into 13 gene clusters. We have isolated single- and low-copy DNA probes from each of these clusters to visualize restriction enzyme site polymorphisms in the DNAs from

Astar Winoto; Michael Steinmetz; Leroy Hood

1983-01-01

210

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

211

Prediction of Protein Interaction Sites From Sequence Profile and Residue Neighbor List  

E-print Network

Prediction of Protein Interaction Sites From Sequence Profile and Residue Neighbor List Huan Protein­protein interaction sites are predicted from a neural network with sequence profiles correctly predicted residues account for 65% of the 11,805 residues making up the 129 interfaces. The main

Weston, Ken

212

Mapping QTLs with epistatic effects and QTL×environment interactions by mixed linear model approaches  

Microsoft Academic Search

A new methodology based on mixed linear models was developed for mapping QTLs with digenic epistasis and QTL?environment (QE)\\u000a interactions. Reliable estimates of QTL main effects (additive and epistasis effects) can be obtained by the maximum-likelihood\\u000a estimation method, while QE interaction effects (additive?environment interaction and epistasis?environment interaction) can\\u000a be predicted by the-best-linear-unbiased-prediction (BLUP) method. Likelihood ratio and t statistics were

D. L. Wang; J. Zhu; Z. K. L. Li; A. H. Paterson

1999-01-01

213

MAPS  

Atmospheric Science Data Center

... MAPS Data and Information Measurement of Air Pollution from Satellites (MAPS) data were collected during Space Shuttle ... NASA Facts Correlative Data  - CDIAC - Spring & Fall 1994 - Field and Aircraft Campaigns SCAR-B Block:  ...

2014-07-03

214

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

USGS Publications Warehouse

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

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

1999-01-01

215

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

NASA Astrophysics Data System (ADS)

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

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

2010-12-01

216

Identifying viral integration sites using SeqMap 2.0  

PubMed Central

Summary: Retroviral integration has been implicated in several biomedical applications, including identification of cancer-associated genes and malignant transformation in gene therapy clinical trials. We introduce an efficient and scalable method for fast identification of viral vector integration sites from long read high-throughput sequencing. Individual sequence reads are masked to remove non-genomic sequence, aligned to the host genome and assembled into contiguous fragments used to pinpoint the position of integration. Availability and Implementation: The method is implemented in a publicly accessible web server platform, SeqMap 2.0, containing analysis tools and both private and shared lab workspaces that facilitate collaboration among researchers. Available at http://seqmap.compbio.iupui.edu/. Contact: troyhawk@iupui.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21245052

Hawkins, Troy B.; Dantzer, Jessica; Peters, Brandon; Dinauer, Mary; Mockaitis, Keithanne; Mooney, Sean; Cornetta, Kenneth

2011-01-01

217

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

218

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

SciTech Connect

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

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

1998-10-05

219

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

PubMed Central

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

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

2007-01-01

220

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

PubMed

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

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

2012-01-01

221

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

PubMed Central

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

2013-01-01

222

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

223

Interaction of Voltage-gated Sodium Channel Nav1.6 (SCN8A) with Microtubule-associated Protein Map1b*  

PubMed Central

The mechanism by which voltage-gated sodium channels are trafficked to the surface of neurons is not well understood. Our previous work implicated the cytoplasmic N terminus of the sodium channel Nav1.6 in this process. We report that the N terminus plus the first transmembrane segment (residues 1–153) is sufficient to direct a reporter to the cell surface. To identify proteins that interact with the 117-residue N-terminal domain, we carried out a yeast two-hybrid screen of a mouse brain cDNA library. Three clones containing overlapping portions of the light chain of microtubule-associated protein Map1b (Mtap1b) were recovered from the screen. Interaction between endogenous Nav1.6 channels and Map1b in mouse brain was confirmed by co-immunoprecipitation. Map1b did not interact with the N terminus of the related channel Nav1.1. Alanine-scanning mutagenesis of the Nav1.6 N terminus demonstrated that residues 77–80 (VAVP) contribute to interaction with Map1b. Co-expression of Nav1.6 with Map1b in neuronal cell line ND7/23 resulted in a 50% increase in current density, demonstrating a functional role for this interaction. Mutation of the Map1b binding site of Nav1.6 prevented generation of sodium current in transfected cells. The data indicate that Map1b facilitates trafficking of Nav1.6 to the neuronal cell surface. PMID:22474336

O'Brien, Janelle E.; Sharkey, Lisa M.; Vallianatos, Christina N.; Han, Chongyang; Blossom, Julie C.; Yu, Ting; Waxman, Stephen G.; Dib-Hajj, Sulayman D.; Meisler, Miriam H.

2012-01-01

224

An Interactive Classification of Web Documents by Self-Organizing Maps and Search Engines  

Microsoft Academic Search

In this paper, we propose an effective classification view mechanism for hypertext data such as web documents based on Kohonen's Self-Organizing Map (SOM) and search engines. Web documents collected by search engines are automatically classified by SOM and the obtained SOMs are incremental- ly modified according to the interaction between users and SOMs. At present, various search engines are designed

Kenji Hatano; Ryouichi Sano; Yiwei Duan; Katsumi Tanaka

1999-01-01

225

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

E-print Network

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

226

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.

227

Mapping Interactions Within the Evolving Science of Science and Innovation Policy Community  

E-print Network

Mapping Interactions Within the Evolving Science of Science and Innovation Policy Community Angela Abstract The Science of Science & Innovation Policy (SciSIP) program at the National Science Foundation (NSF) supports research designed to advance the scientific basis of science and innovation policy

Menczer, Filippo

228

Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment  

E-print Network

analysis of gene expres- sion (SAGE)12,13, but the template for STAGE consists of genomic loci enrichedMapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment gene expression programs. We have developed an unbiased genomic method called sequence tag analysis

Cai, Long

229

A visual bag of words method for interactive qualitative localization and mapping  

E-print Network

A visual bag of words method for interactive qualitative localization and mapping David FILLIAT any robot position. This system is inspired by visual categorization algorithms called bag of words inspired from bag of words methods used in object categories learning developed in the computer vision

Paris-Sud XI, Université de

230

Local dynamic interactions in the collicular motor map: a neural network model  

Microsoft Academic Search

Ahstrad In this paper we explore the possibility that some of the dynamic properties of the neuraI activity in the gazerelated motor map (located in the intermediate layers of the superior colliculus) might be mediated by Id interactions belween movement-related neurons and fixation neurons. More Specifically, the goal of this research is to demonstrate, from a computational standpoint. which classes

Lina L E Massonett; Tony Khoshabat

1995-01-01

231

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

E-print Network

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

Klippel, Alexander

232

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

233

VIMAP: an Interactive Program Providing Radio Spectral Index Maps of Active Galactic Nuclei  

E-print Network

We present a GUI-based interactive Python program, VIMAP, which generates radio spectral index maps of active galactic nuclei (AGN) from Very Long Baseline Interferometry (VLBI) maps obtained at different frequencies. VIMAP is a handy tool for the spectral analysis of synchrotron emission from AGN jets, specifically of spectral index distributions, turn-over frequencies, and core-shifts. In general, the required accurate image alignment is difficult to achieve because of a loss of absolute spatial coordinate information during VLBI data reduction (self-calibration) and/or intrinsic variations of source structure as function of frequency. These issues are overcome by VIMAP which in turn is based on the two-dimensional cross-correlation algorithm of Croke and Gabuzda (2008). In this paper, we briefly review the problem of aligning VLBI AGN maps, describe the workflow of VIMAP, and present an analysis of archival VLBI maps of the active nucleus 3C 120.

Kim, Jae-Young

2014-01-01

234

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

235

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

PubMed

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

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

1994-04-26

236

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

237

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

SciTech Connect

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

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

1998-11-01

238

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

PubMed Central

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

2013-01-01

239

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. PMID:23935524

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

2013-01-01

240

Functionality maps of the ATP binding site of DNA gyrase B: generation of a consensus model of ligand binding.  

PubMed

The Multiple Copy Simultaneous Search method (MCSS) was used to construct consensus functionality maps for functional group binding in the ATP binding site of DNA gyrase B. To account for the conformational flexibility of the protein active site, which involves small side chain fluctuations as well as large-scale loop motions, the calculations were done for three different conformations of the 24 kDa subdomain of DNA gyrase B. A postprocessing procedure that employs a continuum dielectric model to include solvent effects was used to calculate the binding free energy for every functional group. These results were ranked according to their affinity for DNA gyrase B and clustered using a new procedure based on van der Waals contacts that is better adapted for cases where multiple conformations are being considered. A total of 23 different functional groups were tested. The results gave consensus maps that indicate those functional group binding sites that are insensitive to the specific protein conformation. The maps also demonstrate that functional groups other than those found in the known ligands may bind competitively in the binding sites of known ligands. This suggests numerous scaffolds that can be used in the development of new ligands for the ATP and coumarinic binding sites in DNA gyrase B. Finally, the calculations show the existence of alternative binding sites near the known binding sites that could be targeted in the rational design for new inhibitors. PMID:15317451

Schechner, Martina; Sirockin, Finton; Stote, Roland H; Dejaegere, Annick P

2004-08-26

241

Eighty-eight historical and present-day maps of Saint-Domingue/Haiti, its sites, towns, and islands  

E-print Network

Occasional Paper N° 20 Bryant C. Freeman Eighty-Eight Historical and Present-Day Maps of Saint-Domingue/Haiti, its Sites, Towns, and Islands Institute of Haitian Studies University of Kansas Occasional Paper N° 20 Bryant C. Freeman Eighty...-Eight Historical and Present-Day Maps of Saint-Domingue/Haiti, its Sites, Towns, and Islands Institute of Haitian Studies University of Kansas 1999 University of Kansas Institute of Haitian Studies Occasional Papers Bryant C. Freeman, Ph.D. - Series Editor...

Freeman, Bryant C.

1999-01-01

242

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

SciTech Connect

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

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

1996-10-01

243

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

244

Assessing intermolecular RNA:RNA interactions within a ribonucleoprotein complex using heavy metal cleavage mapping.  

PubMed

Heavy metal cleavage mapping analysis of both assembling and fully mature ribonucleoprotein (RNP) complexes are informative techniques for assessing the intermolecular base pairing between small non-coding RNAs and their interacting target RNAs. Lead cleavage of the RNA in partially or fully assembled RNPs in the absence or presence of the interacting RNA can determine both the accessibility of the base pairing sequence within the RNP itself as well as its interaction with the target RNA. In this chapter, we detail how this technique was used to map the intermolecular RNA:RNA base pairing of a box C/D RNA with its target RNA within the assembling archaeal RNP complex. PMID:25352141

Gagnon, Keith T; Maxwell, E Stuart

2015-01-01

245

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. PMID:22848404

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

246

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. PMID:21876146

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

2011-01-01

247

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

248

Toward an integrated linkage map of common bean. III. Mapping genetic factors controlling host-bacteria interactions.  

PubMed

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 F2 of this cross. Seventy F2-derived F3 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. PMID:8514141

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

1993-05-01

249

Mapping Single Cell-Substrate Interactions by Surface Plasmon Resonance Microscopy  

PubMed Central

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

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

2013-01-01

250

Mapping of Protein-Protein Interactions of E. coli RNA Polymerase with Microfluidic Mechanical Trapping  

PubMed Central

The biophysical details of how transcription factors and other proteins interact with RNA polymerase are of great interest as they represent the nexus of how structure and function interact to regulate gene expression in the cell. We used an in vitro microfluidic approach to map interactions between a set of ninety proteins, over a third of which are transcription factors, and each of the four subunits of E. coli RNA polymerase, and we compared our results to those of previous large-scale studies. We detected interactions between RNA polymerase and transcription factors that earlier high-throughput screens missed; our results suggest that such interactions can occur without DNA mediation more commonly than previously appreciated. PMID:24643045

Bates, Steven R.; Quake, Stephen R.

