Note: This page contains sample records for the topic mapping interaction sites from Science.gov.
While these samples are representative of the content of Science.gov,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of Science.gov
to obtain the most current and comprehensive results.
Last update: November 12, 2013.
1

Helical peptide arrays for lead identification and interaction site mapping.  

PubMed

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

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

2011-06-12

2

STATE System Interactive Maps  

MedlinePLUS

... Initiative Global Tobacco Control Spotlight About GTSS GTSS Atlas Publications and Products Printed Material Videos Interagency Committee ... Reproductive Health More CDC Sites STATE System Interactive Maps ? Highlights 2012 Abstract Highlights 2012 (by section) Highlights ...

3

Mapping of Protein-Protein Interaction Sites by the 'Absence of Interference' Approach  

PubMed Central

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

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

2008-01-01

4

Genome-wide mapping of the binding sites of proteins that interact with DNA.  

PubMed

The coordinated regulation of the expression of a group of genes by a specific transcription factor frequently lies at the heart of the ability of a bacterium to respond to an environmental signal, or to progress through a developmental program. Thus, in many situations, it is of interest to identify all of the genes that are under the control of a particular regulatory protein. This chapter begins with a brief overview of some of the methods that have been used in attempts to identify some or all of the members of a regulon (i.e., those genes that are the targets for a transcriptional activator or repressor). Thereafter, the chapter will focus on one technique, chromatin immunoprecipitation and microarray analysis (ChIP-chip) and some of its variants. Design considerations and some protocols for ChIP-chip experiments are provided, along with some considerations related to downstream data analysis. ChIP-chip is a method for the genome-wide localization of protein-binding sites. In a typical ChIP-chip protocol, proteins are cross-linked nonspecifically to DNA in vivo. Chromatin is extracted and sheared, and specific protein-DNA complexes are immunoprecipitated with a suitable antibody. After purification, the DNA is hybridized to a microarray (after an amplification step in some protocols), together with a differentially labeled reference sample. Features on the microarray that show an elevated fluorescence ratio reveal DNA sequences that were enriched by immunoprecipitation. The corresponding genomic locations are those that were enriched, and are therefore close to sites of binding. The use of high-density tiled microarrays allows for binding site localization with quite high resolution. It is likely that ChIP-chip will soon be superseded by ChIP-seq, in which the immunoprecipitated DNA is analyzed directly by next-generation sequencing technologies. ChIP-chip and ChIP-seq applications are not confined to regulatory proteins, since they can be used with any protein that binds to DNA, either directly, or indirectly via an interaction with another protein. Thus, ChIP-chip has been used successfully to map binding sites for nucleoid proteins, and proteins involved in DNA replication. PMID:22639213

Spiro, Stephen

2012-01-01

5

Mapping a Study Site  

NSDL National Science Digital Library

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

Science, Lawrence H.

1982-01-01

6

Mapping sites of interaction of p47-phox and flavocytochrome b with random-sequence peptide phage display libraries.  

PubMed

During assembly of the phagocyte NADPH oxidase, cytosolic p47-phox translocates to the plasma membrane and binds to flavocytochrome b, and binding domains for p47-phox have been identified on the C-terminal tails of both flavocytochrome b subunits. In the present report, we further examine the interaction of these two oxidase components by using random-sequence peptide phage display library analysis. Screening p47-phox with the peptide libraries identified five potential sites of interaction with flavocytochrome b, including three previously reported regions of interaction and two additional regions of interaction of p47-phox with gp91-phox and p22-phox. The additional sites were mapped to a domain on the first predicted cytosolic loop of gp91-phox encompassing residues S86TRVRRQL93 and to a domain near the cytosolic C-terminal tail of gp91-phox encompassing residues F450EWFADLL457. The mapping also confirmed a previously reported binding domain on gp91-phox (E554SGPRGVHFIF564) and putative Src homology 3 domain binding sites on p22-phox (P156PRPP160 and G177GPPGGP183). To demonstrate that the additional regions identified were biologically significant, peptides mimicking the gp91-phox sequences F77LRGSSACCSTRVRRQL93 and E451WFADLLQLLESQ463 were synthesized and assayed for their ability to inhibit NADPH oxidase activity. These peptides had EC50 values of 1 microM and 230 microM, respectively, and inhibited activation when added prior to assembly but did not affect activity of the preassembled oxidase. Our data demonstrate the usefulness of phage display library analysis for the identification of biologically relevant sites of protein-protein interaction and show that the binding of p47-phox to flavocytochrome b involves multiple binding sites along the C-terminal tails of both gp91- and p22-phox and other regions of gp91-phox nearer to the N terminus. PMID:7624379

DeLeo, F R; Yu, L; Burritt, J B; Loetterle, L R; Bond, C W; Jesaitis, A J; Quinn, M T

1995-07-18

7

Humanin binds MPP8: mapping interaction sites of the peptide and protein.  

PubMed

Humanin (HN), a 24-amino acid peptide encoded by the mitochondrial 16S rRNA gene, was discovered by screening a cDNA library from the occipital cortex of a patient with Alzheimer's disease (AD) for a protection factor against AD-relevant insults. Earlier, using the yeast two-hybrid system, we have identified the M-phase phosphoprotein 8 (MPP8) as a binding partner for HN. In the present work, we further confirmed interaction of HN with MPP8 in co-immunoprecipitation experiments and localized an MPP8-binding site in the region between 5 and 12 aa. of HN. We have also shown that an MPP8 fragment (residues 431-560) is sufficient to bind HN. Further studies on functional consequences of the interaction between the potential oncopetide and the oncoprotein may elucidate some aspects of the molecular mechanisms of carcinogenesis. PMID:23532874

Maximov, Vadim V; Martynenko, Alina V; Arman, Inga P; Tarantul, Vyacheslav Z

2013-03-27

8

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

9

SiMMap: a web server for inferring site-moiety map to recognize interaction preferences between protein pockets and compound moieties  

PubMed Central

The protein–ligand interacting mechanism is essential to biological processes and drug discovery. The SiMMap server statistically derives site-moiety map with several anchors, which describe the relationship between the moiety preferences and physico-chemical properties of the binding site, from the interaction profiles between query target protein and its docked (or co-crystallized) compounds. Each anchor includes three basic elements: a binding pocket with conserved interacting residues, the moiety composition of query compounds and pocket–moiety interaction type (electrostatic, hydrogen bonding or van der Waals). We provide initial validation of the site-moiety map on three targets, thymidine kinase, and estrogen receptors of antagonists and agonists. Experimental results show that an anchor is often a hot spot and the site-moiety map can help to assemble potential leads by optimal steric, hydrogen bonding and electronic moieties. When a compound highly agrees with anchors of site-moiety map, this compound often activates or inhibits the target protein. We believe that the site-moiety map is useful for drug discovery and understanding biological mechanisms. The SiMMap web server is available at http://simfam.life.nctu.edu.tw/.

Chen, Yen-Fu; Hsu, Kai-Cheng; Lin, Shen-Rong; Wang, Wen-Ching; Huang, Yu-Chi; Yang, Jinn-Moon

2010-01-01

10

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.

11

Sites of interaction of a precursor polypeptide on the export chaperone SecB mapped by site-directed spin labeling  

PubMed Central

Summary Export of protein into the periplasm of Escherichia coli via the general secretory system requires that the transported polypeptides be devoid of stably folded tertiary structure. Capture of the precursor polypeptides before they fold is achieved by the promiscuous binding to the chaperone SecB. SecB delivers its ligand to export sites through its specific binding to SecA, a peripheral component of the membrane translocon. At the translocon the ligand is passed from SecB to SecA and subsequently through the SecYEG channel. We have previously used site-directed spin labeling and electron paramagnetic resonance spectroscopy to establish a docking model between SecB and SecA. Here we report use of the same strategy to map the pathway of a physiologic ligand, the unfolded form of precursor galactose-binding protein, on SecB. Our set of SecB variants each containing a single cysteine, which was used in the previous study, has been expanded to forty-eight residues which cover 49% of the surface of SecB. The residues on SecB involved in contacts were identified as those that, upon addition of the unfolded polypeptide ligand, showed changes in spectral line shape consistent with restricted motion of the nitroxide. We conclude that the bound precursor makes contact with a large portion of the surface of the small chaperone. The sites on SecB that interact with the ligand are compared with the previously identified sites that interact with SecA and a model for transfer of the ligand is discussed.

Crane, Jennine M.; Suo, Yuying; Lilly, Angela A.; Mao, Chunfeng; Hubbell, Wayne L.; Randall, Linda L.

2010-01-01

12

Policy Manual Site Map  

Cancer.gov

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

13

An expanded, unified substrate recognition site map for mammalian cytochrome P450s: analysis of molecular interactions between 15 mammalian CYP450 isoforms and 868 substrates.  

PubMed

The original map of mammalian cytochrome P450 (CYP450) residues involved in substrate recognition was prepared for the CYP2 family by Gotoh in 1992 by manual alignment of mammalian CYP450 residues with substrate recognition site (SRS) residues manually delimited from a bacterial cytochrome P450-substrate complex. Using modern structural bioinformatics tools, we have identified CYP450-ligand interactions in mammalian complexes to create a "X-ray structures" SRS map. In a parallel approach, we have built a "docking" SRS map by successful docking of 868 known substrates of 10 mammalian CYP450 isoforms and analysis of contacts made in docking solutions. We subsequently combined these maps to create a unified description of SRSs. The new map largely agrees with the original map by Gotoh with the six original SRS regions appearing in similar locations along the CYP450 sequence as in Gotoh's map. However, important differences also occur: Two new SRS regions appear before SRS1 and we have assigned them as SRS1'a and SRS1'b; SRS1 is much bigger in our map than in Gotoh's (49 aligned positions versus 28); & SRS2 and SRS3 are co-joined in our map to give a single large SRS region (60 aligned positions) we have designated as SRS(2,3), in contrast to the 9 and 10 aligned positions individually covered by SRS2 and SRS3 respectively in Gotoh's original map. These differences result in the SRS zone covering 33 % of the mammalian CYP450 sequence in our map as opposed to 16 % in Gotoh's map. PMID:21740382

Zawaira, Alexander; Ching, Lim Yen; Coulson, Lauren; Blackburn, Jonathan; Wei, Yap Chun

2011-09-01

14

Interactive Arctic Climate Map  

NSDL National Science Digital Library

This map shows communities, villages, and research stations throughout the Arctic. You can click on a yellow dot on the map to display current weather information for that location. There are also different maps which show smaller portions of the Arctic as well as explorer maps.

Fries-Gaither, Jessica

2011-09-20

15

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

PubMed

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

2013-04-09

16

Mapping of the CD23 Binding Site on Immunoglobulin E (IgE) and Allosteric Control of the IgE-Fc?RI Interaction*  

PubMed Central

IgE, the antibody that mediates allergic responses, acts as part of a self-regulating protein network. Its unique effector functions are controlled through interactions of its Fc region with two cellular receptors, Fc?RI on mast cells and basophils and CD23 on B cells. IgE cross-linked by allergen triggers mast cell activation via Fc?RI, whereas IgE-CD23 interactions control IgE expression levels. We have determined the CD23 binding site on IgE, using a combination of NMR chemical shift mapping and site-directed mutagenesis. We show that the CD23 and Fc?RI interaction sites are at opposite ends of the C?3 domain of IgE, but that receptor binding is mutually inhibitory, mediated by an allosteric mechanism. This prevents CD23-mediated cross-linking of IgE bound to Fc?RI on mast cells and resulting antigen-independent anaphylaxis. The mutually inhibitory nature of receptor binding provides a degree of autonomy for the individual activities mediated by IgE-Fc?RI and IgE-CD23 interactions.

Borthakur, Susmita; Hibbert, Richard G.; Pang, Marie O. Y.; Yahya, Norhakim; Bax, Heather J.; Kao, Michael W.; Cooper, Alison M.; Beavil, Andrew J.; Sutton, Brian J.; Gould, Hannah J.; McDonnell, James M.

2012-01-01

17

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

PubMed

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

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

2013-08-12

18

Yellowstone National Park Interactive Map  

NSDL National Science Digital Library

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

Census, Nps S.

19

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

PubMed Central

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

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

2012-01-01

20

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 Application

21

Site Map | Cancer Diagnosis Program (CDP)  

Cancer.gov

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

22

An Engineered Aryl Azide Ligase for Site-Specific Mapping of Protein-Protein Interactions via Photocrosslinking**  

PubMed Central

We re-engineered the small-molecule binding site of E. coli lipoic acid ligase (LplA) to accept a fluorinated aryl azide probe in place of lipoic acid. The mutated ligase can covalently attach the aryl azide to recombinant proteins fused to a 17-amino acid recognition sequence for LplA (called "LAP"). Labeling is highly specific, modifying LAP fusion proteins to the exclusion of all endogenous mammalian proteins. In cell lysate, we labeled FKBP with aryl azide and demonstrated rapamycin-dependent photocrosslinking to FRB.

Baruah, Hemanta; Puthenveetil, Sujiet; Choi, Yoon-Aa; Shah, Samit; Ting, Alice Y.

2008-01-01

23

Mapping NEHRP VS30 site classes  

USGS Publications Warehouse

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

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

2005-01-01

24

Mapping the elusive neonicotinoid binding site  

PubMed Central

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

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

2007-01-01

25

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

26

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

27

Designing interactive maps for crisis management  

Microsoft Academic Search

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

D. J. M. Willems; Louis Vuurpijl

2007-01-01

28

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

29

INTERACTIVE DATA EXPLORATION USING MDS MAPPING  

Microsoft Academic Search

Interactive exploratory data analysis can be realised by using dimensionality reduction techniques integrated in data visualization software. This work presents an adaptation of one multidimensional scaling algorithm to provide it with generalization capability, allowing the display of new data on an existing mapping. The ensuing relative mapping is used to help the understanding of classification results.

Antoine Naud; Wøodzisøaw Duch

2000-01-01

30

Interactive Maps for Community in Online Learning  

ERIC Educational Resources Information Center

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

Cavanaugh, Terence W.; Cavanaugh, Cathy

2008-01-01

31

Interactive Maps for Community in Online Learning  

ERIC Educational Resources Information Center

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

Cavanaugh, Terence W.; Cavanaugh, Cathy

2008-01-01

32

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

33

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

34

Characterization of MAP1B heavy chain interaction with actin.  

PubMed

Microtubule-associated protein 1B is an essential protein during brain development and neurite outgrowth and was studied by several assays to further characterize actin as a major interacting partner. Tubulin and actin co-immunoprecipitated with MAP1B at similar ratios throughout development. Their identity was identified by mass spectrometry and was confirmed by Western blots. In contrast to previous reports, the MAP1B-actin interaction was not dependent on the MAP1B phosphorylation state, since actin was precipitated from brain tissue throughout development at similar ratios and equal amounts were precipitated before and after dephosphorylation with alkaline phosphatase. MAP1B heavy chain was able to bind actin directly and therefore the N-terminal part of MAP1B heavy chain must also contain an actin-binding site. The binding force of this interaction was measured by atomic force microscopy and values were in the same range as those of MAP1B binding to tubulin or that measured in MAP1B self-aggregation. Aggregation was confirmed by negative staining and electron microscopy. Experiments including COS-7 cells, PC12 cells, cytochalasin D and immunocytochemistry with subsequent confocal laser microscopy, suggested that MAP1B may bind to actin but has no obvious microfilament stabilizing effect. We conclude, that the MAP1B heavy chain has a microtubule-stabilization effect, and contains an actin-binding site that may play a role in the crosslinking of actin and microtubules, a function that may be important in neurite elongation. PMID:17292804

Cueille, N; Blanc, C Tallichet; Popa-Nita, S; Kasas, S; Catsicas, S; Dietler, G; Riederer, B M

2007-01-03

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

MotifMap: integrative genome-wide maps of regulatory motif sites for model species  

PubMed Central

Background A central challenge of biology is to map and understand gene regulation on a genome-wide scale. For any given genome, only a small fraction of the regulatory elements embedded in the DNA sequence have been characterized, and there is great interest in developing computational methods to systematically map all these elements and understand their relationships. Such computational efforts, however, are significantly hindered by the overwhelming size of non-coding regions and the statistical variability and complex spatial organizations of regulatory elements and interactions. Genome-wide catalogs of regulatory elements for all model species simply do not yet exist. Results The MotifMap system uses databases of transcription factor binding motifs, refined genome alignments, and a comparative genomic statistical approach to provide comprehensive maps of candidate regulatory elements encoded in the genomes of model species. The system is used to derive new genome-wide maps for yeast, fly, worm, mouse, and human. The human map contains 519,108 sites for 570 matrices with a False Discovery Rate of 0.1 or less. The new maps are assessed in several ways, for instance using high-throughput experimental ChIP-seq data and AUC statistics, providing strong evidence for their accuracy and coverage. The maps can be usefully integrated with many other kinds of omic data and are available at http://motifmap.igb.uci.edu/. Conclusions MotifMap and its integration with other data provide a foundation for analyzing gene regulation on a genome-wide scale, and for automatically generating regulatory pathways and hypotheses. The power of this approach is demonstrated and discussed using the P53 apoptotic pathway and the Gli hedgehog pathways as examples.

2011-01-01

37

Protein interaction mapping: a Drosophila case study.  

PubMed

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

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

2005-02-14

38

Interactivity on Traditional Media Web Sites  

Microsoft Academic Search

This study compares the radio industry's use of interactivity to that of other traditional media on the Web such as newspapers and television stations, along the dimensions of audience-oriented interactivity and source-oriented interactivity. A content analysis of 112 traditional radio station Web sites, 282 traditional newspaper Web sites, and 128 traditional television station Web sites found that traditional radio station

Michelle Seelig

2008-01-01

39

The protein interaction map of bacteriophage lambda  

PubMed Central

Background Bacteriophage lambda is a model phage for most other dsDNA phages and has been studied for over 60 years. Although it is probably the best-characterized phage there are still about 20 poorly understood open reading frames in its 48-kb genome. For a complete understanding we need to know all interactions among its proteins. We have manually curated the lambda literature and compiled a total of 33 interactions that have been found among lambda proteins. We set out to find out how many protein-protein interactions remain to be found in this phage. Results In order to map lambda's interactions, we have cloned 68 out of 73 lambda open reading frames (the "ORFeome") into Gateway vectors and systematically tested all proteins for interactions using exhaustive array-based yeast two-hybrid screens. These screens identified 97 interactions. We found 16 out of 30 previously published interactions (53%). We have also found at least 18 new plausible interactions among functionally related proteins. All previously found and new interactions are combined into structural and network models of phage lambda. Conclusions Phage lambda serves as a benchmark for future studies of protein interactions among phage, viruses in general, or large protein assemblies. We conclude that we could not find all the known interactions because they require chaperones, post-translational modifications, or multiple proteins for their interactions. The lambda protein network connects 12 proteins of unknown function with well characterized proteins, which should shed light on the functional associations of these uncharacterized proteins.

2011-01-01

40

Comprehensive mapping of the C-terminus of flap endonuclease-1 reveals distinct interaction sites for five proteins that represent different DNA replication and repair pathways  

PubMed Central

Flap endonuclease 1 (FEN-1) is a multifunctional and structure-specific nuclease that plays a critical role in maintaining human genome stability through RNA primer removal, long-patch base excision repair, resolution of DNA secondary structures and stalled DNA replication forks, and apoptotic DNA fragmentation. How FEN-1 is involved in multiple pathways, some of which are seemingly contradictory, is of considerable interest. To date, at least twenty proteins are known to interact with FEN-1; some form distinct complexes that affect one or more FEN-1 activities presumably to direct FEN-1 to a particular DNA metabolic pathway. FEN-1 consists of a nuclease core domain and a C-terminal extension. While the core domain harbors the nuclease activity, the C-terminal extension may be important for protein-protein interactions. Here, we have truncated or mutated the C-terminus of FEN-1 to identify amino acid residues that are critical for interaction with five proteins representing roles in different DNA replication and repair pathways. We found with all five proteins that the C-terminus is important for binding and that each protein uses a subset of amino acid residues. Replacement of one or more residues with an alanine in many cases leads to the complete loss of interaction, which may consequently lead to severe biological defects in mammals.

Guo, Zhigang; Chavez, Valerie; Singh, Purnima; Finger, L. David; Hang, Haiying; Hegde, Muralidhar L.; Mitra, Sankar; Shen, Binghui

2009-01-01

41

National Site Classification Map for Australia  

Microsoft Academic Search

Historic earthquakes have demonstrated that the properties of geological materials beneath a site have a major influence on the amplitude and frequency content of ground shaking. Consideration of site conditions is therefore an important part of seismic hazard and risk assessment. This study presents a national scale site classification for Australia, for use in regional scale seismic hazard and risk

L. S. Hall; A. A. McPherson

2005-01-01

42

Groundwater maps of the Hanford site, June 1995  

SciTech Connect

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

Sweeney, M.D.

1996-03-15

43

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

44

Phosphospecific proteolysis for mapping sites of protein phosphorylation  

Microsoft Academic Search

Protein phosphorylation is a dominant mechanism of information transfer in cells, and a major goal of current proteomic efforts is to generate a system-level map describing all the sites of protein phosphorylation. Recent efforts have focused on developing technologies for enriching and quantifying phosphopeptides. Identification of the sites of phosphorylation typically relies on tandem mass spectrometry to sequence individual peptides.

Zachary A Knight; Birgit Schilling; Richard H Row; Denise M Kenski; Bradford W Gibson; Kevan M Shokat

2003-01-01

45

Interactive Web Sites for Teens  

ERIC Educational Resources Information Center

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

Haycock, Ken

2005-01-01

46

Mapping key functional sites within yeast TFIID.  

PubMed

The transcription factor TFIID, composed of the TATA box-binding protein (TBP) and 14 TBP-associated factors (TAFs), plays a key role in the regulation of gene expression by RNA polymerase II. The structure of yeast TFIID, as determined by electron microscopy and digital image analysis, is formed by three lobes, labelled A-C, connected by thin linking domains. Immunomapping revealed that TFIID contains two copies of the WD-40 repeat-containing TAF5 and that TAF5 contributes to the linkers since its C- and N-termini were found in different lobes. This property was confirmed by the finding that a recombinant complex containing TAF5 complexed with six histone fold containing TAFs was able to form a trilobed structure. Moreover, the N-terminal domain of TAF1 was mapped in lobe C, whereas the histone acetyltransferase domain resides in lobe A along with TAF7. TBP was found in the linker domain between lobes A and C in a way that the N-terminal 100 residues of TAF1 are spanned over it. The implications of these data with regard to TFIID function are discussed. PMID:14765106

Leurent, Claire; Sanders, Steven L; Demény, Màté A; Garbett, Krassimira A; Ruhlmann, Christine; Weil, P Anthony; Tora, Làszlò; Schultz, Patrick

2004-02-12

47

Research on clustered patent mapping visualization and interaction  

Microsoft Academic Search

Patent mapping, which is a series of mapping process with patent information, especially those unstructured information, such as patent claims, details and patent illustrations, is an important tool of patent analysis. Clustering is a popular method to mining the knowledge hidden in patents and provides abundant information to the visualization and interaction of patent mapping. A method of projecting the

Lingyun Sun; Yu Song

2008-01-01

48

Design Issues for Pen-Centric Interactive Maps  

Microsoft Academic Search

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

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

2010-01-01

49

Mapping of Drosophila Mutations Using Site-Specific Male Recombination  

Microsoft Academic Search

Although recombination does not usually occur in the male Drosophila germline, site-specific recombina- tion can be induced at the ends of P elements. This finding suggested that male recombination could be used to map Drosophila mutations. In this article, we describe the general method and its application to the mapping of two EMS-induced female-sterile mutations, grauzone and cortex. Within two

Bin Chen; Tehyen Chu; Emily Harms; J. Peter Gergen; Sidney Strickland

50

Global Mapping of the Yeast Genetic Interaction Network  

Microsoft Academic Search

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

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

2004-01-01

51

Groundwater maps of the Hanford Site, December 1994  

SciTech Connect

This report is a continuation of a series of reports (see Serkowski et al 1994) that the configuration of the uppermost unconfined aquifer beneath the Hanford Site. This series presents the results of the semiannual water level measurement program and the water table maps generated from these measurements. The reports document the changes in the groundwater level at the Hanford Site during the transition from nuclear material production to environmental restoration and remediation. In addition, these reports provide water level data to support the various site characterization and groundwater monitoring programs currently in progress on the Hanford Site.

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

1995-06-01

52

Global Mapping of the Yeast Genetic Interaction Network  

NASA Astrophysics Data System (ADS)

A genetic interaction network containing ~1000 genes and ~4000 interactions was mapped by crossing mutations in 132 different query genes into a set of ~4700 viable gene yeast deletion mutants and scoring the double mutant progeny for fitness defects. Network connectivity was predictive of function because interactions often occurred among functionally related genes, and similar patterns of interactions tended to identify components of the same pathway. The genetic network exhibited dense local neighborhoods; therefore, the position of a gene on a partially mapped network is predictive of other genetic interactions. Because digenic interactions are common in yeast, similar networks may underlie the complex genetics associated with inherited phenotypes in other organisms.

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

2004-02-01

53

Hanford site Computer Automated Mapping Information System (CAMIS)  

SciTech Connect

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

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

1995-09-01

54

Mapping replicational sites in the eucaryotic cell nucleus  

Microsoft Academic Search

We have used fluorescent microscopy to map DNA replication sites in the interphase cell nu- cleus after incorporation of biotinylated dUTP into permeabilized PtK-1 kangaroo kidney or 3T3 mouse fibroblast cells. Discrete replication granules were found distributed throughout the nuclear interior and along the periphery. Three distinct patterns of replica- tion sites in relationship to chromatin domains in the cell

Hiroshi Nakayasu; Ronald Berezney

1989-01-01

55

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

56

Measurement Sites for Wafer Map Visualization and Process Monitoring  

NASA Astrophysics Data System (ADS)

This paper proposes measurement site selection to visualize a wafer characterization map and also monitor wafer-to-wafer and batch-to-batch variation. In the manufacturing line of thin film devices such as large-scale integrated circuits, magnetic heads of hard disk drives and thin-film-transistor substrates of liquid-crystal projectors, several critical dimensions are generally measured and monitored for quality control. To monitor wafer-to-wafer and batch-to-batch variation, engineers control average and standard deviation of measured dimensions as statistical process control. To monitor characterization across a wafer, the engineers observe an sculptured surface as a wafer map. The paper presents a selection method to decide measurement sites across a wafer for both of the wafer map visualization and the process monitoring and examines their accuracies experimentally.

Ono, Makoto; Hayashi, Hirohito; Kondo, Akira; Hamaguchi, Daisuke; Kaneko, Shun'ichi

57

The International HapMap Project Web site  

PubMed Central

The HapMap Web site at http://www.hapmap.org is the primary portal to genotype data produced as part of the International Haplotype Map Project. In phase I of the project, >1.1 million SNPs were genotyped in 270 individuals from four worldwide populations. The HapMap Web site provides researchers with a number of tools that allow them to analyze the data as well as download data for local analyses. This paper presents step-by-step guides to using those tools, including guides for retrieving genotype and frequency data, picking tag-SNPs for use in association studies, viewing haplotypes graphically, and examining marker-to-marker LD patterns.

Thorisson, Gudmundur A.; Smith, Albert V.; Krishnan, Lalitha; Stein, Lincoln D.

2005-01-01

58

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

PubMed

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

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

2013-06-23

59

From ORFeomes to Protein Interaction Maps in Viruses  

Microsoft Academic Search

Although cloned viral ORFeomes are particularly well suited for genome-wide interaction mapping due to the limited size of viral genomes, only a few such studies have been published. Here, we summarize virus interaction mapping projects involving vaccinia virus, hepatitis C virus (HCV), potato virus A (PVA), pea seed-borne mosaic virus (PSbMV), and bacteriophage T7, as well as some projects in

Peter Uetz; Seesandra V. Rajagopala; Yu-An Dong; Jürgen Haas

2009-01-01

60

GABAC receptor sensitivity is modulated by interaction with MAP1B.  

