GRID-seq reveals the global RNA-chromatin interactome

PubMed Central

Li, Xiao; Zhou, Bing; Chen, Liang; Gou, Lan-Tao; Li, Hairi; Fu, Xiang-Dong

2017-01-01

Higher eukaryotic genomes are bound by a large number of coding and non-coding RNAs, but approaches to comprehensively map the identity and binding sites of these RNAs are lacking. Here we report a method to in situ capture global RNA interactions with DNA by deep sequencing (GRID-seq), which enables the comprehensive identification of the entire repertoire of chromatin-interacting RNAs and their respective binding sites. In human, mouse and Drosophila cells, we detected a large set of tissue-specific coding and non-coding RNAs that are bound to active promoters and enhancers, especially super-enhancers. Assuming that most mRNA-chromatin interactions indicate the physical proximity of a promoter and an enhancer, we constructed a three-dimensional global connectivity map of promoters and enhancers, revealing transcription activity-linked genomic interactions in the nucleus. PMID:28922346

DIMA 3.0: Domain Interaction Map.

PubMed

Luo, Qibin; Pagel, Philipp; Vilne, Baiba; Frishman, Dmitrij

2011-01-01

Domain Interaction MAp (DIMA, available at http://webclu.bio.wzw.tum.de/dima) is a database of predicted and known interactions between protein domains. It integrates 5807 structurally known interactions imported from the iPfam and 3did databases and 46,900 domain interactions predicted by four computational methods: domain phylogenetic profiling, domain pair exclusion algorithm correlated mutations and domain interaction prediction in a discriminative way. Additionally predictions are filtered to exclude those domain pairs that are reported as non-interacting by the Negatome database. The DIMA Web site allows to calculate domain interaction networks either for a domain of interest or for entire organisms, and to explore them interactively using the Flash-based Cytoscape Web software.

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

PubMed Central

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

2010-01-01

In order to fully understand protein kinase networks, new methods are needed to identify regulators and substrates of kinases, especially for weakly expressed proteins. Here we have developed a hybrid computational search algorithm that combines machine learning and expert knowledge to identify kinase docking sites, and used this algorithm to search the human genome for novel MAP kinase substrates and regulators focused on the JNK family of MAP kinases. Predictions were tested by peptide array followed by rigorous biochemical verification with in vitro binding and kinase assays on wild-type and mutant proteins. Using this procedure, we found new ‘D-site’ class docking sites in previously known JNK substrates (hnRNP-K, PPM1J/PP2Czeta), as well as new JNK-interacting proteins (MLL4, NEIL1). Finally, we identified new D-site-dependent MAPK substrates, including the hedgehog-regulated transcription factors Gli1 and Gli3, suggesting that a direct connection between MAP kinase and hedgehog signaling may occur at the level of these key regulators. These results demonstrate that a genome-wide search for MAP kinase docking sites can be used to find new docking sites and substrates. PMID:20865152

CLIP-seq analysis of multi-mapped reads discovers novel functional RNA regulatory sites in the human transcriptome.

PubMed

Zhang, Zijun; Xing, Yi

2017-09-19

Crosslinking or RNA immunoprecipitation followed by sequencing (CLIP-seq or RIP-seq) allows transcriptome-wide discovery of RNA regulatory sites. As CLIP-seq/RIP-seq reads are short, existing computational tools focus on uniquely mapped reads, while reads mapped to multiple loci are discarded. We present CLAM (CLIP-seq Analysis of Multi-mapped reads). CLAM uses an expectation-maximization algorithm to assign multi-mapped reads and calls peaks combining uniquely and multi-mapped reads. To demonstrate the utility of CLAM, we applied it to a wide range of public CLIP-seq/RIP-seq datasets involving numerous splicing factors, microRNAs and m6A RNA methylation. CLAM recovered a large number of novel RNA regulatory sites inaccessible by uniquely mapped reads. The functional significance of these sites was demonstrated by consensus motif patterns and association with alternative splicing (splicing factors), transcript abundance (AGO2) and mRNA half-life (m6A). CLAM provides a useful tool to discover novel protein-RNA interactions and RNA modification sites from CLIP-seq and RIP-seq data, and reveals the significant contribution of repetitive elements to the RNA regulatory landscape of the human transcriptome. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

A Global Survey and Interactive Map Suite of Deep Underground Facilities; Examples of Geotechnical and Engineering Capabilities, Achievements, Challenges: (Mines, Shafts, Tunnels, Boreholes, Sites and Underground Facilities for Nuclear Waste and Physics R&D)

NASA Astrophysics Data System (ADS)

Tynan, M. C.; Russell, G. P.; Perry, F.; Kelley, R.; Champenois, S. T.

2017-12-01

This global survey presents a synthesis of some notable geotechnical and engineering information reflected in four interactive layer maps for selected: 1) deep mines and shafts; 2) existing, considered or planned radioactive waste management deep underground studies, sites, or disposal facilities; 3) deep large diameter boreholes, and 4) physics underground laboratories and facilities from around the world. These data are intended to facilitate user access to basic information and references regarding deep underground "facilities", history, activities, and plans. In general, the interactive maps and database [http://gis.inl.gov/globalsites/] provide each facility's approximate site location, geology, and engineered features (e.g.: access, geometry, depth, diameter, year of operations, groundwater, lithology, host unit name and age, basin; operator, management organization, geographic data, nearby cultural features, other). Although the survey is not all encompassing, it is a comprehensive review of many of the significant existing and historical underground facilities discussed in the literature addressing radioactive waste management and deep mined geologic disposal safety systems. The global survey is intended to support and to inform: 1) interested parties and decision makers; 2) radioactive waste disposal and siting option evaluations, and 3) safety case development as a communication tool applicable to any mined geologic disposal facility as a demonstration of historical and current engineering and geotechnical capabilities available for use in deep underground facility siting, planning, construction, operations and monitoring.

Site-specific Interaction Mapping of Phosphorylated Ubiquitin to Uncover Parkin Activation*♦

PubMed Central

Yamano, Koji; Queliconi, Bruno B.; Koyano, Fumika; Saeki, Yasushi; Hirokawa, Takatsugu; Tanaka, Keiji; Matsuda, Noriyuki

2015-01-01

Damaged mitochondria are eliminated through autophagy machinery. A cytosolic E3 ubiquitin ligase Parkin, a gene product mutated in familial Parkinsonism, is essential for this pathway. Recent progress has revealed that phosphorylation of both Parkin and ubiquitin at Ser65 by PINK1 are crucial for activation and recruitment of Parkin to the damaged mitochondria. However, the mechanism by which phosphorylated ubiquitin associates with and activates phosphorylated Parkin E3 ligase activity remains largely unknown. Here, we analyze interactions between phosphorylated forms of both Parkin and ubiquitin at a spatial resolution of the amino acid residue by site-specific photo-crosslinking. We reveal that the in-between-RING (IBR) domain along with RING1 domain of Parkin preferentially binds to ubiquitin in a phosphorylation-dependent manner. Furthermore, another approach, the Fluoppi (fluorescent-based technology detecting protein-protein interaction) assay, also showed that pathogenic mutations in these domains blocked interactions with phosphomimetic ubiquitin in mammalian cells. Molecular modeling based on the site-specific photo-crosslinking interaction map combined with mass spectrometry strongly suggests that a novel binding mechanism between Parkin and ubiquitin leads to a Parkin conformational change with subsequent activation of Parkin E3 ligase activity. PMID:26260794

Mapping of the Rsd Contact Site on the Sigma 70 Subunit of Escherichia coli RNA Polymerase

PubMed Central

Jishage, Miki; Dasgupta, Dipak; Ishihama, Akira

2001-01-01

Rsd (regulator of sigma D) is an anti-sigma factor for the Escherichia coli RNA polymerase ς70 subunit. The contact site of Rsd on ς70 was analyzed after mapping of the contact-dependent cleavage sites by Rsd-tethered iron-p-bromoacetamidobenzyl EDTA and by analysis of the complex formation between Ala-substituted ς70 and Rsd. Results indicate that the Rsd contact site is located downstream of the promoter −35 recognition helix-turn-helix motif within region 4, overlapping with the regions involved in interaction with both core enzyme and ς70 contact transcription factors. PMID:11292818

Mapping of the Rsd contact site on the sigma 70 subunit of Escherichia coli RNA polymerase.

PubMed

Jishage, M; Dasgupta, D; Ishihama, A

2001-05-01

Rsd (regulator of sigma D) is an anti-sigma factor for the Escherichia coli RNA polymerase sigma(70) subunit. The contact site of Rsd on sigma(70) was analyzed after mapping of the contact-dependent cleavage sites by Rsd-tethered iron-p-bromoacetamidobenzyl EDTA and by analysis of the complex formation between Ala-substituted sigma(70) and Rsd. Results indicate that the Rsd contact site is located downstream of the promoter -35 recognition helix-turn-helix motif within region 4, overlapping with the regions involved in interaction with both core enzyme and sigma(70) contact transcription factors.

Small Molecule Interactome Mapping by Photoaffinity Labeling Reveals Binding Site Hotspots for the NSAIDs.

PubMed

Gao, Jinxu; Mfuh, Adelphe; Amako, Yuka; Woo, Christina M

2018-03-28

Many therapeutics elicit cell-type specific polypharmacology that is executed by a network of molecular recognition events between a small molecule and the whole proteome. However, measurement of the structures that underpin the molecular associations between the proteome and even common therapeutics, such as the nonsteroidal anti-inflammatory drugs (NSAIDs), is limited by the inability to map the small molecule interactome. To address this gap, we developed a platform termed small molecule interactome mapping by photoaffinity labeling (SIM-PAL) and applied it to the in cellulo direct characterization of specific NSAID binding sites. SIM-PAL uses (1) photochemical conjugation of NSAID derivatives in the whole proteome and (2) enrichment and isotope-recoding of the conjugated peptides for (3) targeted mass spectrometry-based assignment. Using SIM-PAL, we identified the NSAID interactome consisting of over 1000 significantly enriched proteins and directly characterized nearly 200 conjugated peptides representing direct binding sites of the photo-NSAIDs with proteins from Jurkat and K562 cells. The enriched proteins were often identified as parts of complexes, including known targets of NSAID activity (e.g., NF-κB) and novel interactions (e.g., AP-2, proteasome). The conjugated peptides revealed direct NSAID binding sites from the cell surface to the nucleus and a specific binding site hotspot for the three photo-NSAIDs on histones H2A and H2B. NSAID binding stabilized COX-2 and histone H2A by cellular thermal shift assay. Since small molecule stabilization of protein complexes is a gain of function regulatory mechanism, it is conceivable that NSAIDs affect biological processes through these broader proteomic interactions. SIM-PAL enabled characterization of NSAID binding site hotspots and is amenable to map global binding sites for virtually any molecule of interest.