2014-01-01

251

Using Mutagenesis and Structural Biology to Map the Binding Site for the Plasmodium falciparum Merozoite Protein PfRh4 on the Human Immune Adherence Receptor*  

PubMed Central

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

252

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

PubMed Central

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

2012-01-01

253

Interaction-site prediction for protein complexes: a critical assessment  

Microsoft Academic Search

Motivation: Proteins function through interactions with other pro- teins and biomolecules. Protein-protein interfaces hold key informa- tion toward molecular understanding of protein function. In the past few years there have been intensive efforts in developing methods for predicting protein interface residues. A review that presents the current status of interface prediction and an overview of its applica- tions and project

Huan-xiang Zhou; Sanbo Qin

2007-01-01

254

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

PubMed Central

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

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

2014-01-01

255

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

256

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

E-print Network

Help Site Map languages China World Opinion Business Sci-Edu Culture/Life Sports Photos Services Ethnic minorities Selected Works of Deng Xiaoping >>Home Sci-Edu UPDATED: 20:06, July 01, 2005 China, near Aix-en-Provence, France, overriding Japan's competition for hosting the innovative reactor

257

Integration of landslide hazard maps into probabilistic risk assessment in context of global changes: an alpine test site  

E-print Network

1 Integration of landslide hazard maps into probabilistic risk assessment in context of global climate on landslides activity and impacts of social changes on exposure to provide a complete evaluation site. Mechanical approaches represent a solution to quantify landslide susceptibility and to model

Paris-Sud XI, Université de

258

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

E-print Network

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

Adams, Christiaan Scott, 1973-

2004-01-01

259

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

PubMed

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

Shimakawa, Yuichi; Mizumaki, Masaichiro

2014-11-26

260

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

PubMed Central

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

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

2012-01-01

261

Fanconi anemia protein complex: mapping protein interactions in the yeast 2- and 3-hybrid systems.  

PubMed

Fanconi anemia (FA) is an autosomal recessive syndrome characterized by progressive bone marrow failure and cancer predisposition. Eight FA complementation groups have been identified. The FANCA, FANCC, FANCE, FANCF, and FANCG proteins form a nuclear complex required for the monoubiquination of the FANCD2 protein. To investigate the architecture of the FA protein complex, the yeast 2-hybrid system was used to map contact points of the FANCA/FANCG, FANCC/FANCE, and FANCF/FANCG interactions. FANCG was shown to interact with both the amino-terminus of FANCA and the carboxyl-terminal region of FANCF. A FANCG mutant truncated at the carboxyl-terminus retained the ability to interact with FANCA. The interaction between FANCG and FANCF was ablated by a Leu71Pro mutant of FANCG. A central region of FANCE was sufficient for FANCC binding. A Leu554Pro mutant of FANCC failed to interact with FANCE. To further examine complex assembly, the yeast 3-hybrid system was used to investigate the ability of FANCG to act as a molecular bridge in mediating interaction between other FA proteins. FANCG was able to mediate interaction between FANCA and FANCF, as well as between monomers of FANCA. Direct interaction between FANCE and FANCD2 was also demonstrated in the yeast 2-hybrid system. This interaction involving an amino-terminal region of FANCD2 may provide a link between the FA protein complex and its downstream targets. PMID:12649160

Gordon, Susan M; Buchwald, Manuel

2003-07-01

262

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. PMID:24860644

Yachdav, Guy

2014-01-01

263

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

PubMed

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

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

2010-01-01

264

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

PubMed Central

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

2010-01-01

265

Polypharmacology rescored: Protein-ligand interaction profiles for remote binding site similarity assessment.  

PubMed

Detection of remote binding site similarity in proteins plays an important role for drug repositioning and off-target effect prediction. Various non-covalent interactions such as hydrogen bonds and van-der-Waals forces drive ligands' molecular recognition by binding sites in proteins. The increasing amount of available structures of protein-small molecule complexes enabled the development of comparative approaches. Several methods have been developed to characterize and compare protein-ligand interaction patterns. Usually implemented as fingerprints, these are mainly used for post processing docking scores and (off-)target prediction. In the latter application, interaction profiles detect similarities in the bound interactions of different ligands and thus identify essential interactions between a protein and its small molecule ligands. Interaction pattern similarity correlates with binding site similarity and is thus contributing to a higher precision in binding site similarity assessment of proteins with distinct global structure. This renders it valuable for existing drug repositioning approaches in structural bioinformatics. Current methods to characterize and compare structure-based interaction patterns - both for protein-small-molecule and protein-protein interactions - as well as their potential in target prediction will be reviewed in this article. The question of how the set of interaction types, flexibility or water-mediated interactions, influence the comparison of interaction patterns will be discussed. Due to the wealth of protein-ligand structures available today, predicted targets can be ranked by comparing their ligand interaction pattern to patterns of the known target. Such knowledge-based methods offer high precision in comparison to methods comparing whole binding sites based on shape and amino acid physicochemical similarity. PMID:24923864

Salentin, Sebastian; Haupt, V Joachim; Daminelli, Simone; Schroeder, Michael

2014-01-01

266

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

2006-01-01

267

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

USGS Publications Warehouse

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

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

2012-01-01

268

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

NASA Astrophysics Data System (ADS)

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.

Li, Rongxing; Archinal, Brent A.; Arvidson, Raymond E.; Bell, Jim; Christensen, Philip; Crumpler, Larry; Des Marais, David J.; Di, Kaichang; Duxbury, Tom; Golombek, Matt; Grant, John; Greeley, Ronald; Guinn, Joe; Johnson, Andrew; Kirk, Randolph L.; Maimone, Mark; Matthies, Larry H.; Malin, Mike; Parker, Tim; Sims, Mike; Thompson, Shane; Squyres, Steven W.; Soderblom, Larry A.

2006-01-01

269

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

PubMed Central

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.

2010-01-01

270

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

271

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

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

2014-08-28

272

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. PMID:22673903

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

2012-01-01

273

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

ERIC Educational Resources Information Center

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

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

2009-01-01

274

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

USGS Publications Warehouse

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

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

1998-01-01

275

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

276

Mapping Plant Interactomes Using Literature Curated and Predicted Protein–Protein Interaction Data Sets[W  

PubMed Central

Most cellular processes are enabled by cohorts of interacting proteins that form dynamic networks within the plant proteome. The study of these networks can provide insight into protein function and provide new avenues for research. This article informs the plant science community of the currently available sources of protein interaction data and discusses how they can be useful to researchers. Using our recently curated IntAct Arabidopsis thaliana protein–protein interaction data set as an example, we discuss potentials and limitations of the plant interactomes generated to date. In addition, we present our efforts to add value to the interaction data by using them to seed a proteome-wide map of predicted protein subcellular locations. PMID:20371643

Lee, KiYoung; Thorneycroft, David; Achuthan, Premanand; Hermjakob, Henning; Ideker, Trey

2010-01-01

277

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

278

PRODISTIN Web Site: a tool for the functional classification of proteins from interaction networks  

Microsoft Academic Search

Summary: The PRODISTIN Web Site is a web service allowing users to functionally classify genes\\/proteins from any type of interaction network. The resulting computation provides a classification tree in which (1) genes\\/proteins are clustered according to the identity of their interaction partners and (2) functional classes are delineated in the tree using the Biological Process Gene Ontology annotations. Availabitily: The

Anaïs Baudot; David Martin; Pierre Mouren; François Chevenet; Alain Guénoche; Bernard Jacq; Christine Brun

2006-01-01

279

Functional genomics platform for pooled screening and mammalian genetic interaction maps  

PubMed Central

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

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

2014-01-01

280

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

281

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. PMID:9194188

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

1997-01-01

282

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.

283

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

284

California Geological Survey: Geologic Maps  

NSDL National Science Digital Library

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

285

Mapping the genetic basis of symbiotic variation in legume-rhizobium interactions in Medicago truncatula.  

PubMed

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. PMID:23173081

Gorton, Amanda J; Heath, Katy D; Pilet-Nayel, Marie-Laure; Baranger, Alain; Stinchcombe, John R

2012-11-01

286

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. PMID:23173081

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

2012-01-01

287

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

Microsoft Academic Search

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

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

2008-01-01

288

Kentucky Mine Mapping Information System  

NSDL National Science Digital Library

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

289

Design and User Satisfaction of Interactive Maps for Visually Impaired People, Anke Brock, Philippe Truillet, Bernard Oriola, Delphine Picard and Christophe  

E-print Network

Design and User Satisfaction of Interactive Maps for Visually Impaired People, Anke Brock, Philippe://www.springerlink.com/content/r7855rjg2t5m7501/ #12;Design and User Satisfaction of Interactive Maps for Visually Impaired People Anke. Multimodal interactive maps are a solution for presenting spatial in- formation to visually impaired people

Boyer, Edmond

290

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

USGS Publications Warehouse

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

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

2007-01-01

291

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

PubMed Central

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

Unneberg, Per; Claverie, Jean-Michel

2007-01-01

292

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

PubMed Central

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

2011-01-01

293

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

PubMed Central

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

Peters, Brandon; Dirscherl, Sara; Dantzer, Jessica; Nowacki, Jonathan; Cross, Scott; Li, Xiaoman; Cornetta, Kenneth; Dinauer, Mary C.; Mooney, Sean D.

2009-01-01

294

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

PubMed

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

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

2008-09-01

295

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

296

Electron microscopic structure of agrin and mapping of its binding site in laminin-1.  

PubMed Central

Agrin is a large, multidomain heparan sulfate proteoglycan that is associated with basement membranes of several tissues. Particular splice variants of agrin are essential for the formation of synaptic structures at the neuromuscular junction. The binding of agrin to laminin appears to be required for its localization to synaptic basal lamina and other basement membranes. Here, electron microscopy was used to determine the structure of agrin and to localize its binding site in laminin-1. Agrin appears as an approximately 95 nm long particle that consists of a globular, N-terminal laminin-binding domain, a central rod predominantly formed by the follistatin-like domains and three globular, C-terminal laminin G-like domains. In a few cases, heparan sulfate glycosaminoglycan chains were seen emerging from the central portion of the core protein. Moreover, we show that agrin binds to the central region of the three-stranded, coiled-coil oligomerization domain in the long arm of laminin-1, which mediates subunit assembly of the native laminin molecule. In summary, our data show for the first time a protein-protein interaction of the extracellular matrix that involves a coiled-coil domain, and they assign a novel role to this domain of laminin-1. Based on this, we propose that agrin associates with basal lamina in a polarized way. PMID:9430625

Denzer, A J; Schulthess, T; Fauser, C; Schumacher, B; Kammerer, R A; Engel, J; Ruegg, M A

1998-01-01

297

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

298

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

299

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

PubMed

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

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

2014-01-01

300

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

PubMed Central

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

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

2014-01-01

301

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

PubMed Central

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

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

2014-01-01

302

Phase resetting reduces theta-gamma rhythmic interaction to a one-dimensional map.  