PubMed

GABA(C) receptors contain rho subunits and mediate feedback inhibition from retinal amacrine cells to bipolar cells. We previously identified the cytoskeletal protein MAP1B as a rho1 subunit anchoring protein. Here, we analyze the structural basis and functional significance of the MAP1B-rho1 interaction. Twelve amino acids at the C terminus of the large intracellular loop of rho1 (and also rho2) are sufficient for interaction with MAP1B. Disruption of the MAP1B-rho interaction in bipolar cells in retinal slices decreased the EC(50) of their GABA(C) receptors, doubling the receptors' current at low GABA concentrations without affecting their maximum current at high concentrations. Thus, anchoring to the cytoskeleton lowers the sensitivity of GABA(C) receptors and provides a likely site for functional modulation of GABA(C) receptor-mediated inhibition. PMID:11102469

Billups, D; Hanley, J G; Orme, M; Attwell, D; Moss, S J

2000-12-01

61

Interactive Journey Through the Innerbody Web Site  

Microsoft Academic Search

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

2008-01-01

62

Mapping of anion binding sites on cytochrome c by differential chemical modification of lysine residues.  

PubMed Central

The carbonate binding site on horse cytochrome c was mapped by comparing the yields of carboxydinitrophenyl-cytochromes c, each with a single carboxydinitrophenyl-substituted lysine residue per molecule, when the modification reaction was carried out in the presence and absence of carbonate. The site is located on the "left surface" of the protein and consists of lysine residues 72 and/or 73 as well as 86 and/or 87 (Carbonate Site). Although one of the binding sites for phosphate on cytochrome c (Phosphat Site I) is located near the carbonate site, the sites are distinctly different since carbonate does not displace bound phosphate, as monitored by 31P NMR. Furthermore, citrate interacts with Phosphate Site I with high affinity, whereas chloride, acetate, borate, and cacodylate have a much lower affinity for this site, if they bind to it at all. The affinity of phosphate for Phosphate Site I (KD = 2 X 10(-4) M) is at least 1 order of magnitude higher than it is for other sites of interaction. Images

Osheroff, N; Brautigan, D L; Margoliash, E

1980-01-01

63

Towards adaptable, interactive and quantitative paleogeographic maps  

NASA Astrophysics Data System (ADS)

A variety of paleogeographic atlases have been constructed, with applications from paleoclimate, ocean circulation and faunal radiation models to resource exploration; yet their uncertainties remain difficult to assess, as they are generally presented as low-resolution static maps. We present a methodology for ground-truthing paleogeographic maps, by linking the GPlates plate reconstruction tool to the global Paleobiology Database and a Phanerozoic plate motion model. We develop a spatio-temporal data mining workflow to compare a Phanerozoic Paleogeographic Atlas of Australia with biogeographic indicators. The agreement between fossil data and paleogeographic maps is quite good, but the methodology also highlights key inconsistencies. The Early Devonian paleogeography of southeastern Australia insufficiently describes the Emsian inundation that is supported by biogeography. Additionally, the Cretaceous inundation of eastern Australia retreats by 110 Ma according to the paleogeography, but the biogeography indicates that inundation prevailed until at least 100 Ma. Paleobiogeography can also be used to refine Gondwana breakup and the extent of pre-breakup Greater India can be inferred from the southward limit of inundation along western Australia. Although paleobiology data provide constraints only for paleoenvironments with high preservation potential of organisms, our approach enables the use of additional proxy data to generate improved paleogeographic reconstructions.

Wright, N.; Zahirovic, S.; Müller, R. D.; Seton, M.

2012-07-01

64

A proteome-wide protein interaction map for Campylobacter jejuni  

PubMed Central

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

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

2007-01-01

65

Towards Interactive Museum: Mapping Cultural Contexts to Historical Objects  

Microsoft Academic Search

In this paper, we present Interactive Museum Interface (IMI) which runs on a wearable computer. It allows people to efficiently and intuitively interact with historical objects in museums. Based on the IMI, the historical objects can be mapped to virtual icons containing cultural contexts as if making a shortcut icon in Desktop. A visitor can collect interesting contexts by pointing

Ki-Woong Park; Sung Kyu Park; Jong-Woon Yoo; Kyu Ho Park

2009-01-01

66

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

67

Mapping of contact sites in the caldesmon-calmodulin complex.  

PubMed Central

The interaction of intact calmodulin and its four tryptic peptides with deletion mutants of caldesmon was analysed by native gel electrophoresis, fluorescence spectroscopy and zero-length cross-linking. Deletion mutants H2 (containing calmodulin-binding sites A and B) and H9 (containing sites B and B') interacted with intact calmodulin to form complexes whose stoichiometries varied from 2:1 to 1:1. The N-terminal peptides of calmodulin (TR1C, residues 1-77, and TR2E, residues 1-90) bound H2 with higher affinity than H9. At the same time H2 was less effective than H9 in binding to the C-terminal peptides of calmodulin TR2C (residues 78-148) and TR3E (residues 107-148). The N-terminal peptides of calmodulin (TR1C and TR2E) could be cross-linked to intact caldesmon and its deletion mutants H2 and H9. The similarity in the primary structures of sites A and B' of caldesmon and our measurements of the affinities of H2 and H9 to calmodulin and its peptides strongly indicate an orientation of the protein complex where sites A and B' interact with the N-terminal domain of calmodulin, whereas site B interacts with the C-terminal domain of calmodulin. The spatial organization of contact sites in the caldesmon-calmodulin complex agrees with the earlier proposed two-dimensional model of interaction of the two proteins [Huber, El-Mezgueldi, Grabarek, Slatter, Levine and Marston (1996) Biochem. J. 316, 413-420].

Medvedeva, M V; Kolobova, E A; Huber, P A; Fraser, I D; Marston, S B; Gusev, N B

1997-01-01

68

Prediction, Assessment and Validation of Protein Interaction Maps in Bacteria  

Microsoft Academic Search

High-throughput proteomics technologies, especially the yeast two-hybrid system, produce large volumes of protein–protein interaction data organized in networks. The complete sequencing of many genomes raises questions about the extent to which such networks can be transferred between organisms. We attempted to answer this question using the experimentally derived Helicobacter pylori interaction map and the recently described interacting domain profile pair

Jérôme Wojcik; Ivo G. Boneca; Pierre Legrain

2002-01-01

69

Microtubule Interaction Site of the Kinesin Motor  

Microsoft Academic Search

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

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

1997-01-01

70

Interactive computer methods for generating mineral-resource maps  

USGS Publications Warehouse

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

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

1980-01-01

71

The interactive multisensor snow and ice mapping system  

NASA Astrophysics Data System (ADS)

The interactive multisensor snow and ice mapping system (IMS) was developed to give snow and ice analysts the tools, on one platform, to inspect visually the imagery and mapped data from various sensor sources to determine the presence of snow and ice and to depict snow- and ice-covered areas on a map on a daily basis, in one hour or less. Snow and ice analysts in the National Environmental Satellite, Data, and Information Service have been creating weekly maps showing the extent of snow cover for the Northern Hemisphere since 1966 using visible imagery from polar-orbiting and geostationary satellites and surface observations as data sources. The current process is mostly manual and time-consuming, taking up to 10 hours to produce a map during the snow season. Where cloud cover precludes an unobstructed view of an area during the entire week, the analysis from the previous week is carried forward. Each week the analyst draws a new map by hand, then digitizes the extent of snow and ice cover using an 89×89 line grid overlaid on a stereographic map of the Northern Hemisphere. The hand-drawn map is photocopied and distributed and the digitized map is saved to a file for use in National Weather Service numerical models and for archival storage. IMS was designed and built to replace and improve this process by producing a more accurate and timely product.

Ramsay, Bruce H.

1998-07-01

72

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

73

Epstein-Barr virus and virus human protein interaction maps  

PubMed Central

A comprehensive mapping of interactions among Epstein–Barr virus (EBV) proteins and interactions of EBV proteins with human proteins should provide specific hypotheses and a broad perspective on EBV strategies for replication and persistence. Interactions of EBV proteins with each other and with human proteins were assessed by using a stringent high-throughput yeast two-hybrid system. Overall, 43 interactions between EBV proteins and 173 interactions between EBV and human proteins were identified. EBV–EBV and EBV–human protein interaction, or “interactome” maps provided a framework for hypotheses of protein function. For example, LF2, an EBV protein of unknown function interacted with the EBV immediate early R transactivator (Rta) and was found to inhibit Rta transactivation. From a broader perspective, EBV genes can be divided into two evolutionary classes, “core” genes, which are conserved across all herpesviruses and subfamily specific, or “noncore” genes. Our EBV–EBV interactome map is enriched for interactions among proteins in the same evolutionary class. Furthermore, human proteins targeted by EBV proteins were enriched for highly connected or “hub” proteins and for proteins with relatively short paths to all other proteins in the human interactome network. Targeting of hubs might be an efficient mechanism for EBV reorganization of cellular processes.

Calderwood, Michael A.; Venkatesan, Kavitha; Xing, Li; Chase, Michael R.; Vazquez, Alexei; Holthaus, Amy M.; Ewence, Alexandra E.; Li, Ning; Hirozane-Kishikawa, Tomoko; Hill, David E.; Vidal, Marc; Kieff, Elliott; Johannsen, Eric

2007-01-01

74

Mapping the phase diagram of strongly interacting matter  

SciTech Connect

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

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

2011-04-01

75

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

PubMed

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

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

2008-11-01

76

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

PubMed Central

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

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

2010-01-01

77

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

PubMed Central

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

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

2012-01-01

78

Gate Map Tunneling Spectroscopy of Interactions in Graphene  

NASA Astrophysics Data System (ADS)

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

Chae, Jungseok

2013-03-01

79

Integrating physical and genetic maps: from genomes to interaction networks  

PubMed Central

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 involves reconciling the wide variety of interaction types that are currently available. For this purpose, recent studies have sought to classify genetic and physical interactions along several complementary dimensions, such as ordered versus unordered, alleviating versus aggravating, and first versus second degree.

Beyer, Andreas; Bandyopadhyay, Sourav; Ideker, Trey

2009-01-01

80

USGS Topographic Maps  

NSDL National Science Digital Library

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

2010-10-26

81

Gestion informatisee du site. Gestion de l'occupation du sol par un plan numerique. (Computer aided site management. Site use management by digital mapping).  

National Technical Information Service (NTIS)

The logistics program developed for assisting the Hague site management is presented. A digital site mapping representation and geographical data bases are used. The digital site map and its integration into a data base are described. The program can be a...

J. C. Chupin

1990-01-01

82

Mutual adaptation to mind mapping in human-agent interaction  

Microsoft Academic Search

This paper describes a human-agent interaction framework in which a user and a life-like agent mutually acquire the other's mind mapping through a mutual mind reading game. Through development of various life-like agents and an internal state (mind) of an agent like emotion, processing load has been recognized to play an important role in making them believable to a user.

Seiji YAMADA; Tomohiro YAMAGUCHI

2002-01-01

83

Evolution of the spatial distribution of MAP1B phosphorylation sites in vertebrate neurons  

PubMed Central

The microtubule-associated protein MAP1B has important roles in neural development, particularly in migrating and differentiating neurons. MAP1B is phosphorylated by glycogen synthase kinase 3? (GSK-3?) at a site that requires prior phosphorylation by another kinase four amino acid residues downstream of the GSK-3? site, a so-called primed site, and at non-primed sites that have no such requirement. In developing mammalian neurons, MAP1B phosphorylated by GSK-3? at primed and non-primed sites is distributed in spatially distinct patterns. Non-primed GSK-3?-phosphorylated MAP1B sites are only expressed in axons and are present in the form of a gradient that is highest distally, towards the growth cone. In contrast, primed GSK-3?-phosphorylated MAP1B sites are present throughout the neuron including the somato-dendritic compartment and uniformly throughout the axon. To examine the function of these two sites, we explored the evolutionary conservation of the spatial distribution of GSK-3? primed and non-primed sites on MAP1B in vertebrate neurons. We immunostained spinal cord sections from embryonic or newly hatched representatives of all of the main vertebrate groups using phospho-specific antibodies to GSK-3? primed and non-primed sites on MAP1B. This revealed a remarkable evolutionary conservation of the distribution of primed and non-primed GSK-3?-phosphorylated MAP1B sites in developing vertebrate neurons. By analysing amino acid sequences of MAP1B we found that non-primed GSK-3? sites are more highly conserved than primed sites throughout the vertebrates, suggesting that the latter evolved later. Finally, distinct distribution patterns of GSK-3? primed and non-primed sites on MAP1B were preserved in cultured rat embryonic cortical neurons, opening up the possibility of studying the two sites in vitro.

Tymanskyj, Stephen R; Lin, Shen; Gordon-Weeks, Phillip R

2010-01-01

84

Methods for Mapping of Interaction Networks Involving Membrane Proteins  

SciTech Connect

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

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

2007-11-23

85

Map Maker  

NSDL National Science Digital Library

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

Interior, United S.

86

MIMO: an efficient tool for molecular interaction maps overlap  

PubMed Central

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

2013-01-01

87

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

PubMed

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

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

2008-05-01

88

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.

89

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

PubMed

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

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

2012-05-19

90

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

Microsoft Academic Search

This eye-opener article aims at introducing the health GIS community to the emerging online consumer geoinformatics services from Google and Microsoft (MSN), and their potential utility in creating custom online interactive health maps. Using the programmable interfaces provided by Google and MSN, we created three interactive demonstrator maps of England's Strategic Health Authorities. These can be browsed online at http:\\/\\/www.healthcybermap.org\\/GoogleMapsAPI\\/

Maged N Kamel Boulos

2005-01-01

91

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

92

Ontology-based web site mapping for information exploration  

Microsoft Academic Search

Centralized search process requires that the whole collection reside at a single site. This imposes a burden on both the system storage of the site and the network traffic near the site. It thus comes to require the search process to be distributed. Recently, more and more Web sites provide the ability to search their local collection of Web pages.

Xiaolan Zhu; Susan Gauch; Lutz Gerhard; Nicholas Kral; Alexander Pretschner

1999-01-01

93

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

Microsoft Academic Search

Physical mapping of DNA can be accomplished by direct AFM imaging of site specific proteins bound to DNA molecules. Using Gln-111, a mutant of EcoRI endonuclease with a specific affinity for EcoRI sites 1000 times greater than wild type enzyme but with cleavage rate constants reduced by a factor of 104, we demonstrate site-specific mapping by direct AFM imaging. Images

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

1995-01-01

94

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

Microsoft Academic Search

Physical mapping of DNA can be accomplished by direct AFM imaging of site specific proteins bound to DNA molecules. Using Gln-111, a mutant of EcoRI endonuclease with a specific affinity for EcoRI sites 1,000 times greater than wild type enzyme but with cleavage rate constants reduced by a factor of 10⁴, the authors demonstrate site-specific mapping by direct AFM imaging.

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

1995-01-01

95

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

Microsoft Academic Search

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

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

2005-01-01

96

The Gunby Site and Late Pickering Interactions  

Microsoft Academic Search

The Gunby site, excavated during the summer and fall of 1977, represents a late Pickering village dating to circa 1300-1320 A.D. Ten longhouses, ranging from 10.0 to 45.2 meters in length, lie within a village estimated at 1.1 hectares (2.7 acres). This constitutes the most longhouses uncovered at a Pickering site to date.\\u000aFaunal and floral samples from Gunby clearly

Robert John Rozel

1979-01-01

97

The Evaluation and Influence of Interaction in Network Supported Collaborative Concept Mapping.  

ERIC Educational Resources Information Center

|This study of inservice and preservice teachers investigated group interaction processes in networked supported collaborative concept mapping and the influence these group interaction processes had upon group concept mapping performance. Results showed that group concept mapping performance was significantly correlated to the quantity of group…

Chiu, Chiung-Hui; Huang, Chun-Chieh; Chang, Wen-Tsung

2000-01-01

98

Mapping Interactions between mRNA Export Factors in Living Cells  

PubMed Central

The TREX complex couples nuclear mRNA processing events with subsequent export to the cytoplasm. TREX also acts as a binding platform for the mRNA export receptor Nxf1. The sites of mRNA transcription and processing within the nucleus have been studied extensively. However, little is known about where TREX assembly takes place and where Nxf1 is recruited to TREX to form the export competent mRNP. Here we have used sensitized emission Förster resonance energy transfer (FRET) and fluorescence lifetime imaging (FLIM)-FRET, to produce a spatial map in living cells of the sites for the interaction of two TREX subunits, Alyref and Chtop, with Nxf1. Prominent assembly sites for export factors are found in the vicinity of nuclear speckles in regions known to be involved in transcription, splicing and exon junction complex formation highlighting the close coupling of mRNA export with mRNP biogenesis.

Teng, I-Fang; Wilson, Stuart A.

2013-01-01

99

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

USGS Publications Warehouse

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

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

2006-01-01

100

Charting the genetic interaction map of a cell.  

PubMed

Genome sequencing projects have revealed a massive catalog of genes and astounding genetic diversity in a variety of organisms. We are now faced with the formidable challenge of assigning functions to thousands of genes, and how to use this information to understand how genes interact and coordinate cell function. Studies indicate that the majority of eukaryotic genes are dispensable, highlighting the extensive buffering of genomes against genetic and environmental perturbations. Such robustness poses a significant challenge to those seeking to understand the wiring diagram of the cell. Genome-scale screens for genetic interactions are an effective means to chart the network that underlies this functional redundancy. A complete atlas of genetic interactions offers the potential to assign functions to most genes identified by whole genome sequencing projects and to delineate a functional wiring diagram of the cell. Perhaps more importantly, mapping genetic networks on a large-scale will shed light on the general principles and rules governing genetic networks and provide valuable information regarding the important but elusive relationship between genotype and phenotype. PMID:21111604

Costanzo, Michael; Baryshnikova, Anastasia; Myers, Chad L; Andrews, Brenda; Boone, Charles

2010-11-24

101

Mapping of RGS12-Cav2.2 channel interaction.  

PubMed

The alpha1 (pore-forming) subunit of the Cav2.2 (N-type) channel is tyrosine phosphorylated by Src kinase upon activation of GABAB receptors. The tyrosine-phosphorylated form of the alpha1 subunit of the Cav2.2 channel becomes a target for the binding of RGS12, a GTPase-accelerating protein. Binding of the phosphotyrosine-binding domain of RGS12 to the tyrosine-phosphorylated channel alters the kinetics of the termination of GABA-mediated inhibition of the calcium current. Using a combination of biochemical and electrophysiological approaches, we have determined that the SNARE binding or "synprint" region of the Cav2.2 binds to RGS12. This article describes the protocols used to map the interaction using primary neuronal cultures. PMID:15488181

Richman, Ryan W; Diversé-Pierluissi, María A

2004-01-01

102

Active site mapping of trypsin, thrombin and matriptase-2 by sulfamoyl benzamidines.  

PubMed

The benzamidine moiety, a well-known arginine mimetic, has been introduced in a variety of ligands, including peptidomimetic inhibitors of trypsin-like serine proteases. According to their primary substrate specificity, the benzamidine residue interacts with the negatively charged aspartate at the bottom of the S1 pocket of such enzymes. Six series of benzamidine derivatives (1-73) were synthesized and evaluated as inhibitors of two prototype serine proteases, that is, bovine trypsin and human thrombin. As a further target, human matriptase-2, a recently discovered type II transmembrane serine protease, was investigated. Matriptase-2 represents an important regulatory protease in iron homeostasis by down-regulation of the hepcidin expression. Compounds 1-73 were designed to contain a fixed sulfamoyl benzamidine moiety as arginine mimetic and a linker-connected additional substructure, such as a tert-butyl ester, carboxylate or second benzamidine functionality. A systematic mapping approach was performed with these inhibitors to scan the active site of the three target proteases. In particular, bisbenzamidines, able to interact with both the S1 and S3/S4 binding sites, showed notable affinity. In branched bisbenzamidines 66-73 containing a third hydrophobic residue, opposite effects of the stereochemistry on trypsin and thrombin inhibition were observed. PMID:23026080

Dosa, Stefan; Stirnberg, Marit; Lülsdorff, Verena; Häußler, Daniela; Maurer, Eva; Gütschow, Michael

2012-09-05

103

A MAP OF IMPORTANT GEOLOGICAL SITES OF SLOVAKIA  

Microsoft Academic Search

The Landscape Atlas of the Slovak Republic is being prepared at the Ministry of the Environment of the Slovak Republic comprising also geological aspects of the environment. The map of geological curiosities at 1 : 1 000 000 scale is the compound of the chapter 8 devoted to protected territories and natural resources (responsible editor: RNDr. Tatiana Hrn?iarová, CSc.). Geological

P. LIŠ?ÁK; M. POLÁK; I. BARÁTH

104

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

PubMed Central

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

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

2011-01-01

105

Mapping the Distribution of Perchlorates on the Martian Surface at the Phoenix Landing Site  

NASA Astrophysics Data System (ADS)

Mapping the distribution of perchlorates near the Phoenix landing site is accomplished using the Phoenix’s Surface Stereo Imager (SSI). Images were chosen for analysis based on the trenching activity of the Phoenix’s Robotic Arm.

Clark, A. S.; Cull, S. C.

2012-03-01

106

Sagamore Hill National Historic Site, New York. Historical Base Map Documentation. Historic Resource Study.  

National Technical Information Service (NTIS)

The historical base map documentation for Sagamore Hill National Historic Site is a description of the physical environment of Theodore Roosevelt's home. The author treats the environment of that Long Island area, the boundaries of Roosevelt's property, v...

F. Wilshin

1972-01-01

107

IMPROVING FARM MANAGEMENT DECISIONS BY ANALYZING SITE-SPECIFIC ECONOMIC DATA DEVELOPED FROM YIELD MAPS  

Microsoft Academic Search

This thesis examines the use of precision agriculture data, specifically yield maps, for makingsite-specific economic decisions for improved farm management. The adoption of precisionagriculture on farms has allowed producers to collect a greater quantity and more specificinformation about production than ever before. With such information, site-specific decisions canbe made. Incorporating economic data with yield map data, two primary decision examples

Laura A. Powers

2002-01-01

108

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

Microsoft Academic Search

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

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

1998-01-01

109

Phosphorylation sites of Arabidopsis MAP kinase substrate 1 (MKS1)  

Microsoft Academic Search

The Arabidopsis MAP kinase 4 (MPK4) substrate MKS1 was expressed in Escherichia coli and purified, full-length, 6x histidine (His)-tagged MKS1 was phosphorylated in vitro by hemagglutinin (HA)-tagged MPK4 immuno-precipitated from plants. MKS1 phosphorylation was initially verified by electrophoresis and gel-staining with ProQ Diamond and the protein was digested by either trypsin or chymotrypsin for maximum sequence coverage to facilitate identification

Mikael B. Caspersen; Jin-Long Qiu; Xumin Zhang; Erik Andreasson; Henrik Næsted; John Mundy; Birte Svensson

2007-01-01

110

Structural mapping of nucleotide binding sites on chloroplast coupling factor  

SciTech Connect

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

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

1982-02-16

111

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

ERIC Educational Resources Information Center

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

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

2008-01-01

112

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

ERIC Educational Resources Information Center

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

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

2008-01-01

113

Mapping Functional Interactions in a Heterodimeric Phospholipid Pump*  

PubMed Central

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

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

2012-01-01

114

Restriction endonucleases functionally interacting with two DNA sites  

Microsoft Academic Search

Simultaneous interaction with two recognition sites was found to be a precondition for DNA cleavage by certain type-II and type-III restriction endonucleases. Nevertheless, the molecular mechanisms of the protein-DNA interaction are different between members of both classes of enzymes.

Detlev H. Krüger; Dagmar Kupper; Andreas Meisel; Mike Tierlich; Monika Reuter; Cornelia Schroeder

1995-01-01

115

Thermal interaction effect on nucleation site distribution in subcooled boiling  

SciTech Connect

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

Ling Zou; Barclay Joned

2012-05-01

116

Drosophila protein interaction map (DPiM): a paradigm for metazoan protein complex interactions.  

PubMed

Proteins perform essential cellular functions as part of protein complexes, often in conjunction with RNA, DNA, metabolites and other small molecules. The genome encodes thousands of proteins but not all of them are expressed in every cell type; and expressed proteins are not active at all times. Such diversity of protein expression and function accounts for the level of biological intricacy seen in nature. Defining protein-protein interactions in protein complexes, and establishing the when, what and where of potential interactions, is therefore crucial to understanding the cellular function of any protein-especially those that have not been well studied by traditional molecular genetic approaches. We generated a large-scale resource of affinity-tagged expression-ready clones and used co-affinity purification combined with tandem mass-spectrometry to identify protein partners of nearly 5,000 Drosophila melanogaster proteins. The resulting protein complex "map" provided a blueprint of metazoan protein complex organization. Here we describe how the map has provided valuable insights into protein function in addition to generating hundreds of testable hypotheses. We also discuss recent technological advancements that will be critical in addressing the next generation of questions arising from the map. PMID:23222005

Guruharsha, K G; Obar, Robert A; Mintseris, Julian; Aishwarya, K; Krishnan, R T; Vijayraghavan, K; Artavanis-Tsakonas, Spyros

117

A Comprehensive Molecular Interaction Map for Rheumatoid Arthritis  

PubMed Central

Background Computational 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 that occur between molecules related to Rheumatoid Arthritis (RA). Methodology Due to the complexity of the disease and the numerous molecular players involved, we devised a method to construct a systemic network of interactions of the processes ongoing in patients affected by RA. The network is based on high-throughput data, refined semi-automatically with carefully curated literature-based information. This global network has then been topologically analysed, as a whole and tissue-specifically, in order to translate the experimental molecular connections into topological motifs meaningful in the identification of tissue-specific markers and targets in the diagnosis, and possibly in the therapy, of RA. Significance We find that some nodes in the network that prove to be topologically important, in particular AKT2, IL6, MAPK1 and TP53, are also known to be associated with drugs used for the treatment of RA. Importantly, based on topological consideration, we are also able to suggest CRKL as a novel potentially relevant molecule for the diagnosis or treatment of RA. This type of finding proves the potential of in silico analyses able to produce highly refined hypotheses, based on vast experimental data, to be tested further and more efficiently. As research on RA is ongoing, the present map is in fieri, despite being -at the moment- a reflection of the state of the art. For this reason we make the network freely available in the standardised and easily exportable .xml CellDesigner format at ‘www.picb.ac.cn/ClinicalGenomicNTW/temp.html’ and ‘www.celldesigner.org’.

Nardini, Christine

2010-01-01

118

Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data  

PubMed Central

Mammalian RNA complexity is regulated through interactions of RNA-binding proteins (RBPs) with their target transcripts. High-throughput sequencing together with UV-crosslinking and immunoprecipitation (HITS-CLIP) is able to globally map RBP-binding footprint regions at the resolution of ~30–60 nucleotides. Here we describe a systematic way to analyze HITS-CLIP data to identify exact crosslink sites, and thereby determine protein-RNA interactions at single-nucleotide resolution. We found that reverse transcriptase used in CLIP frequently skips the crosslinked amino-acid-RNA adduct, resulting in a nucleotide deletion. Genome-wide analysis of these cross-linking induced mutation sites (CIMS) in Nova and Argonaut (Ago) HITS-CLIP data demonstrated deletions in ~8–20% mRNA tags, which mapped to Nova and Ago binding sites on mRNA or miRNA in the mouse brain. CIMS analysis provides a general and more precise means of mapping protein-RNA interactions than currently available, as well as providing insight into the biochemical properties of such interactions in living tissues.

Zhang, Chaolin; Darnell, Robert B.

2012-01-01

119

Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data.  

PubMed

Mammalian RNA complexity is regulated through interactions of RNA-binding proteins (RBPs) with their target transcripts. High-throughput sequencing together with UV-crosslinking and immunoprecipitation (HITS-CLIP) is able to globally map RBP-binding footprint regions at a resolution of ~30-60 nucleotides. Here we describe a systematic way to analyze HITS-CLIP data to identify exact crosslink sites, and thereby determine protein-RNA interactions at single-nucleotide resolution. We found that reverse transcriptase used in CLIP frequently skips the crosslinked amino-acid-RNA adduct, resulting in a nucleotide deletion. Genome-wide analysis of these crosslinking-induced mutation sites (CIMS) in HITS-CLIP data for Nova and Argonaute (Ago) proteins in mouse brain tissue revealed deletions in ~8-20% of mRNA tags, which mapped to Nova and Ago binding sites on mRNA or miRNA. CIMS analysis provides a general and more precise means of mapping protein-RNA interactions than currently available methods and insight into the biochemical properties of such interactions in living tissues. PMID:21633356

Zhang, Chaolin; Darnell, Robert B

2011-06-01

120

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

121

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

National Technical Information Service (NTIS)

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

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

1995-01-01

122

Conserved Sequence-Tagged Sites: A Phylogenetic Approach to Genome Mapping  

Microsoft Academic Search

Cognate sites in genomes that diverged ≈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

Richard Mazzarella; Vittorio Montanaro; Juha Kere; Rolland Reinbold; Alfredo Ciccodicola; Michele D'Urso; David Schlessinger

1992-01-01

123

A novel approach in model-based mapping of soil water conditions at forest sites  

Microsoft Academic Search

Knowledge of site-specific water conditions is important in forestland evaluation and fundamental for a sustainable forest management. In Central Europe, traditional site mapping has followed an integrated ecological approach. The assessment of soil water availability is based on overlaying relief and descriptive soil information. It is a relative system referring to an (hypothetical) equilibrium between relief-dependent soil conditions and the

Kai Schwärzel; Karl-Heinz Feger; Janet Häntzschel; Alexander Menzer; Uwe Spank; Falko Clausnitzer; Barbara Köstner; Christian Bernhofer

2009-01-01

124

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

Microsoft Academic Search

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

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

2003-01-01

125

Nucleocytoplasmic glycosylation, O-GlcNAc: identification and site mapping.  