Interactions between white spruce and shrubby alders at three boreal forest sites in Alaska.

Treesearch

Tricia L. Wurtz

2000-01-01

To document possible soil nitrogen mosaics before timber harvesting on three boreal forest sites in Alaska, maps of the distribution of understory green (Alnus crispa (Ait.) Pursh) and Sitka alder (A. sitchensis(Reg.) Rydb.) stems were made. Understory alders were regularly distributed throughout the northernmost site (Standard...

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

PubMed Central

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

2010-01-01

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

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

PubMed

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

2011-01-01

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

Mapping General Anesthetic Sites in Heteromeric γ-Aminobutyric Acid Type A Receptors Reveals a Potential For Targeting Receptor Subtypes.

PubMed

Forman, Stuart A; Miller, Keith W

2016-11-01

IV general anesthetics, including propofol, etomidate, alphaxalone, and barbiturates, produce important actions by enhancing γ-aminobutyric acid type A (GABAA) receptor activation. In this article, we review scientific studies that have located and mapped IV anesthetic sites using photoaffinity labeling and substituted cysteine modification protection. These anesthetics bind in transmembrane pockets between subunits of typical synaptic GABAA receptors, and drugs that display stereoselectivity also show remarkably selective interactions with distinct interfacial sites. These results suggest strategies for developing new drugs that selectively modulate distinct GABAA receptor subtypes.

Modeling forest site productivity using mapped geospatial attributes within a South Carolina Landscape, USA

DOE PAGES

Parresol, B. R.; Scott, D. A.; Zarnoch, S. J.; ...

2017-12-15

Spatially explicit mapping of forest productivity is important to assess many forest management alternatives. We assessed the relationship between mapped variables and site index of forests ranging from southern pine plantations to natural hardwoods on a 74,000-ha landscape in South Carolina, USA. Mapped features used in the analysis were soil association, land use condition in 1951, depth to groundwater, slope and aspect. Basal area, species composition, age and height were the tree variables measured. Linear modelling identified that plot basal area, depth to groundwater, soils association and the interactions between depth to groundwater and forest group, and between land usemore » in 1951 and forest group were related to site index (SI) (R 2 =0.37), but this model had regression attenuation. We then used structural equation modeling to incorporate error-in-measurement corrections for basal area and groundwater to remove bias in the model. We validated this model using 89 independent observations and found the 95% confidence intervals for the slope and intercept of an observed vs. predicted site index error-corrected regression included zero and one, respectively, indicating a good fit. With error in measurement incorporated, only basal area, soil association, and the interaction between forest groups and land use were important predictors (R2 =0.57). Thus, we were able to develop an unbiased model of SI that could be applied to create a spatially explicit map based primarily on soils as modified by past (land use and forest type) and recent forest management (basal area).« less

Modeling forest site productivity using mapped geospatial attributes within a South Carolina Landscape, USA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parresol, B. R.; Scott, D. A.; Zarnoch, S. J.

Spatially explicit mapping of forest productivity is important to assess many forest management alternatives. We assessed the relationship between mapped variables and site index of forests ranging from southern pine plantations to natural hardwoods on a 74,000-ha landscape in South Carolina, USA. Mapped features used in the analysis were soil association, land use condition in 1951, depth to groundwater, slope and aspect. Basal area, species composition, age and height were the tree variables measured. Linear modelling identified that plot basal area, depth to groundwater, soils association and the interactions between depth to groundwater and forest group, and between land usemore » in 1951 and forest group were related to site index (SI) (R 2 =0.37), but this model had regression attenuation. We then used structural equation modeling to incorporate error-in-measurement corrections for basal area and groundwater to remove bias in the model. We validated this model using 89 independent observations and found the 95% confidence intervals for the slope and intercept of an observed vs. predicted site index error-corrected regression included zero and one, respectively, indicating a good fit. With error in measurement incorporated, only basal area, soil association, and the interaction between forest groups and land use were important predictors (R2 =0.57). Thus, we were able to develop an unbiased model of SI that could be applied to create a spatially explicit map based primarily on soils as modified by past (land use and forest type) and recent forest management (basal area).« less

The Application of Ligand-Mapping Molecular Dynamics Simulations to the Rational Design of Peptidic Modulators of Protein-Protein Interactions.

PubMed

Tan, Yaw Sing; Spring, David R; Abell, Chris; Verma, Chandra S

2015-07-14

A computational ligand-mapping approach to detect protein surface pockets that interact with hydrophobic moieties is presented. In this method, we incorporated benzene molecules into explicit solvent molecular dynamics simulations of various protein targets. The benzene molecules successfully identified the binding locations of hydrophobic hot-spot residues and all-hydrocarbon cross-links from known peptidic ligands. They also unveiled cryptic binding sites that are occluded by side chains and the protein backbone. Our results demonstrate that ligand-mapping molecular dynamics simulations hold immense promise to guide the rational design of peptidic modulators of protein-protein interactions, including that of stapled peptides, which show promise as an exciting new class of cell-penetrating therapeutic molecules.

Hydrographs showing groundwater levels for selected wells in the Puyallup River watershed and vicinity, Pierce and King Counties, Washington

USGS Publications Warehouse

Lane, R.C.; Julich, R.J.; Justin, G.B.

2013-01-01

Hydrographs of groundwater levels for selected wells in and adjacent to the Puyallup River watershed in Pierce and King Counties, Washington, are presented using an interactive Web-based map of the study area to illustrate changes in groundwater levels on a monthly and seasonal basis. The interactive map displays well locations that link to the hydrographs, which in turn link to the U.S. Geological Survey National Water Information System, Groundwater Site Inventory System.

Mapping as a visual health communication tool: promises and dilemmas.

PubMed

Parrott, Roxanne; Hopfer, Suellen; Ghetian, Christie; Lengerich, Eugene

2007-01-01

In the era of evidence-based public health promotion and planning, the use of maps as a form of evidence to communicate about the multiple determinants of cancer is on the rise. Geographic information systems and mapping technologies make future proliferation of this strategy likely. Yet disease maps as a communication form remain largely unexamined. This content analysis considers the presence of multivariate information, credibility cues, and the communication function of publicly accessible maps for cancer control activities. Thirty-six state comprehensive cancer control plans were publicly available in July 2005 and were reviewed for the presence of maps. Fourteen of the 36 state cancer plans (39%) contained map images (N = 59 static maps). A continuum of map inter activity was observed, with 10 states having interactive mapping tools available to query and map cancer information. Four states had both cancer plans with map images and interactive mapping tools available to the public on their Web sites. Of the 14 state cancer plans that depicted map images, two displayed multivariate data in a single map. Nine of the 10 states with interactive mapping capability offered the option to display multivariate health risk messages. The most frequent content category mapped was cancer incidence and mortality, with stage at diagnosis infrequently available. The most frequent communication function served by the maps reviewed was redundancy, as maps repeated information contained in textual forms. The social and ethical implications for communicating about cancer through the use of visual geographic representations are discussed.

Systematic identification of phosphorylation-mediated protein interaction switches

PubMed Central

Wichmann, Oliver; Utz, Mathias; Andre, Timon; Minguez, Pablo; Parca, Luca; Roth, Frederick P.; Gavin, Anne-Claude; Bork, Peer; Russell, Robert B.

2017-01-01

Proteomics techniques can identify thousands of phosphorylation sites in a single experiment, the majority of which are new and lack precise information about function or molecular mechanism. Here we present a fast method to predict potential phosphorylation switches by mapping phosphorylation sites to protein-protein interactions of known structure and analysing the properties of the protein interface. We predict 1024 sites that could potentially enable or disable particular interactions. We tested a selection of these switches and showed that phosphomimetic mutations indeed affect interactions. We estimate that there are likely thousands of phosphorylation mediated switches yet to be uncovered, even among existing phosphorylation datasets. The results suggest that phosphorylation sites on globular, as distinct from disordered, parts of the proteome frequently function as switches, which might be one of the ancient roles for kinase phosphorylation. PMID:28346509

Real-time Shakemap implementation in Austria

NASA Astrophysics Data System (ADS)

Weginger, Stefan; Jia, Yan; Papi Isaba, Maria; Horn, Nikolaus

2017-04-01

ShakeMaps provide near-real-time maps of ground motion and shaking intensity following significant earthquakes. They are automatically generated within a few minutes after occurrence of an earthquake. We tested and included the USGS ShakeMap 4.0 (experimental code) based on python in the Antelope real-time system with local modified GMPE and Site Effects based on the conditions in Austria. The ShakeMaps are provided in terms of Intensity, PGA, PGV and PSA. Future presentation of ShakeMap contour lines and Ground Motion Parameter with interactive maps and data exchange over Web-Services are shown.

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

NASA Astrophysics Data System (ADS)

Licatalosi, Donny D.; Mele, Aldo; Fak, John J.; Ule, Jernej; Kayikci, Melis; Chi, Sung Wook; Clark, Tyson A.; Schweitzer, Anthony C.; Blume, John E.; Wang, Xuning; Darnell, Jennifer C.; Darnell, Robert B.

2008-11-01

Protein-RNA interactions have critical roles in all aspects of gene expression. However, applying biochemical methods to understand such interactions in living tissues has been challenging. Here we develop a genome-wide means of mapping protein-RNA binding sites in vivo, by high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP). HITS-CLIP analysis of the neuron-specific splicing factor Nova revealed extremely reproducible RNA-binding maps in multiple mouse brains. These maps provide genome-wide in vivo biochemical footprints confirming the previous prediction that the position of Nova binding determines the outcome of alternative splicing; moreover, they are sufficiently powerful to predict Nova action de novo. HITS-CLIP revealed a large number of Nova-RNA interactions in 3' untranslated regions, leading to the discovery that Nova regulates alternative polyadenylation in the brain. HITS-CLIP, therefore, provides a robust, unbiased means to identify functional protein-RNA interactions in vivo.