PubMed

Gamma and theta oscillations of the hippocampus are known to interact, but the mechanisms underlying such interaction are not well understood. We focus on a previously published computational model of hippocampal activity that shows the gamma rhythms nesting in the theta rhythms, and investigate the dynamical mechanisms underlying that interaction. There are three types of neurons in the model: pyramidal cells, fast-spiking interneurons, and "oriens lacunosum-moelculare" (O-LM cells); the latter is an inhibitory cell whose inhibition has a longer time scale, and which has currents associated with intrinsic theta-rhythm behavior. We identify two main modes of interaction among the slow and the fast rhythms in the model, modulated by the strength of the excitatory synapse on the O-LM cells. Using resets of phases after each pyramidal cell and O-LM spike, we extend the use of the phase transition map (PTM) to encode the stability type of spiking patterns in networks where different frequencies interact. The tailored application of the PTM to the model network measures how the interaction between the shape of the phase response curves and the length of the gamma period determines the number of gamma spikes in theta cycles, and provides an explicit formula for the length of theta intervals in nesting regimes. Using the PTM, we also explain the covariance of the gamma and theta rhythms as drive is changed over some intervals. PMID:22526842

Malerba, Paola; Kopell, Nancy

2013-06-01

303

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

304

Interactions of the site-specific recombinases XerC and XerD with the recombination site dif.  

PubMed Central

The Xer site-specific recombination system of Escherichia coli is involved in the stable inheritance of circular replicons. Multimeric replicons, produced by homologous recombination, are converted to monomers by the action of two related recombinases XerC and XerD. Site-specific recombination at a locus, dif, within the chromosomal replication terminus region is thought to convert dimeric chromosomes to monomers, which can then be segregated prior to cell division. The recombinases XerC and XerD bind cooperatively to dif, where they catalyse recombination. Chemical modification of specific bases and the phosphate-sugar backbone within dif was used to investigate the requirements for binding of the recombinases. Site-directed mutagenesis was then used to alter bases implicated in recombinase binding. Characterization of these mutants by in vitro recombinase binding and in vivo recombination, has demonstrated that the cooperative interactions between XerC and XerD can partially overcome DNA alterations that should interfere with specific recombinase-dif interactions. Images PMID:7838714

Blakely, G W; Sherratt, D J

1994-01-01

305

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

306

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

307

Highly ionized gas on galaxy scales: mapping the interacting Seyfert galaxy LEDA 135736  

E-print Network

We have used the VIMOS IFU to map the properties of the Seyfert 1.9 galaxy LEDA 135736. These maps reveal a number of interesting features including: an Extended Narrow Line Region detectable out to 9 kpc, an area of intense star formation located at a projected distance of 12 kpc from the centre, an elliptical companion galaxy, and kinematic features, aligned along the long-axis of the ENLR, that are consistent with radio jet-driven mass outflow. We propose that the ENLR results from extra-planar gas ionized by the AGN, and that the AGN in turn might be triggered by interaction with the companion galaxy, which can also explain the burst of star formation and morphological features. Only about two percent of the ENLR's kinetic energy is in the mass outflow. We infer from this that the bulk of mechanical energy imparted by the jet is used to heat this gas.

J. Gerssen; D. J. Wilman; L. Christensen; R. G. Bower; V. Wild

2008-11-10

308

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

NASA Astrophysics Data System (ADS)

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

Shih, Bi-Ching; Zhang, Peihong

2011-03-01

309

The Interaction of Integrin ?IIb?3 with Fibrin Occurs through Multiple Binding Sites in the ?IIb ?-Propeller Domain*  

PubMed Central

The currently available antithrombotic agents target the interaction of platelet integrin ?IIb?3 (GPIIb-IIIa) with fibrinogen during platelet aggregation. Platelets also bind fibrin formed early during thrombus growth. It was proposed that inhibition of platelet-fibrin interactions may be a necessary and important property of ?IIb?3 antagonists; however, the mechanisms by which ?IIb?3 binds fibrin are uncertain. We have previously identified the ?370–381 sequence (P3) in the ?C domain of fibrinogen as the fibrin-specific binding site for ?IIb?3 involved in platelet adhesion and platelet-mediated fibrin clot retraction. In the present study, we have demonstrated that P3 can bind to several discontinuous segments within the ?IIb ?-propeller domain of ?IIb?3 enriched with negatively charged and aromatic residues. By screening peptide libraries spanning the sequence of the ?IIb ?-propeller, several sequences were identified as candidate contact sites for P3. Synthetic peptides duplicating these segments inhibited platelet adhesion and clot retraction but not platelet aggregation, supporting the role of these regions in fibrin recognition. Mutant ?IIb?3 receptors in which residues identified as critical for P3 binding were substituted for homologous residues in the I-less integrin ?M?2 exhibited reduced cell adhesion and clot retraction. These residues are different from those that are involved in the coordination of the fibrinogen ?404–411 sequence and from auxiliary sites implicated in binding of soluble fibrinogen. These results map the binding of fibrin to multiple sites in the ?IIb ?-propeller and further indicate that recognition specificity of ?IIb?3 for fibrin differs from that for soluble fibrinogen. PMID:24338009

Podolnikova, Nataly P.; Yakovlev, Sergiy; Yakubenko, Valentin P.; Wang, Xu; Gorkun, Oleg V.; Ugarova, Tatiana P.

2014-01-01

310

Elucidation of inositol hexaphosphate and heparin interaction sites and conformational changes in arrestin-1 by solution nuclear magnetic resonance.  

PubMed

Arrestins specifically bind activated and phosphorylated G protein-coupled receptors and orchestrate both receptor trafficking and channel signaling through G protein-independent pathways via direct interactions with numerous nonreceptor partners. Here we report the first successful use of solution NMR in mapping 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 an identification of residues involved in the binding with these ligands that was more complete than what has previously been feasible. IP6 and heparin appear to bind to the same site on arrestin-1, centered on a positively charged region in the N-domain. We present the first direct evidence that both IP6 and heparin induced a complete release of the arrestin C-tail. These observations provide novel insight into the nature of the transition of arrestin from the basal to active state and demonstrate the potential of NMR-based methods in the study of protein-protein interactions involving members of the arrestin family. PMID:21050017

Zhuang, Tiandi; Vishnivetskiy, Sergey A; Gurevich, Vsevolod V; Sanders, Charles R

2010-12-14

311

Mapping of the SecA·SecY and SecA·SecG Interfaces by Site-directed in Vivo Photocross-linking  

PubMed Central

The two major components of the Eubacteria Sec-dependent protein translocation system are the heterotrimeric channel-forming component SecYEG and its binding partner, the SecA ATPase nanomotor. Once bound to SecYEG, the preprotein substrate, and ATP, SecA undergoes ATP-hydrolytic cycles that drive the stepwise translocation of proteins. Although a previous site-directed in vivo photocross-linking study (Mori, H., and Ito, K. (2006) Proc. Natl. Acad. Sci. U.S.A. 103, 16159–16164) elucidated residues of SecY needed for interaction with SecA, no reciprocal study for SecA protein has been reported to date. In the present study we mapped residues of SecA that interact with SecY or SecG utilizing this approach. Our results show that distinct domains of SecA on two halves of the molecule interact with two corresponding SecY partners as well as with the central cytoplasmic domain of SecG. Our data support the in vivo relevance of the Thermotoga maritima SecA·SecYEG crystal structure that visualized SecYEG interaction for only one-half of SecA as well as previous studies indicating that SecA normally binds two molecules of SecYEG. PMID:21317284

Das, Sanchaita; Oliver, Donald B.

2011-01-01

312

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

PubMed Central

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

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

2014-01-01

313

Mapping of Interaction Domains Mediating Binding between BACE1 and RTN\\/Nogo Proteins  

Microsoft Academic Search

BACE1 is a membrane-bound aspartyl protease that specifically cleaves amyloid precursor protein (APP) at the ?-secretase site. Membrane bound reticulon (RTN) family proteins interact with BACE1 and negatively modulate BACE1 activity through preventing access of BACE1 to its cellular APP substrate. Here, we focused our study on RTN3 and further show that a C-terminal QID triplet conserved among mammalian RTN

Wanxia He; Xiangyou Hu; Qi Shi; Xiangdong Zhou; Yifeng Lu; Christopher Fisher; Riqiang Yan

2006-01-01

314

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

Microsoft Academic Search

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

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

2005-01-01

315

Genomic mapping of Suppressor of Hairy-wing binding sites in Drosophila  

PubMed Central

Background Insulator elements are proposed to play a key role in the organization of the regulatory architecture of the genome. In Drosophila, one of the best studied is the gypsy retrotransposon insulator, which is bound by the Suppressor of Hairy-wing (Su [Hw]) transcriptional regulator. Immunolocalization studies suggest that there are several hundred Su(Hw) sites in the genome, but few of these endogenous Su(Hw) binding sites have been identified. Results We used chromatin immunopurification with genomic microarray analysis to identify in vivo Su(Hw) binding sites across the 3 megabase Adh region. We find 60 sites, and these enabled the construction of a robust new Su(Hw) binding site consensus. In contrast to the gypsy insulator, which contains tightly clustered Su(Hw) binding sites, endogenous sites generally occur as isolated sites. These endogenous sites have three key features. In contrast to most analyses of DNA-binding protein specificity, we find that strong matches to the binding consensus are good predictors of binding site occupancy. Examination of occupancy in different tissues and developmental stages reveals that most Su(Hw) sites, if not all, are constitutively occupied, and these isolated Su(Hw) sites are generally highly conserved. Analysis of transcript levels in su(Hw) mutants indicate widespread and general changes in gene expression. Importantly, the vast majority of genes with altered expression are not associated with clustering of Su(Hw) binding sites, emphasizing the functional relevance of isolated sites. Conclusion Taken together, our in vivo binding and gene expression data support a role for the Su(Hw) protein in maintaining a constant genomic architecture. PMID:17705839

Adryan, Boris; Woerfel, Gertrud; Birch-Machin, Ian; Gao, Shan; Quick, Marie; Meadows, Lisa; Russell, Steven; White, Robert

2007-01-01

316

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

SciTech Connect

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

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

1986-07-01

317

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

SciTech Connect

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

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

2011-11-21

318

Transition to chaos by interaction of resonances in dissipative systems. I. Circle maps  

SciTech Connect

Dissipative dynamical systems with two competing frequencies exhibit transitions to chaos. We have investigated the transition through a study of discrete maps of the circle onto itself. The transition is caused by interaction and overlap of mode-locked resonances and occurs at a critical line where the map loses invertibility. At this line the mode-locked intervals trace up a complete devil's staircase whose complementary set is a Cantor set with fractal dimension Dapprox.0.87. Numerical results indicate that the dimension is universal for maps with cubic inflection points. Below criticality the staircase is incomplete, leaving room for quasiperiodic behavior. The Lebesgue measure of the quasiperiodic orbits seems to be given by an exponent ..beta..approx.0.35 which can be related to D through the scaling relation D = 1-..beta../..nu... The exponent ..nu.. characterizes the cutoff of narrow plateaus near the transition. A variety of other exponents describing the transition to chaos is defined and estimated numerically.

Jensen, M.H.; Bak, P.; Bohr, T.

1984-10-01

319

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

PubMed

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

Boulos, Maged N Kamel; Burden, David

2007-01-01

320

Topographic Mapping Of The Ocular Fundus By Laser Contour Angiography : The Man-Machine Interaction  

NASA Astrophysics Data System (ADS)

Laser contour angiography is a new technique which was developed by the author for topographically mapping the retina and optic nerve head of the eye. A striped pattern of laser light is projected onto the ocular fundus through one side of the patient's dilated pupil. Photographs, taken through the opposite side of the pupil, reveal the topography as parallactic displacements of the stripes. A topographic map is constructed from tracings of the stripes. The method was shown to produce highly reproducible maps. In order to further improve the reproducibility of the topographic measurements, the effects of the man-machine interaction during the stripe tracing process on measurement error were investigated. The tracing strategy of the operator is to estimate the position along the edge of a stripe at which the perceived light intensity is halfway between the local maximum and minimum. The relationship of errors in the estimates of position to those in perceived intensity was established using a theoretical model. The predictive ability of the model was tested using repeated measurements on the laser contour angiogram of a human eye. The model predicted a position error (standard deviation) of 4.3 micrometers. This agreed remarkably well with the experimental result of 4.5 micrometers. The results indicated that film grain noise and defocussing of the projected pattern are the primary contributors to measurement error. We now use a finer grain film, and have further reduced the position error to 3.4 micrometers.