PubMed

beta-O-linked N-acetylglucosamine (O-GlcNAc) is posttranslationally added to serine and threonine residues of many nuclear and cytoplasmic proteins found in metazoans. This modification is dynamic and responsive to numerous stimuli and conditions, suggesting an important role in many regulatory pathways. Moreover, the O-GlcNAc modification seems to compete with phosphorylation for sites of attachment, indicating a reciprocal relationship with phosphorylation. This chapter includes protocols for: (1) identifying the O-GlcNAc modification on proteins through immunoblotting, lectin affinity chromatography, and galactosyltransferase labeling; and (2) identifying and enriching for the sites of attachment using the mass spectrometry-based beta-elimination followed by Michael addition with dithiothreitol (BEMAD) technique. PMID:15173616

Zachara, Natasha Elizabeth; Cheung, Win Den; Hart, Gerald Warren

2004-01-01

126

Halogenated naphthyl methoxy piperidines for mapping serotonin transporter sites  

DOEpatents

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

Goodman, M.M.; Faraj, B.

1999-07-06

127

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

Microsoft Academic Search

We derive a family of singular iterated maps—closely related to Poincare´ maps—that describe chaotic interactions between colliding solitary waves. The chaotic behavior of such solitary-wave collisions depends on the transfer of energy to a secondary mode of oscillation, often an internal mode of the pulse. This map allows us to go beyond previous analyses and to understand the interactions in

Roy H. Goodman; Roy H

2008-01-01

128

Digital soil mapping at pilot sites in the northwest coast of Egypt: A multinomial logistic regression approach  

Microsoft Academic Search

The study examines a digital soil mapping approach for the production of soil maps by using multinomial logistic regression on soil and terrain information at pilot sites in the Northwestern Coastal region of Egypt. The aim is to reproduce the original map and predict soil distribution in the adherent landscape. Reference soil maps produced by conventional methods at Omayed and

Fawzy Hassan Abdel-Kader

2011-01-01

129

Site assessment guidelines provide road map in due diligence  

SciTech Connect

Buyers, sellers and lenders of commercial and industrial real estate since the 1980s have faced potential liability under CERCLA for property contamination. The law stipulates that buyers must exercise due diligence'', conducting all appropriate inquiry'' to determine past ownership and uses of a property, and whether contamination exists. Buyers of polluted property can avoid liability only by showing that contamination occurred before the property was transferred to them, and that they had no knowledge or reason to know'' about the contamination at the time of purchase. Owners or sellers of contaminated property, as well as buyers aware of the contamination at time of purchase, may be designated potentially responsible parties (PRPs) under CERCLA and held liable for site cleanup. Lenders that participate in managing a contaminated property also may be designated PRPs. EPA in 1992 provided a liability exemption for lenders with limited or no management responsibilities for a contaminated property.

Not Available

1994-03-01

130

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

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

131

Detecting site-specific biochemical constraints through substitution mapping.  

PubMed

The neutral theory of molecular evolution states that most mutations are deleterious or neutral. It results that the evolutionary rate of a given position in an alignment is a function of the level of constraint acting on this position. Inferring evolutionary rates from a set of aligned sequences is hence a powerful method to detect functionally and/or structurally important positions in a protein. Some positions, however, may be constrained while having a high substitution rate, providing these substitutions do not affect the biochemical property under constraint. Here, I introduce a new evolutionary rate measure accounting for the evolution of specific biochemical properties (e.g., volume, polarity, and charge). I then present a new statistical method based on the comparison of two rate measures: a site is said to be constrained for property X if it shows an unexpectedly high conservation of X knowing its total evolutionary rate. Compared to single-rate methods, the two-rate method offers several advantages: it (i) allows assessment of the significance of the constraint, (ii) provides information on the type of constraint acting on each position, and (iii) detects positions that are not proposed by previous methods. I apply this method to a 200-sequence data set of triosephosphate isomerase and report significant cases of positions constrained for polarity, volume, or charge. The three-dimensional localization of these positions shows that they are of potential interest to the molecular evolutionist and to the biochemist. PMID:18696030

Dutheil, Julien

2008-08-12

132

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

PubMed

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

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

2009-11-01

133

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

134

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

PubMed

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

Schwacke, John H; Voit, Eberhard O

2007-01-14

135

An Approach to Intelligent Interactive Social Network Geo Mapping  

Microsoft Academic Search

\\u000a Map-based visualization of different kinds of information, which can be geo-coded to a particular location, becomes more and\\u000a more popular, as it is very well accepted and understood by end-users. However, a simple map interface is not enough if we\\u000a aim to provide information about objects coming from vast and dynamic information spaces such as the Web or social networks

Anton Ben?i?; Márius Šajgalík; Michal Barla; Mária Bieliková

136

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.

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

137

Nucleation site interaction in pool boiling on the artificial surface  

Microsoft Academic Search

The present work aims at studying the physical mechanisms of nucleation site interaction in pool boiling. A series of experiments have been carried out to investigate the average bubble departure frequency fd of two artificial cavities on the thin silicon surface for different dimensionless cavity spacing S\\/Db, that is the ratio of the cavity spacing to the average bubble departure

Lei Zhang; Masahiro Shoji

2003-01-01

138

Using Catalytic Atom Maps to Predict the Catalytic Functions Present in Enzyme Active Sites  

PubMed Central

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

Nosrati, Geoffrey R.; Houk, K. N.

2012-01-01

139

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

140

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

USGS Publications Warehouse

A vegetation mapping and characterization effort was conducted at Fort Bowie National Historic Site in 2008-10 by the Sonoran Desert Network office in collaboration with researchers from the Office of Arid lands studies, Remote Sensing Center at the University of Arizona. This vegetation mapping effort was completed under the National Park Service Vegetation Inventory program which aims to complete baseline mapping inventories at over 270 national park units. The vegetation map data was collected to provide park managers with a digital map product that met national standards of spatial and thematic accuracy, while also placing the vegetation into a regional and even national context. Work comprised of three major field phases 1) concurrent field-based classification data collection and mapping (map unit delineation), 2) development of vegetation community types at the National Vegetation Classification alliance or association level and 3) map accuracy assessment. Phase 1 was completed in late 2008 and early 2009. Community type descriptions were drafted to meet the then-current hierarchy (version 1) of the National Vegetation Classification System (NVCS) and these were applied to each of the mapped areas. This classification was developed from both plot level data and censused polygon data (map units) as this project was conducted as a concurrent mapping and classification effort. The third stage of accuracy assessment completed in the fall of 2010 consisted of a complete census of each map unit and was conducted almost entirely by park staff. Following accuracy assessment the map was amended where needed and final products were developed including this report, a digital map and full vegetation descriptions. Fort Bowie National Historic Site covers only 1000 acres yet has a relatively complex landscape, topography and geology. A total of 16 distinct communities were described and mapped at Fort Bowie NHS. These ranged from lush riparian woodlands lining the ephemeral washes dominated by Ash (Fraxinus), Walnut (Juglans) and Hackberry (Celtis) to drier upland sites typical of desert scrub and semi-desert grassland communities. These shrublands boast a diverse mixture of shrubs, succulents and perennial grasses. In many places the vegetation could be seen to echo the history of the fort site, with management of shrub encroachment apparent in the grasslands and the paucity of trees evidence of historic cutting for timber and fire wood. Seven of the 16 vegetation types were ‘accepted’ types within the NVC while the others have been described here as specific to FOBO and have proposed status within the NVC. The map was designed to facilitate ecologically-based natural resources management and research. The map is in digital format within a geodatabase structure that allows for complex relationships to be established between spatial and tabular data, and makes accessing the product easy and seamless. The GIS format allows user flexibility and will also enable updates to be made as new information becomes available (such as revised NVC codes or vegetation type names) or in the event of major disturbance events that could impact the vegetation.

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

2013-01-01

141

Soil profile mapping in relation to site evaluation for foundations and earthworks  

Microsoft Academic Search

Summary  Site evaluation for foundations and earthworks requires more detailed investigation than that required for the preparation\\u000a of general purpose engineering geological maps. It is generally best carried out in several stages, all of which must take\\u000a account of the functional requirements of the structure planned at the site and the practical problems which may arise during\\u000a construction. Of particular importance

A. Marsland; A. McGown; E. Derbyshire

1980-01-01

142

ICMAP: An interactive tool for concept map generation to facilitate learning process  

Microsoft Academic Search

Human-computer interaction could play an essential role in learning. In distance learning, interactive tools can facilitate the learning process for teachers and students. In this article, the design and implementation of software will be introduced which helps users to learn more with the help of interactive instructions and concept map (Cmap) generation. Cmaps are graphical visualisations of knowledge about a

Hendijanifard Fatemeh; Kardan Ahmad; Dibay Moghadam Mohammad

2011-01-01

143

Learning Consistent, Interactive, and Meaningful Task-Action Mappings: A Computational Model.  

ERIC Educational Resources Information Center

The study of human-computer interactions has revealed that highly interactive devices are often easier to learn to use than keyboard-based devices. Describes an integrated cognitive model designed to exhibit interactions between people and computers while learning task-action mappings such as the action sequences for opening a file in a word…

Howes, Andrew; Young, Richard M.

1996-01-01

144

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

NASA Astrophysics Data System (ADS)

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

Chorianopoulos, Konstantinos; Rieniets, Tim

145

Geological map of the future: digital, interactive, and 3D  

NASA Astrophysics Data System (ADS)

Geological survey agencies are developing methods for government geological mapping in the post-paper map era. Surficial and bedrock maps are being digitized and reconciled, while multiple generations of legends are being made accessible in a categorized format. Regional 3D geological models that integrate soils and geology, surficial and bedrock geology, as well as onshore and offshore are increasingly in demand as the information, technology, and protocols to build them progress. Applications such as regional groundwater modelling require digitizing, reconciliation, and assembly of a digital elevation model, bathymetry, offshore geology, soils, surficial geology, public domain drillhole and geophysical data, bedrock maps, and existing stratigraphic models typically expressed as structure contours. New stratigraphic modelling, particularly required for surficial unconsolidated deposits in many regions, requires information from cored holes logged by geologists as well as geophysical surveys. These high-quality results are extrapolated laterally using drill hole data, commonly large quantities of water well data of varying resolution and reliability. Much effort is required to adequately georeference the drillhole data, and to parse large numbers of unique lithological descriptions. Stratigraphic modelling methods ideally use all data and an approach that permits judgement in the acceptance or rejection of data, while interpolation and extrapolation are guided by genetic insights. Models are best captured as a grid of predicted stratigraphy profiles that convey expert opinion on interpolation and extrapolation from the data points. Reconciliation of mapping with that of neighbouring jurisdictions is a key step, as is balancing subjective definition of strata with more objective geostatistical approaches to characterizing the heterogeneous physical properties of the strata. Progress is readily achievable in undeformed strata, while deformed strata present far greater challenges. Increasingly, databases of observations and measurements are being retained alongside the interpreted model, and models are being assigned varying confidence levels such that the result is seen not as an end but a means for prioritizing new mapping. Current activity is broadening our reliance not only from paper maps to digital models, but also from plan view maps, to drillhole databases, to 3D models, to dynamic models such as groundwater flow models. Pressing user requirements demand that geological survey work rapidly advance along this progression.

Thorleifson, H.

2003-12-01

146

APPLICATION OF THE INTERACTIVE IMAGE MAPPING FOR THE DEVELOPMENT OF KIDS ROBOT DESIGN  

Microsoft Academic Search

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

Jonghwan Seo; Jaehyung Byun; Sungho Yang; Myungseok Kim

147

BacMap: an interactive picture atlas of annotated bacterial genomes.  

PubMed

BacMap is an interactive visual database containing fully labeled, zoomable and searchable chromosome maps from more than 170 bacterial (archaebacterial and eubacterial) species. It uses a recently developed visualization tool (CGView) to generate high-resolution circular genome maps from sequence feature information. Each map includes an interface that allows the image to be expanded and rotated. In the default view, identified genes are drawn to scale and colored according to coding directions. When a region of interest is expanded, gene labels are displayed. Each label is hyperlinked to a custom 'gene card' which provides several fields of information concerning the corresponding DNA and protein sequences. Each genome map is searchable via a local BLAST search and a gene name/synonym search. BacMap is freely available at http://wishart.biology.ualberta.ca/BacMap/. PMID:15608206

Stothard, Paul; Van Domselaar, Gary; Shrivastava, Savita; Guo, Anchi; O'Neill, Brian; Cruz, Joseph; Ellison, Michael; Wishart, David S

2005-01-01

148

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

149

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

Microsoft Academic Search

Current yeast interactome network maps contain several hundred molecular complexes with limited and somewhat controversial representation of direct binary interactions. We carried out a comparative quality assessment of current yeast interactome data sets, demonstrating that high-throughput yeast two-hybrid (Y2H) screening provides high-quality binary interaction information. Because a large fraction of the yeast binary interactome remains to be mapped, we developed

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

2008-01-01

150

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

151

Interaction Between Digital Road Map Systems And Trinocular Autonomous Driving  

Microsoft Academic Search

In addition to vehicles that are guided automatically along roads of preselected types, a project is described that guides a road vehicle to execute a complete driving mission. To increase the robustness of the current implementation a-priori knowledge about the vehicle’s environment is extensively used. A digital road map can provide long range knowledge. The navigation system Travelpilot@, commercially offered

G. Struck; J. Geisler; F. Laubenstein; H.-H. Nagel; G. Siegle

1993-01-01

152

Interactive Computer Programs for Sorting and Mapping Dialect Data.  

ERIC Educational Resources Information Center

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

Herrick, Earl M.

153

Mapping the Manipulator Workspace Using Interactive Computer Graphics  

Microsoft Academic Search

This paper describes an algorithm to map the workspace of a generalized manipulator on computer graphics. A workspace that can be simulated, displayed, and manipulated in real time on computer graphics is a very useful and efficient tool for the analysis, design, and motion planning of a manipula tor. The algorithm is developed for generalized manipulators with constrained revolute and

A. Kumar; Mayank S. Patel

1986-01-01

154

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

155

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

156

National Geographic Society Map Machine  

NSDL National Science Digital Library

For those interested in map information, National Geographic's Map Machine is an effective place to start. Map Machine's Atlas allows users to click on a world map or on continent or country menus to retrieve country maps, with concise information and flags. There are also selected area maps available, created from weather satellite data, as well as political and physical maps and a Macromedia Shockwave enhanced world map that allows users to view a world map interactively. The quality of the maps is the quality of the site.

1996-01-01

157

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

158

Mapping the Frame: Locative Media and Interactive Art Environments  

Microsoft Academic Search

In this paper we will be examining the relevance of interactivity, locativity and visualization to the process of making computational art. In addition we will be making much needed interconnections between instances of modern and contemporary fine art and interactive and locative art. Such connections are necessary due to both the rudimentary aesthetic condition of new media art and the

Elizabeth Coulter-Smith; Graham Coulter-Smith

159

Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data  

Microsoft Academic Search

Recently, a number of advanced screening technologies have allowed for the comprehensive quantification of aggravating and alleviating genetic interactions among gene pairs. In parallel, TAP-MS studies (tandem affinity purification followed by mass spectroscopy) have been successful at identifying physical protein interactions that can indicate proteins participating in the same molecular complex. Here, we propose a method for the joint learning

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

2008-01-01

160

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

161

[What defines the genetic map? The specification of meiotic recombination sites].  

PubMed

During meiosis, homologous reciprocal recombination events or crossing-over determine the genetic map and are known not to be randomly distributed in the genome. Recent studies in yeasts and mammals reveal some key features of the molecular mechanism involved in this distribution. Through different molecular processes, specific histone post-translational modifications are induced at specific genomic sites, called hotspots, where initiation of meiotic recombination takes place. These sites are some transcription promoters in S. cerevisiae or binding sites for transcription factors in S. pombe, where chromatin modifiers are recruited. In mammals, the sites are DNA sequences recognized by the PRDM9 protein which has the ability both to bind DNA and to induce the trimethylation of the lysine 4 of histone H3. The properties of the chromatin at these sites, and potentially the binding of additional factors, allow the recruitment of proteins involved in the formation of DNA double strand breaks that initiate meiotic recombination. PMID:21299964

Grey, Corinne; Sommermeyer, Vérane; Borde, Valérie; de Massy, Bernard

2011-01-01

162

Understanding Human-Computer Interactions in Map Revision  

Microsoft Academic Search

Tracking, parsing and modeling human-computer interac- tions to edit, revise documents is di-cult but necessary if we are to develop automated technologies that will aid or replace humans. This paper introduces a system for accessing and recording a stream of events related to human actions in a real-time map (cartographic) revision sys- tem. The recorded events are parsed into a

Jun Zhou; Walter F. Bischof; Terry Caelli

2004-01-01

163

Toward accelerating landslide mapping with interactive machine learning techniques  

NASA Astrophysics Data System (ADS)

Despite important advances in the development of more automated methods for landslide mapping from optical remote sensing images, the elaboration of inventory maps after major triggering events still remains a tedious task. Image classification with expert defined rules typically still requires significant manual labour for the elaboration and adaption of rule sets for each particular case. Machine learning algorithm, on the contrary, have the ability to learn and identify complex image patterns from labelled examples but may require relatively large amounts of training data. In order to reduce the amount of required training data active learning has evolved as key concept to guide the sampling for applications such as document classification, genetics and remote sensing. The general underlying idea of most active learning approaches is to initialize a machine learning model with a small training set, and to subsequently exploit the model state and/or the data structure to iteratively select the most valuable samples that should be labelled by the user and added in the training set. With relatively few queries and labelled samples, an active learning strategy should ideally yield at least the same accuracy than an equivalent classifier trained with many randomly selected samples. Our study was dedicated to the development of an active learning approach for landslide mapping from VHR remote sensing images with special consideration of the spatial distribution of the samples. The developed approach is a region-based query heuristic that enables to guide the user attention towards few compact spatial batches rather than distributed points resulting in time savings of 50% and more compared to standard active learning techniques. The approach was tested with multi-temporal and multi-sensor satellite images capturing recent large scale triggering events in Brazil and China and demonstrated balanced user's and producer's accuracies between 74% and 80%. The assessment also included an experimental evaluation of the uncertainties of manual mappings from multiple experts and demonstrated strong relationships between the uncertainty of the experts and the machine learning model.

Stumpf, André; Lachiche, Nicolas; Malet, Jean-Philippe; Kerle, Norman; Puissant, Anne

2013-04-01

164

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

PubMed

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

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

2013-04-18

165

Mapping the specific cytoprotective interaction of humanin with the pro-apoptotic protein bid.  

PubMed

Humanin is a short endogenous peptide, which can provide protection from cell death through its association with various receptors, including the pro-apoptotic Bcl-2 family proteins Bid, Bim, and Bax. By using NMR chemical shift mapping experiments, we demonstrate that the interaction between Humanin-derived peptides and Bid is specific, and we localize the binding site to a region on the surface of Bid, which includes residues from the conserved helical BH3 domain of the protein. The BH3 domain mediates the association of Bid with other Bcl-2 family members and is essential for the protein's cytotoxic activity. The data suggest that Humanin exerts its cytoprotective activity by engaging the Bid BH3 domain; this would hinder the association of Bid with other Bcl-2 family proteins, thereby mitigating its toxicity. The identification of a Humanin-specific binding site on the surface of Bid reinforces its importance as a direct modulator of programmed cell death, and suggests a strategy for the design of cytoprotective peptide inhibitors of Bid. PMID:17927731

Choi, Jungyuen; Zhai, Dayong; Zhou, Xin; Satterthwait, Arnold; Reed, John C; Marassi, Francesca M

2007-10-10

166

Site specific endonucleases for human genome mapping. Final report, April 1, 1992--March 31, 1994  

SciTech Connect

Current large scale genome mapping methodology suffers from a lack of tools for generating specific DNA fragments in the megabase size range. While technology such as pulsed field gel electrophoresis can resolve DNA fragments greater than 10 megabases in size, current methods for cleaving mammalian DNA using bacterial restriction enzymes are incapable of producing such fragments. Though several multidimensional approaches are underway to overcome this limitation, there currently is no single step procedure to generate specific DNA fragments in the 2-100 megabase size range. In order to overcome these limitations, we proposed to develop a family of site-specific endonucleases capable of generating DNA fragments in the 2-100 megabase size range in a single step. Additionally, we proposed to accomplish this by relaxing the specificity of a very-rare cutting intron-encoded endonucleases, I-Ppo I, and potentially using the process as a model for development of other enzymes. Our research has uncovered a great deal of information about intron-encoded endonucleases. We have found that I-Ppo I has a remarkable ability to tolerate degeneracy within its recognition sequence, and we have shown that the recognition sequence is larger than 15 base pairs. These findings suggest that a detailed study of the mechanism by which intron-encoded endonucleases recognize their target sequences should provide new sights into DNA-protein interactions; this had led to a continuation of the study of I-Ppo I in Dr. Raines` laboratory and we expect a more detailed understanding of the mechanism of I-Ppo I action to result.

Knoche, K.; Selman, S.; Hung, L. [and others

1994-06-01

167

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

PubMed

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

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

2009-08-03

168

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

169

The protein-protein interaction map of Helicobacter pylori  

Microsoft Academic Search

With the availability of complete DNA sequences for many prokaryotic and eukaryotic genomes, and soon for the human genome itself, it is important to develop reliable proteome-wide approaches for a better understanding of protein function. As elementary constituents of cellular protein complexes and pathways, protein-protein interactions are key determinants of protein function. Here we have built a large-scale protein-protein interaction

Jean-Christophe Rain; Luc Selig; Hilde De Reuse; Véronique Battaglia; Céline Reverdy; Stéphane Simon; Gerlinde Lenzen; Fabien Petel; Jérôme Wojcik; Vincent Schächter; Y. Chemama; Agnès Labigne; Pierre Legrain

2001-01-01

170

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

171

Mapping physical interactions within chromatin by proteomic approaches.  

PubMed

Our ability to study protein-protein interactions has grown by leaps and bounds in recent years, enabling numerous large-scale studies to be performed in a variety of organisms. Despite this success, some classes of proteins, including those bound to chromatin, remain difficult to characterize through proteomic approaches. Some of the problems faced by researchers studying chromatin-bound proteins include low complex solubility, heterogeneous sample composition, and numerous transient interactions, which can be further complicated by the presence of DNA itself. To tackle these issues, a number of innovative protocols have been developed to better study the various facets of chromatin biology. In this review, we will discuss novel approaches to study protein-DNA interactions as well as protein complexes affecting chromatin. PMID:22611019

Lambert, Jean-Philippe; Pawson, Tony; Gingras, Anne-Claude

2012-05-01

172

WebCutter: A System for Dynamic and Tailorable Site Mapping  

Microsoft Academic Search

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

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

1997-01-01

173

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

SciTech Connect

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

Not Available

1988-03-01

174

Protein–protein interaction maps: a lead towards cellular functions  

Microsoft Academic Search

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

Pierre Legrain; Jérôme Wojcik; Jean-Michel Gauthier

2001-01-01

175

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

Microsoft Academic Search

\\u000a This chapter describes the design and development of an interactive video installation that allows participants to explore\\u000a a map narrative, and engage in group interactions through a shared screen. For this purpose, several layers of cartographic\\u000a information were employed in a computer application, which was programmed with motion-tracking libraries in the open source\\u000a tool processing. The interactive video installation has

Konstantinos Chorianopoulos; Tim Rieniets

2010-01-01

176

Mapping adaptation opportunities and activities in an interactive atlas.  

PubMed

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

Morris, Daniel F; Krishnan, Nisha

2012-01-01

177

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

PubMed Central

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

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

2007-01-01

178

Mapping interaction forces with the atomic force microscope.  

PubMed Central

Force curves were recorded as the sample was raster-scanned under the tip. This opens new opportunities for imaging with the atomic force microscope: several characteristics of the samples can be measured simultaneously, for example, topography, adhesion forces, elasticity, van der Waals, and electrostatic interactions. The new opportunities are illustrated by images of several characteristics of thin metal films, aggregates of lysozyme, and single molecules of DNA. Images FIGURE 1 FIGURE 3 FIGURE 4 FIGURE 5 FIGURE 6

Radmacher, M; Cleveland, J P; Fritz, M; Hansma, H G; Hansma, P K

1994-01-01

179

Interacting damage models mapped onto ising and percolation models  

SciTech Connect

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

Toussaint, Renaud; Pride, Steven R.

2004-03-23

180

Extended DFT + U + V method with on-site and inter-site electronic interactions.  

PubMed

In this paper we introduce a generalization of the popular DFT + U method based on the extended Hubbard model that includes on-site and inter-site electronic interactions. The novel corrective Hamiltonian is designed to study systems for which electrons are not completely localized on atomic states (according to the general scheme of Mott localization) and hybridization between orbitals from different sites plays an important role. The application of the extended functional to archetypal Mott-charge-transfer (NiO) and covalently bonded insulators (Si and GaAs) demonstrates its accuracy and versatility and the possibility to obtain a unifying and equally accurate description for a broad range of very diverse systems. PMID:21386347

Campo, Vivaldo Leiria; Cococcioni, Matteo

2010-01-19

181

iGMT: Interactive Mapping of Geoscientific Datasets. User manual for version 1.2  

Microsoft Academic Search

iGMT is a Tcl\\/Tk package for interactive mapping of geoscientific datasets, built around the generic mapping tools (GMT). Our software is intended to assist in the creation of GMT scripts and has built-in data processing capabilities for raster data sets such as topography, sea-floor age, free air-gravity, the geoid, and various polygon data files such as earthquake hypocentre lists or

Thorsten W. Becker; Alexander Braun

182

Gitools: Analysis and Visualisation of Genomic Data Using Interactive Heat-Maps  

Microsoft Academic Search

Intuitive visualization of data and results is very important in genomics, especially when many conditions are to be analyzed and compared. Heat-maps have proven very useful for the representation of biological data. Here we present Gitools (http:\\/\\/www.gitools.org), an open-source tool to perform analyses and visualize data and results as interactive heat-maps. Gitools contains data import systems from several sources (i.e.

Christian Perez-Llamas; Nuria Lopez-Bigas

2011-01-01

183

A comprehensive modular map of molecular interactions in RB\\/E2F pathway  

Microsoft Academic Search

We present, here, a detailed and curated map of molecular interactions taking place in the regulation of the cell cycle by the retinoblastoma protein (RB\\/RB1). Deregulations and\\/or mutations in this pathway are observed in most human cancers. The map was created using Systems Biology Graphical Notation language with the help of CellDesigner 3.5 software and converted into BioPAX 2.0 pathway

Laurence Calzone; Amélie Gelay; François Radvanyi; Emmanuel Barillot; Andrei Zinovyev

2008-01-01

184

Mapping metal-binding sites in the catalytic domain of bacterial RNase P RNA  

PubMed Central

Ribonuclease P (RNase P) is a ribonucleoprotein enzyme that contains a universally conserved, catalytically active RNA component. RNase P RNA requires divalent metal ions for folding, substrate binding, and catalysis. Despite recent advances in understanding the structure of RNase P RNA, no comprehensive analysis of metal-binding sites has been reported, in part due to the poor crystallization properties of this large RNA. We have developed an abbreviated yet still catalytic construct, Bst P7? RNA, which contains the catalytic domain of the bacterial RNase P RNA and has improved crystallization properties. We use this mutant RNA as well as the native RNA to map metal-binding sites in the catalytic core of the bacterial RNase P RNA, by anomalous scattering in diffraction analysis. The results provide insight into the interplay between RNA structure and focalization of metal ions, and a structural basis for some previous biochemical observations with RNase P. We use electrostatic calculations to extract the potential functional significance of these metal-binding sites with respect to binding Mg2+. The results suggest that with at least one important exception of specific binding, these sites mainly map areas of diffuse association of magnesium ions.