NHS-Esters As Versatile Reactivity-Based Probes for Mapping Proteome-Wide Ligandable Hotspots.

PubMed

Ward, Carl C; Kleinman, Jordan I; Nomura, Daniel K

2017-06-16

Most of the proteome is considered undruggable, oftentimes hindering translational efforts for drug discovery. Identifying previously unknown druggable hotspots in proteins would enable strategies for pharmacologically interrogating these sites with small molecules. Activity-based protein profiling (ABPP) has arisen as a powerful chemoproteomic strategy that uses reactivity-based chemical probes to map reactive, functional, and ligandable hotspots in complex proteomes, which has enabled inhibitor discovery against various therapeutic protein targets. Here, we report an alkyne-functionalized N-hydroxysuccinimide-ester (NHS-ester) as a versatile reactivity-based probe for mapping the reactivity of a wide range of nucleophilic ligandable hotspots, including lysines, serines, threonines, and tyrosines, encompassing active sites, allosteric sites, post-translational modification sites, protein interaction sites, and previously uncharacterized potential binding sites. Surprisingly, we also show that fragment-based NHS-ester ligands can be made to confer selectivity for specific lysine hotspots on specific targets including Dpyd, Aldh2, and Gstt1. We thus put forth NHS-esters as promising reactivity-based probes and chemical scaffolds for covalent ligand discovery.

Arabidopsis Microtubule-Associated Protein MAP65-3 Cross-Links Antiparallel Microtubules toward Their Plus Ends in the Phragmoplast via Its Distinct C-Terminal Microtubule Binding Domain[W

PubMed Central

Ho, Chin-Min Kimmy; Lee, Yuh-Ru Julie; Kiyama, Lindsay D.; Dinesh-Kumar, Savithramma P.; Liu, Bo

2012-01-01

Plant cytokinesis is brought about by the phragmoplast, which contains an antiparallel microtubule (MT) array. The MT-associated protein MAP65-3 acts as an MT-bundling factor that specifically cross-links antiparallel MTs near their plus ends. MAP65 family proteins contain an N-terminal dimerization domain and C-terminal MT interaction domain. Compared with other MAP65 isoforms, MAP65-3 contains an extended C terminus. A MT binding site was discovered in the region between amino acids 496 and 588 and found to be essential for the organization of phragmoplast MTs. The frequent cytokinetic failure caused by loss of MAP65-3 was not rescued by ectopic expression of MAP65-1 under the control of the MAP65-3 promoter, indicating nonoverlapping functions between the two isoforms. In the presence of MAP65-3, however, ectopic MAP65-1 appeared in the phragmoplast midline. We show that MAP65-1 could acquire the function of MAP65-3 when the C terminus of MAP65-3, which contains the MT binding site, was grafted to it. Our results also show that MAP65-1 and MAP65-3 may share redundant functions in MT stabilization. Such a stabilization effect was likely brought about by MT binding and bundling. We conclude that MAP65-3 contains a distinct C-terminal MT binding site with a specific role in cross-linking antiparallel MTs toward their plus ends in the phragmoplast. PMID:22570443

A Global Survey of Deep Underground Facilities; Examples of Geotechnical and Engineering Capabilities, Achievements, Challenges (Mines, Shafts, Tunnels, Boreholes, Sites and Underground Facilities for Nuclear Waste and Physics R&D): A Guide to Interactive Global Map Layers, Table Database, References and Notes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tynan, Mark C.; Russell, Glenn P.; Perry, Frank V.

These associated tables, references, notes, and report present a synthesis of some notable geotechnical and engineering information used to create four interactive layer maps for selected: 1) deep mines and shafts; 2) existing, considered or planned radioactive waste management deep underground studies or disposal facilities 3) deep large diameter boreholes, and 4) physics underground laboratories and facilities from around the world. These data are intended to facilitate user access to basic information and references regarding “deep underground” facilities, history, activities, and plans. In general, the interactive maps and database provide each facility’s approximate site location, geology, and engineered features (e.g.:more » access, geometry, depth, diameter, year of operations, groundwater, lithology, host unit name and age, basin; operator, management organization, geographic data, nearby cultural features, other). Although the survey is not comprehensive, it is representative of many of the significant existing and historical underground facilities discussed in the literature addressing radioactive waste management and deep mined geologic disposal safety systems. The global survey is intended to support and to inform: 1) interested parties and decision makers; 2) radioactive waste disposal and siting option evaluations, and 3) safety case development applicable to any mined geologic disposal facility as a demonstration of historical and current engineering and geotechnical capabilities available for use in deep underground facility siting, planning, construction, operations and monitoring.« less

Data visualization in interactive maps and time series

NASA Astrophysics Data System (ADS)

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

2014-05-01

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

Hydrogen Production Cost Analysis | Hydrogen and Fuel Cells | NREL

Science.gov Websites

Analysis Hydrogen Production Cost Analysis This interactive map displays the results of a 2011 NREL analysis on the cost of hydrogen from electrolysis at potential sites across the United States. NREL analyzed the cost of hydrogen production via wind-based water electrolysis at 42 potential sites in 11

Lunar Reconnaissance Orbiter Camera

Science.gov Websites

them out » Traverse featurette Traverse the Apollo Landing Sites & More. By combining LROC imagery , data, and historical data, we've created detailed, interactive maps of the Apollo Landing Sites and taken by the original Apollo crews. ASU maintains the Apollo Digital Image Archive and the March to the

Indentification and Analysis of Occludin Phosphosites: A Combined Mass Spectroscoy and Bioinformatics Approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sundstrom, J.; Tash, B; Murakami, T

2009-01-01

The molecular function of occludin, an integral membrane component of tight junctions, remains unclear. VEGF-induced phosphorylation sites were mapped on occludin by combining MS data analysis with bioinformatics. In vivo phosphorylation of Ser490 was validated and protein interaction studies combined with crystal structure analysis suggest that Ser490 phosphorylation attenuates the interaction between occludin and ZO-1. This study demonstrates that combining MS data and bioinformatics can successfully identify novel phosphorylation sites from limiting samples.

Documentation for the 2008 Update of the United States National Seismic Hazard Maps

USGS Publications Warehouse

Petersen, Mark D.; Frankel, Arthur D.; Harmsen, Stephen C.; Mueller, Charles S.; Haller, Kathleen M.; Wheeler, Russell L.; Wesson, Robert L.; Zeng, Yuehua; Boyd, Oliver S.; Perkins, David M.; Luco, Nicolas; Field, Edward H.; Wills, Chris J.; Rukstales, Kenneth S.

2008-01-01

The 2008 U.S. Geological Survey (USGS) National Seismic Hazard Maps display earthquake ground motions for various probability levels across the United States and are applied in seismic provisions of building codes, insurance rate structures, risk assessments, and other public policy. This update of the maps incorporates new findings on earthquake ground shaking, faults, seismicity, and geodesy. The resulting maps are derived from seismic hazard curves calculated on a grid of sites across the United States that describe the frequency of exceeding a set of ground motions. The USGS National Seismic Hazard Mapping Project developed these maps by incorporating information on potential earthquakes and associated ground shaking obtained from interaction in science and engineering workshops involving hundreds of participants, review by several science organizations and State surveys, and advice from two expert panels. The National Seismic Hazard Maps represent our assessment of the 'best available science' in earthquake hazards estimation for the United States (maps of Alaska and Hawaii as well as further information on hazard across the United States are available on our Web site at http://earthquake.usgs.gov/research/hazmaps/).

Water-Level and land-subsidence studies in the Mojave River and Morongo groundwater basins

USGS Publications Warehouse

Stamos, Christina L.; Glockhoff, Carolyn S.; McPherson, Kelly R.; Julich, Raymond J.

2007-01-01

What's New! Water-level data, contours, and meta data for spring 2008 are included in Version 2.0 of SIR 2007-5097 (http://ca.water.usgs.gov/mojave/wl_studies/wl2008.html). All the original data are still available on the web site. Introduction Since 1992, the U.S. Geological Survey (USGS), in cooperation with the Mojave Water Agency (MWA), has constructed a series of regional water-table maps for intermittent years in a continuing effort to monitor groundwater conditions in the Mojave River and Morongo groundwater basins. The previously published data, which were used to construct these maps, can be accessed on the interactive map. The associated reports describing the groundwater conditions for the Mojave River groundwater basin for 1992 (Stamos and Predmore, 1995), the Morongo groundwater basin for 1994 (Trayler and Koczot, 1995), and for both groundwater basins for 1996 (Mendez and Christensen, 1997); for 1998 (Smith and Pimentel, 2000), for 2000 (Smith, 2002), for 2002 (Smith and others, 2004), for 2004 (Stamos and others, 2004), and for 2006 (Stamos and others, 2007) can be accessed using this web site. Spatially detailed maps of interferometric synthetic aperture radar (InSAR) methods were used to characterize land subsidence associated with groundwater-level declines during various intervals of time between 1992 and 1999 in the Mojave River and Morongo groundwater basins (Sneed and others, 2003). Concerns related to the potential for new or renewed land subsidence in the basins resulted in a cooperative study between the MWA and the USGS in 2006. InSAR data were developed to determine the location, extent, and magnitude of vertical land-surface changes in the Mojave River and Morongo groundwater basins for time intervals ranging from about 35 days to 14 months between 1999 and 2000 and between 2003 and 2004. (interactive Google map) The results from many future land-subsidence studies, which are scheduled about every 10 years, will be available on this website. Mapping of water-level contours, water-level change and numerous InSAR images were combined in an interactive map. This interactive map may be customized to your needs and viewed at a scale that is appropriate for the data.

Technical Analysis and Characterization of Southern Cayo, Belize for Tropical Testing and Evaluation of Foliage Penetration Remote Sensing Systems

DTIC Science & Technology

2011-05-01

Characterization of Test Sites 57 Appendix 4 – Interactive Maps and Images...issued by the tropical test study panel, reporting the results of work conducted at 24 sites. The evolution of tropical testing to the suite of sites...macrophylla, Terminalia amazonia, Virola brachycarpa, and the palm Astrocaryum mexicanum. The mangrove and littoral forest are ecologically important to the

Genetics Home Reference: vitiligo

MedlinePlus

... PubMed or Free article on PubMed Central Smith AG, Sturm RA. Multiple genes and locus interactions in ... qualified healthcare professional . About Selection Criteria for Links Data Files & API Site Map Subscribe Customer Support USA. ...