Shapiro, Jerrold M.

1980-07-01

321

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

PubMed

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

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

2012-10-01

322

Interaction of Antiparallel Microtubules in the Phragmoplast Is Mediated by the Microtubule-Associated Protein MAP65-3 in Arabidopsis[W  

PubMed Central

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

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

2011-01-01

323

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...

324

Equilibrium self-assembly of colloids with distinct interaction sites: Thermodynamics, percolation, and cluster distribution functions  

E-print Network

of self-assembly, which can be quantified by the maxima of the specific heat at constant volumeEquilibrium self-assembly of colloids with distinct interaction sites: Thermodynamics, percolation for functional materials and devices. A promising approach is self-assembly, which is the spontaneous

Sciortino, Francesco

325

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

E-print Network

Where Do Web Sites Come From? Capturing and Interacting with Design History Scott R. Klemmer1@daimi.au.dk ABSTRACT To form a deep understanding of the present; we need to Ã?nd and engage history. We present an informal history capture and retrieval mechanism for collaborative, early- stage information design

Klemmer, Scott

326

Prediction of protein-protein interaction sites using an ensemble method  

Microsoft Academic Search

BACKGROUND: Prediction of protein-protein interaction sites is one of the most challenging and intriguing problems in the field of computational biology. Although much progress has been achieved by using various machine learning methods and a variety of available features, the problem is still far from being solved. RESULTS: In this paper, an ensemble method is proposed, which combines bootstrap resampling

Lei Deng; Jihong Guan; Qiwen Dong; Shuigeng Zhou

2009-01-01

327

Deformable spin-2 XX chain with three-site interactions at zero and finite temperatures  

E-print Network

and the specific heat illustrating the changes in these quantities due to lattice instabilities. DOI: 10.1103/Phys energy of the spin chain with exchange couplings varying coherently with a possible static lattice present phase diagrams illustrating the effect of the three-site interaction on the spin-Peierls lattice

Kierfeld, Jan

328

Understanding and Designing for Interactional Privacy Needs within Social Networking Sites  

ERIC Educational Resources Information Center

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

Wisniewski, Pamela J.

2012-01-01

329

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

E-print Network

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

Brutlag, Doug

330

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

NASA Technical Reports Server (NTRS)

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

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

2003-01-01

331

Prediction of protein-protein interaction sites in heterocomplexes with neural networks  

Microsoft Academic Search

In this paper we address the problem of extracting features relevant for predicting protein-protein interaction sites from the three-dimensional structures of protein complexes. Our approach is based on information about evolutionary con- servation and surface disposition. We implement a neural network based system, which uses a cross validation proce- dure and allows the correct detection of 73% of the residues

Piero Fariselli; Florencio Pazos; Alfonso Valencia; Rita Casadio

2002-01-01

332

Combining solvent thermodynamic profiles with functionality maps of the Hsp90 binding site to predict the displacement of water molecules.  

PubMed

Intermolecular interactions in the aqueous phase must compete with the interactions between the two binding partners and their solvating water molecules. In biological systems, water molecules in protein binding sites cluster at well-defined hydration sites and can form strong hydrogen-bonding interactions with backbone and side-chain atoms. Displacement of such water molecules is only favorable when the ligand can form strong compensating hydrogen bonds. Conversely, water molecules in hydrophobic regions of protein binding sites make only weak interactions, and the requirements for favorable displacement are less stringent. The propensity of water molecules for displacement can be identified using inhomogeneous fluid solvation theory (IFST), a statistical mechanical method that decomposes the solvation free energy of a solute into the contributions from different spatial regions and identifies potential binding hotspots. In this study, we employed IFST to study the displacement of water molecules from the ATP binding site of Hsp90, using a test set of 103 ligands. The predicted contribution of a hydration site to the hydration free energy was found to correlate well with the observed displacement. Additionally, we investigated if this correlation could be improved by using the energetic scores of favorable probe groups binding at the location of hydration sites, derived from a multiple copy simultaneous search (MCSS) method. The probe binding scores were not highly predictive of the observed displacement and did not improve the predictivity when used in combination with IFST-based hydration free energies. The results show that IFST alone can be used to reliably predict the observed displacement of water molecules in Hsp90. However, MCSS can augment IFST calculations by suggesting which functional groups should be used to replace highly displaceable water molecules. Such an approach could be very useful in improving the hit-to-lead process for new drug targets. PMID:24070451

Haider, Kamran; Huggins, David J

2013-10-28

333

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

PubMed Central

Intermolecular interactions in the aqueous phase must compete with the interactions between the two binding partners and their solvating water molecules. In biological systems, water molecules in protein binding sites cluster at well-defined hydration sites and can form strong hydrogen-bonding interactions with backbone and side-chain atoms. Displacement of such water molecules is only favorable when the ligand can form strong compensating hydrogen bonds. Conversely, water molecules in hydrophobic regions of protein binding sites make only weak interactions, and the requirements for favorable displacement are less stringent. The propensity of water molecules for displacement can be identified using inhomogeneous fluid solvation theory (IFST), a statistical mechanical method that decomposes the solvation free energy of a solute into the contributions from different spatial regions and identifies potential binding hotspots. In this study, we employed IFST to study the displacement of water molecules from the ATP binding site of Hsp90, using a test set of 103 ligands. The predicted contribution of a hydration site to the hydration free energy was found to correlate well with the observed displacement. Additionally, we investigated if this correlation could be improved by using the energetic scores of favorable probe groups binding at the location of hydration sites, derived from a multiple copy simultaneous search (MCSS) method. The probe binding scores were not highly predictive of the observed displacement and did not improve the predictivity when used in combination with IFST-based hydration free energies. The results show that IFST alone can be used to reliably predict the observed displacement of water molecules in Hsp90. However, MCSS can augment IFST calculations by suggesting which functional groups should be used to replace highly displaceable water molecules. Such an approach could be very useful in improving the hit-to-lead process for new drug targets. PMID:24070451

2013-01-01

334

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

335

Profitability Maps as an Input for Site-Specific Management Decision Making  

Technology Transfer Automated Retrieval System (TEKTRAN)

For over a decade, farmers have been collecting site-specific yield data. Many have formed doubts about this investment because of their inability to directly apply this information as feedback for improving management. The objective of this case-study analysis was to investigate how site-specific d...

336

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

USGS Publications Warehouse

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

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

2013-01-01

337

Genome-wide mapping and characterization of hypomethylated sites in human tissues and breast cancer cell lines  

PubMed Central

We have developed a method for mapping unmethylated sites in the human genome based on the resistance of TspRI-digested ends to ExoIII nuclease degradation. Digestion with TspRI and methylation-sensitive restriction endonuclease HpaII, followed by ExoIII and single-strand DNA nuclease allowed removal of DNA fragments containing unmethylated HpaII sites. We then used array comparative genomic hybridization (CGH) to map the sequences depleted by these procedures in human genomes derived from five human tissues, a primary breast tumor, and two breast tumor cell lines. Analysis of methylation patterns of the normal tissue genomes indicates that the hypomethylated sites are enriched in the 5? end of widely expressed genes, including promoter, first exon, and first intron. In contrast, genomes of the MCF-7 and MDA-MB-231 cell lines show extensive hypomethylation in the intragenic and intergenic regions whereas the primary tumor exhibits a pattern between those of the normal tissue and the cell lines. A striking characteristic of tumor cell lines is the presence of megabase-sized hypomethylated zones. These hypomethylated zones are associated with large genes, fragile sites, evolutionary breakpoints, chromosomal rearrangement breakpoints, tumor suppressor genes, and with regions containing tissue-specific gene clusters or with gene-poor regions containing novel tissue-specific genes. Correlation with microarray analysis shows that genes with a hypomethylated sequence 2 kb up- or downstream of the transcription start site are highly expressed, whereas genes with extensive intragenic and 3? untranslated region (UTR) hypomethylation are silenced. The method described herein can be used for large-scale screening of changes in the methylation pattern in the genome of interest. PMID:18256232

Shann, Yih-Jyh; Cheng, Ching; Chiao, Chun-Hui; Chen, Dow-Tien; Li, Pei-Hsin; Hsu, Ming-Ta

2008-01-01

338

Genome-wide mapping and characterization of hypomethylated sites in human tissues and breast cancer cell lines.  

PubMed

We have developed a method for mapping unmethylated sites in the human genome based on the resistance of TspRI-digested ends to ExoIII nuclease degradation. Digestion with TspRI and methylation-sensitive restriction endonuclease HpaII, followed by ExoIII and single-strand DNA nuclease allowed removal of DNA fragments containing unmethylated HpaII sites. We then used array comparative genomic hybridization (CGH) to map the sequences depleted by these procedures in human genomes derived from five human tissues, a primary breast tumor, and two breast tumor cell lines. Analysis of methylation patterns of the normal tissue genomes indicates that the hypomethylated sites are enriched in the 5' end of widely expressed genes, including promoter, first exon, and first intron. In contrast, genomes of the MCF-7 and MDA-MB-231 cell lines show extensive hypomethylation in the intragenic and intergenic regions whereas the primary tumor exhibits a pattern between those of the normal tissue and the cell lines. A striking characteristic of tumor cell lines is the presence of megabase-sized hypomethylated zones. These hypomethylated zones are associated with large genes, fragile sites, evolutionary breakpoints, chromosomal rearrangement breakpoints, tumor suppressor genes, and with regions containing tissue-specific gene clusters or with gene-poor regions containing novel tissue-specific genes. Correlation with microarray analysis shows that genes with a hypomethylated sequence 2 kb up- or downstream of the transcription start site are highly expressed, whereas genes with extensive intragenic and 3' untranslated region (UTR) hypomethylation are silenced. The method described herein can be used for large-scale screening of changes in the methylation pattern in the genome of interest. PMID:18256232

Shann, Yih-Jyh; Cheng, Ching; Chiao, Chun-Hui; Chen, Dow-Tien; Li, Pei-Hsin; Hsu, Ming-Ta

2008-05-01

339

A new approach for facility siting using mapping risks on a plant grid area and optimization  

Microsoft Academic Search

The present work is focused on developing a methodology to find the optimal placement of a hazardous process unit and other facilities using optimization theory while considering a risk map in the plant area. Incidents can have possible consequences resulting from flammable gas releases, which can be evaluated by using consequence modeling programs. The probability of each incident can be

Seungho Jung; Dedy Ng; Carl D. Laird; M. Sam Mannan

2010-01-01

340

Human MutationREVIEW Mapping Structural Landmarks, Ligand Binding Sites, and  

E-print Network

proximity, for example, between integrins, matrix metalloproteinases, and heparin. The maps indicated, Pennsylvania; 3 Center for Matrix Biology and Department of Medicine, Vanderbilt University Medical Center represent the major proteins of the extracellular matrix and 29 types (I­XXIX) assembled from at least 44

Jensen, Shane T.