Kazantsev, Alexei V.; Krivenko, Angelika A.; Pace, Norman R.

2009-01-01

185

Extracting Between-Pathway Models from E-MAP Interactions Using Expected Graph Compression  

NASA Astrophysics Data System (ADS)

Genetic interactions (such as synthetic lethal interactions) have become quantifiable on a large-scale using the epistatic miniarray profile (E-MAP) method. An E-MAP allows the construction of a large, weighted network of both aggravating and alleviating genetic interactions between genes. By clustering genes into modules and establishing relationships between those modules, we can discover compensatory pathways. We introduce a general framework for applying greedy clustering heuristics to probabilistic graphs. We use this framework to apply a graph clustering method called graph summarization to an E-MAP that targets yeast chromosome biology. This results in a new method for clustering E-MAP data that we call Expected Graph Compression (EGC). We validate modules and compensatory pathways using enriched Gene Ontology annotations and a novel method based on correlated gene expression. EGC finds a number of modules that are not found by any previous methods to cluster E-MAP data. EGC also uncovers core submodules contained within several previously found modules, suggesting that EGC can reveal the finer structure of E-MAP networks.

Kelley, David R.; Kingsford, Carl

186

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

187

Mapping of the nick site on conjugative plasmid pVT745 by interrupted mating  

PubMed Central

Conjugal transfer of plasmid DNA initiates and terminates at a specific non-coding site called the origin of transfer (oriT). Previous analysis of conjugative plasmid pVT745 from Aggregatibacter actinomycetemcomitans suggested that oriT was located adjacent to the operon responsible for initiation of ssDNA transfer. The location of oriT was confirmed by assaying both subclones of the region as well as a pVT745 deletion derivative for mobilization. The precise DNA nick site (nic) and polarity of DNA transfer were identified by use of interrupted mating assays, a technique originally used for the mapping of bacterial chromosomes. Nucleotide sequence analysis revealed that the pVT745-specific nick region was similar to the consensus nick sequence of the IncP family albeit the actual cleavage site differed. Functionality of nic was confirmed by point mutations.

Chen, Jinbiao; Pappas, Donald L.; Galli, Dominique M.

2010-01-01

188

Physical map of infectious baboon type C viral DNA and sites of integration in infected cells.  

PubMed Central

Three species of unintegrated viral DNAs were found in permissive cells infected with baboon type C virus. The major species was a 9.0-kilobase (kb) linear DNA that was infectious. A restriction endonuclease map of this DNA was constructed and oriented with respect to the viral RNA. The linear DNA had a 0.6-kb sequence repeated at each terminus. These terminal repeat sequences were required for infectivity of the viral DNA. The minor species of the unintegrated viral DNAs were covalently closed circles of 9.0 and 8.4 kb. The smaller circle was in two- to threefold excess over the larger circle. The difference appeared to be that the smaller circle lacked one of the two 0.6-kb repeat sequences found in the larger circle. Restriction endonuclease maps of the integrated viral DNAs were constructed, and the sequences on both viral DNA and cellular DNA that are involved in integration were determined. The integrated viral DNA map was identical to that of the unintegrated infectious 9.0-kb linear DNA. Therefore, a specific site in the terminal repeat sequence of the viral DNA was used to integrate with the host cell DNA. The sizes of the cellular DNA fragments were different from clone to clone but stable with cell passage. Therefore, many sites in the cell DNA can recombine with the viral DNA. Images

Battula, N; Todaro, G J

1980-01-01

189

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

PubMed

Soil texture varies significantly within many agricultural fields. The physical properties of soil, such as soil texture, have a direct effect on water holding capacity, cation exchange capacity, crop yield, production capability, and nitrogen (N) loss variations within a field. In short, mobile nutrients are used, lost, and stored differently as soil textures vary. A uniform application of N to varying soils results in a wide range of N availability to the crop. N applied in excess of crop usage results in a waste of the grower"s input expense, a potential negative effect on the environment, and in some crops a reduction of crop quality, yield, and harvestability. Inadequate N levels represent a lost opportunity for crop yield and profit. The global positioning system (GPS)-referenced mapping of bulk soil electrical conductivity (EC) has been shown to serve as an effective proxy for soil texture and other soil properties. Soils with a high clay content conduct more electricity than coarser textured soils, which results in higher EC values. This paper will describe the EC mapping process and provide case studies of site-specific N applications based on EC maps. Results of these case studies suggest that N can be managed site-specifically using a variety of management practices, including soil sampling, variable yield goals, and cropping history. PMID:12805883

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

2001-10-16

190

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

SciTech Connect

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

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

1995-04-01

191

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

SciTech Connect

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

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

1982-08-01

192

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

PubMed Central

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

2010-01-01

193

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

NASA Astrophysics Data System (ADS)

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

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

2005-08-01

194

Generalized theory of site-specific DNA-protein interactions.  

PubMed

We develop a generalized theory of the site-specific DNA-protein interactions, which includes both the static as well as the dynamical factors influencing the one-dimensional diffusion of the nonspecifically bound protein molecule which is in the process of searching for the specific site on the DNA lattice. We argue that the chemically driven condensation of the DNA molecule introduces a static distribution in the one-dimensional phenomenological diffusion coefficient associated with the protein molecule and the conformational dynamics of the DNA introduces temporal fluctuations in the one-dimensional diffusion coefficient over the static distribution. We further derive the generalized inequality conditions and the scaling laws which are required to enhance the three-dimensional diffusion controlled site-specific association rate to an arbitrary order. Our model predicts that when the degree of condensation of the DNA molecule under consideration is very high, then the probability distribution associated with the stationary state one-dimensional diffusion coefficient variable as well as the stationary state one-dimensional diffusion length variable will be a flat one. Further analysis reveals that to achieve a site-specific association rate which is higher than that of the three-dimensional diffusion controlled rate, the one-dimensional diffusion length associated with the dynamics of the nonspecifically bound protein molecule on the DNA lattice should fall in certain critical ranges. Comparison of our theoretical results with the recent experimental observations reveals that when the DNA molecule is under a stretched condition, then the static distribution of the one-dimensional diffusion coefficient associated with the dynamics of the protein molecule on the DNA lattice is a Gaussian and therefore the fluctuations in the one-dimensional diffusion coefficient generated by the dynamical factors are confined in a harmonic type potential. PMID:17677488

Murugan, R

2007-07-02

195

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

Microsoft Academic Search

This digital geologic map of the Nevada Test Site (NTS) and vicinity, as well as its accompanying digital geophysical maps, are compiled at 1:100,000 scale. The map area covers two 30 Ã 60-minute quadrangles-the Pahute Mesa quadrangle to the north and the Beatty quadrangle to the south-plus a strip of 7 1\\/2-minute quadrangles on the east side. In addition to

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

2000-01-01

196

VS30 mapping and soil classification for seismic site effect evaluation in Dinar region, SW Turkey  

NASA Astrophysics Data System (ADS)

The Dinar earthquake (MS= 6.1) of 1995 October 1 killed 90 people and destroyed more than 4000 buildings. Despite the moderate size of the earthquake, the level of damage was extremely high, which led to many studies that were carried out in the region. The majority of these studies concluded that the main reasons for the damage were the construction errors and the poor soil conditions. However, at that time no appropriate soil condition map based on extended, high density measurements was available. Shear wave velocity is an important parameter for evaluating the dynamic behaviour of soil in the shallow subsurface. Thus site characterization in calculating seismic hazards is usually based on the near surface shear wave velocity values. The average shear wave velocity for the top 30 m of soil is referred to as VS30. For earthquake engineering design purposes, both the Uniform Building Code (UBC) and Eurocode 8 (EC8) codes use VS30 to classify sites according to the soil type. The Vs30 values calculated by using multichannel analysis of surface waves (MASW) were used to create a new soil classification map of the Dinar region. Surface seismic measurements were carried out at 50 locations mostly in Dinar city and its surroundings. The dispersion data of the recorded Rayleigh waves were inverted using a Genetic Algorithm (GA) method to obtain shear wave velocity profiles of the investigated sites. Thus the derived Vs30 map of the Dinar region was transformed to the UBC and EC8 standards. Soil classification results show that most parts of the region, located in alluvial basin, have low shear wave velocity values. These values are within the range of 160-240 m s-1 and thus fall into the SD and SE categories according to the UBC and the C and D categories according to EC8. Within the region, some parts located on the hill zone and the transition zone have better soil conditions [corresponding to SC (UBC) and B (EC8) categories] and have comparatively high shear wave velocities in the range of 500-740 m s-1 and 350-450 m s-1, respectively. VS30 and soil classification maps were compared with the damage distribution associated with the earthquake. In possession of a detailed shear wave velocity map of Dinar City, in general, the results show that there is a correlation between the VS30 values and the damage distribution of the region. In addition to the low VS30 values, the likely causes of the damage were investigated, and it is observed that one of the major factors for high levels of damage is 3-D variations of geological structures.

Ismet Kanl?, Ali; Tildy, Péter; Prónay, Zsolt; P?nar, Ali; Hermann, László

2006-04-01

197

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

PubMed Central

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

2011-01-01

198

Unbiased Mapping of Transcription Factor Binding Sites along Human Chromosomes 21 and 22 Points to Widespread Regulation of Noncoding RNAs  

Microsoft Academic Search

Using high-density oligonucleotide arrays representing essentially all nonrepetitive sequences on human chromosomes 21 and 22, we map the binding sites in vivo for three DNA binding transcription factors, Sp1, cMyc, and p53, in an unbiased manner. This mapping reveals an unexpectedly large number of transcription factor binding site (TFBS) regions, with a minimal estimate of 12,000 for Sp1, 25,000 for

Simon Cawley; Stefan Bekiranov; Huck H. Ng; Philipp Kapranov; Edward A. Sekinger; Dione Kampa; Antonio Piccolboni; Victor Sementchenko; Jill Cheng; Alan J. Williams; Raymond Wheeler; Brant Wong; Jorg Drenkow; Mark Yamanaka; Sandeep Patel; Shane Brubaker; Hari Tammana; Gregg Helt; Kevin Struhl; Thomas R Gingeras

2004-01-01

199

MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations.  

PubMed

With the advent of RFLPs, genetic linkage maps are now being assembled for a number of organisms including both inbred experimental populations such as maize and outbred natural populations such as humans. Accurate construction of such genetic maps requires multipoint linkage analysis of particular types of pedigrees. We describe here a computer package, called MAPMAKER, designed specifically for this purpose. The program uses an efficient algorithm that allows simultaneous multipoint analysis of any number of loci. MAPMAKER also includes an interactive command language that makes it easy for a geneticist to explore linkage data. MAPMAKER has been applied to the construction of linkage maps in a number of organisms, including the human and several plants, and we outline the mapping strategies that have been used. PMID:3692487

Lander, E S; Green, P; Abrahamson, J; Barlow, A; Daly, M J; Lincoln, S E; Newberg, L A; Newburg, L

1987-10-01

200

Limitation of application of conformal mapping on the interaction of an edge dislocation and a crack  

SciTech Connect

The limitation of application of conformal mapping on the interaction between an edge dislocation and a crack is investigated. The in-plane fracture is usually obtained by the method of the Muskhelishvili complex potential. The equation obtained by the method of Muskhelishvili can be solved by Cauchy integral if it is analytic. Based on this point of view, an exact solution of an edge dislocation near a semi-infinite crack is obtained using conformal mapping. However, the conformal mapping cannot be applied to the problem of a wedge crack because the ratio of mapping function to the conjugate of its derivative is not analytic. Generally, most crack problems encounter the same difficulty as the wedge crack in obtaining the analytic form. 11 refs.

Wang, S.; Hu, C.; Lee, S. [Natl Tsing Hua Univ, Hsinchu, Taiwan (China)

1994-06-01

201

Complete Switchgrass Genetic Maps Reveal Subgenome Collinearity, Preferential Pairing and Multilocus Interactions  

PubMed Central

Polyploidy is an important aspect of the evolution of flowering plants. The potential of gene copies to diverge and evolve new functions is influenced by meiotic behavior of chromosomes leading to segregation as a single locus or duplicated loci. Switchgrass (Panicum virgatum) linkage maps were constructed using a full-sib population of 238 plants and SSR and STS markers to access the degree of preferential pairing and the structure of the tetraploid genome and as a step toward identification of loci underlying biomass feedstock quality and yield. The male and female framework map lengths were 1645 and 1376 cM with 97% of the genome estimated to be within 10 cM of a mapped marker in both maps. Each map coalesced into 18 linkage groups arranged into nine homeologous pairs. Comparative analysis of each homology group to the diploid sorghum genome identified clear syntenic relationships and collinear tracts. The number of markers with PCR amplicons that mapped across subgenomes was significantly fewer than expected, suggesting substantial subgenome divergence, while both the ratio of coupling to repulsion phase linkages and pattern of marker segregation indicated complete or near complete disomic inheritance. The proportion of transmission ratio distorted markers was relatively low, but the male map was more extensively affected by distorted transmission ratios and multilocus interactions, associated with spurious linkages.

Okada, Miki; Lanzatella, Christina; Saha, Malay C.; Bouton, Joe; Wu, Rongling; Tobias, Christian M.

2010-01-01

202

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

PubMed

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

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

2008-08-21

203

Mapping of complex fractionated atrial electrograms as target sites for AF ablation.  

PubMed

The myriad pathologies leading to and resulting from atrial fibrillation (AF) have led to many theories regarding how substrate should be defined and how to reconcile substrate ablation with trigger ablation. The identification of spatiotemporally stable areas of very low amplitude short cycle length CFAE in a sea of otherwise discrete normal amplitude and relatively longer cycle length electrograms led to ablate the complex fractionated atrial electrogram (CFAE) as a marker of abnormal substrate. This pure substrate-based ablation strategy has shown promising result of benefit in stroke and mortality reduction in high-risk patients. In this review which has been modified and abridged from the recent publication on this subject [1], we discuss the prevailing mechanisms underlying CFAE, how to map and ablate CFAE sites, correlation of CFAE areas to those of ganglionic plexi, clinical outcomes of the approach, and the controversy surrounding targeting CFAE as substrate sites for AF ablation. PMID:22255593

Nademanee, Koonlawee

2011-01-01

204

Multiple interaction sites of galnon trigger its biological effects.  

PubMed

Galnon was first reported as a low molecular weight non-peptide agonist at galanin receptors [Saar et al. (2002) Proc. Natl. Acad. Sci. USA 99, 7136-7141]. Following its systemic administration, this synthetic ligand affected a range of important physiological processes including appetite, seizures and pain. Physiological activity of galnon could not be explained solely by the activation of the three known galanin receptors, GalR1, GalR2 and GalR3. Consequently, it was possible that galnon generates its manifold effects by interacting with other signaling pathway components, in addition to via GalR1-3. In this report, we establish that galnon: (i) can penetrate across the plasma membrane of cells, (ii) can activate intracellular G-proteins directly independent of receptor activation thereby triggering downstream signaling, (iii) demonstrates selectivity for different G-proteins, and (iiii) is a ligand to other G-protein coupled receptors (GPCRs) in addition to via GalR1-3. We conclude that galnon has multiple sites of interaction within the GPCR signaling cascade which mediate its physiological effects. PMID:16297447

Florén, Anders; Sollenberg, Ulla; Lundström, Linda; Zorko, Matjaz; Stojan, Jure; Budihna, Metka; Wheatley, Mark; Martin, Negin P; Kilk, Kalle; Mazarati, Andrey; Bartfai, Tamas; Lindgren, Maria; Langel, Ulo

2005-11-16

205

Discovery and characterization of non-ATP site inhibitors of the mitogen activated protein (MAP) kinases.  

PubMed

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? (involved in the formation of TNF? 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 (1)H/(13)C NMR spectroscopy, protein X-ray crystallography, surface plasmon resonance, and direct enzymatic activity and activation cascade assays. Jnk-1 and p38? 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. PMID:21090814

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

2011-01-20

206

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

207

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

PubMed Central

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

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

2003-01-01

208

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

209

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

PubMed Central

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

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

2012-01-01

210

Distance mapping of protein-binding sites using spin-labeled oligosaccharide ligands  

PubMed Central

The binding of a nitroxide spin-labeled analog of N-acetyllactosamine to galectin-3, a mammalian lectin of 26 kD size, is studied to map the binding sites of this small oligosaccharide on the protein surface. Perturbation of intensities of cross-peaks in the 15N heteronuclear single quantum coherence (HSQC) spectrum of full-length galectin-3 owing to the bound spin label is used qualitatively to idey protein residues proximate to the binding site for N-acetyllactosamine. A protocol for converting intensity measurements to a more quantitative determination of distances between discrete protein amide protons and the bound spin label is then described. This protocol is discussed as part of a drug design strategy in which subsequent perturbation of chemical shifts of distance mapped amide cross-peaks can be used effectively to screen a library of compounds for other ligands that bind to the target protein at distances suitable for chemical linkage to the primary ligand. This approach is novel in that it bypasses the need for structure determination and resonance assignment of the target protein.

Jain, Nitin U.; Venot, Andre; Umemoto, Kimiko; Leffler, Hakon; Prestegard, James H.

2001-01-01

211

Genome-Wide Characterization of Tetrahymena thermophila Chromosome Breakage Sites. II. Physical and Genetic Mapping  

PubMed Central

The chromosomes of the macronuclear (expressed) genome of Tetrahymena thermophila are generated by developmental fragmentation of the five micronuclear (germline) chromosomes. This fragmentation is site specific, directed by a conserved chromosome breakage sequence (Cbs element). An accompanying article in this issue reports the development of a successful scheme for the genome-wide cloning and identification of functional chromosome breakage sites. This article reports the physical and genetic characterization of 30 functional chromosome breakage junctions. Unique sequence tags and physical sizes were obtained for the pair of macronuclear chromosomes generated by fragmentation at each Cbs. Cbs-associated polymorphisms were used to genetically map 11 junctions to micronuclear linkage groups and macronuclear coassortment groups. Two pairs of junctions showed statistically significant similarity of the sequences flanking the Cbs, suggestive of relatively recent duplications of entire Cbs junctions during Tetrahymena genome evolution. Two macronuclear chromosomes that lose at least one end in an age-related manner were also identified. The whole-genome shotgun sequencing of the Tetrahymena macronucleus has recently been completed at The Institute for Genome Research (TIGR). By providing unique sequence from natural ends of macronuclear chromosomes, Cbs junctions will provide useful sequence tags for relating macro- and micronuclear genetic, physical, and whole-genome sequence maps.

Cassidy-Hanley, Donna; Bisharyan, Yelena; Fridman, Vladimir; Gerber, Joseph; Lin, Cindy; Orias, Eduardo; Orias, Judith D.; Ryder, Hilary; Vong, Linh; Hamilton, Eileen P.

2005-01-01

212

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

Technology Transfer Automated Retrieval System (TEKTRAN)

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

213

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

PubMed Central

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

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

2012-01-01

214

Human papilloma viruses and cervical tumours: mapping of integration sites and analysis of adjacent cellular sequences  

PubMed Central

Background In cervical tumours the integration of human papilloma viruses (HPV) transcripts often results in the generation of transcripts that consist of hybrids of viral and cellular sequences. Mapping data using a variety of techniques has demonstrated that HPV integration occurred without obvious specificity into human genome. However, these techniques could not demonstrate whether integration resulted in the generation of transcripts encoding viral or viral-cellular sequences. The aim of this work was to map the integration sites of HPV DNA and to analyse the adjacent cellular sequences. Methods Amplification of the INTs was done by the APOT technique. The APOT products were sequenced according to standard protocols. The analysis of the sequences was performed using BLASTN program and public databases. To localise the INTs PCR-based screening of GeneBridge4-RH-panel was used. Results Twelve cellular sequences adjacent to integrated HPV16 (INT markers) expressed in squamous cell cervical carcinomas were isolated. For 11 INT markers homologous human genomic sequences were readily identified and 9 of these showed significant homologies to known genes/ESTs. Using the known locations of homologous cDNAs and the RH-mapping techniques, mapping studies showed that the INTs are distributed among different human chromosomes for each tumour sample and are located in regions with the high levels of expression. Conclusions Integration of HPV genomes occurs into the different human chromosomes but into regions that contain highly transcribed genes. One interpretation of these studies is that integration of HPV occurs into decondensed regions, which are more accessible for integration of foreign DNA.

Klimov, Eugene; Vinokourova, Svetlana; Moisjak, Elena; Rakhmanaliev, Elian; Kobseva, Vera; Laimins, Laimonis; Kisseljov, Fjodor; Sulimova, Galina

2002-01-01

215

Chromatin Interaction Analysis with Paired-End Tag Sequencing (ChIA-PET) for Mapping Chromatin Interactions and Understanding Transcription Regulation  

PubMed Central

Genomes are organized into three-dimensional structures, adopting higher-order conformations inside the micron-sized nuclear spaces 7, 2, 12. Such architectures are not random and involve interactions between gene promoters and regulatory elements 13. The binding of transcription factors to specific regulatory sequences brings about a network of transcription regulation and coordination 1, 14. Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET) was developed to identify these higher-order chromatin structures 5,6. Cells are fixed and interacting loci are captured by covalent DNA-protein cross-links. To minimize non-specific noise and reduce complexity, as well as to increase the specificity of the chromatin interaction analysis, chromatin immunoprecipitation (ChIP) is used against specific protein factors to enrich chromatin fragments of interest before proximity ligation. Ligation involving half-linkers subsequently forms covalent links between pairs of DNA fragments tethered together within individual chromatin complexes. The flanking MmeI restriction enzyme sites in the half-linkers allow extraction of paired end tag-linker-tag constructs (PETs) upon MmeI digestion. As the half-linkers are biotinylated, these PET constructs are purified using streptavidin-magnetic beads. The purified PETs are ligated with next-generation sequencing adaptors and a catalog of interacting fragments is generated via next-generation sequencers such as the Illumina Genome Analyzer. Mapping and bioinformatics analysis is then performed to identify ChIP-enriched binding sites and ChIP-enriched chromatin interactions 8. We have produced a video to demonstrate critical aspects of the ChIA-PET protocol, especially the preparation of ChIP as the quality of ChIP plays a major role in the outcome of a ChIA-PET library. As the protocols are very long, only the critical steps are shown in the video.

Poh, Huay Mei; Peh, Su Qin; Ong, Chin Thing; Zhang, Jingyao; Ruan, Xiaoan; Ruan, Yijun

2012-01-01

216

Chromatin Interaction Analysis with Paired-End Tag Sequencing (ChIA-PET) for mapping chromatin interactions and understanding transcription regulation.  

PubMed

Genomes are organized into three-dimensional structures, adopting higher-order conformations inside the micron-sized nuclear spaces (7, 2, 12). Such architectures are not random and involve interactions between gene promoters and regulatory elements (13). The binding of transcription factors to specific regulatory sequences brings about a network of transcription regulation and coordination (1, 14). Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET) was developed to identify these higher-order chromatin structures (5,6). Cells are fixed and interacting loci are captured by covalent DNA-protein cross-links. To minimize non-specific noise and reduce complexity, as well as to increase the specificity of the chromatin interaction analysis, chromatin immunoprecipitation (ChIP) is used against specific protein factors to enrich chromatin fragments of interest before proximity ligation. Ligation involving half-linkers subsequently forms covalent links between pairs of DNA fragments tethered together within individual chromatin complexes. The flanking MmeI restriction enzyme sites in the half-linkers allow extraction of paired end tag-linker-tag constructs (PETs) upon MmeI digestion. As the half-linkers are biotinylated, these PET constructs are purified using streptavidin-magnetic beads. The purified PETs are ligated with next-generation sequencing adaptors and a catalog of interacting fragments is generated via next-generation sequencers such as the Illumina Genome Analyzer. Mapping and bioinformatics analysis is then performed to identify ChIP-enriched binding sites and ChIP-enriched chromatin interactions (8). We have produced a video to demonstrate critical aspects of the ChIA-PET protocol, especially the preparation of ChIP as the quality of ChIP plays a major role in the outcome of a ChIA-PET library. As the protocols are very long, only the critical steps are shown in the video. PMID:22564980

Goh, Yufen; Fullwood, Melissa J; Poh, Huay Mei; Peh, Su Qin; Ong, Chin Thing; Zhang, Jingyao; Ruan, Xiaoan; Ruan, Yijun

2012-04-30

217

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

PubMed Central

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

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

2008-01-01

218

Ontology Mapping: An Information Retrieval and Interactive Activation Network Based Approach  

NASA Astrophysics Data System (ADS)

Ontology mapping is to find semantic correspondences between similar elements of different ontologies. It is critical to achieve semantic interoperability in the WWW. This paper proposes a new generic and scalable ontology mapping approach based on propagation theory, information retrieval technique and artificial intelligence model. The approach utilizes both linguistic and structural information, measures the similarity of different elements of ontologies in a vector space model, and deals with constraints using the interactive activation network. The results of pilot study, the PRIOR, are promising and scalable.

Mao, Ming

219

Gitools: Analysis and Visualisation of Genomic Data Using Interactive Heat-Maps  

PubMed Central

Intuitive visualization of data and results is very important in genomics, especially when many conditions are to be analyzed and compared. Heat-maps have proven very useful for the representation of biological data. Here we present Gitools (http://www.gitools.org), an open-source tool to perform analyses and visualize data and results as interactive heat-maps. Gitools contains data import systems from several sources (i.e. IntOGen, Biomart, KEGG, Gene Ontology), which facilitate the integration of novel data with previous knowledge.

Perez-Llamas, Christian; Lopez-Bigas, Nuria

2011-01-01

220

Mapping Single Cell-Substrate Interactions by Surface Plasmon Resonance Microscopy  

PubMed Central

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

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

2013-01-01

221

A map of specific cleavage sites and tRNA genes in the chloroplast genome of Euglena gracilis bacillaris  

Microsoft Academic Search

A map showing locations of 22 of the 30 endonuclease EcoRI cleavage sites and 54 additional sites for eight other restriction endonucleases is presented. The regions of chloroplast DNA that hybridize with chloroplast tRNA are also shown.

M. Raafat El-Gewely; Margaret I. Lomax; Elizabeth T. Lau; Robert B. Helling; William Farmerie; W. Edgar Barnett

1981-01-01

222

Comprehensive Identification and Modified-Site Mapping of S-Nitrosylated Targets in Prostate Epithelial Cells  

PubMed Central

Background Although overexpression of nitric oxide synthases (NOSs) has been found associated with prostate diseases, the underlying mechanisms for NOS-related prostatic diseases remain unclear. One proposed mechanism is related to the S-nitrosylation of key regulatory proteins in cell-signaling pathways due to elevated levels of NO in the prostate. Thus, our primary objective was to identify S-nitrosylated targets in an immortalized normal prostate epithelial cell line, NPrEC. Methodology/Principal Findings We treated NPrEC with nitroso-cysteine and used the biotin switch technique followed by gel-based separation and mass spectrometry protein identification (using the LTQ-Orbitrap) to discover S-nitrosylated (SNO) proteins in the treated cells. In parallel, we adapted a peptide pull-down methodology to locate the site(s) of S-nitrosylation on the protein SNO targets identified by the first technique. This combined approach identified 116 SNO proteins and determined the sites of modification for 82 of them. Over 60% of these proteins belong to four functional groups: cell structure/cell motility/protein trafficking, protein folding/protein response/protein assembly, mRNA splicing/processing/transcriptional regulation, and metabolism. Western blot analysis validated a subset of targets related to disease development (proliferating cell nuclear antigen, maspin, integrin ?4, ?-catenin, karyopherin [importin] ?1, and elongation factor 1A1). We analyzed the SNO sequences for their primary and secondary structures, solvent accessibility, and three-dimensional structural context. We found that about 80% of the SNO sites that can be mapped into resolved structures are buried, of which approximately half have charged amino acids in their three-dimensional neighborhood, and the other half residing within primarily hydrophobic pockets. Conclusions/Significance We here identified 116 potential SNO targets and mapped their putative SNO sites in NPrEC. Elucidation of how this post-translational modification alters the function of these proteins should shed light on the role of NO in prostate pathologies. To our knowledge, this is the first report identifying SNO targets in prostate epithelial cells.

Lam, Ying Wai; Yuan, Yong; Isaac, Jared; Babu, C. V. Suresh; Meller, Jarek; Ho, Shuk-Mei

2010-01-01

223

Identification of new G?? interaction sites in adenylyl cyclase 2.  