"Where On Mars?": An Open Planetary Mapping Platform for Researchers, Educators, and the General Public

NASA Astrophysics Data System (ADS)

Manaud, Nicolas; Carter, John; Boix, Oriol

2016-10-01

The "Where On Mars?" project is essentially the evolution of an existing outreach product developed in collaboration between ESA and CartoDB; an interactive map visualisation of the ESA's ExoMars Rover candidate landing sites (whereonmars.co). Planetary imagery data and maps are increasingly produced by the scientific community, and shared typically as images, in scientific publications, presentations or public outreach websites. However, this media lacks of interactivity and contextual information available for further exploration, making it difficult for any audience to relate one location-based information to another. We believe that interactive web maps are a powerful way of telling stories, engaging with and educating people who, over the last decade, have become familiar with tools such as Google Maps. A few planetary web maps exist but they are either too complex for non-experts, or are closed-systems that do not allows anyone to publish and share content. The long-term vision for the project is to provide researchers, communicators, educators and a worldwide public with an open planetary mapping and social platform enabling them to create, share, communicate and consume research-based content. We aim for this platform to become the reference website everyone will go to learn about Mars and other planets in our Solar System; just like people head to Google Maps to find their bearings or any location-based information. The driver is clearly to create for people an emotional connection with Mars. The short-term objectives for the project are (1) to produce and curate an open repository of basemaps, geospatial data sets, map visualisations, and story maps; (2) to develop a beautifully crafted and engaging interactive map of Mars. Based on user-generated content, the underlying framework should (3) make it easy to create and share additional interactive maps telling specific stories.

KIDFamMap: a database of kinase-inhibitor-disease family maps for kinase inhibitor selectivity and binding mechanisms

PubMed Central

Chiu, Yi-Yuan; Lin, Chih-Ta; Huang, Jhang-Wei; Hsu, Kai-Cheng; Tseng, Jen-Hu; You, Syuan-Ren; Yang, Jinn-Moon

2013-01-01

Kinases play central roles in signaling pathways and are promising therapeutic targets for many diseases. Designing selective kinase inhibitors is an emergent and challenging task, because kinases share an evolutionary conserved ATP-binding site. KIDFamMap (http://gemdock.life.nctu.edu.tw/KIDFamMap/) is the first database to explore kinase-inhibitor families (KIFs) and kinase-inhibitor-disease (KID) relationships for kinase inhibitor selectivity and mechanisms. This database includes 1208 KIFs, 962 KIDs, 55 603 kinase-inhibitor interactions (KIIs), 35 788 kinase inhibitors, 399 human protein kinases, 339 diseases and 638 disease allelic variants. Here, a KIF can be defined as follows: (i) the kinases in the KIF with significant sequence similarity, (ii) the inhibitors in the KIF with significant topology similarity and (iii) the KIIs in the KIF with significant interaction similarity. The KIIs within a KIF are often conserved on some consensus KIDFamMap anchors, which represent conserved interactions between the kinase subsites and consensus moieties of their inhibitors. Our experimental results reveal that the members of a KIF often possess similar inhibition profiles. The KIDFamMap anchors can reflect kinase conformations types, kinase functions and kinase inhibitor selectivity. We believe that KIDFamMap provides biological insights into kinase inhibitor selectivity and binding mechanisms. PMID:23193279

Hydrographs Showing Groundwater Level Changes for Selected Wells in the Chambers-Clover Creek Watershed and Vicinity, Pierce County, Washington

USGS Publications Warehouse

Justin, G.B.; Julich, R.; Payne, K.L.

2009-01-01

Selected groundwater level hydrographs for the Chambers-Clover Creek watershed (CCCW) and vicinity, Washington, are presented in an interactive web-based map to illustrate changes in groundwater levels in and near the CCCW on a monthly and seasonal basis. Hydrographs are linked to points corresponding to the well location on an interactive map of the study area. Groundwater level data and well information from Federal, State, and local agencies were obtained from the U.S. Geological Survey National Water Information System (NWIS), Groundwater Site Inventory (GWSI) System.

WatAA: Atlas of Protein Hydration. Exploring synergies between data mining and ab initio calculations.

PubMed

Černý, Jiří; Schneider, Bohdan; Biedermannová, Lada

2017-07-14

Water molecules represent an integral part of proteins and a key determinant of protein structure, dynamics and function. WatAA is a newly developed, web-based atlas of amino-acid hydration in proteins. The atlas provides information about the ordered first hydration shell of the most populated amino-acid conformers in proteins. The data presented in the atlas are drawn from two sources: experimental data and ab initio quantum-mechanics calculations. The experimental part is based on a data-mining study of a large set of high-resolution protein crystal structures. The crystal-derived data include 3D maps of water distribution around amino-acids and probability of occurrence of each of the identified hydration sites. The quantum mechanics calculations validate and extend this primary description by optimizing the water position for each hydration site, by providing hydrogen atom positions and by quantifying the interaction energy that stabilizes the water molecule at the particular hydration site position. The calculations show that the majority of experimentally derived hydration sites are positioned near local energy minima for water, and the calculated interaction energies help to assess the preference of water for the individual hydration sites. We propose that the atlas can be used to validate water placement in electron density maps in crystallographic refinement, to locate water molecules mediating protein-ligand interactions in drug design, and to prepare and evaluate molecular dynamics simulations. WatAA: Atlas of Protein Hydration is freely available without login at .

Real-Time Mapping alert system; user's manual

USGS Publications Warehouse

Torres, L.A.

1996-01-01

The U.S. Geological Survey has an extensive hydrologic network that records and transmits precipitation, stage, discharge, and other water- related data on a real-time basis to an automated data processing system. Data values are recorded on electronic data collection platforms at field monitoring sites. These values are transmitted by means of orbiting satellites to receiving ground stations, and by way of telecommunication lines to a U.S. Geological Survey office where they are processed on a computer system. Data that exceed predefined thresholds are identified as alert values. These alert values can help keep water- resource specialists informed of current hydrologic conditions. The current alert status at monitoring sites is of critical importance during floods, hurricanes, and other extreme hydrologic events where quick analysis of the situation is needed. This manual provides instructions for using the Real-Time Mapping software, a series of computer programs developed by the U.S. Geological Survey for quick analysis of hydrologic conditions, and guides users through a basic interactive session. The software provides interactive graphics display and query of real-time information in a map-based, menu-driven environment.

Genotype to Phenotype Mapping of the E. coli lac Promoter

NASA Astrophysics Data System (ADS)

Otwinowski, Jakub; Nemenman, Ilya

2014-03-01

Genotype-to-phenotype maps and the related fitness landscapes that include epistatic interactions are difficult to measure because of their high dimensional structure. Here we construct such a map using the recently collected corpora of high-throughput sequence data from the 75 base pairs long mutagenized E. coli lac promoter region, where each sequence is associated with induced transcriptional activity measured by a fluorescent reporter. We find that the additive (non-epistatic) contributions of individual mutations account for about two-thirds of the explainable phenotype variance, while pairwise epistasis explains about 7% of the variance for the full mutagenized sequence and about 15% for the subsequence associated with protein binding sites. Surprisingly, there is no evidence for third order epistatic contributions, and our inferred fitness landscape is essentially single peaked, with a small amount of antagonistic epistasis. We identify transcription factor (CRP) and RNA polymerase binding sites in the promotor region and their interactions. We conclude with a cautionary note that inferred properties of fitness landscapes may be severely influenced by biases in the sequence data. Funded in part by HFSP and James S. McDonnell Foundation.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cao, Zhen; Voth, Gregory A., E-mail: gavoth@uchicago.edu

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

A 20-residue peptide of the inner membrane protein OutC mediates interaction with two distinct sites of the outer membrane secretin OutD and is essential for the functional type II secretion system in Erwinia chrysanthemi.

PubMed

Login, Frédéric H; Fries, Markus; Wang, Xiaohui; Pickersgill, Richard W; Shevchik, Vladimir E

2010-05-01

The type II secretion system (T2SS) is widely exploited by proteobacteria to secrete enzymes and toxins involved in bacterial survival and pathogenesis. The outer membrane pore formed by the secretin OutD and the inner membrane protein OutC are two key components of the secretion complex, involved in secretion specificity. Here, we show that the periplasmic regions of OutC and OutD interact directly and map the interaction site of OutC to a 20-residue peptide named OutCsip (secretin interacting peptide, residues 139-158). This peptide interacts in vitro with two distinct sites of the periplasmic region of OutD, one located on the N0 subdomain and another overlapping the N2-N3' subdomains. The two interaction sites of OutD have different modes of binding to OutCsip. A single substitution, V143S, located within OutCsip prevents its interaction with one of the two binding sites of OutD and fully inactivates the T2SS. We show that the N0 subdomain of OutD interacts also with a second binding site within OutC located in the region proximal to the transmembrane segment. We suggest that successive interactions between these distinct regions of OutC and OutD may have functional importance in switching the secretion machine.

Mapping contacts between gRNA and mRNA in trypanosome RNA editing.

PubMed

Leung, S S; Koslowsky, D J

1999-02-01

All guide RNAs (gRNAs) identified to date have defined 5' anchor sequences, guiding sequences and a non-encoded 3' uridylate tail. The 5' anchor is required for in vitro editing and is thought to be responsible for selection and binding to the pre-edited mRNA. Little is known, however, about how the gRNAs are used to direct RNA editing. Utilizing the photo-reactive crosslinking agent, azidophenacyl (APA), attached to the 5'- or 3'-terminus of the gRNA, we have begun to map the structural relationships between the different defined regions of the gRNA with the pre-edited mRNA. Analyses of crosslinked conjugates produced with a 5'-terminal APA group confirm that the anchor of the gRNA is correctly positioning the interacting molecules. 3' Crosslinks (X-linker placed at the 3'-end of a U10tail) have also been mapped for three different gRNA/mRNA pairs. In all cases, analyses indicate that the U-tail can interact with a range of nucleotides located upstream of the first edited site. It appears that the U-tail prefers purine-rich sites, close to the first few editing sites. These results suggest that the U-tail may act in concert with the anchor to melt out secondary structure in the mRNA in the immediate editing domain, possibly increasing the accessibility of the editing complex to the proper editing sites.