341

An Overview of Tubulin Inhibitors That Interact with the Colchicine Binding Site  

PubMed Central

Tubulin dynamics is a promising target for new chemotherapeutic agents. The colchicine binding site is one of the most important pockets for potential tubulin polymerization destabilizers. Colchicine binding site inhibitors (CBSI) exert their biological effects by inhibiting tubulin assembly and suppressing microtubule formation. A large number of molecules interacting with the colchicine binding site have been designed and synthesized with significant structural diversity. CBSIs have been modified as to chemical structure as well as pharmacokinetic properties, and tested in order to find a highly potent, low toxicity agent for treatment of cancers. CBSIs are believed to act by a common mechanism via binding to the colchicine site on tubulin. The present review is a synopsis of compounds that have been reported in the past decade that have provided an increase in our understanding of the actions of CBSIs. PMID:22814904

Lu, Yan; Chen, Jianjun; Xiao, Min; Li, Wei

2013-01-01

342

Selection of optimal recording sites for limited lead body surface potential mapping: A sequential selection based approach  

PubMed Central

Background In this study we propose the development of a new algorithm for selecting optimal recording sites for limited lead body surface potential mapping. The proposed algorithm differs from previously reported methods in that it is based upon a simple and intuitive data driven technique that does not make any presumptions about deterministic characteristics of the data. It uses a forward selection based search technique to find the best combination of electrocardiographic leads. Methods The study was conducted using a dataset consisting of body surface potential maps (BSPM) recorded from 116 subjects which included 59 normals and 57 subjects exhibiting evidence of old Myocardial Infarction (MI). The performance of the algorithm was evaluated using spatial RMS voltage error and correlation coefficient to compare original and reconstructed map frames. Results In all, three configurations of the algorithm were evaluated and it was concluded that there was little difference in the performance of the various configurations. In addition to observing the performance of the selection algorithm, several lead subsets of 32 electrodes as chosen by the various configurations of the algorithm were evaluated. The rationale for choosing this number of recording sites was to allow comparison with a previous study that used a different algorithm, where 32 leads were deemed to provide an acceptable level of reconstruction performance. Conclusion It was observed that although the lead configurations suggested in this study were not identical to that suggested in the previous work, the systems did bear similar characteristics in that recording sites were chosen with greatest density in the precordial region. PMID:16503972

Finlay, Dewar D; Nugent, Chris D; Donnelly, Mark P; Lux, Robert L; McCullagh, Paul J; Black, Norman D

2006-01-01

343

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

344

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

PubMed Central

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

2013-01-01

345

Historic Maps  

NSDL National Science Digital Library

The first site about historical maps is the US Military Academy at West Point's History Department's Map Library (1). The page contains links to dozens of maps related to warfare from ancient times, the American Revolution, and the Napoleonic wars to the World Wars and other modern conflicts. Although map descriptions are not given and the main page seemed to have a problem loading correctly, the site does give a very interesting glimpse into the geography and history of conflict. The second offering is from The Dalton School called Maps of the Roman Empire (2). Visitors will find dozens of interesting maps with titles such as the Roman Empire circa 120 AD; Trade Routes; 18 Centuries of Roman Empire; and maps of how the empire expanded, barbarian migrations, and more. Next, the History of Cartography (3) Web site is maintained by the University of Wisconsin Geography Department. The well designed page contains six volumes of information relating to cartographic changes from ancient times to the twentieth century. Full descriptions and images are available from this unique research, editorial, and publishing project. The fourth site from the Library of Congress Historical Collections is entitled American Memory Collections (4). The page contains various links to civil war maps, panoramic maps, revolutionary era maps, and other very impressive collections. The Perry-Castañeda Library Map Collection: Historical Maps Web site (5) of the University of Texas at Austin is the next offering. This extensive site contains a well organized collection of historical maps of Africa, the Americas, Asia, Australia and the Pacific, Europe, the Middle East, Polar Regions and Oceans, Russia and the Former Soviet Republics, Texas, the US, and the World. The sixth site is maintained by John Hopkins University called Color Landforms Atlas of the United States (6). The main page contains links to maps from all fifty states, which include large historical maps from 1895, county maps, and shaded relief maps. The next site, old-maps.co.uk (7), is provided by Britain's national mapping agency and the Landmark Information Group. The site gives online access to Britain's most extensive digital historical map archive, which can be searched and browsed by a variety of subjects to view maps of Buckingham Palace, Edinburgh Castle, and Oxford University, among others. The last historical maps Web site is the Maps and Geography (8) search engine from National Geographic online. Users can search by general historical maps, Lewis and Clark maps, New England and New York maps, Civil War, and World Maps to find and view an impressive and interesting collection.

Brieske, Joel A.

2003-01-01

346

The interaction of borate ions with cytochrome c surface sites: a molecular dynamics study.  

PubMed Central

Ionic interactions of cytochrome c play an important role in the electron transfer process. Molecular dynamics simulations of the binding of borate ion, which serves as a model ion, at three different cytochrome c surface sites are performed. This work is motivated by previous NMR studies of cytochrome c in borate solution, which indicate the existence of two types of binding sites, a slow exchange site and a fast exchange site. These two types of binding behavior were observed in the dynamic simulations, offering a molecular interpretation of "loose" and "tight" binding. At the "loose" binding sites (near Lys25/Lys27 and Lys55/Lys73) the ion forms two to three hydrogen bonds to the nearest lysine residue. This binding is transient on the time scale of the simulation, demonstrating the feasibility of fast exchange. At the "tight" binding site (near Lys13/Lys86), on the other hand, the ion becomes integrated into the protein hydrogen bond network and remains there for the duration of the simulation (exemplifying slow exchange). Binding simulations of the ion at the "tight" site of H26Q mutant cytochrome c also showed integration of the ion into the protein's hydrogen bond network. However, this integration differs in details from the binding of the ion to the native protein, in agreement with previous NMR observations. PMID:9788941

Taler, G; Navon, G; Becker, O M

1998-01-01

347

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

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

348

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

349

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

350

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

351

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

PubMed

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

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

2014-06-11

352

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

USGS Publications Warehouse

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

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

2008-01-01

353

Land cover mapping and GIS processing for the Savannah River Site Database  

SciTech Connect

The Savannah River Site (SRS) is owned by the U.S. Department of Energy and operated by Westinghouse Savannah River Company. Located in Barnwell, Aiken, and Allendale counties in South Carolina, SRS covers an area of approximately 77,700 hectares. Land cover information for SRS was interpreted from color and color infrared aerial photography acquired between 1980 and 1989. The data were then used as the source of the land cover data layer for the SRS sitewide Geographic Information System database. This database provides SRS managers with recent land use information and has been successfully used to support cost-effective site characterization and reclamation.

Christel, L.M.; Guber, A.L.

1994-07-01

354

Isolation of ATMEKK1 (a MAP Kinase Kinase Kinase)Interacting Proteins and Analysis of a MAP Kinase Cascade in Arabidopsis  

Microsoft Academic Search

In plants, a number of MAP kinase (MAPK), MAPK kinase (MAPKK), and MAPKK kinase (MAPKKK) homologues have been reported. However, there have been no reports of protein–protein interactions between these kinases or molecular analysis of MAPK cascades in higher plants. To analyze a possible MAPK cascade inArabidopsis thaliana,we took two molecular approaches. One is the two-hybrid screening of ATMEKK1 (a

Kazuya Ichimura; Tsuyoshi Mizoguchi; Kenji Irie; Peter Morris; Jérôme Giraudat; Kunihiro Matsumoto; Kazuo Shinozaki

1998-01-01

355

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

PubMed Central

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

2014-01-01

356

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

PubMed

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

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

2011-05-01

357

Help Shopping Cart Contact Site Map Member Login Logout Annual Report  

E-print Network

logging as theft of timber or logs, cutting in parks, reserves or similar areas, and cutting where Pulp & Paper Wood Products Environment & Recycling Policy Issues Career Center Marketplace News Room. All rights reserved. Privacy Policy Site designed and developed by Active Matter http

358

Mapping shallow underground features that influence site-specific agricultural production  

Microsoft Academic Search

Modern agricultural production practices are rapidly evolving in the United States of America (USA). These new production practices present significant applications for nonintrusive subsurface imaging. One such imaging technology is GPR, and it is now being incorporated within site-specific agriculture in the detection of soil horizons, perched water (episaturation), fragipans, hydrological preferential flow paths, and soil compaction. These features traditionally

Robert S Freeland; Ronald E Yoder; John T Ammons

1998-01-01

359

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

PubMed Central

A synthetic peptide modeled on residues 45 to 60 of the 1A protein of respiratory syncytial (RS) virus [1A(45-60)] was constructed and used for immunization of mice and rabbits. The immunoglobulin G fraction of the resulting rabbit antibody, purified on protein A-Sepharose, immunoprecipitated from RS-infected HEp-2 cells a protein with a molecular size of approximately 9.5 kilodaltons, which corresponds to the previously published molecular size of the 1A protein (Y. T. Huang, P. L. Collins, and G. W. Wertz, Virus Res. 2:157-173, 1985). To investigate the T-cell-inducing properties of 1A(45-60), six strains of mice were immunized and their popliteal lymph node cells were tested for proliferation upon restimulation with peptide in vitro. The lymph node cells of all six strains of mice were responsive to restimulation with 1A(45-60) and showed high- and low-responder strain variation. These peptide-primed lymph node cells also proliferated upon in vitro restimulation with RS virus-infected cells. Correlation of proliferation with interleukin 2 production suggested that the responding lymphocytes were T-helper cells. The antibody-binding and T-cell-stimulating sites of 1A were mapped by constructing a series of overlapping synthetic peptides and testing each for ability to react with antiserum prepared by immunization of BALB/C mice with free peptide 1A(45-60) or for ability to restimulate proliferation in 1A(45-60)-primed lymph node cells of BALB/C mice. Human antibody, obtained during confirmed RS virus infection, was similarly tested with the truncated peptides. Antibody-binding activity was reduced after truncation from the carboxy terminus, and a binding site was mapped to residues 51 through 60, the smallest peptide tested. T-cell-stimulating activity in mice was relatively resistant to truncation from the carboxy terminus and sensitive to truncation from the amino terminus. The smallest region which retained significant T-cell-stimulating activity mapped to residues 46 through 56. However, addition of the naturally occurring Cys at residue 45 and extension of the C terminus to residue 62 resulted in maximum T-cell-stimulating activity of the peptide. These data define both a T-cell epitope and a B-cell epitope of the 1A protein of RS virus and suggest that the carboxy terminus of 1A contains a B-cell epitope, involving residues 51 through 60, which is recognized during natural human infection. Images PMID:2460636

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

1988-01-01

360

Cross-cultural comparison of interactivity and advertising appeals on antismoking web sites in the United States and South Korea  

Microsoft Academic Search

Purpose – This study aims to examine the content of health promotional web sites in two culturally distinct countries, the USA and South Korea, by investigating the level of interactivity and types of advertising appeals presented on antismoking web sites. Design\\/methodology\\/approach – Antismoking web sites in the two countries were collected through the three major search engines (msn, Yahoo and

Hye-jin Paek; Bumjun Bae

2008-01-01

361

Mapping substrate interactions of the human membrane-associated neuraminidase, NEU3, using STD NMR.  

PubMed

Saturation transfer difference (STD) nuclear magnetic resonance (NMR) is a powerful technique which can be used to investigate interactions between proteins and their substrates. The method identifies specific sites of interaction found on a small molecule ligand when in complex with a protein. The ability of STD NMR to provide specific insight into binding interactions in the absence of other structural data is an attractive feature for its use with membrane proteins. We chose to employ STD NMR in our ongoing investigations of the human membrane-associated neuraminidase NEU3 and its interaction with glycolipid substrates (e.g., GM3). In order to identify critical substrate-enzyme interactions, we performed STD NMR with a catalytically inactive form of the enzyme, NEU3(Y370F), containing an N-terminal maltose-binding protein (MBP)-affinity tag. In the absence of crystallographic data on the enzyme, these data represent a critical experimental test of proposed homology models, as well as valuable new structural data. To aid interpretation of the STD NMR data, we compared the results with molecular dynamics (MD) simulations of the enzyme-substrate complexes. We find that the homology model is able to predict essential features of the experimental data, including close contact of the hydrophobic aglycone and the Neu5Ac residue with the enzyme. Additionally, the model and STD NMR data agree on the facial recognition of the galactose and glucose residues of the GM3-analog studied. We conclude that the homology model of NEU3 can be used to predict substrate recognition, but our data indicate that unstructured portions of the NEU3 model may require further refinement. PMID:25294388

Albohy, Amgad; Richards, Michele R; Cairo, Christopher W

2015-03-01

362

A new tool to quantify receptor recruitment to cell contact sites during host-pathogen interaction.  