PubMed

The role of G?? in adenylyl cyclase (AC) signaling is complicated due to its role as a conditional activator (AC2, AC4 and AC7) and an inhibitor (AC1, AC3 and AC8). AC2 is stimulated by G?(s) and if G?? is present the stimulation is synergistic. The precise mechanism of this synergistic activation is still not known. In order to further elucidate the role of G?? in AC2 activation by G?(s), peptides derived from the C1 domains of AC2 were synthesized and the ability of the various peptides to regulate AC2 function was tested. Our results identify two new G??-binding sites in the AC2 C1 domain, AC2 C1a 339-360 and AC2 C1b 578-602 that are involved with stimulation of AC2 by G??. These two regions are different from the previously described QEHA motif in the C2 domain of AC2. Further, the recently discovered PFAHL motif was confirmed to bind and to be involved with stimulation of AC2 by G??. These functional studies indicate that multiple regions of AC2 are involved in the interaction with G??. PMID:21596131

Boran, Aislyn D W; Chen, Yibang; Iyengar, Ravi

2011-05-08

224

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

2010-03-03

225

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

Microsoft Academic Search

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

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

2008-01-01

226

Mapping of matrix metalloproteinase cleavage sites on syndecan-1 and syndecan-4 ectodomains.  

PubMed

Syndecans are transmembrane heparan sulfate proteoglycans with roles in cell proliferation, differentiation, adhesion, and migration. They have been associated with multiple functions in tumour progression, through their ability to interact with a wide range of ligands as well as other receptors, which makes them key effectors in the pericellular microenvironment. Extracellular shedding of syndecans by tumour-associated matrix metalloproteinases (MMPs) may have an important role in tumour progression. Such ectodomain shedding generates soluble ectodomains that may function as paracrine or autocrine effectors, or as competitive inhibitors of the intact proteoglycan. Tumour-associated MMPs are shown here to cleave the ectodomains of human syndecan-1 and syndecan-4. Two membrane proximal regions of both syndecan-1 and syndecan-4 are favoured MMP cleavage sites, six and 15 residues from the transmembrane domain. Other sites are 35-40 residues C-terminal from the heparan sulfate chain substitution sites in both syndecans. The MT1-MMP cleavage sites in syndecan-1 and syndecan-4 were confirmed by site-directed mutagenesis. These findings provide insights into the characteristics of syndecan shedding. PMID:23384311

Manon-Jensen, Tina; Multhaupt, Hinke A B; Couchman, John R

2013-03-04

227

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

228

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

229

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

PubMed Central

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

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

2011-01-01

230

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

PubMed Central

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

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

2011-01-01

231

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

PubMed

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

Gurevitz, Michael

2012-04-04

232

Jules Map Server  

NSDL National Science Digital Library

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

Estey, Lou

2004-05-18

233

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

NASA Astrophysics Data System (ADS)

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

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

1992-11-01

234

Phosphorylation of microtubule-associated proteins MAP2 and MAP4 by the protein kinase p110mark. Phosphorylation sites and regulation of microtubule dynamics.  

PubMed

The phosphorylation of microtubule-associated proteins (MAPs) is thought to be a key factor in the regulation of microtubule stability. We have shown recently that a novel protein kinase, termed p110 microtubule-affinity regulating kinase ("MARK"), phosphorylates microtubule-associated protein tau at the KXGS motifs in the region of internal repeats and causes the detachment of tau from microtubules (Drewes, G., Trinczek, B., Illenberger, S., Biernat, J., Schmitt-Ulms, G., Meyer, H.E., Mandelkow, E.-M., and Mandelkow, E. (1995) J. Biol. Chem. 270, 7679-7688). Here we show that p110mark phosphorylates analogous KXGS sites in the microtubule binding domains of the neuronal MAP2 and the ubiquitous MAP4. Phosphorylation in vitro leads to the dissociation of MAP2 and MAP4 from microtubules and to a pronounced increase in dynamic instability. Thus, the phosphorylation of the repeated motifs in the microtubule binding domains of MAPs by p110mark might provide a mechanism for the regulation of microtubule dynamics in cells. PMID:8631898

Illenberger, S; Drewes, G; Trinczek, B; Biernat, J; Meyer, H E; Olmsted, J B; Mandelkow, E M; Mandelkow, E

1996-05-01

235

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

Microsoft Academic Search

BrainMaps.org is an interactive high-resolution digital brain atlas and virtual microscope that is based on over 20 million megapixels of scanned images of serial sections of both primate and non-primate brains and that is integrated with a high-speed database for querying and retrieving data about brain structure and function over the internet. Complete brain datasets for various species, including Homo

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

236

Molecular Maps of the Reorganization of Genome-Nuclear Lamina Interactions during Differentiation  

Microsoft Academic Search

The three-dimensional organization of chromosomes within the nucleus and its dynamics during differentiation are largely unknown. To visualize this process in molecular detail, we generated high-resolution maps of genome-nuclear lamina interactions during subsequent differentiation of mouse embryonic stem cells via lineage-committed neural precursor cells into terminally differentiated astrocytes. This reveals that a basal chromosome architecture present in embryonic stem cells

Daan Peric-Hupkes; Wouter Meuleman; Ludo Pagie; Sophia W. M. Bruggeman; Irina Solovei; Wim Brugman; Stefan Gräf; Paul Flicek; Ron M. Kerkhoven; Maarten van Lohuizen; Marcel Reinders; Lodewyk Wessels; Bas van Steensel

2010-01-01

237

Geologic Maps  

NSDL National Science Digital Library

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

Graymer, Russell

238

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

PubMed Central

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

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

2010-01-01

239

Mapping dynamic protein interactions to insulin secretory granule behavior with TIRF-FRET.  

PubMed

Biological processes are governed by extensive networks of dynamic molecular interactions. Yet, establishing a spatial and temporal map of these interactions and their direct relationship to specific cell functions has remained a challenge. Here, we implement sensitized emission Förster resonance energy transfer (FRET) stoichiometry under total internal reflection fluorescence (TIRF) microscopy. We demonstrate through quantitative analysis and modeling that evanescent fields must be precisely matched between FRET excitation wavelengths to isolate dynamic interactions between bimolecular FRET pairs that are not entirely membrane-delimited. We then use TIRF-FRET to monitor the behavior of individual insulin-containing secretory granules at the plasma membrane of living cells, while simultaneously tracking the dynamic interaction between the GTPase Rab27A and its effector Slp4A, on those same granules. Notably, insulin granules that underwent exocytosis demonstrated a specific increase in Rab27A-GTP/Slp4A FRET in the 5 s before membrane fusion, which coincided temporally with an increase in granule displacement and mobility. These results demonstrate an initial spatiotemporal mapping of a dynamic protein-protein interaction on individual secretory granules that is linked to a specific granule behavior in living cells. PMID:20713017

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

2010-08-01

240

A Rice Kinase-Protein Interaction Map1[W][OA  

PubMed Central

Plants uniquely contain large numbers of protein kinases, and for the vast majority of the 1,429 kinases predicted in the rice (Oryza sativa) genome, little is known of their functions. Genetic approaches often fail to produce observable phenotypes; thus, new strategies are needed to delineate kinase function. We previously developed a cost-effective high-throughput yeast two-hybrid system. Using this system, we have generated a protein interaction map of 116 representative rice kinases and 254 of their interacting proteins. Overall, the resulting interaction map supports a large number of known or predicted kinase-protein interactions from both plants and animals and reveals many new functional insights. Notably, we found a potential widespread role for E3 ubiquitin ligases in pathogen defense signaling mediated by receptor-like kinases, particularly by the kinases that may have evolved from recently expanded kinase subfamilies in rice. We anticipate that the data provided here will serve as a foundation for targeted functional studies in rice and other plants. The application of yeast two-hybrid and TAPtag analyses for large-scale plant protein interaction studies is also discussed.

Ding, Xiaodong; Richter, Todd; Chen, Mei; Fujii, Hiroaki; Seo, Young Su; Xie, Mingtang; Zheng, Xianwu; Kanrar, Siddhartha; Stevenson, Rebecca A.; Dardick, Christopher; Li, Ying; Jiang, Hao; Zhang, Yan; Yu, Fahong; Bartley, Laura E.; Chern, Mawsheng; Bart, Rebecca; Chen, Xiuhua; Zhu, Lihuang; Farmerie, William G.; Gribskov, Michael; Zhu, Jian-Kang; Fromm, Michael E.; Ronald, Pamela C.; Song, Wen-Yuan

2009-01-01

241

Mapping the ligand-binding sites and disease-associated mutations on the most abundant protein in the human, type I collagen.  

PubMed

Type I collagen is the most abundant protein in humans, and it helps to maintain the integrity of many tissues via its interactions with cell surfaces, other extracellular matrix molecules, and growth and differentiation factors. Nearly 50 molecules have been found to interact with type I collagen, and for about half of them, binding sites on this collagen have been elucidated. In addition, over 300 mutations in type I collagen associated with human connective tissue disorders have been described. However, the spatial relationships between the known ligand-binding sites and mutation positions have not been examined. To this end, here we have created a map of type I collagen that includes all of its ligand-binding sites and mutations. The map reveals the existence of several hot spots for ligand interactions on type I collagen and that most of the binding sites locate to its C-terminal half. Moreover, on the collagen fibril some potentially relevant relationships between binding sites were observed including the following: fibronectin- and certain integrin-binding regions are near neighbors, which may mechanistically relate to fibronectin-dependent cell-collagen attachment; proteoglycan binding may potentially impact upon collagen fibrillogenesis, cell-collagen attachment, and collagen glycation seen in diabetes and aging; and mutations associated with osteogenesis imperfecta and other disorders show apparently nonrandom distribution patterns within both the monomer and fibril, implying that mutation positions correlate with disease phenotype. These and other observations presented here may provide novel insights into evaluating type I collagen functions and the relationships between its binding partners and mutations. PMID:11704682

Di Lullo, Gloria A; Sweeney, Shawn M; Korkko, Jarmo; Ala-Kokko, Leena; San Antonio, James D

2001-11-09

242

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

PubMed

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

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

2013-04-18

243

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.

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

1996-01-01

244

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

245

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

PubMed Central

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

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

2007-01-01

246

Mapping sites of O-GlcNAc modification using affinity tags for serine and threonine post-translational modifications.  

PubMed

Identifying sites of post-translational modifications on proteins is a major challenge in proteomics. O-Linked beta-N-acetylglucosamine (O-GlcNAc) is a dynamic nucleocytoplasmic modification more analogous to phosphorylation than to classical complex O-glycosylation. We describe a mass spectrometry-based method for the identification of sites modified by O-GlcNAc that relies on mild beta-elimination followed by Michael addition with dithiothreitol (BEMAD). Using synthetic peptides, we also show that biotin pentylamine can replace dithiothreitol as the nucleophile. The modified peptides can be efficiently enriched by affinity chromatography, and the sites can be mapped using tandem mass spectrometry. This same methodology can be applied to mapping sites of serine and threonine phosphorylation, and we provide a strategy that uses modification-specific antibodies and enzymes to discriminate between the two post-translational modifications. The BEMAD methodology was validated by mapping three previously identified O-GlcNAc sites, as well as three novel sites, on Synapsin I purified from rat brain. BEMAD was then used on a purified nuclear pore complex preparation to map novel sites of O-GlcNAc modification on the Lamin B receptor and the nucleoporin Nup155. This method is amenable for performing quantitative mass spectrometry and can also be adapted to quantify cysteine residues. In addition, our studies emphasize the importance of distinguishing between O-phosphate versus O-GlcNAc when mapping sites of serine and threonine post-translational modification using beta-elimination/Michael addition methods. PMID:12438562

Wells, Lance; Vosseller, Keith; Cole, Robert N; Cronshaw, Janet M; Matunis, Michael J; Hart, Gerald W

2002-10-01

247

Nicotinic Agonist Binding Site Mapped by Methionine- and Tyrosine-Scanning Coupled with Azidochloropyridinyl Photoaffinity Labeling  

PubMed Central

Agonists activating nicotinic acetylcholine receptors (nAChR) include potential therapeutic agents and also toxicants such as epibatidine and neonicotinoid insecticides with a chloropyridinyl substituent. Nicotinic agonist interactions with mollusk (Aplysia californica) acetylcholine binding protein, a soluble surrogate of the nAChR extracellular domain, are precisely defined by scanning with 17 methionine and tyrosine mutants within the binding site by photoaffinity labeling with 5-azido-6-chloropyridin-3-yl probes that have similar affinities to their nonazido counterparts. Methionine and tryrosine are the only residues found derivatized, and their reactivity exquisitely depends on the direction of the azido moiety and its apposition to the reactive amino acid side chains.

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

2009-01-01

248

Predictions for Cholesterol Interaction Sites on the A2A Adenosine Receptor  

PubMed Central

Molecular dynamics simulations of the A2A adenosine receptor totaling 1.4 ?sec show clear evidence for specific sites mediating interactions between adenosinebound A2A and cholesterol. The strongest evidence is for three binding sites. Two are in the extracellular leaflet, with one site interacting with helices VII and I, and the other with helices II and III. One site is located in the intracellular leaflet, interacting with helices III and IV. One of our three predicted binding sites is confirmed by a just-published high resolution structure of A2A cocrystallized with an antagonist.

Lee, Ji Young; Lyman, Edward

2012-01-01

249

Binding site mapping of a photoaffinity-labeled juvenile hormone binding protein.  

PubMed

The juvenile hormone binding protein (JHBP) of larval Manduca sexta was labeled by a photoaffinity analog of JH II and purified by preparative IEF and ion-exchange HPLC. The purified [3H]EHDA-labeled JHBP was selectively cleaved by CNBr and by endoproteinases Lys-C and Glu-C. The radioactive peptides were separated by tricine SDS-PAGE and sequenced after blotting to a PVDF membrane. The sequence revealed that Ala184-Asn226 contained a primary binding site of [3H]EHDA. Furthermore, peptide mapping indicated that Asp1-Glu34 also contained a second covalent attachment site of [3H]EHDA. Labeling of the N-terminal region increased when the photolysis was performed at lower temperature. Since Ala184-Asn226 is predicted to be a hydrophobic beta-sheet region, it may participate in the recognition of lipophilic backbone of JH. Five out of six cysteines are located in these two regions, consistent with a model in which the two binding regions connected by disulfide bridges provide a two-sided binding pocket for juvenile hormone. PMID:1734862

Touhara, K; Prestwich, G D

1992-01-31

250

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

PubMed Central

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

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

1986-01-01

251

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

252

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

253

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

PubMed Central

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

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

2010-01-01

254

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

PubMed

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

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

2012-01-11

255

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

PubMed Central

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

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

2012-01-01

256

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

PubMed Central

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

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

2010-01-01

257

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

258

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

2013-03-14

259

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

PubMed Central

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

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

2012-01-01

260

Protein interactions: mapping interactome networks to support drug target discovery and selection.  

PubMed

Proteins are biomolecular structures that build the microscopic working machinery of any living system. Proteins within the cells and biological systems do not act alone, but rather team up into macromolecular structures enclosing intricate physicochemical dynamic connections to undertake biological functions. A critical step towards unraveling the complex molecular relationships in living systems is the mapping of protein-to-protein physical "interactions". The complete map of protein interactions that can occur in a living organism is called the "interactome". Achieving an adequate atlas of all the protein interactions within a living system should allow to build its interaction network and to identity the "central nodes" that can be critical for the function, the homeostasis, and the movement of such system. Focusing on human studies, the data about the human interactome are most relevant for current biomedical research, because it is clear that the location of the proteins in the interactome network will allow to evaluate their centrality and to redefine the potential value of each protein as a drug target. This chapter presents our current knowledge on the human protein-protein interactome and explains how such knowledge can help us to select adequate targets for drugs. PMID:22821600

De Las Rivas, Javier; Prieto, Carlos

2012-01-01

261

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.

262

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.

Unneberg, Per; Claverie, Jean-Michel

2007-01-01

263

Estramustine phosphate but not estramustine inhibits the interaction of microtubule associated protein 2 (MAP2) with actin filaments  

Microsoft Academic Search

The effect of estramustine and estramustine phosphate (EP) on the interaction of microtubule associated protein 2 (MAP2) with actin has been examined. We show that (a) neither estramustine nor EP influences actin polymerisation (b) EP, but not estramustine, reduces the amount of MAP2 which co-sediments with F-actin in a dose-dependent manner and (c) EP decreases the MAP2-induced crosslinking of F-actin

Barbara Pedrotti; Khalid Islam

1997-01-01

264

Mapping the binding-site crevice of the dopamine D2 receptor by the substituted-cysteine accessibility method  

Microsoft Academic Search

The binding site of the dopamine D2 receptor, like that of other homologous G protein-coupled receptors, is contained within a water-accessible crevice formed among its seven membrane-spanning segments. We have developed a method to map systematically all the residues forming the surface of this binding-site crevice, and we have applied this method to the third membrane-spanning segment (M3). We mutated,

Jonathan A Javitch; Dingyi Fu; Jiayun Chen; Arthur Karlin

1995-01-01

265

Real-time PCR mapping of DNaseI-hypersensitive sites using a novel ligation-mediated amplification technique  

Microsoft Academic Search

Mapping sites within the genome that are hyper- sensitive to digestion with DNaseI is an important method for identifying DNA elements that regulate transcription. The standard approach to locating these DNaseI-hypersensitive sites (DHSs) has been to use Southern blotting techniques, although we, and others, have recently published alternative methods using a range of technologies including high-throughput sequencing and genomic array

George A. Follows; Mary E. Janes; Ludovic Vallier; Anthony R. Green; Berthold Gottgens

2007-01-01

266

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

267

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

Microsoft Academic Search

Identifying protein-protein interaction sites is crucial for understanding of the principles of biological systems and processes, as well as mutant design. This paper describes a novel method that can predict protein interaction sites in heterocomplexes using information of evolutionary conservation and spatial sequence profile. A predictor was generated to distinguish the interface residues from protein surface region by radial basis

Bing Wang; Hau-san Wong; Peng Chen; Hong-qiang Wang; De-shuang Huang

2006-01-01

268

Retail web site interactivity : How does it influence customer satisfaction and behavioral intentions?  

Microsoft Academic Search

Purpose – Since web sites are collection of several features, this paper examines web site interactivity – objective and subjective – at the feature level in terms of three underlying dimensions. The purpose of this paper is to understand the distinction between objective and subjective interactivity and to investigate their effects on customer satisfaction, behavioral intention, and telepresence. Design\\/methodology\\/approach –

Ruby Roy Dholakia; Miao Zhao

2009-01-01

269

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

ERIC Educational Resources Information Center

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

Ko, Moo Nam

2011-01-01

270

Mapping of Quantitative Trait Loci Controlling Adaptive Traits in Coastal Douglas Fir. III. Quantitative Trait Loci-by-Environment Interactions  

Microsoft Academic Search

Quantitative trait loci (QTL) were mapped in the woody perennial Douglas fir (Pseudotsuga menziesii var. menziesii (Mirb.) Franco) for complex traits controlling the timing of growth initiation and growth cessation. QTL were estimated under controlled environmental conditions to identify QTL interactions with photoperiod, moisture stress, winter chilling, and spring temperatures. A three-generation mapping population of 460 cloned progeny was used

Kathleen D. Jermstad; Daniel L. Bassoni; Keith S. Jech; Gary A. Ritchie; Nicholas C. Wheeler; David B. Neale

271

Precise mapping of an IGF-I-binding site on the IGF-1R  

PubMed Central

The IGF-1R [type 1 IGF (insulin-like growth factor) receptor] is activated upon binding to IGF-I and IGF-II leading to cell growth, survival and migration of both normal and cancerous cells. We have characterized the binding interaction between the IGF-1R and its ligands using two high-affinity mouse anti-IGF-1R mAbs (monoclonal antibodies), 7C2 and 9E11. These mAbs both block IGF-I binding to the IGF-1R but have no effect on IGF-II binding. Epitope mapping using chimaeras of the IGF-1R and insulin receptor revealed that the mAbs bind to the CR (cysteine-rich) domain of IGF-1R. The epitope was finely mapped using single point mutations in the IGF-1R. Mutation of Phe241, Phe251 or Phe266 completely abolished 7C2 and 9E11 binding. The three-dimensional structure showed that these residues cluster on the surface of the CR-domain. BIAcore analyses revealed that IGF-I and a chimaeric IGF-II with the IGF-I C-domain competed for the binding of both mAbs with the IGF-1R, whereas neither IGF-II nor a chimaeric IGF-I with the IGF-II C-domain affected antibody binding. We therefore conclude the IGF-I C-domain interacts with the CR (cysteine-rich) domain of the receptor at the cluster of residues Phe241, Phe251 and Phe266. These results allow precise orientation of IGF-I within the IGF-I–IGF-1R complex involving the IGF-I C-domain binding to the IGF-1R CR domain. In addition, mAbs 7C2 and 9E11 inhibited both IGF-I- and IGF-II-induced cancer cell proliferation, migration and IGF-1R down-regulation, demonstrating that targeting the IGF-1R is an effective strategy for inhibition of cancer cell growth.

Keyhanfar, Mehrnaz; Booker, Grant W.; Whittaker, Jonathan; Wallace, John C.; Forbes, Briony E.

2006-01-01

272

Snowpack: Decadal Averages Map  

NSDL National Science Digital Library

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

Commission, California E.

273

NMR Mapping and Functional Confirmation of the Collagen Binding Sites of MMP-2†  

PubMed Central

Interactions of matrix metalloproteinase-2 (MMP-2)1 with native and denatured forms of several types of collagen are mediated by the collagen-binding domain (CBD). CBD positions substrates relative to the catalytic site and is essential for their cleavage. Our previous studies identified an CBD binding site on the ?1(I) collagen chain. The corresponding synthetic collagen peptide P713 bound CBD with high affinity and was used in this study to identify specific collagen binding residues by NMR analysis of 15N-labeled CBD complexed with P713. Results obtained showed that P713 caused chemical shifts perturbations of several surface exposed CBD backbone amide resonances in a concentration dependent manner. The ten residues that underwent the largest chemical shift perturbations (R252 in module 1, R296, F297, Y302, E321, Y323, Y329 in module 2, and R368, W374, and Y381, in module 3), were investigated by site-specific substitution with alanine. The structural integrity of the CBD variants was also analyzed by 1D 1H NMR. Surface plasmon resonance and microwell protein binding assays of control and CBD variants showed that residues in all three CBD modules contributed to collagen binding. Single residue substitutions altered the affinity for peptide P713, as well as native and denatured type I collagen, with the greatest effects observed for residues in modules 2 and 3. Additional alanine substitutions involving residues in two or three modules simultaneously further reduced the binding of CBD to native and denatured type I collagen and demonstrated that all three modules contribute to the substrate binding. These results have localized and confirmed the key collagen binding site residues in the three fibronectin type II-like modules of MMP-2.

Xu, Xiaoping; Mikhailova, Margarita; Ilangovan, Udayar; Chen, Zhihua; Yu, Agnes; Pal, Sanjay; Hinck, Andrew P.; Steffensen, Bjorn

2009-01-01

274

Real-time PCR mapping of DNaseI-hypersensitive sites using a novel ligation-mediated amplification technique  

PubMed Central

Mapping sites within the genome that are hypersensitive to digestion with DNaseI is an important method for identifying DNA elements that regulate transcription. The standard approach to locating these DNaseI-hypersensitive sites (DHSs) has been to use Southern blotting techniques, although we, and others, have recently published alternative methods using a range of technologies including high-throughput sequencing and genomic array tiling paths. In this article, we describe a novel protocol to use real-time PCR to map DHS. Advantages of the technique reported here include the small cell numbers required for each analysis, rapid, relatively low-cost experiments with minimal need for specialist equipment. Presented examples include comparative DHS mapping of known TAL1/SCL regulatory elements between human embryonic stem cells and K562 cells.

Follows, George A.; Janes, Mary E.; Vallier, Ludovic; Green, Anthony R.; Gottgens, Berthold

2007-01-01

275

Site Mapping, Geophysical Investigation, and Geomorphic Reconnaissance at Site 9 ME 395 Upatoi Town, Fort Benning, Georgia.  

National Technical Information Service (NTIS)

An interdisciplinary team was tasked to support archaeologists in evaluating an historic Creek Indian village and cemetery site located on Fort Benning, Georgia. The investigations demonstrated that conditions at the site were excellent for the use of non...

F. L. Briuer J. E. Simms L. M. Smith

1997-01-01

276

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

National Technical Information Service (NTIS)

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 estimat...

A. W. Stevens D. P. Finlayson G. Gelfenbaum J. R. Lacy

2008-01-01

277

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

Microsoft Academic Search

This paper describes our photogrammetric analysis of the Imager for Mars Pathfinder data, part of a broader program of mapping the Mars Pathfinder landing site in support of geoscience investigations. This analysis, carried out primarily with a commercial digital photogrammetric system, supported by our in-house Integrated Software for Imagers and Spectrometers (ISIS), consists of three steps: (1) geometric control: simultaneous

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

1999-01-01

278

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

Microsoft Academic Search

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

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

2010-01-01

279

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

PubMed Central

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

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

2012-01-01

280

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

PubMed Central

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

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

2012-01-01

281

Mapping of antigenic sites of foot-and-mouth disease virus serotype Asia 1 and relationships with sites described in other serotypes.  

PubMed

Knowledge of the antigenic structure of foot-and-mouth disease virus (FMDV) has relevance in the development of diagnostic assays, in the evaluation of the antigenic variability and in the selection of appropriate vaccine strains. Antigenic sites have been investigated only in FMDVs of serotypes O, A and C, while it would be valuable to extend studies also to other serotypes. This paper reports the identification of antigenic sites involved in virus neutralization in the FMDV serotype Asia 1 by using a new panel of mAbs and their relation with sites described in other serotypes is discussed. Out of 24 mAbs raised against the FMDV serotype Asia 1, 10 neutralize viral infectivity and were used to select FMDV mutants resistant to neutralization. On the basis of their reactivity profile with virus mutants, the 10 neutralizing mAbs were clustered in four groups corresponding to four independent antigenic sites. By comparing the amino acid sequence of the parental virus and of virus mutants, the amino acids crucial for the four sites were mapped at the following positions: VP1 140-142, VP2 67-79, VP3 58/59 and VP3 218. Three of the four neutralizing sites identified and mapped on FMDV serotype Asia 1 correspond structurally and functionally to analogous sites described in FMDV serotypes O, A and C, enforcing the evidence that these are dominant antigenic sites in the FMDV structure. The fourth site, located at the C terminus of VP3, is a new independent site, described for the first time in FMDV. PMID:23197575

Grazioli, Santina; Fallacara, Francesca; Brocchi, Emiliana

2012-11-28

282

A remote characterization system for subsurface mapping of buried waste sites  

SciTech Connect

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

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

1992-10-01

283

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.

284

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

PubMed

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

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

2010-03-01

285

Rational manipulation of amyloidogenesis using an atomic level map of peptide-fibril interactions.  

PubMed

Amyloidogenic aggregation has been the subject of intense research over the past few decades, but the mechanisms underlying the early stages of amyloidogenesis remain elusive. Here we demonstrate for the first time manipulation of amyloidogenesis based on an atomic level map of peptide-fibril interactions in early- and late-stage ordered aggregation. Several point mutants with specific amyloidogenic properties are introduced, including one that "stalls" early in the aggregation process, forming early-stage fibrillar aggregates, but not mature fibrils. PMID:20560641

Liang, Yanfang; Jasbi, Shohreh Zahedi; Morin, Sylvie; Wilson, Derek J

2010-07-20

286

Nonprimed and DYRK1A-primed GSK3 beta-phosphorylation sites on MAP1B regulate microtubule dynamics in growing axons.  

PubMed

MAP1B is a developmentally regulated microtubule-associated phosphoprotein that regulates microtubule dynamics in growing axons and growth cones. We used mass spectrometry to map 28 phosphorylation sites on MAP1B, and selected for further study a putative primed GSK3 beta site and compared it with two nonprimed GSK3 beta sites that we had previously characterised. We raised a panel of phosphospecific antibodies to these sites on MAP1B and used it to assess the distribution of phosphorylated MAP1B in the developing nervous system. This showed that the nonprimed sites are restricted to growing axons, whereas the primed sites are also expressed in the neuronal cell body. To identify kinases phosphorylating MAP1B, we added kinase inhibitors to cultured embryonic cortical neurons and monitored MAP1B phosphorylation with our panel of phosphospecific antibodies. These experiments identified dual-specificity tyrosine-phosphorylation-regulated kinase (DYRK1A) as the kinase that primes sites of GSK3 beta phosphorylation in MAP1B, and we confirmed this by knocking down DYRK1A in cultured embryonic cortical neurons by using shRNA. DYRK1A knockdown compromised neuritogenesis and was associated with alterations in microtubule stability. These experiments demonstrate that MAP1B has DYRK1A-primed and nonprimed GSK3 beta sites that are involved in the regulation of microtubule stability in growing axons. PMID:19549690

Scales, Timothy M E; Lin, Shen; Kraus, Michaela; Goold, Robert G; Gordon-Weeks, Phillip R

2009-06-23

287

Mapping of accessible sites for oligonucleotide hybridization on hepatitis delta virus ribozymes.  