Design Considerations for Computer-Based Interactive Map Display Systems

DTIC Science & Technology

1979-02-01

11 Five Dimensions for Map Display System Options . . . . . . . . . . . . . . . 12 Summary of...most advanced and exotic technologies- space , optical, computer, and graphic pro- duction; the focusing of vast organizational efforts; and the results...Information retrieval: "Where are all the radar sites in sector 12 ?," "What’s the name of this hill?," "Where’s the hill named B243?" Information storage

Site-directed DNA crosslinking of large multisubunit protein-DNA complexes.

PubMed

Persinger, Jim; Bartholomew, Blaine

2009-01-01

Several methods have been developed to site-specifically incorporate photoreactive nucleotide analogs into DNA for the purpose of identifying the proteins and their domains that are in contact with particular regions of DNA. The synthesis of several deoxynucleotide analogs that have a photoreactive group tethered to the nucleotide base and the incorporation of these analogs into DNA are described. In a second approach, oligonucleotide with a photoreactive group attached to the phosphate backbone is chemically synthesized. The photoreactive oligonucleotide is then enzymatically incorporated into DNA by annealing it to a complementary DNA template and extending with DNA polymerase. Both approaches have been effectively used to map protein-DNA interactions in large multisubunit complexes such as the eukaryotic transcription or ATP-dependent chromatin remodeling complexes. Not only do these techniques map the binding sites of the various subunits in these complexes, but when coupled with peptide mapping also determine the protein domain that is in close proximity to the different DNA sites. The strength of these techniques is the ability to scan a large number of potential sites by making combinations of different DNA probes and is facilitated by using an immobilized DNA template for synthesis.

Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein-Protein Interfaces

PubMed Central

Zerbe, Brandon S.; Hall, David R.

2013-01-01

In the context of protein-protein interactions, the term “hot spot” refers to a residue or cluster of residues that makes a major contribution to the binding free energy, as determined by alanine scanning mutagenesis. In contrast, in pharmaceutical research a hot spot is a site on a target protein that has high propensity for ligand binding and hence is potentially important for drug discovery. Here we examine the relationship between these two hot spot concepts by comparing alanine scanning data for a set of 15 proteins with results from mapping the protein surfaces for sites that can bind fragment-sized small molecules. We find the two types of hot spots are largely complementary; the residues protruding into hot spot regions identified by computational mapping or experimental fragment screening are almost always themselves hot spot residues as defined by alanine scanning experiments. Conversely, a residue that is found by alanine scanning to contribute little to binding rarely interacts with hot spot regions on the partner protein identified by fragment mapping. In spite of the strong correlation between the two hot spot concepts, they fundamentally differ, however. In particular, while identification of a hot spot by alanine scanning establishes the potential to generate substantial interaction energy with a binding partner, there are additional topological requirements to be a hot spot for small molecule binding. Hence, only a minority of hot spots identified by alanine scanning represent sites that are potentially useful for small inhibitor binding, and it is this subset that is identified by experimental or computational fragment screening. PMID:22770357

Relationship between hot spot residues and ligand binding hot spots in protein-protein interfaces.

PubMed

Zerbe, Brandon S; Hall, David R; Vajda, Sandor; Whitty, Adrian; Kozakov, Dima

2012-08-27

In the context of protein-protein interactions, the term "hot spot" refers to a residue or cluster of residues that makes a major contribution to the binding free energy, as determined by alanine scanning mutagenesis. In contrast, in pharmaceutical research, a hot spot is a site on a target protein that has high propensity for ligand binding and hence is potentially important for drug discovery. Here we examine the relationship between these two hot spot concepts by comparing alanine scanning data for a set of 15 proteins with results from mapping the protein surfaces for sites that can bind fragment-sized small molecules. We find the two types of hot spots are largely complementary; the residues protruding into hot spot regions identified by computational mapping or experimental fragment screening are almost always themselves hot spot residues as defined by alanine scanning experiments. Conversely, a residue that is found by alanine scanning to contribute little to binding rarely interacts with hot spot regions on the partner protein identified by fragment mapping. In spite of the strong correlation between the two hot spot concepts, they fundamentally differ, however. In particular, while identification of a hot spot by alanine scanning establishes the potential to generate substantial interaction energy with a binding partner, there are additional topological requirements to be a hot spot for small molecule binding. Hence, only a minority of hot spots identified by alanine scanning represent sites that are potentially useful for small inhibitor binding, and it is this subset that is identified by experimental or computational fragment screening.

Probing the communication of deoxythymidine triphosphate in HIV-1 reverse transcriptase by communication maps and interaction energy studies.

PubMed

Gnanasekaran, Ramachandran

2017-11-08

We calculate communication maps for HIV-1 Reverse Transcriptase (RT) to elucidate energy transfer pathways between deoxythymidine triphosphate (dTTP) and other parts of the protein. This approach locates energy transport channels from the dTTP to remote regions of the protein via residues and water molecules. We examine the water dynamics near the catalytic site of HIV-1 RT by molecular dynamics (MD) simulations. We find that, within the catalytic site, the relaxation of water molecules is similar to that of the hydration water molecules present in other proteins and the relaxation time scale is fast enough to transport energy and helps in communication between dTTP and other residues in the system. To quantify energy transfer, we also calculate the interaction energies of dTTP, 2Mg 2+ , doxy-guanosine nucleotide (DG22) with their surrounding residues by using the B3LYP-D3 method. The results, from classical vibrational energy diffusivity and QM interaction energy, are complementary to identify the important residues involved in the process of polymerization. The positive and negative interactions by dTTP with different types of residues in the catalytic region make the residues transfer energy through vibrational communication.

Peeking Beneath the Caldera: Communicating Subsurface Knowledge of Newberry Volcano

NASA Astrophysics Data System (ADS)

Mark-Moser, M.; Rose, K.; Schultz, J.; Cameron, E.

2016-12-01

"Imaging the Subsurface: Enhanced Geothermal Systems and Exploring Beneath Newberry Volcano" is an interactive website that presents a three-dimensional subsurface model of Newberry Volcano developed at National Energy Technology Laboratory (NETL). Created using the Story Maps application by ArcGIS Online, this format's dynamic capabilities provide the user the opportunity for multimedia engagement with the datasets and information used to build the subsurface model. This website allows for an interactive experience that the user dictates, including interactive maps, instructive videos and video capture of the subsurface model, and linked information throughout the text. This Story Map offers a general background on the technology of enhanced geothermal systems and the geologic and development history of Newberry Volcano before presenting NETL's modeling efforts that support the installation of enhanced geothermal systems. The model is driven by multiple geologic and geophysical datasets to compare and contrast results which allow for the targeting of potential EGS sites and the reduction of subsurface uncertainty. This Story Map aims to communicate to a broad audience, and provides a platform to effectively introduce the model to researchers and stakeholders.

Mapping DNA damage-dependent genetic interactions in yeast via party mating and barcode fusion genetics.

PubMed

Díaz-Mejía, J Javier; Celaj, Albi; Mellor, Joseph C; Coté, Atina; Balint, Attila; Ho, Brandon; Bansal, Pritpal; Shaeri, Fatemeh; Gebbia, Marinella; Weile, Jochen; Verby, Marta; Karkhanina, Anna; Zhang, YiFan; Wong, Cassandra; Rich, Justin; Prendergast, D'Arcy; Gupta, Gaurav; Öztürk, Sedide; Durocher, Daniel; Brown, Grant W; Roth, Frederick P

2018-05-28

Condition-dependent genetic interactions can reveal functional relationships between genes that are not evident under standard culture conditions. State-of-the-art yeast genetic interaction mapping, which relies on robotic manipulation of arrays of double-mutant strains, does not scale readily to multi-condition studies. Here, we describe barcode fusion genetics to map genetic interactions (BFG-GI), by which double-mutant strains generated via en masse "party" mating can also be monitored en masse for growth to detect genetic interactions. By using site-specific recombination to fuse two DNA barcodes, each representing a specific gene deletion, BFG-GI enables multiplexed quantitative tracking of double mutants via next-generation sequencing. We applied BFG-GI to a matrix of DNA repair genes under nine different conditions, including methyl methanesulfonate (MMS), 4-nitroquinoline 1-oxide (4NQO), bleomycin, zeocin, and three other DNA-damaging environments. BFG-GI recapitulated known genetic interactions and yielded new condition-dependent genetic interactions. We validated and further explored a subnetwork of condition-dependent genetic interactions involving MAG1 , SLX4, and genes encoding the Shu complex, and inferred that loss of the Shu complex leads to an increase in the activation of the checkpoint protein kinase Rad53. © 2018 The Authors. Published under the terms of the CC BY 4.0 license.

Facilitation or Competition? Tree Effects on Grass Biomass across a Precipitation Gradient

PubMed Central

Moustakas, Aristides; Kunin, William E.; Cameron, Tom C.; Sankaran, Mahesh

2013-01-01

Savanna ecosystems are dominated by two distinct plant life forms, grasses and trees, but the interactions between them are poorly understood. Here, we quantified the effects of isolated savanna trees on grass biomass as a function of distance from the base of the tree and tree height, across a precipitation gradient in the Kruger National Park, South Africa. Our results suggest that mean annual precipitation (MAP) mediates the nature of tree-grass interactions in these ecosystems, with the impact of trees on grass biomass shifting qualitatively between 550 and 737 mm MAP. Tree effects on grass biomass were facilitative in drier sites (MAP≤550 mm), with higher grass biomass observed beneath tree canopies than outside. In contrast, at the wettest site (MAP = 737 mm), grass biomass did not differ significantly beneath and outside tree canopies. Within this overall precipitation-driven pattern, tree height had positive effect on sub-canopy grass biomass at some sites, but these effects were weak and not consistent across the rainfall gradient. For a more synthetic understanding of tree-grass interactions in savannas, future studies should focus on isolating the different mechanisms by which trees influence grass biomass, both positively and negatively, and elucidate how their relative strengths change over broad environmental gradients. PMID:23451137

Crystal structure and functional interpretation of the erythrocyte spectrin tetramerization domain complex

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ipsaro, Jonathan J.; Harper, Sandra L.; Messick, Troy E.