PubMed

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

Graus, Matthew S; Pehlke, Carolyn; Wester, Michael J; Davidson, Lisa B; Steinberg, Stanly L; Neumann, Aaron K

2014-05-01

363

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

USGS Publications Warehouse

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

Kucks, Robert P.; Hill, Patricia L.

2005-01-01

364

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

NASA Astrophysics Data System (ADS)

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

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

2007-02-01

365

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

USGS Publications Warehouse

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

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

2003-01-01

366

Voltage sensor interaction site for selective small molecule inhibitors of voltage-gated sodium channels  

PubMed Central

Voltage-gated sodium (Nav) channels play a fundamental role in the generation and propagation of electrical impulses in excitable cells. Here we describe two unique structurally related nanomolar potent small molecule Nav channel inhibitors that exhibit up to 1,000-fold selectivity for human Nav1.3/Nav1.1 (ICA-121431, IC50, 19 nM) or Nav1.7 (PF-04856264, IC50, 28 nM) vs. other TTX-sensitive or resistant (i.e., Nav1.5) sodium channels. Using both chimeras and single point mutations, we demonstrate that this unique class of sodium channel inhibitor interacts with the S1–S4 voltage sensor segment of homologous Domain 4. Amino acid residues in the “extracellular” facing regions of the S2 and S3 transmembrane segments of Nav1.3 and Nav1.7 seem to be major determinants of Nav subtype selectivity and to confer differences in species sensitivity to these inhibitors. The unique interaction region on the Domain 4 voltage sensor segment is distinct from the structural domains forming the channel pore, as well as previously characterized interaction sites for other small molecule inhibitors, including local anesthetics and TTX. However, this interaction region does include at least one amino acid residue [E1559 (Nav1.3)/D1586 (Nav1.7)] that is important for Site 3 ?-scorpion and anemone polypeptide toxin modulators of Nav channel inactivation. The present study provides a potential framework for identifying subtype selective small molecule sodium channel inhibitors targeting interaction sites away from the pore region. PMID:23818614

McCormack, Ken; Santos, Sonia; Chapman, Mark L.; Krafte, Douglas S.; Marron, Brian E.; West, Christopher W.; Krambis, Michael J.; Antonio, Brett M.; Zellmer, Shannon G.; Printzenhoff, David; Padilla, Karen M.; Lin, Zhixin; Wagoner, P. Kay; Swain, Nigel A.; Stupple, Paul A.; de Groot, Marcel; Butt, Richard P.; Castle, Neil A.

2013-01-01

367

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

PubMed Central

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

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

2003-01-01

368

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

PubMed Central

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

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

2013-01-01

369

Fractionation profiling: a fast and versatile approach for mapping vesicle proteomes and protein–protein interactions  

PubMed Central

We developed “fractionation profiling,” a method for rapid proteomic analysis of membrane vesicles and protein particles. The approach combines quantitative proteomics with subcellular fractionation to generate signature protein abundance distribution profiles. Functionally associated groups of proteins are revealed through cluster analysis. To validate the method, we first profiled >3500 proteins from HeLa cells and identified known clathrin-coated vesicle proteins with >90% accuracy. We then profiled >2400 proteins from Drosophila S2 cells, and we report the first comprehensive insect clathrin-coated vesicle proteome. Of importance, the cluster analysis extends to all profiled proteins and thus identifies a diverse range of known and novel cytosolic and membrane-associated protein complexes. We show that it also allows the detailed compositional characterization of complexes, including the delineation of subcomplexes and subunit stoichiometry. Our predictions are presented in an interactive database. Fractionation profiling is a universal method for defining the clathrin-coated vesicle proteome and may be adapted for the analysis of other types of vesicles and particles. In addition, it provides a versatile tool for the rapid generation of large-scale protein interaction maps. PMID:25165137

Borner, Georg H. H.; Hein, Marco Y.; Hirst, Jennifer; Edgar, James R.; Mann, Matthias; Robinson, Margaret S.

2014-01-01

370

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

PubMed

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

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

2013-11-21

371

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

NASA Astrophysics Data System (ADS)

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

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

2014-11-01

372

Kinetics of the bosonic A+B-->0 reaction with on-site attractive interaction.  

PubMed

We investigate kinetics of the uniformly driven bosonic A+B-->0 reaction with on-site attractive interaction in one dimension. In this model, n(i)(lambda) particles from a site with n(i) particles are driven to the right. When particles of opposite species occupy the same site, the reaction takes place instantaneously. Since n(i)(lambda)site attractive interaction between like particles. The lambda=0 case corresponds to the hard-core (HC) particle model. With equal initial densities of both species, we numerically confirm that the scaling behaviors of density and lengths are the same as those of the uniformly driven HC particle system. Especially the domain length l satisfies the power law l approximately t(2/3). The kinetics of the reaction is independent of lambda as long as lambda<1. The lambda -independent kinetics results from the lambda -independent collective motions of single species domains. PMID:17358328

Kwon, Sungchul; Kim, Yup

2007-02-01

373

Target detection and mapping of aquatic hazardous waste sites in Massachusetts Bay utilizing sidescan sonar  

SciTech Connect

The oceans have frequently been used for disposal for a variety of industrial, chemical, and low-level radioactive wastes. In Massachusetts Bay, several areas have been used for the permitted and possible non-permitted disposal of waste containers with environmentally sensitive materials. During the Summer and Fall of 1991, the Industrial Waste Site (IWS) and the Boston Lightship Dumping Ground (BLDG) in Massachusetts Bay were the subject of intensive surveys to determine the areal extent, distribution and location of waste containers.

Keith, D.J.; Capone, V.; Cook, G.S.; Casey, D.A.; Wiley, D.N.

1992-01-01

374

Functional mapping of SPARC: peptides from two distinct Ca+(+)-binding sites modulate cell shape  

Microsoft Academic Search

Abstract. Using synthetic peptides, we have identified two distinct regions of the glycoprotein SPARC (Secreted Protein Acidic and Rich in Cysteine) (os- teonectin\\/BM-40) that inhibit cell spreading. One of these sites also contributes to the affinity of SPARC for extracellular matrix components.,Peptides representing subregions,of SPARC were synthesized and antipeptide antibodies were produced. Immuno- globulin fractions of sera recognizing,an NH2-terminal peptide

E. Helene Sage

1990-01-01

375

Fragile X syndrome: genetic localisation by linkage mapping of two microsatellite repeats FRAXAC1 and FRAXAC2 which immediately flank the fragile site  

Microsoft Academic Search

We report the genetic localisation of the fragile site at Xq27.3 associated with fragile X syndrome. The position of the fragile site within the multipoint linkage map was determined using two polymorphic microsatellite AC repeat markers FRAXAC1 and FRAXAC2. These markers were physically located within 10 kilobases and on either side of the p(CCG)n repeat responsible for the fragile site.

R I Richards; K Holman; H Kozman; E Kremer; M Lynch; M Pritchard; S Yu; J Mulley; G R Sutherland

1991-01-01

376

Fat-soluble vitamin intestinal absorption: Absorption sites in the intestine and interactions for absorption.  

PubMed

The interactions occurring at the intestinal level between the fat-soluble vitamins A, D, E and K (FSVs) are poorly documented. We first determined each FSV absorption profile along the duodenal-colonic axis of mouse intestine to clarify their respective absorption sites. We then investigated the interactions between FSVs during their uptake by Caco-2 cells. Our data show that vitamin A was mostly absorbed in the mouse proximal intestine, while vitamin D was absorbed in the median intestine, and vitamin E and K in the distal intestine. Significant competitive interactions for uptake were then elucidated among vitamin D, E and K, supporting the hypothesis of common absorption pathways. Vitamin A also significantly decreased the uptake of the other FSVs but, conversely, its uptake was not impaired by vitamins D and K and even promoted by vitamin E. These results should be taken into account, especially for supplement formulation, to optimise FSV absorption. PMID:25442537

Goncalves, Aurélie; Roi, Stéphanie; Nowicki, Marion; Dhaussy, Amélie; Huertas, Alain; Amiot, Marie-Josèphe; Reboul, Emmanuelle

2015-04-01

377

Interactive Radiative Transfer Modeling Tools to Map Volcanic Emissions with Thermal Infrared Remote Sensing  

NASA Astrophysics Data System (ADS)

The estimation of plume composition from thermal infrared (TIR) radiance measurements is based in radiative transfer (RT) modeling. To model the observed spectra we must consider the temperature, emissivity, and elevation of the surface beneath the plume, plume altitude and thickness, and the local atmospheric temperature and humidity. Our knowledge of these parameters is never perfect, and interactive RT modeling allows us to evaluate the impact of these uncertainties on our estimates of plume composition. Interactive RT modeling has three main components: retrieval procedures for plume components, an engine for RT calculations, and a graphic user interface (GUI) to input radiance data, modify model parameters, launch retrievals, and visualize the resulting estimates of plume composition. The Jet Propulsion Laboratory (JPL), in collaboration with Spectral Sciences, Inc. (SSI), is developing a new class of tools for interactive RT modeling. We will implement RT modeling on graphics processors (GPU) to achieve a 100-fold increase in processing speed, relative to conventional CPU-based processing, and thus enable fully-interactive estimation and visualization of plume composition. The heritage for our new tools is based on the Plume Tracker toolkit, developed at JPL, and MODTRAN RT model, developed by SSI. Plume Tracker integrates retrieval procedures, interactive visualization tools, and an interface to a modified version of MODTRAN under a single GUI. Our new tools will incorporate refinements from a recent adaptation of MODTRAN to optimize modeling the radiative properties of chemical clouds. This presentation will include a review of the foundations of plume mapping in the TIR and examples of the application of Plume Tracker to ASTER, MODIS, and AIRS data. We will present an overview of our tool development effort and discuss the application of these tools to data from new and future instruments, such as the airborne Hyperspectral Thermal Emission Spectrometer and TIR data from the upcoming Hyperspectral Infrared Imager mission. Portions of this research were conducted at the Jet Propulsion Laboratory, California Institute of Technology, under contract to the National Aeronautics and Space Administration.

Realmuto, V. J.