PubMed

Semi-random libraries of DNA 6mers and RNase H digestion were applied to search for sites accessible to hybridization on the genomic and antigenomic HDV ribozymes and their 3' truncated derivatives. An approach was proposed to correlate the cleavage sites and most likely sequences of oligomers, members of the oligonucleotide libraries, which were engaged in the formation of RNA-DNA hybrids. The predicted positions of oligomers hybridizing to the genomic ribozyme were compared with the fold of polynucleotide chain in the ribozyme crystal structure. The data exemplified the crucial role of target RNA structural features in the binding of antisense oligonucleotides. It turned out that cleavages were induced if the bound oligomer could adapt an ordered helical conformation even when it required partial penetration of an adjacent double-stranded region. The major features of RNA structure disfavoring hybridization and/or RNase H hydrolysis were sharp turns of the polynucleotide chain and breaks in stacking interactions of bases. Based on the predicted positions of oligomers hybridizing to the antigenomic ribozyme we chose and synthesized four antisense DNA 6mers which were shown to direct hydrolysis in the desired, earlier predicted regions of the molecule. PMID:10734198

Wrzesinski, J; Legiewicz, M; Ciesio?ka, J

2000-04-15

288

Mapping of accessible sites for oligonucleotide hybridization on hepatitis delta virus ribozymes  

PubMed Central

Semi-random libraries of DNA 6mers and RNase H digestion were applied to search for sites accessible to hybridization on the genomic and antigenomic HDV ribozymes and their 3? truncated derivatives. An approach was proposed to correlate the cleavage sites and most likely sequences of oligomers, members of the oligonucleotide libraries, which were engaged in the formation of RNA–DNA hybrids. The predicted positions of oligomers hybridizing to the genomic ribozyme were compared with the fold of polynucleotide chain in the ribozyme crystal structure. The data exemplified the crucial role of target RNA structural features in the binding of antisense oligonucleotides. It turned out that cleavages were induced if the bound oligomer could adapt an ordered helical conformation even when it required partial penetration of an adjacent double-stranded region. The major features of RNA structure disfavoring hybridization and/or RNase H hydrolysis were sharp turns of the polynucleotide chain and breaks in stacking interactions of bases. Based on the predicted positions of oligomers hybridizing to the antigenomic ribozyme we chose and synthesized four antisense DNA 6mers which were shown to direct hydrolysis in the desired, earlier predicted regions of the molecule.

Wrzesinski, Jan; Legiewicz, Micha; Ciesiolka, Jerzy

2000-01-01

289

Far upstream element binding protein 2 interacts with enterovirus 71 internal ribosomal entry site and negatively regulates viral translation  

PubMed Central

An internal ribosomal entry site (IRES) that directs the initiation of viral protein translation is a potential drug target for enterovirus 71 (EV71). Regulation of internal initiation requires the interaction of IRES trans-acting factors (ITAFs) with the internal ribosomal entry site. Biotinylated RNA-affinity chromatography and proteomic approaches were employed to identify far upstream element (FUSE) binding protein 2 (FBP2) as an ITAF for EV71. The interactions of FBP2 with EV71 IRES were confirmed by competition assay and by mapping the association sites in both viral IRES and FBP2 protein. During EV71 infection, FBP2 was enriched in cytoplasm where viral replication occurs, whereas FBP2 was localized in the nucleus in mock-infected cells. The synthesis of viral proteins increased in FBP2-knockdown cells that were infected by EV71. IRES activity in FBP2-knockdown cells exceeded that in the negative control (NC) siRNA-treated cells. On the other hand, IRES activity decreased when FBP2 was over-expressed in the cells. Results of this study suggest that FBP2 is a novel ITAF that interacts with EV71 IRES and negatively regulates viral translation.

Lin, Jing-Yi; Li, Mei-Ling; Shih, Shin-Ru

2009-01-01

290

Far upstream element binding protein 2 interacts with enterovirus 71 internal ribosomal entry site and negatively regulates viral translation.  

PubMed

An internal ribosomal entry site (IRES) that directs the initiation of viral protein translation is a potential drug target for enterovirus 71 (EV71). Regulation of internal initiation requires the interaction of IRES trans-acting factors (ITAFs) with the internal ribosomal entry site. Biotinylated RNA-affinity chromatography and proteomic approaches were employed to identify far upstream element (FUSE) binding protein 2 (FBP2) as an ITAF for EV71. The interactions of FBP2 with EV71 IRES were confirmed by competition assay and by mapping the association sites in both viral IRES and FBP2 protein. During EV71 infection, FBP2 was enriched in cytoplasm where viral replication occurs, whereas FBP2 was localized in the nucleus in mock-infected cells. The synthesis of viral proteins increased in FBP2-knockdown cells that were infected by EV71. IRES activity in FBP2-knockdown cells exceeded that in the negative control (NC) siRNA-treated cells. On the other hand, IRES activity decreased when FBP2 was over-expressed in the cells. Results of this study suggest that FBP2 is a novel ITAF that interacts with EV71 IRES and negatively regulates viral translation. PMID:19010963

Lin, Jing-Yi; Li, Mei-Ling; Shih, Shin-Ru

2008-11-14

291

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

292

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

2007-11-27

293

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

NASA Astrophysics Data System (ADS)

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

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

294

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

PubMed

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

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

2005-07-14

295

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

296

Magnetization reversal within Dzyaloshinskii—Moriya interaction under on-site Coulomb interaction in BiCrO3  

NASA Astrophysics Data System (ADS)

First-principals calculations show that magnetization reversal is accompanied by the opposite sense of rotation of the neighboring oxygen octahedra along the [1 1 1] direction which is called the antiferrodistortive displacement in BiCrO3. The coupling between magnetization and antiferrodistortive distortion is mainly caused by Dzyaloshinskii—Moriya interaction which is driven by the eg-eg states antiferromagnetic interaction in Cr-3d. A critical value of on-site Coulomb interaction prohibiting the Dzyaloshinskii—Moriya interaction and thus the magnetization reversal is found to be 1.3 eV.

Feng, Hong-Jian

2012-08-01

297

A protein-protein interaction map of yeast RNA polymerase III  

PubMed Central

The structure of the yeast RNA polymerase (pol) III was investigated by exhaustive two-hybrid screening using a library of random genomic fragments fused to the Gal4 activation domain. This procedure allowed us to identify contacts between individual polypeptides, localize the contact domains, and deduce a protein–protein interaction map of the multisubunit enzyme. In all but one case, pol III subunits were able to interact in vivo with one or sometimes two partner subunits of the enzyme or with subunits of TFIIIC. Four subunits that are common to pol I, II, and III (ABC27, ABC14.5, ABC10?, and ABC10?), two that are common to pol I and III (AC40 and AC19), and one pol III-specific subunit (C11) can associate with defined regions of the two large subunits. These regions overlapped with highly conserved domains. C53, a pol III-specific subunit, interacted with a 37-kDa polypeptide that copurifies with the enzyme and therefore appears to be a unique pol III subunit (C37). Together with parallel interaction studies based on dosage-dependent suppression of conditional mutants, our data suggest a model of the pol III preinitiation complex.

Flores, A.; Briand, J.-F.; Gadal, O.; Andrau, J.-C.; Rubbi, L.; Van Mullem, V.; Boschiero, C.; Goussot, M.; Marck, C.; Carles, C.; Thuriaux, P.; Sentenac, A.; Werner, M.

1999-01-01

298

Groundwater vulnerability: interactions of chemical and site properties  

Microsoft Academic Search

This study brings together extensive, multi-annual groundwater monitoring datasets from the UK and Midwestern US to test the relative importance of site (e.g. land use, soil and aquifer type) and chemical factors (e.g. solubility in water) and between and within year variations in controlling groundwater contamination by pesticides. ANOVA (general linear modelling) was used to test the significance and proportion

Fred Worrall; Tim Besien; Dana W Kolpin

2002-01-01

299

Sites, sacredness, and stories: Interactions of archaeology and contemporary paganism  

Microsoft Academic Search

Folklore has, until very recently, been at the fringes of archaeological research. Post-processual archaeology has promoted plurality in interpretation, however, and archaeology more widely is required to make itself relevant to contemporary society; so, contemporary folkloric practices vis-à-vis archaeological remains are once again receiving attention. In this paper we examine contemporary Pagan understandings of and engagements with 'sacred sites' in

Robert J. Wallis; Jenny Blain

2003-01-01

300

Linkage map organization of expressed sequence tags and sequence tagged sites in the mosquito, Aedes aegypti  

Microsoft Academic Search

A composite genetic linkage map for the yellow fever mosquito Aedes aegypti was constructed based on restriction fragment length polymorphism (RFLP), single nucleotide polymorphism (SNP) and single strand conformation polymorphism (SSCP) markers. The map consists of 146 marker loci distributed across 205 cM, and includes several morphological mutant marker loci. Most of the genetic markers are derived from random cDNAs

D. W. Severson; J. K. Meece; D. D. Lovin; G. Saha; I. Morlais

2002-01-01

301

A Comprehensive Rice Transcript Map Containing 6591 Expressed Sequence Tag Sites  

Microsoft Academic Search

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

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

2002-01-01

302

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

Microsoft Academic Search

Graptemys flavimaculata, the yellow-blotched map turtle, is a long-lived, threatened, species, endemic to the Pascagoula River drainage in Mississippi. During the 1980s, one branch of the drainage (i.e. the Leaf River) was impacted by effluent from a wood pulp processing plant known to contain endocrine disrupters. A decade later, we examined seasonal reproductive parameters (i.e. monthly plasma estradiol-17? (E2), testosterone

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

2009-01-01

303

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

SciTech Connect

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

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

2009-01-01

304

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.

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

2011-01-01

305

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

PubMed Central

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

2013-01-01

306

Mapping the nucleotide binding site of uncoupling protein 1 using atomic force microscopy.  

PubMed

A tight regulation of proton transport in the inner mitochondrial membrane is crucial for physiological processes such as ATP synthesis, heat production, or regulation of the reactive oxygen species as proposed for the uncoupling protein family members (UCP). Specific regulation of proton transport is thus becoming increasingly important in the therapy of obesity and inflammatory, neurodegenerative, and ischemic diseases. We and other research groups have shown previously that UCP1- and UCP2-mediated proton transport is inhibited by purine nucleotides. Several hypotheses have been proposed to explain the inhibitory effect of ATP, although structural details are still lacking. Moreover, the unresolved mystery is how UCP operates in vivo despite the permanent presence of high (millimolar) concentrations of ATP in mitochondria. Here we use the topographic and recognition (TREC) mode of an atomic force microscope to visualize UCP1 reconstituted into lipid bilayers and to analyze the ATP-protein interaction at a single molecule level. The comparison of recognition patterns obtained with anti-UCP1 antibody and ATP led to the conclusion that the ATP binding site can be accessed from both sides of the membrane. Using cantilever tips with different cross-linker lengths, we determined the location of the nucleotide binding site inside the membrane with 1 Å precision. Together with the recently published NMR structure of a UCP family member (Berardi et al. Nature, 2011, 476, 109-113), our data provide a valuable insight into the mechanism of the nucleotide binding and pave the way for new pharmacological approaches against the diseases mentioned above. PMID:23414455

Zhu, Rong; Rupprecht, Anne; Ebner, Andreas; Haselgrübler, Thomas; Gruber, Hermann J; Hinterdorfer, Peter; Pohl, Elena E

2013-02-26

307

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

PubMed Central

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

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

2009-01-01

308

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

Microsoft Academic Search

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

Karen A. Alexander; Ron Janssen; Gustavo Arciniegas; Timothy G. OHiggins; Tessa Eikelboom; Thomas A. Wilding

2012-01-01

309

Site-condition map for Portugal based on Vs30 values and evaluation of the applicability of Vs30 proxies  

NASA Astrophysics Data System (ADS)

Maps providing information on site conditions are essential tools to accurately represent the spatial distribution of ground motions, both in seismic hazard maps and in instrumental intensity maps (ShakeMaps). Project SCENE, funded by the Portuguese Foundation for Science and Technology, aims at characterizing the site conditions for Portugal and to outline a first-order site effects map to be used in seismic hazard assessment at a national level. In the context of project SCENE we developed a database of available shear-wave velocity profiles together with surface-geology data and geotechnical data. Currently the database includes around 60 profiles dispersed in a variety of lithological and geological units. The vast majority of data consist of seismic refraction sections that were acquired both within the scope of ongoing research projects SCENE and NEFITAG, and previously performed CAPSA and ERSTA campaigns. Few sites analyzed with multichannel analysis of surface waves by Lopes et al. (2005) were also included. The Vs30 values calculated from the profiles range from 100 m/s to1000 m/s, but the higher values are poorly represented. We performed a careful evaluation of the geological conditions at database sites, using the smallest scale available maps (usually 1:50000), and grouped it into six generalized geological units. The variability of the distribution of Vs30 values varies significantly with the generalized geological unit. Holocene deposits and Pliocene units display the lowest variance. On the other hand the Pleistocene and Miocene units, which are characterized in Portugal by a large lithological variety, display a large dispersion. Geological outcrop studies and the analysis of geotechnical data in close association the seismic refraction data acquisition are currently under way to better understand this velocity-lithology relation. The use of proxies based either on exogenous geological-geographical defined units (Wills et al., 2006) or topographic slope shows relatively unbiased residual distributions of the logarithm of Vs30. Although the variance is large for both methods the geological/geographical-defined units method shows a better performance with respect to the topographic slope method. Lemoine et al. (2012) evaluated the applicability of the topographic slope method for stable and active regions of Europe using the Vs30 dataset compiled in the context of project SHARE. The variability of the entire residuals distribution is larger for the Portuguese dataset than for the European dataset, suggesting that the European database is far from being representative of the near-surface conditions in Europe.

Narciso, Joao; Vilanova, Susana; Carvalho, Joao; Pinto, Carlos; Lopes, Isabel; Nemser, Eliza; Sousa Oliveira, Carlos; Borges, Jose

2013-04-01

310

Method of predicting Splice Sites based on signal interactions  

PubMed Central

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

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

2006-01-01

311

Phosphorylation of the Synaptic Protein Interaction Site on N-type Calcium Channels Inhibits Interactions with SNARE Proteins  

Microsoft Academic Search

binant syntaxin or SNAP-25, even at a level of free calcium (15 mM) that stimulates maximal binding. In contrast, phosphoryla- tion of syntaxin and SNAP-25 with PKC and CaM KII did not affect interactions with the synprint site. Binding assays with polypeptides representing the N- and C-terminal halves of the synprint site indicate that the PKC- and CaM KII-mediated inhibition

Charles T. Yokoyama; Zu-Hang Sheng; William A. Catterall

1997-01-01

312

Interaction Maps of the Saccharomyces cerevisiae ESCRT-III Protein Snf7.  

PubMed

The Saccharomyces cerevisiae ESCRT-III protein Snf7 is part of an intricate interaction network at the endosomal membrane. Interaction maps of Snf7 were established by measuring the degree of binding of individual binding partners to putative binding motifs along the Snf7 sequence by glutathione S-transferase (GST) pulldown. For each interaction partner, distinct binding profiles were obtained. The following observations were made. The ESCRT-III subunits Vps20 and Vps24 showed a complementary binding pattern, suggesting a model for the series of events in the ESCRT-III functional cycle. Vps4 bound to individual Snf7 motifs but not to full-length Snf7. This suggests that Vps4 does not bind to the closed conformation of Snf7. We also demonstrate for the first time that the ALIX/Bro1 homologue Rim20 binds to the ?6 helix of Snf7. Analysis of a Snf7 ?6 deletion mutant showed that the ?6 helix is crucial for binding of Bro1 and Rim20 in vivo and is indispensable for the multivesicular body (MVB)-sorting and Rim-signaling functions of Snf7. The Snf7??6 protein still appeared to be incorporated into ESCRT-III complexes at the endosomal membrane, but disassembly of the complex seemed to be defective. In summary, our study argues against the view that the ESCRT cycle is governed by single one-to-one interactions between individual components and emphasizes the network character of the ESCRT interactions. PMID:24058170

Sciskala, Barbara; Kölling, Ralf

2013-09-20

313

A fast method to predict protein interaction sites from sequences 1 1 Edited by B. Holland  

Microsoft Academic Search

A simple method for predicting residues involved in protein interaction sites is proposed. In the absence of any structural report, the procedure identifies linear stretches of sequences as “receptor-binding domains” (RBDs) by analysing hydrophobicity distribution. The sequences of two databases of non-homologous interaction sites eliciting various biological activities were tested; 59–80 % were detected as RBDs. A statistical analysis of

Xavier Gallet; Benoit Charloteaux; Annick Thomas; Robert Brasseur

2000-01-01

314

Protein binding site analysis by means of structural interaction fingerprint patterns.  

PubMed

We introduce a new approach to the known concept of interaction profiles, based on Structural Interaction Fingerprints (SIFt), for precise and rapid binding site description. A set of scripts for batch generation and analysis of SIFt were prepared, and the implementation is computationally efficient and supports parallelization. It is based on a 9-digit binary interaction pattern that describes physical ligand-protein interactions in structures and models of ligand-protein complexes. The tool performs analysis and identifies binding site residues (crucial and auxiliary) and classifies interactions according to type (hydrophobic, aromatic, charge, polar, side chain, and backbone). It is convenient and easy to use, and gives manageable output data for both, interpretation and further processing. In the presented Letter, SIFts are applied to analyze binding sites in models of antagonist-5-HT7 receptor complexes and structures of cyclin dependent kinase 2-ligand complexes. PMID:21974955

Mordalski, Stefan; Kosciolek, Tomasz; Kristiansen, Kurt; Sylte, Ingebrigt; Bojarski, Andrzej J

2011-09-14

315

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

316

Escherichia coli Dam-methylase as a molecular tool for mapping binding sites of the yeast transcription factor Rpn4  

Microsoft Academic Search

Rpn4p is a transcription factor responsible for coordinated regulation of proteasomal genes in Saccharomyces cerevisiae. There are data suggesting an involvement of this factor in regulation of many other genes that comprise more than one tenth\\u000a part of the yeast genome. Traditional methods are inapplicable for mapping of Rpn4p binding sites because of their extremely\\u000a low level. We have developed

D. S. Spasskaya; D. S. Karpov; V. L. Karpov

2011-01-01

317

Mapping the Hsp90 Genetic Interaction Network in Candida albicans Reveals Environmental Contingency and Rewired Circuitry  

PubMed Central

The molecular chaperone Hsp90 regulates the folding of diverse signal transducers in all eukaryotes, profoundly affecting cellular circuitry. In fungi, Hsp90 influences development, drug resistance, and evolution. Hsp90 interacts with ?10% of the proteome in the model yeast Saccharomyces cerevisiae, while only two interactions have been identified in Candida albicans, the leading fungal pathogen of humans. Utilizing a chemical genomic approach, we mapped the C. albicans Hsp90 interaction network under diverse stress conditions. The chaperone network is environmentally contingent, and most of the 226 genetic interactors are important for growth only under specific conditions, suggesting that they operate downstream of Hsp90, as with the MAPK Hog1. Few interactors are important for growth in many environments, and these are poised to operate upstream of Hsp90, as with the protein kinase CK2 and the transcription factor Ahr1. We establish environmental contingency in the first chaperone network of a fungal pathogen, novel effectors upstream and downstream of Hsp90, and network rewiring over evolutionary time.

Diezmann, Stephanie; Michaut, Magali; Shapiro, Rebecca S.; Bader, Gary D.; Cowen, Leah E.

2012-01-01

318

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

PubMed Central

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

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

2012-01-01

319

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

320

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

PubMed Central

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

2012-01-01

321

Mapping key interactions in the dimerization process of HBHA from Mycobacterium tuberculosis, insights into bacterial agglutination.  

PubMed

HBHA is a cell-surface protein implicated in the dissemination of Mycobacterium tuberculosis (Mtb) from the site of primary infection. Its N-terminal coiled-coil region is also involved in bacterial agglutination. However, despite the importance of HBHA dimerization in agglutination, protein regions involved in dimerization are hitherto not known. Here, we mapped these regions by coupling peptide synthesis, biochemical and computational analyses, and identified structural determinants for HBHA monomer-monomer recognition. Importantly, we obtained the first molecule able to induce HBHA dimer disaggregation at 37°C, the typical growth temperature of Mtb. This result provides new opportunities towards the development of Mtb anti-aggregation molecules with therapeutic interest. PMID:22306117

Esposito, Carla; Cantisani, Marco; D'Auria, Gabriella; Falcigno, Lucia; Pedone, Emilia; Galdiero, Stefania; Berisio, Rita

2012-01-31

322

USGS - Coastal and Marine Geology Program Internet Map Server  

NSDL National Science Digital Library

This site from the USGS features marine geology resources, including the Coastal and Marine Map Server, the Gloria Mapping Program and data, and the Coastal and Marine Geology Program. Each of these resources presents data, maps, and publications. For example, the GLORIA system was developed specifically to map the morphology and texture of seafloor features in the deep ocean, while the Coastal and Marine Geology program features an interactive map server to view and create maps using available CMGP data sets.

Usgs

323

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

PubMed

Telomerase, the enzyme that extends single-stranded telomeric DNA, consists of an RNA subunit (TER) including a short template sequence, a catalytic protein (TERT) and accessory proteins. We used site-specific UV cross-linking to map the binding sites for DNA primers in TER within active Tetrahymena telomerase holoenzyme complexes. The mapping was performed at single-nucleotide resolution by a novel technique based on RNase H digestion of RNA-DNA hybrids made with overlapping complementary oligodeoxynucleotides. These data allowed tracing of the DNA path through the telomerase complexes from the template to the TERT binding element (TBE) region of TER. TBE is known to bind TERT and to be involved in the template 5'-boundary definition. Based on these findings, we propose that upstream sequences of each growing telomeric DNA chain are involved in regulation of its growth arrest at the 5'-end of the RNA template. The upstream DNA-TBE interaction may also function as an anchor for the subsequent realignment of the 3'-end of the DNA with the 3'-end of the template to enable initiation of synthesis of a new telomeric repeat. PMID:22584626

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

2012-05-14

324

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

PubMed Central

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

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

2012-01-01

325

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

ERIC Educational Resources Information Center

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

Hochheiser, Harry; Shneiderman, Ben

1999-01-01

326

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

327

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

328

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

PubMed Central

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

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

2011-01-01

329

Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways.  

PubMed

As the interface between a microbe and its environment, the bacterial cell envelope has broad biological and clinical significance. While numerous biosynthesis genes and pathways have been identified and studied in isolation, how these intersect functionally to ensure envelope integrity during adaptive responses to environmental challenge remains unclear. To this end, we performed high-density synthetic genetic screens to generate quantitative functional association maps encompassing virtually the entire cell envelope biosynthetic machinery of Escherichia coli under both auxotrophic (rich medium) and prototrophic (minimal medium) culture conditions. The differential patterns of genetic interactions detected among > 235,000 digenic mutant combinations tested reveal unexpected condition-specific functional crosstalk and genetic backup mechanisms that ensure stress-resistant envelope assembly and maintenance. These networks also provide insights into the global systems connectivity and dynamic functional reorganization of a universal bacterial structure that is both broadly conserved among eubacteria (including pathogens) and an important target. PMID:22125496

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

2011-11-17

330

Interactive panoramic map-like views for 3D mountain navigation  

NASA Astrophysics Data System (ADS)

In 3D terrain navigation applications, the views based on general perspective projection often find features of interest (FOIs) being occluded. As an alternative, panorama-like views preserve the similarity between 3D scenes before and after the deformations while ensuring the visibility of interested features. In this paper, an automatic method for generating panoramic map-like views is proposed in mountainous areas. The created panorama-like views by moving up the view position as well as the terrain deformation can successfully avoid occlusions of the FOIs. The final views also ensure the resemblance in appearance for the FOIs and landscapes, and thus satisfy the demand for interactive occlusion-free navigation in 3D complex terrain environments.

Deng, Hao; Zhang, Liqiang; Ma, Jingtao; Kang, Zhizhong

2011-11-01

331

Point Navigation Map method to track low-income mobile user's interaction.  

PubMed

Mobile phones obtained large popularization in Brazil thanks to pre-paid (pay as you go) contracts. This kind of contract represents 82% of mobile phone connections in Brazil, corresponding to 143 million in a total of 174 million mobile phone accesses in the country. In this scenario, a research about the usability of mobile phones with 17 to 24 year old youngsters, living in poor communities, enrolled in the NGO Spectaculu. Usability tests were carried through with 30 youngsters from a NGO in Rio de Janeiro. Was made a extraction of the navigation sequence with data information of input and output from the system. Point Navigation Map was created to track low-income mobile user's interaction. PMID:22317244

Abreu, Leonardo; de Moraes, Anamaria

2012-01-01

332

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

ERIC Educational Resources Information Center

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

Ko, Moo Nam

2011-01-01

333

Mapping of interaction domains between human repair proteins ERCC1 and XPF.  

PubMed

ERCC1-XPF is a heterodimeric protein complexinvolved in nucleotide excision repair and recombinational processes. Like its homologous complex in Saccharomyces cerevisiae , Rad10-Rad1, it acts as a structure-specific DNA endonuclease, cleaving at duplex-single-stranded DNA junctions. In repair, ERCC1-XPF and Rad10-Rad1 make an incision on the the 5'-side of the lesion. No humans with a defect in the ERCC1 subunit of this protein complex have been identified and ERCC1-deficient mice suffer from severe developmental problems and signs of premature aging on top of a repair-deficient phenotype. Xeroderma pigmentosum group F patients carry mutations in the XPF subunit and generally show the clinical symptoms of mild DNA repair deficiency. All XP-F patients examined demonstrate reduced levels of XPF and ERCC1 protein, suggesting that proper complex formation is required for stability of the two proteins. To better understand the molecular and clinical consequences of mutations in the ERCC1-XPF complex, we decided to map the interaction domains between the two subunits. The XPF-binding domain comprises C-terminal residues 224-297 of ERCC1. Intriguingly, this domain resides outside the region of homology with its yeast Rad10 counterpart. The ERCC1-binding domain in XPF maps to C-terminal residues 814-905. ERCC1-XPF complex formation is established by a direct interaction between these two binding domains. A mutation from an XP-F patient that alters the ERCC1-binding domain in XPF indeed affects complex formation with ERCC1. PMID:9722633

de Laat, W L; Sijbers, A M; Odijk, H; Jaspers, N G; Hoeijmakers, J H

1998-09-15

334

Mapping the Gbetagamma-binding sites in GIRK1 and GIRK2 subunits of the G protein-activated K+ channel.  