2010-09-07

As the principal component of the membrane skeleton, spectrin confers integrity and flexibility to red cell membranes. Although this network involves many interactions, the most common hemolytic anemia mutations that disrupt erythrocyte morphology affect the spectrin tetramerization domains. Although much is known clinically about the resulting conditions (hereditary elliptocytosis and pyropoikilocytosis), the detailed structural basis for spectrin tetramerization and its disruption by hereditary anemia mutations remains elusive. Thus, to provide further insights into spectrin assembly and tetramer site mutations, a crystal structure of the spectrin tetramerization domain complex has been determined. Architecturally, this complex shows striking resemblance to multirepeat spectrinmore » fragments, with the interacting tetramer site region forming a central, composite repeat. This structure identifies conformational changes in {alpha}-spectrin that occur upon binding to {beta}-spectrin, and it reports the first structure of the {beta}-spectrin tetramerization domain. Analysis of the interaction surfaces indicates an extensive interface dominated by hydrophobic contacts and supplemented by electrostatic complementarity. Analysis of evolutionarily conserved residues suggests additional surfaces that may form important interactions. Finally, mapping of hereditary anemia-related mutations onto the structure demonstrate that most, but not all, local hereditary anemia mutations map to the interacting domains. The potential molecular effects of these mutations are described.« less

Crystal Structure and Functional Interpretation of the Erythrocyte spectrin Tetramerization Domain Complex

DOE Office of Scientific and Technical Information (OSTI.GOV)

J Ipsaro; S Harper; T Messick

2011-12-31

As the principal component of the membrane skeleton, spectrin confers integrity and flexibility to red cell membranes. Although this network involves many interactions, the most common hemolytic anemia mutations that disrupt erythrocyte morphology affect the spectrin tetramerization domains. Although much is known clinically about the resulting conditions (hereditary elliptocytosis and pyropoikilocytosis), the detailed structural basis for spectrin tetramerization and its disruption by hereditary anemia mutations remains elusive. Thus, to provide further insights into spectrin assembly and tetramer site mutations, a crystal structure of the spectrin tetramerization domain complex has been determined. Architecturally, this complex shows striking resemblance to multirepeat spectrinmore » fragments, with the interacting tetramer site region forming a central, composite repeat. This structure identifies conformational changes in {alpha}-spectrin that occur upon binding to {beta}-spectrin, and it reports the first structure of the {beta}-spectrin tetramerization domain. Analysis of the interaction surfaces indicates an extensive interface dominated by hydrophobic contacts and supplemented by electrostatic complementarity. Analysis of evolutionarily conserved residues suggests additional surfaces that may form important interactions. Finally, mapping of hereditary anemia-related mutations onto the structure demonstrate that most, but not all, local hereditary anemia mutations map to the interacting domains. The potential molecular effects of these mutations are described.« less

SELMAP - SELEX affinity landscape MAPping of transcription factor binding sites using integrated microfluidics

PubMed Central

Chen, Dana; Orenstein, Yaron; Golodnitsky, Rada; Pellach, Michal; Avrahami, Dorit; Wachtel, Chaim; Ovadia-Shochat, Avital; Shir-Shapira, Hila; Kedmi, Adi; Juven-Gershon, Tamar; Shamir, Ron; Gerber, Doron

2016-01-01

Transcription factors (TFs) alter gene expression in response to changes in the environment through sequence-specific interactions with the DNA. These interactions are best portrayed as a landscape of TF binding affinities. Current methods to study sequence-specific binding preferences suffer from limited dynamic range, sequence bias, lack of specificity and limited throughput. We have developed a microfluidic-based device for SELEX Affinity Landscape MAPping (SELMAP) of TF binding, which allows high-throughput measurement of 16 proteins in parallel. We used it to measure the relative affinities of Pho4, AtERF2 and Btd full-length proteins to millions of different DNA binding sites, and detected both high and low-affinity interactions in equilibrium conditions, generating a comprehensive landscape of the relative TF affinities to all possible DNA 6-mers, and even DNA10-mers with increased sequencing depth. Low quantities of both the TFs and DNA oligomers were sufficient for obtaining high-quality results, significantly reducing experimental costs. SELMAP allows in-depth screening of hundreds of TFs, and provides a means for better understanding of the regulatory processes that govern gene expression. PMID:27628341

Genetic interaction analysis of point mutations enables interrogation of gene function at a residue-level resolution

PubMed Central

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

2014-01-01

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

In situ dissection of RNA functional subunits by domain-specific chromatin isolation by RNA purification (dChIRP).

PubMed

Quinn, Jeffrey J; Chang, Howard Y

2015-01-01

Here we describe domain-specific chromatin isolation by RNA purification (dChIRP), a technique for dissecting the functional domains of a target RNA in situ. For an RNA of interest, dChIRP can identify domain-level intramolecular and intermolecular RNA-RNA, RNA-protein, and RNA-DNA interactions and maps the RNA's genomic binding sites with higher precision than domain-agnostic methods. We illustrate how this technique has been applied to the roX1 lncRNA to resolve its domain-level architecture, discover its protein- and chromatin-interacting domains, and map its occupancy on the X chromosome.

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

NASA Technical Reports Server (NTRS)

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

1988-01-01

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

LC-MS/MS Peptide Mapping with Automated Data Processing for Routine Profiling of N-Glycans in Immunoglobulins

NASA Astrophysics Data System (ADS)

Shah, Bhavana; Jiang, Xinzhao Grace; Chen, Louise; Zhang, Zhongqi

2014-06-01

Protein N-Glycan analysis is traditionally performed by high pH anion exchange chromatography (HPAEC), reversed phase liquid chromatography (RPLC), or hydrophilic interaction liquid chromatography (HILIC) on fluorescence-labeled glycans enzymatically released from the glycoprotein. These methods require time-consuming sample preparations and do not provide site-specific glycosylation information. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) peptide mapping is frequently used for protein structural characterization and, as a bonus, can potentially provide glycan profile on each individual glycosylation site. In this work, a recently developed glycopeptide fragmentation model was used for automated identification, based on their MS/MS, of N-glycopeptides from proteolytic digestion of monoclonal antibodies (mAbs). Experimental conditions were optimized to achieve accurate profiling of glycoforms. Glycan profiles obtained from LC-MS/MS peptide mapping were compared with those obtained from HPAEC, RPLC, and HILIC analyses of released glycans for several mAb molecules. Accuracy, reproducibility, and linearity of the LC-MS/MS peptide mapping method for glycan profiling were evaluated. The LC-MS/MS peptide mapping method with fully automated data analysis requires less sample preparation, provides site-specific information, and may serve as an alternative method for routine profiling of N-glycans on immunoglobulins as well as other glycoproteins with simple N-glycans.

Reports on Cancer - Cancer Statistics

Cancer.gov

Interactive tools for access to statistics for a cancer site by gender, race, ethnicity, calendar year, age, state, county, stage, and histology. Statistics include incidence, mortality, prevalence, cost, risk factors, behaviors, tobacco use, and policies and are presented as graphs, tables, or maps.

Analysis of In Vivo Chromatin and Protein Interactions of Arabidopsis Transcript Elongation Factors.

PubMed

Pfab, Alexander; Antosz, Wojciech; Holzinger, Philipp; Bruckmann, Astrid; Griesenbeck, Joachim; Grasser, Klaus D

2017-01-01

A central step to elucidate the function of proteins commonly comprises the analysis of their molecular interactions in vivo. For nuclear regulatory proteins this involves determining protein-protein interactions as well as mapping of chromatin binding sites. Here, we present two protocols to identify protein-protein and chromatin interactions of transcript elongation factors (TEFs) in Arabidopsis. The first protocol (Subheading 3.1) describes protein affinity-purification coupled to mass spectrometry (AP-MS) that utilizes suspension cultured cells as experimental system. This approach provides an unbiased view of proteins interacting with epitope-tagged TEFs. The second protocol (Subheading 3.2) depicts details about a chromatin immunoprecipitation (ChIP) procedure to characterize genomic binding sites of TEFs. These methods should be valuable tools for the analysis of a broad variety of nuclear proteins.

DNA Polymerase α Subunit Residues and Interactions Required for Efficient Initiation Complex Formation Identified by a Genetic Selection.

PubMed

Lindow, Janet C; Dohrmann, Paul R; McHenry, Charles S

2015-07-03

Biophysical and structural studies have defined many of the interactions that occur between individual components or subassemblies of the bacterial replicase, DNA polymerase III holoenzyme (Pol III HE). Here, we extended our knowledge of residues and interactions that are important for the first step of the replicase reaction: the ATP-dependent formation of an initiation complex between the Pol III HE and primed DNA. We exploited a genetic selection using a dominant negative variant of the polymerase catalytic subunit that can effectively compete with wild-type Pol III α and form initiation complexes, but cannot elongate. Suppression of the dominant negative phenotype was achieved by secondary mutations that were ineffective in initiation complex formation. The corresponding proteins were purified and characterized. One class of mutant mapped to the PHP domain of Pol III α, ablating interaction with the ϵ proofreading subunit and distorting the polymerase active site in the adjacent polymerase domain. Another class of mutation, found near the C terminus, interfered with τ binding. A third class mapped within the known β-binding domain, decreasing interaction with the β2 processivity factor. Surprisingly, mutations within the β binding domain also ablated interaction with τ, suggesting a larger τ binding site than previously recognized. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Interactive Web Interface to the Global Strain Rate Map Project

NASA Astrophysics Data System (ADS)

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

2004-05-01

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

JET2 Viewer: a database of predicted multiple, possibly overlapping, protein-protein interaction sites for PDB structures.

PubMed

Ripoche, Hugues; Laine, Elodie; Ceres, Nicoletta; Carbone, Alessandra

2017-01-04

The database JET2 Viewer, openly accessible at http://www.jet2viewer.upmc.fr/, reports putative protein binding sites for all three-dimensional (3D) structures available in the Protein Data Bank (PDB). This knowledge base was generated by applying the computational method JET 2 at large-scale on more than 20 000 chains. JET 2 strategy yields very precise predictions of interacting surfaces and unravels their evolutionary process and complexity. JET2 Viewer provides an online intelligent display, including interactive 3D visualization of the binding sites mapped onto PDB structures and suitable files recording JET 2 analyses. Predictions were evaluated on more than 15 000 experimentally characterized protein interfaces. This is, to our knowledge, the largest evaluation of a protein binding site prediction method. The overall performance of JET 2 on all interfaces are: Sen = 52.52, PPV = 51.24, Spe = 80.05, Acc = 75.89. The data can be used to foster new strategies for protein-protein interactions modulation and interaction surface redesign. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

DARC: Mapping Surface Topography by Ray-Casting for Effective Virtual Screening at Protein Interaction Sites.