2012-12-01

378

Signatures of Pleiotropy, Economy and Convergent Evolution in a Domain-Resolved Map of Human–Virus Protein–Protein Interaction Networks  

PubMed Central

A central challenge in host-pathogen systems biology is the elucidation of general, systems-level principles that distinguish host-pathogen interactions from within-host interactions. Current analyses of host-pathogen and within-host protein-protein interaction networks are largely limited by their resolution, treating proteins as nodes and interactions as edges. Here, we construct a domain-resolved map of human-virus and within-human protein-protein interaction networks by annotating protein interactions with high-coverage, high-accuracy, domain-centric interaction mechanisms: (1) domain-domain interactions, in which a domain in one protein binds to a domain in a second protein, and (2) domain-motif interactions, in which a domain in one protein binds to a short, linear peptide motif in a second protein. Analysis of these domain-resolved networks reveals, for the first time, significant mechanistic differences between virus-human and within-human interactions at the resolution of single domains. While human proteins tend to compete with each other for domain binding sites by means of sequence similarity, viral proteins tend to compete with human proteins for domain binding sites in the absence of sequence similarity. Independent of their previously established preference for targeting human protein hubs, viral proteins also preferentially target human proteins containing linear motif-binding domains. Compared to human proteins, viral proteins participate in more domain-motif interactions, target more unique linear motif-binding domains per residue, and contain more unique linear motifs per residue. Together, these results suggest that viruses surmount genome size constraints by convergently evolving multiple short linear motifs in order to effectively mimic, hijack, and manipulate complex host processes for their survival. Our domain-resolved analyses reveal unique signatures of pleiotropy, economy, and convergent evolution in viral-host interactions that are otherwise hidden in the traditional binary network, highlighting the power and necessity of high-resolution approaches in host-pathogen systems biology. PMID:24339775

Garamszegi, Sara; Franzosa, Eric A.; Xia, Yu

2013-01-01

379

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

PubMed Central

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

Boulos, Maged N Kamel

2003-01-01

380

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

NASA Astrophysics Data System (ADS)

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

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

2010-12-01

381

Mapping the complement C1q binding site in Haemonchus contortus calreticulin  

Microsoft Academic Search

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

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

2009-01-01

382

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

PubMed Central

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

Mourez, M; Hofnung, M; Dassa, E

1997-01-01

383

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

PubMed

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

Mourez, M; Hofnung, M; Dassa, E

1997-06-01

384

Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution.  

PubMed

Understanding translational control in gene expression relies on precise and comprehensive determination of translation initiation sites (TIS) across the entire transcriptome. The recently developed ribosome-profiling technique enables global translation analysis, providing a wealth of information about both the position and the density of ribosomes on mRNAs. Here we present an approach, global translation initiation sequencing, applying in parallel the ribosome E-site translation inhibitors lactimidomycin and cycloheximide to achieve simultaneous detection of both initiation and elongation events on a genome-wide scale. This approach provides a view of alternative translation initiation in mammalian cells with single-nucleotide resolution. Systemic analysis of TIS positions supports the ribosome linear-scanning mechanism in TIS selection. The alternative TIS positions and the associated ORFs identified by global translation initiation sequencing are conserved between human and mouse cells, implying physiological significance of alternative translation. Our study establishes a practical platform for uncovering the hidden coding potential of the transcriptome and offers a greater understanding of the complexity of translation initiation. PMID:22927429

Lee, Sooncheol; Liu, Botao; Lee, Soohyun; Huang, Sheng-Xiong; Shen, Ben; Qian, Shu-Bing

2012-09-11

385

Reconstructing Genome-Wide Protein–Protein Interaction Networks Using Multiple Strategies with Homologous Mapping  

PubMed Central

Background One of the crucial steps toward understanding the biological functions of a cellular system is to investigate protein–protein interaction (PPI) networks. As an increasing number of reliable PPIs become available, there is a growing need for discovering PPIs to reconstruct PPI networks of interesting organisms. Some interolog-based methods and homologous PPI families have been proposed for predicting PPIs from the known PPIs of source organisms. Results Here, we propose a multiple-strategy scoring method to identify reliable PPIs for reconstructing the mouse PPI network from two well-known organisms: human and fly. We firstly identified the PPI candidates of target organisms based on homologous PPIs, sharing significant sequence similarities (joint E-value ? 1 × 10?40), from source organisms using generalized interolog mapping. These PPI candidates were evaluated by our multiple-strategy scoring method, combining sequence similarities, normalized ranks, and conservation scores across multiple organisms. According to 106,825 PPI candidates in yeast derived from human and fly, our scoring method can achieve high prediction accuracy and outperform generalized interolog mapping. Experiment results show that our multiple-strategy score can avoid the influence of the protein family size and length to significantly improve PPI prediction accuracy and reflect the biological functions. In addition, the top-ranked and conserved PPIs are often orthologous/essential interactions and share the functional similarity. Based on these reliable predicted PPIs, we reconstructed a comprehensive mouse PPI network, which is a scale-free network and can reflect the biological functions and high connectivity of 292 KEGG modules, including 216 pathways and 76 structural complexes. Conclusions Experimental results show that our scoring method can improve the predicting accuracy based on the normalized rank and evolutionary conservation from multiple organisms. Our predicted PPIs share similar biological processes and cellular components, and the reconstructed genome-wide PPI network can reflect network topology and modularity. We believe that our method is useful for inferring reliable PPIs and reconstructing a comprehensive PPI network of an interesting organism. PMID:25602759

Lo, Yu-Shu; Huang, Sing-Han; Luo, Yong-Chun; Lin, Chun-Yu; Yang, Jinn-Moon

2015-01-01

386

A comprehensive approach to mapping the interacting surfaces of murine amphotropic and feline subgroup B leukemia viruses with their cell surface receptors.  

PubMed

Because mutations in envelope glycoproteins of retroviruses or in their cell surface receptors can eliminate function by multiple mechanisms, it has been difficult to unambiguously identify sites for their interactions by site-directed mutagenesis. Recently, we developed a gain-of-function approach to overcome this problem. Our strategy relies on the fact that feline leukemia virus subgroup B (FeLV-B) and amphotropic murine leukemia virus (A-MLV) have closely related gp70 surface envelope glycoproteins and use related Na(+)-dependent phosphate symporters, Pit1 and Pit2, respectively, as their receptors. We previously observed that FeLV-B/A-MLV envelope glycoprotein chimeras spliced between the variable regions VRA and VRB were unable to use Pit1 or Pit2 as a receptor but could efficiently use specific Pit1/Pit2 chimeras. The latter study suggested that the VRA of A-MLV and FeLV-B functionally interact with the presumptive extracellular loops 4 and 5 (ECL4 and -5) of their respective receptors, whereas VRB interacts with ECL2. We also found that FeLV-B gp70 residues F60 and P61 and A-MLV residues Y60 and V61 in the first disulfide-bonded loop of VRA were important for functional interaction with the receptor's ECL4 or -5. We have now extended this approach to identify additional VRA and VRB residues that are involved in receptor recognition. Our studies imply that FeLV-B VRA residues F60 and P61 interact with the Pit1 ECL5 region, whereas VRA residues 66 to 78 interact with Pit1 ECL4. Correspondingly, A-MLV VRA residues Y60 and V61 interact with the Pit2 ECL5 region, whereas residues 66 to 78 interact with Pit2 ECL4. Similar studies that focused on the gp70 VRB implicated residues 129 to 139 as contributing to specific interactions with the receptor ECL2. These results identify three regions of gp70 that interact in a specific manner with distinct portions of their receptors, thereby providing a map of the functionally interacting surfaces. PMID:10590111

Tailor, C S; Nouri, A; Kabat, D

2000-01-01

387

Use of Bedrock and Geomorphic Mapping Compilations in Assessing Geologic Hazards at Recreation Sites on National Forests in NW California  

NASA Astrophysics Data System (ADS)

Geologic hazards on US Forest Service lands have a long history of producing catastrophic events. In 1890 (prior to the establishment of the Forest Service), the China Mine landslide buried a miner’s camp along the Trinity River in NW California, killing a number of miners. An earthquake in southwestern Montana triggered a massive landslide which killed 28 people in a US Forest Service campground in 1959. In 1980, Mount St. Helens erupted in Oregon, killing 57 people. Debris flows from a winter storm in 2003 on the burned hillslopes of the San Bernardino National Forest in California killed 14 people at the St. Sophia youth Camp. A rockfall in the summer of 2009 in Lassen National Park killed a 9 year old boy. The most recent catastrophe occurred on June 11, 2010 when 20 people died in a flash flood at the Albert Pike Campground on the Ouachita National Forest. These and other disasters point out the need for geologic hazard mapping and assessments on the National Forests. The US Forest Service (USFS) is currently assessing geologic hazards in the Northern Province of USFS Region 5 (Pacific Southwest Region), which includes the Klamath, Mendocino, Shasta-Trinity, and Six Rivers National Forests. The most common geologic hazards (relatively short return intervals) in this area include landslides, rock falls, debris flows, flooding, temporary dam failures (landslide or woody debris), naturally occurring hazardous materials, (asbestos radon, etc), and rarely, karst subsidence. Seismic and volcanic hazards are also important at longer return intervals. This assessment will be conducted in three phases, and is patterned after a process developed by Region 8 of the US Forest Service. The first phase is a reconnaissance level assessment based on existing information such as spatial databases, aerial photos, Digital Elevation Models, State of California Alquist-Priolo Earthquake Fault Zone maps, previous investigations and anecdotal accounts of past events. The bedrock coverage is a compilation of the best available mapping for all National Forests in California. The geomorphic coverage includes features such as active and dormant landslides, alluvial fans, headwall basins, glacial features, and valley inner gorge. Criteria will be developed which utilize elements of this data to evaluate geologic hazards in the vicinity of developed recreation sites. The second phase will be conducted later and involves site specific analyses focusing on areas identified as higher hazard in the first phase, along with verification and updating of phase 1 findings. The third phase will complete any site level geologic or hydrologic investigations, and wrap up the hazard assessment process. A summary report with hazard maps and recommendations will be prepared at the end of each phase. The overriding goal of this project is to provide sound geologic information to managers so they can use a science-based approach in recognizing and managing geologic hazards at recreation sites.

de La Fuente, J. A.; Bell, A.; Elder, D.; Mowery, R.; Mikulovsky, R.; Klingel, H.; Stevens, M.

2010-12-01

388

Mapping topoisomerase sites in mitochondrial DNA with a poisonous mitochondrial topoisomerase I (Top1mt).  

PubMed

Mitochondrial topoisomerase I (Top1mt) is a type IB topoisomerase present in vertebrates and exclusively targeted to mitochondria. Top1mt relaxes mitochondrial DNA (mtDNA) supercoiling by introducing transient cleavage complexes wherein the broken DNA strand swivels around the intact strand. Top1mt cleavage complexes (Top1mtcc) can be stabilized in vitro by camptothecin (CPT). However, CPT does not trap Top1mtcc efficiently in cells and is highly cytotoxic due to nuclear Top1 targeting. To map Top1mtcc on mtDNA in vivo and to overcome the limitations of CPT, we designed two substitutions (T546A and N550H) in Top1mt to stabilize Top1mtcc. We refer to the double-mutant enzyme as Top1mt*. Using retroviral transduction and ChIP-on-chip assays with Top1mt* in Top1mt knock-out murine embryonic fibroblasts, we demonstrate that Top1mt* forms high levels of cleavage complexes preferentially in the noncoding regulatory region of mtDNA, accumulating especially at the heavy strand replication origin OH, in the ribosomal genes (12S and 16S) and at the light strand replication origin OL. Expression of Top1mt* also caused rapid mtDNA depletion without affecting mitochondria mass, suggesting the existence of specific mitochondrial pathways for the removal of damaged mtDNA. PMID:24798329

Dalla Rosa, Ilaria; Huang, Shar-Yin N; Agama, Keli; Khiati, Salim; Zhang, Hongliang; Pommier, Yves

2014-06-27

389

Fluid expulsion sites on the Cascadia accretionary prism: mapping diagenetic deposits with processed GLORIA imagery  

USGS Publications Warehouse

 Point-discharge fluid expulsion on accretionary prisms is commonly indicated by diagenetic deposition of calcium carbonate cements and gas hydrates in near-surface (<10 m below seafloor; mbsf) hemipelagic sediment. The contrasting clastic and diagenetic lithologies should be apparent in side scan images. However, sonar also responds to variations in bottom slope, so unprocessed images mix topographic and lithologic information. We have processed GLORIA imagery from the Oregon continental margin to remove topographic effects. A synthetic side scan image was created initially from Sea Beam bathymetric data and then was subtracted iteratively from the original GLORIA data until topographic features disappeared. The residual image contains high-amplitude backscattering that we attribute to diagenetic deposits associated with fluid discharge, based on submersible mapping, Ocean Drilling Program drilling, and collected samples. Diagenetic deposits are concentrated (1) near an out-of-sequence thrust fault on the second ridge landward of the base of the continental slope, (2) along zones characterized by deep-seated strikeslip faults that cut transversely across the margin, and (3) in undeformed Cascadia Basin deposits which overlie incipient thrust faults seaward of the toe of the prism. There is no evidence of diagenetic deposition associated with the frontal thrust that rises from the dècollement. If the dècollement is an important aquifer, apparently the fluids are passed either to the strike-slip faults which intersect the dècollement or to the incipient faults in Cascadia Basin for expulsion. Diagenetic deposits seaward of the prism toe probably consist dominantly of gas hydrates

Carson, Bobb; Seke, Erol; Paskevich, Valerie F.; Holmes, Mark L.