PubMed

G protein-activated K+ channels (Kir3 or GIRK) are activated by direct binding of Gbetagamma. The binding sites of Gbetagamma in the ubiquitous GIRK1 (Kir3.1) subunit have not been unequivocally charted, and in the neuronal GIRK2 (Kir3.2) subunit the binding of Gbetagamma has not been studied. We verified and extended the map of Gbetagamma-binding sites in GIRK1 by using two approaches: direct binding of Gbetagamma to fragments of GIRK subunits (pull down), and competition of these fragments with the Galphai1 subunit for binding to Gbetagamma. We also mapped the Gbetagamma-binding sites in GIRK2. In both subunits, the N terminus binds Gbetagamma. In the C terminus, the Gbetagamma-binding sites in the two subunits are not identical; GIRK1, but not GIRK2, has a previously unrecognized Gbetagamma-interacting segments in the first half of the C terminus. The main C-terminal Gbetagamma-binding segment found in both subunits is located approximately between amino acids 320 and 409 (by GIRK1 count). Mutation of C-terminal leucines 262 or 333 in GIRK1, recognized previously as crucial for Gbetagamma regulation of the channel, and of the corresponding leucines 273 and 344 in GIRK2 dramatically altered the properties of K+ currents via GIRK1/GIRK2 channels expressed in Xenopus oocytes but did not appreciably reduce the binding of Gbetagamma to the corresponding fusion proteins, indicating that these residues are mainly important for the regulation of Gbetagamma-induced changes in channel gating rather than Gbetagamma binding. PMID:12743112

Ivanina, Tatiana; Rishal, Ida; Varon, Dalia; Mullner, Carmen; Frohnwieser-Steinecke, Bibiane; Schreibmayer, Wolfgang; Dessauer, Carmen W; Dascal, Nathan

2003-05-12

335

Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome  

Microsoft Academic Search

BACKGROUND: Extensive protein interaction maps are being constructed for yeast, worm, and fly to ask how the proteins organize into pathways and systems, but no such genome-wide interaction map yet exists for the set of human proteins. To prepare for studies in humans, we wished to establish tests for the accuracy of future interaction assays and to consolidate the known

Arun K Ramani; Razvan C Bunescu; Raymond J Mooney; Edward M Marcotte

2005-01-01

336

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

PubMed Central

Using synthetic peptides, we have identified two distinct regions of the glycoprotein SPARC (Secreted Protein Acidic and Rich in Cysteine) (osteonectin/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. Immunoglobulin fractions of sera recognizing an NH2-terminal peptide (designated 1.1) blocked SPARC- mediated anti-spreading activity. Furthermore, when peptides were added to newly plated endothelial cells or fibroblasts, peptide 1.1 and a peptide corresponding to the COOH terminal EF-hand domain (designated 4.2) inhibited cell spreading in a dose-dependent manner. These peptides exhibited anti-spreading activity at concentrations from 0.1 to 1 mM. The ability of peptides 1.1 and 4.2 to modulate cell shape was augmented by an inhibitor of protein synthesis and was blocked by specific antipeptide immunoglobulins. In addition to blocking cell spreading, peptide 4.2 competed for binding of [125I]SPARC and exhibited differential affinity for extracellular matrix molecules in solid-phase binding assays. The binding of peptide 4.2 to matrix components was Ca+(+)-dependent and displayed specificities similar to those of native SPARC. These studies demonstrate that both anti- spreading activity and affinity for collagens are functions of unique regions within the SPARC amino acid sequence. The finding that two separate regions of the SPARC protein contribute to its anti-spreading activity lead us to propose that multiple regions of the protein act in concert to regulate the interactions of cells with their extracellular matrix.

1990-01-01

337

A genetic map in the Mimulus guttatus species complex reveals transmission ratio distortion due to heterospecific interactions.  

PubMed Central

As part of a study of the genetics of floral adaptation and speciation in the Mimulus guttatus species complex, we constructed a genetic linkage map of an interspecific cross between M. guttatus and M. nasutus. We genotyped an F(2) mapping population (N = 526) at 255 AFLP, microsatellite, and gene-based markers and derived a framework map through repeated rounds of ordering and marker elimination. The final framework map consists of 174 marker loci on 14 linkage groups with a total map length of 1780 cM Kosambi. Genome length estimates (2011-2096 cM) indicate that this map provides thorough coverage of the hybrid genome, an important consideration for QTL mapping. Nearly half of the markers in the full data set (49%) and on the framework map (48%) exhibited significant transmission ratio distortion (alpha = 0.05). We localized a minimum of 11 transmission ratio distorting loci (TRDLs) throughout the genome, 9 of which generate an excess of M. guttatus alleles and a deficit of M. nasutus alleles. This pattern indicates that the transmission ratio distortion results from particular interactions between the heterospecific genomes and suggests that substantial genetic divergence has occurred between these Mimulus species. We discuss possible causes of the unequal representation of parental genomes in the F(2) generation.

Fishman, L; Kelly, A J; Morgan, E; Willis, J H

2001-01-01

338

POWER TO DETECT HIGHER-ORDER EPISTATIC INTERACTIONS IN A METABOLIC PATHWAY USING NESTED ASSOCIATION MAPPING AND DIALLEL ASSOCIATION MAPPING  

Technology Transfer Automated Retrieval System (TEKTRAN)

Epistatic interactions among quantitative trait loci (QTL) contribute substantially to the variation in complex traits. The main objectives of this study were to (i) compare two- vs. four-step genome scans to identify four-way interactions among QTL belonging to a metabolic pathway, (ii) investigat...

339

Accurate thermodynamics for short-ranged truncations of Coulomb interactions in site-site molecular models  

NASA Astrophysics Data System (ADS)

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

Rodgers, Jocelyn M.; Weeks, John D.

2009-12-01

340

Characteristics of [3H]hemicholinium-3 binding to rat striatal membranes: evidence for negative cooperative site-site interactions.  

PubMed

The characteristics of [3H]hemicholinium-3 ([3H]HC-3) interactions with rat striatal membranes were investigated. Under the described assay conditions, [3H]-HC-3 binds with a saturable population of membrane binding sites having the following regional distribution: striatum much greater than hippocampus greater than or equal to cerebral cortex greater than cerebellum. The specific binding of [3H]HC-3 showed an obligatory requirement for NaCl; other halide salts of sodium or KCl failed to substitute for NaCl. The Scatchard transformation of saturation isotherm data generated a curvilinear plot with high- and low-affinity components of binding. The dissociation of [3H]HC-3 at infinite dilution was also multiexponential. The dissociation could, however, be accelerated if unlabeled HC-3 was included in the diluting buffer, and this increase in dissociation appeared to be dependent on the concentrations of unlabeled HC-3 used, with the maximal increase demonstrable at 100 nM. The dissociation was also dependent on the fractional saturation of binding sites with labeled HC-3, such that, at higher fractional saturation of binding sites, the overall dissociation was faster and the difference in the dissociation observed between "dilution only" and "dilution + unlabeled HC-3" was reduced. This occupancy-dependent change in dissociation could also be influenced by temperature and pH. Based on the results of these kinetic studies, the steady-state [3H]HC-3 binding data were analyzed for a homogeneous population of binding sites undergoing site-site interactions of the negative cooperative type. Such an analysis yielded a KD of 9.3 nM for the high-affinity state and a KD of 22.8 nM for the low-affinity state of binding sites, with a Bmax of 434 fmol/mg of protein. Competitive binding studies showed that unlabeled HC-3 was most potent in displacing [3H]HC-3, followed by choline. Other drugs known to have little influence on the synaptosomal sodium-dependent high-affinity choline uptake system (SDHACU) had no significant effect on [3H]HC-3 binding sites. Similarities in ionic dependencies, regional distributions, and pharmacological selectivities of [3H]HC-3 binding with synaptosomal SDHACU suggest that [3H]HC-3 selectively labels SDHACU sites located on presynaptic cholinergic neurons in rat CNS. We suggest that the two affinity states of [3H]HC-3 binding sites represent the different "functional" states of the SDHACU system. The binding of HC-3 (or choline) with the high-affinity state of the binding sites induces negative cooperative site-site interactions among the binding sites, resulting in the formation of a low-affinity binding state.(ABSTRACT TRUNCATED AT 400 WORDS) PMID:3625204

Chatterjee, T K; Cannon, J G; Bhatnagar, R K

1987-10-01

341

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

2013-10-16

342

Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas fir. III. Quantitative trait loci-by-environment interactions.  

PubMed Central

Quantitative trait loci (QTL) were mapped in the woody perennial Douglas fir (Pseudotsuga menziesii var. menziesii [Mirb.] Franco) for complex traits controlling the timing of growth initiation and growth cessation. QTL were estimated under controlled environmental conditions to identify QTL interactions with photoperiod, moisture stress, winter chilling, and spring temperatures. A three-generation mapping population of 460 cloned progeny was used for genetic mapping and phenotypic evaluations. An all-marker interval mapping method was used for scanning the genome for the presence of QTL and single-factor ANOVA was used for estimating QTL-by-environment interactions. A modest number of QTL were detected per trait, with individual QTL explaining up to 9.5% of the phenotypic variation. Two QTL-by-treatment interactions were found for growth initiation, whereas several QTL-by-treatment interactions were detected among growth cessation traits. This is the first report of QTL interactions with specific environmental signals in forest trees and will assist in the identification of candidate genes controlling these important adaptive traits in perennial plants.

Jermstad, Kathleen D; Bassoni, Daniel L; Jech, Keith S; Ritchie, Gary A; Wheeler, Nicholas C; Neale, David B

2003-01-01

343

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

344

Functional analysis of interaction sites on the N-terminal domain of clathrin heavy chain  

PubMed Central

In clathrin-mediated membrane traffic, clathrin does not bind directly to cargo and instead binds to adaptors that mediate this function. For endocytosis, the main adaptor is the AP-2 complex but it is uncertain how clathrin contacts AP-2. Here, we tested in human cells the importance of the three binding sites that have been identified so far on the N-terminal domain (NTD) of clathrin. We find that mutation of each of the three sites on the NTD, alone or in combination, does not block clathrin/AP-2-mediated endocytosis in the same way as deletion of the NTD. We report here the fourth and final site on the NTD that is required for clathrin/AP-2-mediated endocytic function. Each of the four interaction sites can operate alone to mediate endocytosis. The observed functional redundancy between interaction sites on the NTD explains how productivity of clathrin-coated vesicle formation is ensured.

Willox, Anna K.; Royle, Stephen J.

2012-01-01

345

X-ray mapping and scatter diagram analysis of the discoloring products resulting from the interaction of artist's pigments.  

PubMed

The discoloring interaction between the artist's pigments cadmium yellow and the copper-containing malachite, an interaction that is conjectured to cause black spotting in oil paintings of the 19th and early 20th centuries, was examined using X-ray mapping and scatter diagram analysis. The application of these coupled techniques confirmed that copper sulfide phases were produced during discoloration reaction. Scatter diagram analysis indicated that two copper sulfide stoichiometries (CuS and Cu3S2) were present as reaction products where previously only crystalline CuS (covellite) had been identified by X-ray diffraction. The results demonstrate the potential of X-ray mapping coupled with scatter diagram analysis for the identification of both crystalline and X-ray amorphous phases produced by such complex heterogeneous interactions and their applicability to the investigation of interactions of artists' pigments. PMID:20804641

White, Rachel; Thomas, Paul; Phillips, Matthew R; Moran, Ken; Wuhrer, Richard

2010-08-31

346

Cembranoid and long-chain alkanol sites on the nicotinic acetylcholine receptor and their allosteric interaction.  

PubMed

Long-chain alkanols are general anesthetics which can also act as uncharged noncompetitive inhibitors of the peripheral nicotinic acetylcholine receptor (AChR) by binding to one or more specific sites on the AChR. Cembranoids are naturally occurring, uncharged noncompetitive inhibitors of peripheral and neuronal AChRs, which have no demonstrable general anesthetic activity in vivo. In this study, [3H]tenocyclidine ([3H]TCP), an analogue of the cationic noncompetitive inhibitor phencyclidine (PCP), was used to characterize the cembranoid and long-chain alkanol sites on the desensitized Torpedo californica AChR and to investigate if these sites interact. These studies confirm that there is a single cembranoid site which sterically overlaps the [3H]TCP channel site. This cembranoid site probably also overlaps the sites for the cationic noncompetitive inhibitors, procaine and quinacrine. Evidence is also presented for one or more allosteric cembranoid sites which negatively modulate cembranoid affinity for the inhibitory site. In contrast, long-chain alkanols inhibit [3H]TCP binding through an allosteric mechanism involving two or more alkanol sites which display positive cooperativity toward each other. Double inhibitor studies show that the cembranoid inhibitory site and the alkanol sites are not independent of each other but interfere allosterically with each other's inhibition of [3H]TCP binding. The simplest models consistent with the observed data are presented and discussed. PMID:11551210

Pagán, O R; Eterovi?, V A; Garcia, M; Vergne, D; Basilio, C M; Rodríguez, A D; Hann, R M

2001-09-18

347

MAPPING OF ARCHAEOLOGICAL AREAS USING A LOW-COST UAV THE AUGUSTA BAGIENNORUM TEST SITE  

Microsoft Academic Search

In the archaeological area of Augusta Bagiennorum different tests have been performed since 1990, in order to support the archaeological scientists using geomatics techniques. Photogrammetric aerial surveys (both helicopter and aircraft platforms were used) for large scale mapping, implementation of Geographic Information System devoted to archaeological investigations and Lidar surveys have been performed. This archaeological scenario is an optimal test

H. Bendea; F. Giulio Tonolo; D. Marenchino

348

Mapping the protein-DNA interface and the metal-binding site of the major human apurinic/apyrimidinic endonuclease.  

PubMed

Apurinic/apyrimidinic (AP) endonuclease Ape1 is a key enzyme in the mammalian base excision repair pathway that corrects AP sites in the genome. Ape1 cleaves the phosphodiester bond immediately 5' to AP sites through a hydrolytic reaction involving a divalent metal co-factor. Here, site-directed mutagenesis, chemical footprinting techniques, and molecular dynamics simulations were employed to gain insights into how Ape1 interacts with its metal cation and AP DNA. It was found that Ape1 binds predominantly to the minor groove of AP DNA, and that residues R156 and Y128 contribute to protein-DNA complex stability. Furthermore, the Ape1-AP DNA footprint does not change along its reaction pathway upon active-site coordination of Mg(2+) or in the presence of DNA polymerase beta (polbeta), an interactive protein partner in AP site repair. The DNA region immediately 5' to the abasic residue was determined to be in close proximity to the Ape1 metal-binding site. Experimental evidence is provided that amino acid residues E96, D70, and D308 of Ape1 are involved in metal coordination. Molecular dynamics simulations, starting from the active site of the Ape1 crystal structure, suggest that D70 and E96 bind directly to the metal, while D308 coordinates the cation through the first hydration shell. These studies define the Ape1-AP DNA interface, determine the effect of polbeta on the Ape1-DNA interaction, and reveal new insights into the Ape1 active site and overall protein dynamics. PMID:10772862

Nguyen, L H; Barsky, D; Erzberger, J P; Wilson, D M

2000-05-01

349

Cone arrestin binding to JNK3 and Mdm2: conformational preference and localization of interaction sites  

PubMed Central

Arrestins are multi-functional regulators of G protein-coupled receptors. Receptor-bound arrestins interact with >30 remarkably diverse proteins and redirect the signaling to G protein-independent pathways. The functions of free arrestins are poorly understood, and the interaction sites of the non-receptor arrestin partners are largely unknown. In this study, we show that cone arrestin, the least studied member of the family, binds c-Jun N-terminal kinase (JNK3) and Mdm2 and regulates their subcellular distribution. Using arrestin mutants with increased or reduced structural flexibility, we demonstrate that arrestin in all conformations binds JNK3 comparably, whereas Mdm2 preferentially binds cone arrestin ‘frozen’ in the basal state. To localize the interaction sites, we expressed separate N- and C-domains of cone and rod arrestins and found that individual domains bind JNK3 and remove it from the nucleus as efficiently as full-length proteins. Thus, the arrestin binding site for JNK3 includes elements in both domains with the affinity of partial sites on individual domains sufficient for JNK3 relocalization. N-domain of rod arrestin binds Mdm2, which localizes its main interaction site to this region. Comparable binding of JNK3 and Mdm2 to four arrestin subtypes allowed us to identify conserved residues likely involved in these interactions.

Song, Xiufeng; Gurevich, Eugenia V.; Gurevich, Vsevolod V.

2008-01-01

350

A road map on human-human interaction and fine-function collaboration in collaborative integrated design environments  

Microsoft Academic Search

From human-computer interaction to human-human interaction and from information sharing to function collaborative are major advances from traditional single-user design to collaborative design. This work presents a road map to achieve this goal with computer-aided tools. The models, methods and techniques in developing collaborative tools for collaborative integrated design environment are discussed in details. The proposed ideas have been implemented

Fazhi He; Soonhung Han; Shaomei Wang; Guozheng Sun

2004-01-01

351

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

SciTech Connect

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

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

1996-09-01

352

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

SciTech Connect

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

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

1995-06-01

353

Mapping protein-protein interactions by localized oxidation: consequences of the reach of hydroxyl radical.  

PubMed

Hydroxyl radicals generated from a variety of methods, including not only synchrotron radiation but also Fenton reactions involving chelated iron, have become an accepted macromolecular footprinting tool. Hydroxyl radicals react with proteins via multiple mechanisms that lead to both polypeptide backbone cleavage events and side chain modifications (e.g., hydroxylation and carbonyl formation). The use of site-specifically tethered iron chelates can reveal protein-protein interactions, but the interpretation of such experiments will be strengthened by improving our understanding of how hydroxyl radicals produced at a point on a protein react with other protein sites. We have developed methods for monitoring carbonyl formation on proteins as a function of distance from a hydroxyl generator, iron-(S)-1-[p-(bromoacetamido)benzyl]EDTA (FeBABE), conjugated to an engineered cysteine residue. After activation of the chelated iron with ascorbate and peroxide produces new protein carbonyl groups, their positions can be identified using element-coded affinity tagging (ECAT), with carbonyl-specific tags {e.g., rare earth chelates of (S)-2-[4-(2-aminooxy)acetamidobenzyl]-1,4,7,10-tetraazacyclododecane-N,N',N'',N'''-tetraacetic acid (AOD)} that allow for affinity purification, identification, and relative quantitation of oxidation sites using mass spectrometry. Intraprotein oxidation of single-cysteine mutants of Escherichia coli sigma(70) by tethered FeBABE was used to calibrate the reach of hydroxyl radical by comparison to the crystal structure; the application to protein-protein interactions was demonstrated using the same sigma(70) FeBABE conjugates in complexes with the RNA polymerase core enzyme. The results provide fundamental information for interpreting protein footprinting experiments in other systems. PMID:19354299

Cheal, Sarah M; Ng, Mindy; Barrios, Brianda; Miao, Zheng; Kalani, Amir K; Meares, Claude F

2009-06-01

354

Genomic maps of lincRNA occupancy reveal principles of RNA-chromatin interactions  

PubMed Central

SUMMARY Long intergenic noncoding RNAs (lincRNAs) are key regulators of chromatin state, yet the nature and sites of RNA-chromatin interaction are mostly unknown. Here we introduce Chromatin Isolation by RNA Purification (ChIRP), where tiling oligonucleotides retrieve specific lincRNAs with bound protein and DNA sequences, which are enumerated by deep sequencing. ChIRP-seq of three lincRNAs reveal that RNA occupancy sites in the genome are focal, sequence-specific, and numerous. Drosophila roX2 RNA occupies male X-linked gene bodies with increasing tendency toward the 3’ end, peaking at CES sites. Human telomerase RNA TERC occupies telomeres and Wnt pathway genes. HOTAIR lincRNA preferentially occupies a GA-rich DNA motif to nucleate broad domains of Polycomb occupancy and histone H3 lysine 27 trimethylation. HOTAIR occupancy occurs independently of EZH2, suggesting the order of RNA guidance of Polycomb occupancy. ChIRP-seq is generally applicable to illuminate the intersection of RNA and chromatin with newfound precision genome-wide.

Chu, Ci; Qu, Kun; Zhong, Franklin; Artandi, Steven E.; Chang, Howard Y.

2011-01-01

355

Interaction between Solar Wind and Lunar Magnetic Anomalies observed by Kaguya MAP-PACE  

NASA Astrophysics Data System (ADS)

It is known that Moon has neither global intrinsic magnetic field nor thick atmosphere. Different from the Earth's case where the intrinsic global magnetic field prevents the solar wind from penetrating into the magnetosphere, solar wind directly impacts the lunar surface. Since the discovery of the lunar crustal magnetic field in 1960s, several papers have been published concerning the interaction between the solar wind and the lunar magnetic anomalies. MAG/ER on Lunar Prospector found heating of the solar wind electrons presumably due to the interaction between the solar wind and the lunar magnetic anomalies and the existence of the mini-magnetosphere was suggested. However, the detailed mechanism of the interaction has been unclear mainly due to the lack of the in-situ observed data of low energy ions. MAgnetic field and Plasma experiment - Plasma energy Angle and Composition Experiment (MAP-PACE) on Kaguya (SELENE) completed its ˜1.5-year observation of the low energy charged particles around the Moon on 10 June, 2009. Kaguya was launched on 14 September 2007 by H2A launch vehicle from Tanegashima Space Center in Japan. Kaguya was inserted into a circular lunar polar orbit of 100km altitude and continued observation for nearly 1.5 years till it impacted the Moon on 10 June 2009. During the last 5 months, the orbit was lowered to ˜50km-altitude between January 2009 and April 2009, and some orbits had further lower perilune altitude of ˜10km after April 2009. MAP-PACE consisted of 4 sensors: ESA (Electron Spectrum Analyzer)-S1, ESA-S2, IMA (Ion Mass Analyzer), and IEA (Ion Energy Analyzer). All the sensors performed quite well as expected from the laboratory experiment carried out before launch. Since each sensor had hemispherical field of view, two electron sensors and two ion sensors that were installed on the spacecraft panels opposite to each other could cover full 3-dimensional phase space of low energy electrons and ions. One of the ion sensors IMA was an energy mass spectrometer. IMA measured mass identified ion energy spectra that had never been obtained at 100km altitude polar orbit around the Moon. When Kaguya flew over South Pole Aitken region, where strong magnetic anomalies exist, solar wind ions reflected by magnetic anomalies were observed. These ions had much higher flux than the solar wind protons scattered at the lunar surface. The magnetically reflected ions had nearly the same energy as the incident solar wind ions while the solar wind protons scattered at the lunar surface had slightly lower energy than the incident solar wind ions. At 100km altitude, when the reflected ions were observed, the simultaneously measured electrons were often heated and the incident solar wind ions were sometimes slightly decelerated. At ~50km altitude, when the reflected ions were observed, proton scattering at the lunar surface clearly disappeared. It suggests that there exists an area on the lunar surface where solar wind does not impact. At ~10km altitude, the interaction between the solar wind ions and the lunar magnetic anomalies was remarkable with clear deceleration of the incident solar wind ions and heating of the reflected ions as well as significant heating of the electrons. Calculating velocity moments including density, velocity, temperature of the ions and electrons, we have found that there exists 100km scale regions over strong magnetic anomalies where plasma parameters are quite different from the outside. Solar wind ions observed at 10km altitude show several different behaviors such as deceleration without heating and heating in a limited region inside the magnetic anomalies that may be caused by the magnetic field structure. The deceleration of the solar wind has the same ?E/q (?E : deceleration energy, q: charge) for different species, which constraints the possible mechanisms of the interaction between solar wind and magnetic anomalies.

Saito, Yoshifumi; Yokota, Shoichiro; Tanaka, Takaaki; Asamura, Kazushi; Nishino, Masaki; Yamamoto, Tadateru; Uemura, Kota; Tsunakawa, Hideo

2010-05-01

356

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

PubMed Central

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

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

2010-01-01

357

Mapping Solvation Dynamics at the Function Site of Flavodoxin in Three Redox States  

PubMed Central

Flavoproteins are unique redox coenzymes and the dynamic solvation at their function sites is critical to the understanding of their electron-transfer properties. Here, we report our complete characterization of the function-site solvation of holoflavodoxin in three redox states and of the binding-site solvation of apoflavodoxin. Using intrinsic flavin cofactor and tryptophan residue as the local optical probes with two site-specific mutations, we observed distinct ultrafast solvation dynamics at the function site in the three states and at the related recognition site of the cofactor, ranging from a few to hundreds of picoseconds. The initial ultrafast motion in 1–2.6 ps reflects the local water-network relaxation around the shallow, solvent-exposed function site. The second relaxation in 20–40 ps results from the coupled local water-protein fluctuation. The third dynamics in hundreds of picoseconds is from the intrinsic fluctuation of the loose loops flanking the cofactor at the function site. These solvation dynamics with different amplitudes well correlate with the redox states from the oxidized form, to the more rigid semiquinone and to the much looser hydroquinone. This observation of the redox control of local protein conformation plasticity and water network flexibility is significant and such an intimate relationship is essential to the biological function of interprotein electron transfer.

Chang, Chih-Wei; He, Ting-Fang; Guo, Lijun; Stevens, Jeffrey A.; Li, Tanping; Wang, Lijuan; Zhong, Dongping

2010-01-01

358

Using Self Organizing Feature Maps to Acquire Knowledge about Visitor Behavior in a Web Site  

Microsoft Academic Search

When a user visits a web site, important information con- cerning his\\/her preferences and behavior is stored implicitly in the asso- ciated log files. This information can be revealed by using data mining techniques and can be used in order to improve both, content and struc- ture of the respective web site. From the set of possible that define the

Juan D. Velásquez; Hiroshi Yasuda; Terumasa Aoki; Richard Weber; Eduardo S. Vera

2003-01-01

359

Mapping Neuronal Inputs to REM Sleep Induction Sites with Carbachol-Fluorescent Microspheres  

Microsoft Academic Search

The cholinergic agonist carbachol was conjugated to latex microspheres that were fluorescently labeled with rhodamine and used as neuroanatomical probes that show little diffusion from their injection site and retrogradely label neurons projecting to the injection site. Microinjection of this pharmacologically active probe into the gigantocellular field of the cat pontine brain stem caused the awake cats to fall into

James J. Quattrochi; Adam N. Mamelak; Roger D. Madison; Jeffrey D. Macklis; J. Allan Hobson

1989-01-01

360

Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells  

Microsoft Academic Search

Background: Transcription by RNA polymerase II is regulated at many steps including initiation, promoter release, elongation and termination. Accumulation of RNA polymerase II at particular locations across genes can be indicative of sites of regulation. RNA polymerase II is thought to accumulate at the promoter and at sites of co-transcriptional alternative splicing where the rate of RNA synthesis slows. Results:

Alexander S Brodsky; Clifford A Meyer; Ian A Swinburne; Giles Hall; Benjamin J Keenan; Xiaole S Liu; Edward A Fox; Pamela A Silver

2005-01-01

361

Nonparametric disequilibrium mapping of functional sites using haplotypes of multiple tightly linked single-nucleotide polymorphism markers.  

PubMed Central

As the speed and efficiency of genotyping single-nucleotide polymorphisms (SNPs) increase, using the SNP map, it becomes possible to evaluate the extent to which a common haplotype contributes to the risk of disease. In this study we propose a new procedure for mapping functional sites or regions of a candidate gene of interest using multiple linked SNPs. Based on a case-parent trio family design, we use expectation-maximization (EM) algorithm-derived haplotype frequency estimates of multiple tightly linked SNPs from both unambiguous and ambiguous families to construct a contingency statistic S for linkage disequilibrium (LD) analysis. In the procedure, a moving-window scan for functional SNP sites or regions can cover an unlimited number of loci except for the limitation of computer storage. Within a window, all possible widths of haplotypes are utilized to find the maximum statistic S* for each site (or locus). Furthermore, this method can be applied to regional or genome-wide scanning for determining linkage disequilibrium using SNPs. The sensitivity of the proposed procedure was examined on the simulated data set from the Genetic Analysis Workshop (GAW) 12. Compared with the conventional and generalized TDT methods, our procedure is more flexible and powerful.

Cheng, Rong; Ma, Jennie Z; Wright, Fred A; Lin, Shili; Gao, Xin; Wang, Daolong; Elston, Robert C; Li, Ming D

2003-01-01

362

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...

363

Map Maker  

NSDL National Science Digital Library

This resource allows users to create interactive maps with layers using census data for the following topics: agriculture, biology, boundaries, climate, environment, geology, history, map reference, people, transportation, and water.

Bureau, Us C.

364

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

PubMed Central

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

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

2001-01-01

365

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

2013-10-15

366

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.

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

2008-01-01

367

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

USGS Publications Warehouse

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

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

1999-01-01

368

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

PubMed Central

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

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

2013-01-01

369

Interaction Sites of Tropomyosin in Muscle Thin Filament as Identified by Site-Directed Spin-Labeling  

PubMed Central

To identify interaction sites we measured the rotational motion of a spin label covalently bound to the side chain of a cysteine genetically incorporated into rabbit skeletal muscle tropomyosin (Tm) at positions 13, 36, 146, 160, 174, 190, 209, 230, 271, and 279. Upon the addition of F-actin, the mobility of all the spin labels, especially at position 13, 271, or 279, of Tm was inhibited significantly. Slow spin-label motion at the C-terminus (at the 230th and 271st residues) was observed upon addition of troponin. The binding of myosin-head S1 fragments without troponin immobilized Tm residues at 146, 160, 190, 209, 230, 271, and 279, suggesting that these residues are involved in a direct interaction between Tm and actin in its open state. As immobilization occurred at substoichiometric amounts of S1 binding to actin (a 1:7 molar ratio), the structural changes induced by S1 binding to one actin subunit must have propagated and influenced interaction sites over seven actin subunits.