PubMed

Gowthaman, Ragul; Miller, Sven A; Rogers, Steven; Khowsathit, Jittasak; Lan, Lan; Bai, Nan; Johnson, David K; Liu, Chunjing; Xu, Liang; Anbanandam, Asokan; Aubé, Jeffrey; Roy, Anuradha; Karanicolas, John

2016-05-12

Protein-protein interactions represent an exciting and challenging target class for therapeutic intervention using small molecules. Protein interaction sites are often devoid of the deep surface pockets presented by "traditional" drug targets, and crystal structures reveal that inhibitors typically engage these sites using very shallow binding modes. As a consequence, modern virtual screening tools developed to identify inhibitors of traditional drug targets do not perform as well when they are instead deployed at protein interaction sites. To address the need for novel inhibitors of important protein interactions, here we introduce an alternate docking strategy specifically designed for this regime. Our method, termed DARC (Docking Approach using Ray-Casting), matches the topography of a surface pocket "observed" from within the protein to the topography "observed" when viewing a potential ligand from the same vantage point. We applied DARC to carry out a virtual screen against the protein interaction site of human antiapoptotic protein Mcl-1 and found that four of the top-scoring 21 compounds showed clear inhibition in a biochemical assay. The Ki values for these compounds ranged from 1.2 to 21 μM, and each had ligand efficiency comparable to promising small-molecule inhibitors of other protein-protein interactions. These hit compounds do not resemble the natural (protein) binding partner of Mcl-1, nor do they resemble any known inhibitors of Mcl-1. Our results thus demonstrate the utility of DARC for identifying novel inhibitors of protein-protein interactions.

The Microtubule-Associated Protein MAP18 Affects ROP2 GTPase Activity during Root Hair Growth1[OPEN

PubMed Central

Kang, Erfang; Zheng, Mingzhi; Zhang, Yan; Yuan, Ming; Fu, Ying

2017-01-01

Establishment and maintenance of the polar site are important for root hair tip growth. We previously reported that Arabidopsis (Arabidopsis thaliana) MICROTUBULE-ASSOCIATED PROTEIN18 (MAP18) functions in controlling the direction of pollen tube growth and root hair elongation. Additionally, the Rop GTPase ROP2 was reported as a positive regulator of both root hair initiation and tip growth in Arabidopsis. Both loss of function of ROP2 and knockdown of MAP18 lead to a decrease in root hair length, whereas overexpression of either MAP18 or ROP2 causes multiple tips or a branching hair phenotype. However, it is unclear whether MAP18 and ROP2 coordinately regulate root hair growth. In this study, we demonstrate that MAP18 and ROP2 interact genetically and functionally. MAP18 interacts physically with ROP2 in vitro and in vivo and preferentially binds to the inactive form of the ROP2 protein. MAP18 promotes ROP2 activity during root hair tip growth. Further investigation revealed that MAP18 competes with RhoGTPase GDP DISSOCIATION INHIBITOR1/SUPERCENTIPEDE1 for binding to ROP2, in turn affecting the localization of active ROP2 in the plasma membrane of the root hair tip. These results reveal a novel function of MAP18 in the regulation of ROP2 activation during root hair growth. PMID:28314794

Real-Time Mapping alert system; characteristics and capabilities

USGS Publications Warehouse

Torres, L.A.; Lambert, S.C.; Liebermann, T.D.

1995-01-01

The U.S. Geological Survey has an extensive hydrologic network that records and transmits precipitation, stage, discharge, and other water-related data on a real-time basis to an automated data processing system. Data values are recorded on electronic data collection platforms at field sampling sites. These values are transmitted by means of orbiting satellites to receiving ground stations, and by way of telecommunication lines to a U.S. Geological Survey office where they are processed on a computer system. Data that exceed predefined thresholds are identified as alert values. The current alert status at monitoring sites within a state or region is of critical importance during floods, hurricanes, and other extreme hydrologic events. This report describes the characteristics and capabilities of a series of computer programs for real-time mapping of hydrologic data. The software provides interactive graphics display and query of hydrologic information from the network in a real-time, map-based, menu-driven environment.

Probing Protein Structure by Amino Acid-Specific Covalent Labeling and Mass Spectrometry

PubMed Central

Mendoza, Vanessa Leah; Vachet, Richard W.

2009-01-01

For many years, amino acid-specific covalent labeling has been a valuable tool to study protein structure and protein interactions, especially for systems that are difficult to study by other means. These covalent labeling methods typically map protein structure and interactions by measuring the differential reactivity of amino acid side chains. The reactivity of amino acids in proteins generally depends on the accessibility of the side chain to the reagent, the inherent reactivity of the label and the reactivity of the amino acid side chain. Peptide mass mapping with ESI- or MALDI-MS and peptide sequencing with tandem MS are typically employed to identify modification sites to provide site-specific structural information. In this review, we describe the reagents that are most commonly used in these residue-specific modification reactions, details about the proper use of these covalent labeling reagents, and information about the specific biochemical problems that have been addressed with covalent labeling strategies. PMID:19016300

Semantic Data And Visualization Techniques Applied To Geologic Field Mapping

NASA Astrophysics Data System (ADS)

Houser, P. I. Q.; Royo-Leon, M.; Munoz, R.; Estrada, E.; Villanueva-Rosales, N.; Pennington, D. D.

2015-12-01

Geologic field mapping involves the use of technology before, during, and after visiting a site. Geologists utilize hardware such as Global Positioning Systems (GPS) connected to mobile computing platforms such as tablets that include software such as ESRI's ArcPad and other software to produce maps and figures for a final analysis and report. Hand written field notes contain important information and drawings or sketches of specific areas within the field study. Our goal is to collect and geo-tag final and raw field data into a cyber-infrastructure environment with an ontology that allows for large data processing, visualization, sharing, and searching, aiding in connecting field research with prior research in the same area and/or aid with experiment replication. Online searches of a specific field area return results such as weather data from NOAA and QuakeML seismic data from USGS. These results that can then be saved to a field mobile device and searched while in the field where there is no Internet connection. To accomplish this we created the GeoField ontology service using the Web Ontology Language (OWL) and Protégé software. Advanced queries on the dataset can be made using reasoning capabilities can be supported that go beyond a standard database service. These improvements include the automated discovery of data relevant to a specific field site and visualization techniques aimed at enhancing analysis and collaboration while in the field by draping data over mobile views of the site using augmented reality. A case study is being performed at University of Texas at El Paso's Indio Mountains Research Station located near Van Horn, Texas, an active multi-disciplinary field study site. The user can interactively move the camera around the study site and view their data digitally. Geologist's can check their data against the site in real-time and improve collaboration with another person as both parties have the same interactive view of the data.

Interactive Geophysical Mapping on the Web

NASA Astrophysics Data System (ADS)

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

2002-12-01

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

Structure of the PSD-95/MAP1A complex reveals a unique target recognition mode of the MAGUK GK domain.

PubMed

Xia, Yitian; Shang, Yuan; Zhang, Rongguang; Zhu, Jinwei

2017-08-10

The PSD-95 family of membrane-associated guanylate kinases (MAGUKs) are major synaptic scaffold proteins and play crucial roles in the dynamic regulation of dendritic remodelling, which is understood to be the foundation of synaptogenesis and synaptic plasticity. The guanylate kinase (GK) domain of MAGUK family proteins functions as a phosphor-peptide binding module. However, the GK domain of PSD-95 has been found to directly bind to a peptide sequence within the C-terminal region of neuronal-specific microtubule-associated protein 1A (MAP1A), although the detailed molecular mechanism governing this phosphorylation-independent interaction at the atomic level is missing. In the present study, we determine the crystal structure of PSD-95 GK in complex with the MAP1A peptide at 2.6-Å resolution. The complex structure reveals that, unlike a linear and elongated conformation in the phosphor-peptide/GK complexes, the MAP1A peptide adopts a unique conformation with a stretch of hydrophobic residues far from each other in the primary sequence clustering and interacting with the 'hydrophobic site' of PSD-95 GK and a highly conserved aspartic acid of MAP1A (D2117) mimicking the phosphor-serine/threonine in binding to the 'phosphor-site' of PSD-95 GK. We demonstrate that the MAP1A peptide may undergo a conformational transition upon binding to PSD-95 GK. Further structural comparison of known DLG GK-mediated complexes reveals the target recognition specificity and versatility of DLG GKs. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Geological mapping in northwestern Saudi Arabia using LANDSAT multispectral techniques

NASA Technical Reports Server (NTRS)

Blodget, H. W.; Brown, G. F.; Moik, J. G.

1975-01-01

Various computer enhancement and data extraction systems using LANDSAT data were assessed and used to complement a continuing geologic mapping program. Interactive digital classification techniques using both the parallel-piped and maximum-likelihood statistical approaches achieve very limited success in areas of highly dissected terrain. Computer enhanced imagery developed by color compositing stretched MSS ratio data was constructed for a test site in northwestern Saudi Arabia. Initial results indicate that several igneous and sedimentary rock types can be discriminated.

RIPiT-Seq: A high-throughput approach for footprinting RNA:protein complexes

PubMed Central

Singh, Guramrit; Ricci, Emiliano P.; Moore, Melissa J.