1994-01-01

390

Using Process Mining to Generate Accurate and Interactive Business Process Maps  

E-print Network

as illustrated by modern car navigation sys- tems (e.g., TomTom, Garmin, etc.), Google maps, Google Street View limits, etc.). Maps do not only play an important role in car navigation, but are also crucial for all]. Besides navigation systems, there are many applications based on Google maps. For example, real

van der Aalst, Wil

391

Modeling LAI based on land cover map and NDVI using SPOT and Landsat data in two Mediterranean sites: preliminary results  

NASA Astrophysics Data System (ADS)

Leaf Area Index (LAI) is considered to be a key parameter of ecosystem processes and it is widely used as input to biogeochemical process models that predict net primary production (NPP) or can be a useful parameter for crop yield prediction and crop stress assessment as well as estimation of the exchanges of carbon dioxide, water, and nutrients in forests. LAI can be derived from satellite optical data using models referred to physical-based approaches, which describe the physical processes of energy flow in the soil-vegetation-atmosphere system, and models using empirically derived regression relationships based on spectral vegetation indices (VIs). The first category of models are more general in application because they can account for the different sources of variability, although in many cases the information needed to constrain model inputs is not available. In contrast, empirical models depend on the site and time. The aim of this paper is to create a reliable semi-empirical method, applied in two Mediterranean sites, to estimate LAI with high spatial resolution images. The model uses a minimum dataset of a Landsat 5 TM or SPOT 4 XS image, land cover map and DEM for each area. Specifically, this model calculates the reflectance of initial bands implementing topographic correction with the aid of DEM and metadata of the images and afterwards uses a list of NDVI values that correspond to certain LAI values on different land cover types which has been proposed by the MODIS Land Team. This model has been applied in two areas; in the river basin of Nestos (Greece and Bulgaria) and in the river basin of Tamega (Portugal). The predicted LAI map was validated with ground truth data from hemispherical images showing high correlation, with r reaching 0.79 and RMSE less than 1 m2/m2.

Topaloglou, Charalampos; Monachou, Styliani; Strati, Stavroula; Alexandridis, Thomas; Stavridou, Domna; Silleos, Nikolaos; Misopolinos, Nikolaos; Nunes, Antonio; Araújo, Antonio

2013-08-01

392

Coupling interactions between voltage sensors of the sodium channel as revealed by site-specific measurements.  

PubMed

The voltage-sensing S4 segments in the sodium channel undergo conformational rearrangements in response to changes in the electric field. However, it remains unclear whether these structures move independently or in a coordinated manner. Previously, site-directed fluorescence measurements were shown to track S4 transitions in each of the four domains. Here, using a similar technique, we provide direct evidence of coupling interactions between voltage sensors in the sodium channel. Pairwise interactions between S4s were evaluated by comparing site-specific conformational changes in the presence and absence of a gating perturbation in a distal domain. Reciprocity of effect, a fundamental property of thermodynamically coupled systems, was measured by generating converse mutants. The magnitude of a local gating perturbation induced by a remote S4 mutation depends on the coupling strength and the relative equilibrium positions of the two voltage sensors. In general, our data indicates that the movement of all four voltage sensors in the sodium channel are coupled to a varying extent. Moreover, a gating perturbation in S4-DI has the largest effect on the activation of S4-DIV and vice versa, demonstrating an energetic linkage between S4-DI and S4-DIV. This result suggests a physical mechanism by which the activation and inactivation process may be coupled in voltage-gated sodium channels. In addition, we propose that cooperative interactions between voltage sensors may be the mechanistic basis for the fast activation kinetics of the sodium channel. PMID:14981134

Chanda, Baron; Asamoah, Osei Kwame; Bezanilla, Francisco

2004-03-01

393

Functional Mapping of the Lectin Activity Site on the ?-Prism Domain of Vibrio cholerae Cytolysin  

PubMed Central

Vibrio cholerae cytolysin (VCC) is a prominent member in the family of ?-barrel pore-forming toxins. It induces lysis of target eukaryotic cells by forming transmembrane oligomeric ?-barrel channels. VCC also exhibits prominent lectin-like activity in interacting with ?1-galactosyl-terminated glycoconjugates. Apart from the cytolysin domain, VCC harbors two lectin-like domains: the ?-Trefoil and the ?-Prism domains; however, precise contribution of these domains in the lectin property of VCC is not known. Also, role(s) of these lectin-like domains in the mode of action of VCC remain obscure. In the present study, we show that the ?-Prism domain of VCC acts as the structural scaffold to determine the lectin activity of the protein toward ?1-galactosyl-terminated glycoconjugates. Toward exploring the physiological implication of the ?-Prism domain, we demonstrate that the presence of the ?-Prism domain-mediated lectin activity is crucial for an efficient interaction of the toxin toward the target cells. Our results also suggest that such lectin activity may act to regulate the oligomerization ability of the membrane-bound VCC toxin. Based on the data presented here, and also consistent with the existing structural information, we propose a novel mechanism of regulation imposed by the ?-Prism domain's lectin activity, implicated in the process of membrane pore formation by VCC. PMID:23209283

Rai, Anand Kumar; Paul, Karan; Chattopadhyay, Kausik

2013-01-01

394

RICH MAPS  

EPA Science Inventory

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

395

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

PubMed Central

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

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

2014-01-01

396

High Resolution Mapping of an Alleged Chemical Weapons Dump Site in the Santa Cruz Basin, offshore California  

NASA Astrophysics Data System (ADS)

Nautical charts record seven locations off the coast of California labeled as 'Chemical Munitions Dumping Area, Disused' that together cover some 12,000 km2 of sea floor. However only one such chemical munitions site is officially documented and no record exists of any chemical munitions disposed of at other locations, thus creating confusion. We have executed a one day AUV mapping survey of a corner of one such site in the Santa Cruz Basin, south of Port Hueneme, to examine and investigate the debris field. The region is covered with soft sediment and the overlying water is very low in oxygen at ~10 ?mol/kg. The processed 110 kHz sidescan data revealed some 754 targets in 25.6 km2 for an average of 29 targets per km2. This was followed by two ROV dives to investigate the targets identified. We found but one false positives among the over 40 targets visited, and found items ranging from two distinct lines of unmarked or labeled and now empty barrels, two target drones, and much miscellaneous debris including 4-packs of cat food cans and a large ships mast over 30m in length. There was zero evidence of chemical weapons materiel as expected given the lack of official records. Almost all of the targets were covered in dense and colorful assemblages of invertebrates: sponges, anemones, and crabs. Where barrels were sufficiently open for full visual inspection, the interior sea floor appeared to have become fully anoxic and was covered in white and yellow bacterial mat. The area chosen for our survey (centered at 33.76 deg N 119.56 deg W) was across the north western boundary of the marked site, and represents only ~ 10% percent of the designated area. Our expectation, that human nature would drive the disposal activities to the nearest corner of the chosen area rather than the center of the field appears to have been confirmed. Objects were found both within and outside of the boundary of the dump site. We have not surveyed the full marked area but there appears to be the substantial possibility of a gross error in the labeling of charts. Our results show that simple, rapid, and cost effective surveys of these sites can be made, that the found debris field of rusted barrels and other objects appears to have contained more mundane waste material that long ago dissipated or hydrolyzed. It is likely that the majority of disposed material is far from the center of the charted area and thus a re-drawing of the warning zone following additional surveying of the actual extent of the dump site to reflect this would be a significant improvement.

Brewer, P. G.; Peltzer, E. T.; Walz, P. M.; Caress, D. W.; Thomas, H. J.

2013-12-01

397

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

USGS Publications Warehouse

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

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

2002-01-01

398

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

PubMed

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

Huang, Edgar; Chang, Chiu-Chi Angela

2012-01-01

399

Baseline mapping study of the Steed Pond aquifer and vadose zone beneath A/M Area, Savannah River Site, Aiken, South Carolina  

SciTech Connect

This report presents the second phase of a baseline mapping project conducted for the Environmental Restoration Department (ERD) at Savannah River Site. The purpose of this second phase is to map the structure and distribution of mud (clay and silt-sized sediment) within the vadose zone beneath A/M Area. The results presented in this report will assist future characterization and remediation activities in the vadose zone and upper aquifer zones in A/M Area.

Jackson, D.G. Jr.

2000-01-27

400

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

PubMed Central

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

Lind, K E; Moller, J V

1976-01-01

401

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

NASA Astrophysics Data System (ADS)

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

Setiawan, Budi; Mila, Oktri; Safni

2014-03-01

402

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

SciTech Connect

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

Setiawan, Budi, E-mail: bravo@batan.go.id [Radwaste Technology Center-National Nuclear Energy Agency, PUSPIPTEK, Serpong-Tangerang 15310 (Indonesia); Mila, Oktri; Safni [Dept. of Chemistry, Fac. of Math. and Nat. Sci., Andalas University, Kampus Limau Manis, Padang-West Sumatra 25163 (Indonesia)

2014-03-24

403

A novel feature extraction scheme for prediction of protein-protein interaction sites.  

PubMed

Identifying protein-protein interaction (PPI) sites plays an important and challenging role in some topics of biology. Although many methods have been proposed, this problem is still far away to be solved. Here, a feature selection approach with an 11-sliding window and random forest algorithm is proposed, which is called DX-RF. This method has achieved an accuracy of 88.79%, recall of 82.09%, and precision of 85.76% with top-ranked 34 features on the Hetero test dataset and has 91.6% accuracy, 89.2% precision, 83.54% recall with top-ranked 25 features set on the Homo test dataset. Compared to other methods, the results indicate that the DX-RF method has a strong ability to select relevance features to get a higher performance. Moreover, in order to further understand protein interactions, feature analysis in this study is also performed. PMID:25413666

Du, Xiuquan; Jing, Anqi; Hu, Xinying

2015-02-20

404

Association mapping of disease resistance traits in rainbow trout using restriction site associated DNA sequencing.  

PubMed

Recent advances in genotyping-by-sequencing have enabled genome-wide association studies in nonmodel species including those in aquaculture programs. As with other aquaculture species, rainbow trout and steelhead (Oncorhynchus mykiss) are susceptible to disease and outbreaks can lead to significant losses. Fish culturists have therefore been pursuing strategies to prevent losses to common pathogens such as Flavobacterium psychrophilum (the etiological agent for bacterial cold water disease [CWD]) and infectious hematopoietic necrosis virus (IHNV) by adjusting feed formulations, vaccine development, and selective breeding. However, discovery of genetic markers linked to disease resistance offers the potential to use marker-assisted selection to increase resistance and reduce outbreaks. For this study we sampled juvenile fish from 40 families f