Ueda, Keisuke; Kimura-Sakiyama, Chieko; Aihara, Tomoki; Miki, Masao; Arata, Toshiaki

2011-01-01

370

Missouri aeromagnetic 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 Missouri magnetic map is constructed from grids that combine information collected in 25 separate magnetic surveys conducted between 1943 and 1987. The data from these surveys are of varying quality. The design and specifications (terrain clearance, sampling rates, line spacing, and reduction procedures) varied from survey to survey depending on the purpose of the project and the technology of that time. Every attempt was made to acquire the data in digital form.

Kucks, Robert P.; Hill, Patricia L.

2005-01-01

371

Restriction endonuclease cleavage site map of safflower ( Carthamus tinctorius L.) chloroplast DNA  

Microsoft Academic Search

The restriction endonucleases SalI, PstI, KpnI and HindIII have been used to construct a physical map of safflower (Carthamus tinctorius L.) chloroplast DNA. This was accomplished by hybridizing Southern blots of single and double digested chloroplast DNA with 32P-dCTP nick-translated SalI, KpnI and HindIII probes which were individually isolated from agarose gels. The chloroplast DNA was found to be circular

M. A. Smith; C. Ma

1985-01-01

372

New class of microRNA targets containing simultaneous 5?-UTR and 3?-UTR interaction sites  

PubMed Central

MicroRNAs (miRNAs) are known to post-transcriptionally regulate target mRNAs through the 3?-UTR, which interacts mainly with the 5?-end of miRNA in animals. Here we identify many endogenous motifs within human 5?-UTRs specific to the 3?-ends of miRNAs. The 3?-end of conserved miRNAs in particular has significant interaction sites in the human-enriched, less conserved 5?-UTR miRNA motifs, while human-specific miRNAs have significant interaction sites only in the conserved 5?-UTR motifs, implying both miRNA and 5?-UTR are actively evolving in response to each other. Additionally, many miRNAs with their 3?-end interaction sites in the 5?-UTRs turn out to simultaneously contain 5?-end interaction sites in the 3?-UTRs. Based on these findings we demonstrate combinatory interactions between a single miRNA and both end regions of an mRNA using model systems. We further show that genes exhibiting large-scale protein changes due to miRNA overexpression or deletion contain both UTR interaction sites predicted. We provide the predicted targets of this new miRNA target class, miBridge, as an efficient way to screen potential targets, especially for nonconserved miRNAs, since the target search space is reduced by an order of magnitude compared with the 3?-UTR alone. Efficacy is confirmed by showing SEC24D regulation with hsa-miR-605, a miRNA identified only in primate, opening the door to the study of nonconserved miRNAs. Finally, miRNAs (and associated proteins) involved in this new targeting class may prevent 40S ribosome scanning through the 5?-UTR and keep it from reaching the start-codon, preventing 60S association.

Lee, Inhan; Ajay, Subramanian S.; Yook, Jong In; Kim, Hyun Sil; Hong, Su Hyung; Kim, Nam Hee; Dhanasekaran, Saravana M.; Chinnaiyan, Arul M.; Athey, Brian D.

2009-01-01

373

Structural basis of allosteric interactions among Ca2+-binding sites in a K+ channel RCK domain  

NASA Astrophysics Data System (ADS)

Ligand binding sites within proteins can interact by allosteric mechanisms to modulate binding affinities and control protein function. Here we present crystal structures of the regulator of K+ conductance (RCK) domain from a K+ channel, MthK, which reveal the structural basis of allosteric coupling between two Ca2+ regulatory sites within the domain. Comparison of RCK domain crystal structures in a range of conformations and with different numbers of regulatory Ca2+ ions bound, combined with complementary electrophysiological analysis of channel gating, suggests chemical interactions that are important for modulation of ligand binding and subsequent channel opening.

Smith, Frank J.; Pau, Victor P. T.; Cingolani, Gino; Rothberg, Brad S.

2013-10-01

374

Structural basis of allosteric interactions among Ca(2+)-binding sites in a K(+) channel RCK domain.  

PubMed

Ligand binding sites within proteins can interact by allosteric mechanisms to modulate binding affinities and control protein function. Here we present crystal structures of the regulator of K(+) conductance (RCK) domain from a K(+) channel, MthK, which reveal the structural basis of allosteric coupling between two Ca(2+) regulatory sites within the domain. Comparison of RCK domain crystal structures in a range of conformations and with different numbers of regulatory Ca(2+) ions bound, combined with complementary electrophysiological analysis of channel gating, suggests chemical interactions that are important for modulation of ligand binding and subsequent channel opening. PMID:24126388

Smith, Frank J; Pau, Victor P T; Cingolani, Gino; Rothberg, Brad S

2013-01-01

375

Off-site interaction effect in the Extended Hubbard Model with the SCRPA method  

Microsoft Academic Search

The self consistent random phase approximation (SCRPA) and a direct analytical (DA) method are proposed to solve the Extended Hubbard Model (EHM) in one dimension (1D). We have considered an EHM including on-site and off-site interactions for closed chains in 1D with periodic boundary conditions. The comparison of the SCRPA results with the ones obtained by a DA approach shows

S. Harir; M. Bennai; Y. Boughaleb

2007-01-01

376

A Remote Characterization System for subsurface mapping of buried waste sites  

SciTech Connect

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

Sandness, G.A.; Bennett, D.W. [Pacific Northwest Lab., Richland, WA (United States); Martinson, L. [Idaho National Engineering Lab., Idaho Falls, ID (United States)

1992-06-01

377

The solar wind - Moon interaction discovered by MAP-PACE on KAGUYA  

NASA Astrophysics Data System (ADS)

Magnetic field And Plasma experiment - Plasma energy Angle and Composition Experiment (MAP-PACE) on KAGUYA (SELENE) completed its ˜1.5-year observation of the low energy charged particles around the Moon. SELENE was successfully launched on 14 September 2007 by H2A launch vehicle from Tanegashima Space Center in Japan. SELENE was inserted into a circular lunar polar orbit of 100km altitude and continued observation for nearly 1.5 years till it impacted the Moon on 10 June 2009. During the last 5 months, the orbit was lowered to ˜50km-altitude between January 2009 and April 2009, and some orbits had further lower perilune altitude of ˜10km after April 2009. The newly observed data showed characteristic ion distributions around the Moon. Besides the solar wind, one of the MAP-PACE sensors MAP-PACE-IMA (Ion Mass Analyzer) discovered four clearly distinguishable ion distributions on the dayside of the Moon: 1) Solar wind ions backscattered at the lunar surface, 2) Solar wind ions reflected by magnetic anomalies on the lunar surface, 3) Ions that are originating from the reflected / backscattered solar wind ions and are pick-up accelerated by the solar wind convection electric field, and 4) Ions originating from the lunar surface / lunar atmosphere. One of the most important discoveries of the ion mass spectrometer (MAP-PACE-IMA) is the first in-situ measurements of the alkali ions originating from the Moon surface / atmosphere. The ions generated on the lunar surface by solar wind sputtering, solar photon stimulated desorption, or micro-meteorite vaporization are accelerated by the solar wind convection electric field and detected by IMA. The mass profiles of these ions show ions including He+, C+, O+, Na+, and K+/Ar+. The heavy ions were also observed when the Moon was in the Earth’s magnetotail where no solar wind ions impinged on the lunar surface. This discovery strongly restricts the possible generation mechanisms of the ionized alkali atmosphere around the Moon. When KAGUYA flew over South Pole Aitken region, where strong magnetic anomalies exist, solar wind ions reflected by magnetic anomalies were observed. These reflected ions had nearly the same energy as the incident solar wind ions, and their flux was more than 10% of the incident solar wind ions. At 100km altitude, when the reflected ions were observed, the simultaneously measured electrons were often heated and the incident solar wind ions were sometimes slightly decelerated. At ~50km altitude, when the reflected ions were observed, proton scattering at the lunar surface clearly disappeared. At ~10km altitude, the interaction between the solar wind ions and the lunar magnetic anomalies was remarkable with clear deceleration of the incident solar wind ions and heating of the reflected ions as well as significant heating of the electrons. These newly discovered plasma signatures around the Moon are the evidences of the smallest magnetosphere ever observed.

Saito, Y.; Yokota, S.; Tanaka, T.; Asamura, K.; Nishino, M. N.; Yamamoto, T.; Tsunakawa, H.; Shibuya, H.; Shimizu, H.; Takahashi, F.

2009-12-01

378

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

PubMed

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

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

2005-01-01

379

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

PubMed Central

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

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

2005-01-01

380

Extended Hubbard model with off-site interactions: Two-particle spectrum and Auger line shapes  

Microsoft Academic Search

We present a method for calculating the Green's function of two particles on a periodic lattice, with arbitrary distance-dependent interactions (extended Hubbard model). We develop the exact results together with their dispersionless limit (local approximation) for the sake of comparison. Numerical calculations for a repulsive, Thomas-Fermi-like potential illustrate the effects of including off-site interactions in a simple cubic lattice. For

C. Verdozzi; M. Cini

1995-01-01

381

Genetic interaction and mapping studies on the leaflet development (lld) mutant in Pisum sativum.  

PubMed

In Pisum sativum, the completely penetrant leaflet development (lld) mutation is known to sporadically abort pinnae suborgans in the unipinnate compound leaf. Here, the frequency and morphology of abortion was studied in each of the leaf suborgans in 36 genotypes and in presence of auxin and gibberellin, and their antagonists. Various lld genotypes were constructed by multifariously recombining lld with a coch homeotic stipule mutation and with af, ins, mare, mfp, tl and uni-tac leaf morphology mutations. It was observed that the suborgans at all levels of pinna subdivisions underwent lld-led abortion events at different stages of development. As in leafblades, lld aborted the pinnae in leaf-like compound coch stipules. The lld mutation interacted with mfp synergistically and with other leaf mutations additively. The rod-shaped and trumpet-shaped aborted pea leaf suborgans mimicked the phenotype of aborted leaves in HD-ZIP-III-deficient Arabidopsis thaliana mutants. Suborganwise aborted morphologies in lld gnotypes were in agreement with basipetal differentiation of leaflets and acropetal differentiation in tendrils. Altogether, the observations suggested that LLD was the master regulator of pinna development. On the basis of molecular markers found linked to lld, its locus was positioned on the linkage group III of the P. sativum genetic map. PMID:23271018

Kumar, Sushil; Mishra, Raghvendra Kumar; Kumar, Arvind; Chaudhary, Swati; Sharma, Vishakha; Kumari, Renu

2012-12-01

382

An interactive mapping tool to assess individual mobility patterns in neighborhood studies.  

PubMed

As their most critical limitation, neighborhood and health studies published to date have not taken into account nonresidential activity places where individuals travel in their daily lives. However, identifying low-mobility populations residing in low-resource environments, assessing cumulative environmental exposures over multiple activity places, and identifying specific activity locations for targeting interventions are important for health promotion. Daily mobility has not been given due consideration in part because of a lack of tools to collect locational information on activity spaces. Thus, the first aim of the current article is to describe VERITAS (Visualization and Evaluation of Route Itineraries, Travel Destinations, and Activity Spaces), an interactive web mapping application that can geolocate individuals' activity places, routes between locations, and relevant areas such as experienced or perceived neighborhoods. The second aim is to formalize the theoretic grounds of a contextual expology as a subdiscipline to better assess the spatiotemporal configuration of environmental exposures. Based on activity place data, various indicators of individual patterns of movement in space (spatial behavior) are described. Successive steps are outlined for elaborating variables of multiplace environmental exposure (collection of raw locational information, selection/exclusion of locational data, defining an exposure area for measurement, and calculation). Travel and activity place network areas are discussed as a relevant construct for environmental exposure assessment. Finally, a note of caution is provided that these measures require careful handling to avoid increasing the magnitude of confounding (selective daily mobility bias). PMID:22992364

Chaix, Basile; Kestens, Yan; Perchoux, Camille; Karusisi, Noëlla; Merlo, Juan; Labadi, Karima

2012-10-01

383

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

PubMed Central

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.

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

2012-01-01

384

Mapping of contact sites in complex formation between transducin and light-activated rhodopsin by covalent crosslinking: use of a photoactivatable reagent.  

PubMed

Interaction of light-activated rhodopsin with transducin (T) is the first event in visual signal transduction. We use covalent crosslinking approaches to map the contact sites in interaction between the two proteins. Here we use a photoactivatable reagent, N-[(2-pyridyldithio)-ethyl], 4-azido salicylamide. The reagent is attached to the SH group of cytoplasmic monocysteine rhodopsin mutants by a disulfide-exchange reaction with the pyridylthio group, and the derivatized rhodopsin then is complexed with T by illumination at lambda >495 nm. Subsequent irradiation of the complex at lambda310 nm generates covalent crosslinks between the two proteins. Crosslinking was demonstrated between T and a number of single cysteine rhodopsin mutants. However, sites of crosslinks were investigated in detail only between T and the rhodopsin mutant S240C (cytoplasmic loop V-VI). Crosslinking occurred predominantly with T(alpha). For identification of the sites of crosslinks in T(alpha), the strategy used involved: (i) derivatization of all of the free cysteines in the crosslinked proteins with N-ethylmaleimide; (ii) reduction of the disulfide bond linking the two proteins and isolation of all of the T(alpha) species carrying the crosslinked moiety with a free SH group; (iii) adduct formation of the latter with the N-maleimide moiety of the reagent, maleimido-butyryl-biocytin, containing a biotinyl group; (iv) trypsin degradation of the resulting T(alpha) derivatives and isolation of T(alpha) peptides carrying maleimido-butyryl-biocytin by avidin-agarose chromatography; and (v) identification of the isolated peptides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. We found that crosslinking occurred mainly to two C-terminal peptides in T(alpha) containing the amino acid sequences 310-313 and 342-345. PMID:11320237

Cai, K; Itoh, Y; Khorana, H G

2001-04-24

385

Genome-scale identification of Caenorhabditis elegans regulatory elements by tiling-array mapping of DNase I hypersensitive sites  

PubMed Central

Background A major goal of post-genomics research is the integrated analysis of genes, regulatory elements and the chromatin architecture on a genome-wide scale. Mapping DNase I hypersensitive sites within the nuclear chromatin is a powerful and well-established method of identifying regulatory element candidates. Results Here, we report the first genome-wide analysis of DNase I hypersensitive sites (DHSs) in Caenorhabditis elegans. The data was obtained by hybridizing DNase I-treated and end-captured material from young adult worms to a high-resolution tiling microarray. The data show that C. elegans DHSs were significantly enriched within intergenic regions located 2 kb upstream and downstream of coding genes, and also that a considerable fraction of all DHSs mapped to intergenic positions distant to annotated coding genes. Annotated transcribed loci were generally depleted in DHSs relative to intergenic regions, but DHSs were nonetheless enriched in coding exons and UTRs, whereas introns were significantly depleted in DHSs. Many DHSs appeared to be associated with annotated non-coding RNAs and recently detected transcripts of unknown function. It has been reported that nematode highly conserved non-coding elements were associated with cis-regulatory elements, and we also found that DHSs, particularly distal intergenic DHSs, were significantly enriched in regions that were conserved between the C. elegans and C. briggsae genomes. Conclusion We describe the first genome-wide analysis of C. elegans DHSs, and show that the distribution of DHSs is strongly associated with functional elements in the genome.

Shi, Baochen; Guo, Xiangqian; Wu, Tao; Sheng, Sitong; Wang, Jie; Skogerb?, Geir; Zhu, Xiaopeng; Chen, Runsheng

2009-01-01

386

Gene-environment interactions in complex diseases: genetic models and methods for QTL mapping in multiple half-sib populations.  

PubMed

An interval quantitative trait locus (QTL) mapping method for complex polygenic diseases (as binary traits) showing QTL by environment interactions (QEI) was developed for outbred populations on a within-family basis. The main objectives, within the above context, were to investigate selection of genetic models and to compare liability or generalized interval mapping (GIM) and linear regression interval mapping (RIM) methods. Two different genetic models were used: one with main QTL and QEI effects (QEI model) and the other with only a main QTL effect (QTL model). Over 30 types of binary disease data as well as six types of continuous data were simulated and analysed by RIM and GIM. Using table values for significance testing, results show that RIM had an increased false detection rate (FDR) for testing interactions which was attributable to scale effects on the binary scale. GIM did not suffer from a high FDR for testing interactions. The use of empirical thresholds, which effectively means higher thresholds for RIM for testing interactions, could repair this increased FDR for RIM, but such empirical thresholds would have to be derived for each case because the amount of FDR depends on the incidence on the binary scale. RIM still suffered from higher biases (15-100% over- or under-estimation of true values) and high standard errors in QTL variance and location estimates than GIM for QEI models. Hence GIM is recommended for disease QTL mapping with QEI. In the presence of QEI, the model including QEI has more power (20-80% increase) to detect the QTL when the average QTL effect is small (in a situation where the model with a main QTL only is not too powerful). Top-down model selection is proposed in which a full test for QEI is conducted first and then the model is subsequently simplified. Methods and results will be applicable to human, plant and animal QTL mapping experiments. PMID:16978428

Kadarmideen, Haja N; Li, Yongjun; Janss, Luc L G

2006-09-15

387

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

USGS Publications Warehouse

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

Sweeney, Ronald E.; Hill, Patricia L.

2003-01-01

388

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

389

Fine mapping of antigenic site II of herpes simplex virus glycoprotein D.  

PubMed Central

Glycoprotein D (gD) is a virion envelope component of herpes simplex virus types 1 (HSV-1) and 2 (HSV-2) which plays an important role in viral infection and pathogenesis. Previously, anti-gD monoclonal antibodies (MAbs) were arranged into groups which recognize distinct type-common and type-specific sites on HSV-1 gD (gD-1) and HSV-2 gD (gD-2). Several groups recognize discontinuous epitopes which are dependent on tertiary structure. Three groups, VII, II, and V, recognize continuous epitopes present in both native and denatured gD. Previously, group II consisted of a single MAb, DL6, whose epitope was localized between amino acids 268 and 287. In the study reported here, we extended our analysis of the antigenic structure of gD, concentrating on continuous epitopes. The DL6 epitope was localized with greater precision to residues 272 to 279. Four additional MAbs including BD78 were identified, each of which recognizes an epitope within residues 264 to 275. BD78 and DL6 blocked each other in binding to gD. In addition, a mutant form of gD was constructed in which the proline at 273 was replaced by serine. This change removes a predicted beta turn in gD. Neither antibody reacted with this mutant, indicating that the BD78 and DL6 epitopes overlap and constitute an antigenic site (site II) within residues 264 to 279. A separate antigenic site (site XI) was recognized by MAb BD66 (residues 284 to 301). This site was only six amino acids downstream of site II, but was distinct as demonstrated by blocking studies. Synthetic peptides mimicking these and other regions of gD were screened with polyclonal antisera to native gD-1 or gD-2. The results indicate that sites II, V, VII, and XI, as well as the carboxy terminus, are the major continuous antigenic determinants on gD. In addition, the results show that the region from residues 264 through 369, except the transmembrane anchor, contains a series of continuous epitopes. Images

Isola, V J; Eisenberg, R J; Siebert, G R; Heilman, C J; Wilcox, W C; Cohen, G H

1989-01-01

390

Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells  

Microsoft Academic Search

Background  Transcription by RNA polymerase II is regulated at many steps including initiation, promoter release, elongation and termination.\\u000a Accumulation of RNA polymerase II at particular locations across genes can be indicative of sites of regulation. RNA polymerase\\u000a II is thought to accumulate at the promoter and at sites of co-transcriptional alternative splicing where the rate of RNA\\u000a synthesis slows.\\u000a \\u000a \\u000a \\u000a \\u000a Results  To further

Alexander S Brodsky; Clifford A Meyer; Ian A Swinburne; Giles Hall; Benjamin J Keenan; Xiaole S Liu; Edward A Fox; Pamela A Silver

2004-01-01

391

Mutational Mapping and Modeling of the Binding Site for (S)-Citalopram in the Human Serotonin Transporter*  

PubMed Central

The serotonin transporter (SERT) regulates extracellular levels of the neurotransmitter serotonin (5-hydroxytryptamine) in the brain by facilitating uptake of released 5-hydroxytryptamine into neuronal cells. SERT is the target for widely used antidepressant drugs, including imipramine, fluoxetine, and (S)-citalopram, which are competitive inhibitors of the transport function. Knowledge of the molecular details of the antidepressant binding sites in SERT has been limited due to lack of structural data on SERT. Here, we present a characterization of the (S)-citalopram binding pocket in human SERT (hSERT) using mutational and computational approaches. Comparative modeling and ligand docking reveal that (S)-citalopram fits into the hSERT substrate binding pocket, where (S)-citalopram can adopt a number of different binding orientations. We find, however, that only one of these binding modes is functionally relevant from studying the effects of 64 point mutations around the putative substrate binding site. The mutational mapping also identify novel hSERT residues that are crucial for (S)-citalopram binding. The model defines the molecular determinants for (S)-citalopram binding to hSERT and demonstrates that the antidepressant binding site overlaps with the substrate binding site.

Andersen, Jacob; Olsen, Lars; Hansen, Kasper B.; Taboureau, Olivier; J?rgensen, Flemming S.; J?rgensen, Anne Marie; Bang-Andersen, Benny; Egebjerg, Jan; Str?mgaard, Kristian; Kristensen, Anders S.

2010-01-01

392

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

393

Interaction of p53 with its consensus DNA-binding site.  

PubMed

We have analyzed the specific interaction of murine p53 with the consensus DNA-binding sequence 5'-AGACATGCCT-AGACATGCCT-3'. We used segments of p53 lacking the C-terminal, nonspecific DNA-binding domain because the presence of an autonomous nonspecific DNA-binding domain in wild-type p53 would complicate analysis of site-specific DNA binding. p53 amino acids 1 to 360 bind the consensus sequence as tetramers, and DNA binding promotes tetramer-tetramer interactions. p53 amino acids 80 to 290, lacking both the nonspecific DNA-binding and tetramerization domains, consistently bind consensus DNA as four monomers and only as four monomers. The virtual absence of stable binding by fewer than four monomers, even at low concentrations of p53, argues that binding by amino acids 80 to 290 is strongly cooperative. Because p53 tetramers and monomers do not simultaneously bind a single DNA consensus sequence, we conclude that a single tetramer of wild-type p53 engages the recognition sequences of the entire DNA consensus site. We further show that consensus DNA consists of two functional half-sites. Insertions, deletions, or rearrangements within the half-sites reduce DNA binding dramatically. In contrast, two half-sites separated by insertions bind p53 relatively efficiently. Insertions that place half-sites on opposite faces of the DNA helix reduce DNA binding more than insertions that place half-sites on the same face of the helix. Transcription studies, in vivo, strongly confirm the rotational specificity of the p53 interaction with consensus DNA. The ability of single p53 tetramers to bind separated DNA half-sites argues that p53 has a flexible tetramerization region. PMID:7891710

Wang, Y; Schwedes, J F; Parks, D; Mann, K; Tegtmeyer, P

1995-04-01

394

Interaction of p53 with its consensus DNA-binding site.  

PubMed Central

We have analyzed the specific interaction of murine p53 with the consensus DNA-binding sequence 5'-AGACATGCCT-AGACATGCCT-3'. We used segments of p53 lacking the C-terminal, nonspecific DNA-binding domain because the presence of an autonomous nonspecific DNA-binding domain in wild-type p53 would complicate analysis of site-specific DNA binding. p53 amino acids 1 to 360 bind the consensus sequence as tetramers, and DNA binding promotes tetramer-tetramer interactions. p53 amino acids 80 to 290, lacking both the nonspecific DNA-binding and tetramerization domains, consistently bind consensus DNA as four monomers and only as four monomers. The virtual absence of stable binding by fewer than four monomers, even at low concentrations of p53, argues that binding by amino acids 80 to 290 is strongly cooperative. Because p53 tetramers and monomers do not simultaneously bind a single DNA consensus sequence, we conclude that a single tetramer of wild-type p53 engages the recognition sequences of the entire DNA consensus site. We further show that consensus DNA consists of two functional half-sites. Insertions, deletions, or rearrangements within the half-sites reduce DNA binding dramatically. In contrast, two half-sites separated by insertions bind p53 relatively efficiently. Insertions that place half-sites on opposite faces of the DNA helix reduce DNA binding more than insertions that place half-sites on the same face of the helix. Transcription studies, in vivo, strongly confirm the rotational specificity of the p53 interaction with consensus DNA. The ability of single p53 tetramers to bind separated DNA half-sites argues that p53 has a flexible tetramerization region.

Wang, Y; Schwedes, J F; Parks, D; Mann, K; Tegtmeyer, P

1995-01-01

395

Soil formation in post mining sites: the role of vegatation soil microflora and fauna interactions  

Microsoft Academic Search

The role of vegetation and soil micro flora and fauna interaction during soil formation was studied in post mining sites in Czech Republic, Germany and USA. Vegetation and character of substrate substantially effect, micro flora, namely fungal bacterial ration, fauna composition and resulting microstructure of soil. Plants that bring more nitrogen in to the system support larger biomass of soil

J. Frouz

2009-01-01

396

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

ERIC Educational Resources Information Center

|Discusses the use of Web log analysis to help understand user visit patterns to Web sites and describes the use of computer software to generate a variety of interactive visualizations of log data that can be used to explore server data across various dimensions. Explores difficulties of data collection, presentation, and interpretation.…

Hochheiser, Harry; Shneiderman, Ben

2001-01-01

397

Evolutionary, Structural and Biochemical Evidence for a New Interaction Site of the Leptin Obesity Protein  

Microsoft Academic Search

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.

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

398

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

Microsoft Academic Search

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

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

2006-01-01

399

Satellite Power System (SPS) Mapping of Exclusion Areas for Rectenna Sites.  

National Technical Information Service (NTIS)

This report sets forth the results of a study by Rice University to determine those areas of the United States that were not available as potential sites for receiving antennas that are an integral part of the Satellite Power System (SPS) concept. Under t...

J. B. Blackburn B. A. Bavinger

1978-01-01

400

Interaction between solar wind and lunar magnetic anomalies observed by MAP-PACE on Kaguya  

NASA Astrophysics Data System (ADS)

It is well known that the Moon has neither global intrinsic magnetic field nor thick atmosphere. Different from the Earth's case where the intrinsic global magnetic field prevents the solar wind from penetrating into the magnetosphere, solar wind directly impacts the lunar surface. MAgnetic field and Plasma experiment -Plasma energy Angle and Composition Experiment (MAP-PACE) on Kaguya (SELENE) completed its 1.5-year observation of the low energy charged particles around the Moon on 10 June 2009. Kaguya was launched on 14 September 2007 by H2A launch vehicle from Tanegashima Space Center in Japan. Kaguya was inserted into a circular lunar polar orbit of 100km altitude and continued observation for nearly 1.5 years till it impacted the Moon on 10 June 2009. During the last 5 months, the orbit was lowered to 50km-altitude between January 2009 and April 2009, and some orbits had further lower perilune altitude of 10km after April 2009. MAP-PACE consisted of 4 sensors: ESA (Electron Spectrum Analyzer)-S1, ESA-S2, IMA (Ion Mass Analyzer), and IEA (Ion Energy Analyzer). Since each sensor had hemispherical field of view, two electron sensors and two ion sensors that were installed on the spacecraft panels opposite to each other could cover full 3-dimensional phase space of low energy electrons and ions. One of the ion sensors IMA was an energy mass spectrometer. IMA measured mass identified ion energy spectra that had never been obtained at 100km altitude polar orbit around the Moon. When Kaguya flew over South Pole Aitken region, where strong magnetic anomalies exist, solar wind ions reflected by magnetic anomalies were observed. These ions had much higher flux than the solar wind protons scattered at the lunar surface. The magnetically reflected ions had nearly the same energy as the incident solar wind ions while the solar wind protons scattered at the lunar surface had slightly lower energy than the incident solar wind ions. At 100km altitude, when the reflected ions were observed, the simultaneously measured electrons were often heated and the incident solar wind ions were sometimes slightly decelerated. At 50km altitude, when the reflected ions were observed, proton scattering at the lunar surface clearly disappeared. It suggests that there exists an area on the lunar surface where solar wind does not impact. At 10km altitude, the interaction between the solar wind ions and the lunar magnetic anomalies was remarkable with clear deceleration of the incident solar wind ions and heating of the reflected ions as well as significant heating of the electrons. Calculating velocity moments including density, velocity, temperature of the ions and electrons, we have found that there exists 100km scale regions over strong magnetic anomalies where plasma parameters are quite different from the outside. Solar wind ions observed at 10km altitude show several different behaviors such as deceleration without heating and heating in a limited region inside the magnetic an