2013-01-01

Development of high-throughput approaches to map the RNA interaction sites of individual RNA binding proteins (RBPs) transcriptome-wide is rapidly transforming our understanding of post-transcriptional gene regulatory mechanisms. Here we describe a ribonucleoprotein (RNP) footprinting approach we recently developed for identifying occupancy sites of both individual RBPs and multi-subunit RNP complexes. RNA:protein immunoprecipitation in tandem (RIPiT) yields highly specific RNA footprints of cellular RNPs isolated via two sequential purifications; the resulting RNA footprints can then be identified by high-throughput sequencing (Seq). RIPiT-Seq is broadly applicable to all RBPs regardless of their RNA binding mode and thus provides a means to map the RNA binding sites of RBPs with poor inherent ultraviolet (UV) crosslinkability. Further, among current high-throughput approaches, RIPiT has the unique capacity to differentiate binding sites of RNPs with overlapping protein composition. It is therefore particularly suited for studying dynamic RNP assemblages whose composition evolves as gene expression proceeds. PMID:24096052

Mapping the binding site of snurportin 1 on native U1 snRNP by cross-linking and mass spectrometry

PubMed Central

Kühn-Hölsken, Eva; Lenz, Christof; Dickmanns, Achim; Hsiao, He-Hsuan; Richter, Florian M.; Kastner, Berthold; Ficner, Ralf; Urlaub, Henning

2010-01-01

Mass spectrometry allows the elucidation of molecular details of the interaction domains of the individual components in macromolecular complexes subsequent to cross-linking of the individual components. Here, we applied chemical and UV cross-linking combined with tandem mass-spectrometric analysis to identify contact sites of the nuclear import adaptor snurportin 1 to the small ribonucleoprotein particle U1 snRNP in addition to the known interaction of m3G cap and snurportin 1. We were able to define previously unknown sites of protein–protein and protein–RNA interactions on the molecular level within U1 snRNP. We show that snurportin 1 interacts with its central m3G-cap-binding domain with Sm proteins and with its extreme C-terminus with stem-loop III of U1 snRNA. The crosslinking data support the idea of a larger interaction area between snurportin 1 and U snRNPs and the contact sites identified prove useful for modeling the spatial arrangement of snurportin 1 domains when bound to U1 snRNP. Moreover, this suggests a functional nuclear import complex that assembles around the m3G cap and the Sm proteins only when the Sm proteins are bound and arranged in the proper orientation to the cognate Sm site in U snRNA. PMID:20421206

NASA's Solar System Treks: Online Portals for Planetary Mapping and Modeling

NASA Technical Reports Server (NTRS)

Day, Brian

2017-01-01

NASA's Solar System Treks are a suite of web-based of lunar and planetary mapping and modeling portals providing interactive visualization and analysis tools enabling mission planners, planetary scientists, students, and the general public to access mapped lunar data products from past and current missions for the Moon, Mars, Vesta, and more. New portals for additional planetary bodies are being planned. This presentation will recap significant enhancements to these toolsets during the past year and look ahead to future features and releases. Moon Trek is a new portal replacing its predecessor, the Lunar Mapping and Modeling Portal (LMMP), that significantly upgrades and builds upon the capabilities of LMMP. It features greatly improved navigation, 3D visualization, fly-overs, performance, and reliability. Additional data products and tools continue to be added. These include both generalized products as well as polar data products specifically targeting potential sites for NASA's Resource Prospector mission as well as for missions being planned by NASA's international partners. The latest release of Mars Trek includes new tools and data products requested by NASA's Planetary Science Division to support site selection and analysis for Mars Human Landing Exploration Zone Sites. Also being given very high priority by NASA Headquarters is Mars Trek's use as a means to directly involve the public in upcoming missions, letting them explore the areas the agency is focusing upon, understand what makes these sites so fascinating, follow the selection process, and get caught up in the excitement of exploring Mars. Phobos Trek, the latest effort in the Solar System Treks suite, is being developed in coordination with the International Phobos/Deimos Landing Site Working Group, with landing site selection and analysis for JAXA's MMX (Martian Moons eXploration) mission as a primary driver.

NASA's Solar System Treks: Online Portals for Planetary Mapping and Modeling

NASA Astrophysics Data System (ADS)

Day, B. H.; Law, E.

2017-12-01

NASA's Solar System Treks are a suite of web-based of lunar and planetary mapping and modeling portals providing interactive visualization and analysis tools enabling mission planners, planetary scientists, students, and the general public to access mapped lunar data products from past and current missions for the Moon, Mars, Vesta, and more. New portals for additional planetary bodies are being planned. This presentation will recap significant enhancements to these toolsets during the past year and look ahead to future features and releases. Moon Trek is a new portal replacing its predecessor, the Lunar Mapping and Modeling Portal (LMMP), that significantly upgrades and builds upon the capabilities of LMMP. It features greatly improved navigation, 3D visualization, fly-overs, performance, and reliability. Additional data products and tools continue to be added. These include both generalized products as well as polar data products specifically targeting potential sites for NASA's Resource Prospector mission as well as for missions being planned by NASA's international partners. The latest release of Mars Trek includes new tools and data products requested by NASA's Planetary Science Division to support site selection and analysis for Mars Human Landing Exploration Zone Sites. Also being given very high priority by NASA Headquarters is Mars Trek's use as a means to directly involve the public in upcoming missions, letting them explore the areas the agency is focusing upon, understand what makes these sites so fascinating, follow the selection process, and get caught up in the excitement of exploring Mars. Phobos Trek, the latest effort in the Solar System Treks suite, is being developed in coordination with the International Phobos/Deimos Landing Site Working Group, with landing site selection and analysis for JAXA's MMX mission as a primary driver.

Estimating net solar radiation using Landsat Thematic Mapper and digital elevation data

NASA Technical Reports Server (NTRS)

Dubayah, R.

1992-01-01

A radiative transfer algorithm is combined with digital elevation and satellite reflectance data to model spatial variability in net solar radiation at fine spatial resolution. The method is applied to the tall-grass prairie of the 16 x 16 sq km FIFE site (First ISLSCP Field Experiment) of the International Satellite Land Surface Climatology Project. Spectral reflectances as measured by the Landsat Thematic Mapper (TM) are corrected for atmospheric and topographic effects using field measurements and accurate 30-m digital elevation data in a detailed model of atmosphere-surface interaction. The spectral reflectances are then integrated to produce estimates of surface albedo in the range 0.3-3.0 microns. This map of albedo is used in an atmospheric and topographic radiative transfer model to produce a map of net solar radiation. A map of apparent net solar radiation is also derived using only the TM reflectance data, uncorrected for topography, and the average field-measured downwelling solar irradiance. Comparison with field measurements at 10 sites on the prairie shows that the topographically derived radiation map accurately captures the spatial variability in net solar radiation, but the apparent map does not.

Unified superresolution experiments and stochastic theory provide mechanistic insight into protein ion-exchange adsorptive separations

PubMed Central

Kisley, Lydia; Chen, Jixin; Mansur, Andrea P.; Shuang, Bo; Kourentzi, Katerina; Poongavanam, Mohan-Vivekanandan; Chen, Wen-Hsiang; Dhamane, Sagar; Willson, Richard C.; Landes, Christy F.

2014-01-01

Chromatographic protein separations, immunoassays, and biosensing all typically involve the adsorption of proteins to surfaces decorated with charged, hydrophobic, or affinity ligands. Despite increasingly widespread use throughout the pharmaceutical industry, mechanistic detail about the interactions of proteins with individual chromatographic adsorbent sites is available only via inference from ensemble measurements such as binding isotherms, calorimetry, and chromatography. In this work, we present the direct superresolution mapping and kinetic characterization of functional sites on ion-exchange ligands based on agarose, a support matrix routinely used in protein chromatography. By quantifying the interactions of single proteins with individual charged ligands, we demonstrate that clusters of charges are necessary to create detectable adsorption sites and that even chemically identical ligands create adsorption sites of varying kinetic properties that depend on steric availability at the interface. Additionally, we relate experimental results to the stochastic theory of chromatography. Simulated elution profiles calculated from the molecular-scale data suggest that, if it were possible to engineer uniform optimal interactions into ion-exchange systems, separation efficiencies could be improved by as much as a factor of five by deliberately exploiting clustered interactions that currently dominate the ion-exchange process only accidentally. PMID:24459184

Unified superresolution experiments and stochastic theory provide mechanistic insight into protein ion-exchange adsorptive separations.

PubMed

Kisley, Lydia; Chen, Jixin; Mansur, Andrea P; Shuang, Bo; Kourentzi, Katerina; Poongavanam, Mohan-Vivekanandan; Chen, Wen-Hsiang; Dhamane, Sagar; Willson, Richard C; Landes, Christy F

2014-02-11

Chromatographic protein separations, immunoassays, and biosensing all typically involve the adsorption of proteins to surfaces decorated with charged, hydrophobic, or affinity ligands. Despite increasingly widespread use throughout the pharmaceutical industry, mechanistic detail about the interactions of proteins with individual chromatographic adsorbent sites is available only via inference from ensemble measurements such as binding isotherms, calorimetry, and chromatography. In this work, we present the direct superresolution mapping and kinetic characterization of functional sites on ion-exchange ligands based on agarose, a support matrix routinely used in protein chromatography. By quantifying the interactions of single proteins with individual charged ligands, we demonstrate that clusters of charges are necessary to create detectable adsorption sites and that even chemically identical ligands create adsorption sites of varying kinetic properties that depend on steric availability at the interface. Additionally, we relate experimental results to the stochastic theory of chromatography. Simulated elution profiles calculated from the molecular-scale data suggest that, if it were possible to engineer uniform optimal interactions into ion-exchange systems, separation efficiencies could be improved by as much as a factor of five by deliberately exploiting clustered interactions that currently dominate the ion-exchange process only accidentally.

Identification of continuous interaction sites in PLA(2)-based protein complexes by peptide arrays.

PubMed

Fortes-Dias, Consuelo Latorre; Santos, Roberta Márcia Marques dos; Magro, Angelo José; Fontes, Marcos Roberto de Mattos; Chávez-Olórtegui, Carlos; Granier, Claude

2009-01-01

Crotoxin (CA.CB) is a beta-neurotoxin from Crotalus durissus terrificus snake venom that is responsible for main envenomation effects upon biting by this snake. It is a heterodimer of an acidic protein (CA) devoid of any biological activity per se and a basic, enzymatically active, PLA(2) counterpart (CB). Both lethal and enzymatic activities of crotoxin have been shown to be inhibited by CNF, a protein from the blood of C. d. terrificus snakes. CNF replaces CA in the CA.CB complex, forming a stable, non-toxic complex CNF.CB. The molecular sites involved in the tight interfacial protein-protein interactions in these PLA(2)-based complexes have not been clearly determined. To help address this question, we used the peptide arrays approach to map possible interfacial interaction sites in CA.CB and CNF.CB. Amino acid stretches putatively involved in these interactions were firstly identified in the primary structure of CB. Further analysis of the interfacial availability of these stretches in the presumed biologically active structure of CB, suggested two interaction main sites, located at the amino-terminus and beta-wing regions. Peptide segments at the carboxyl-terminus of CB were also suggested to play a secondary role in the binding of both CA and CNF.

Viral Organization of Human Proteins

PubMed Central

Wuchty, Stefan; Siwo, Geoffrey; Ferdig, Michael T.

2010-01-01

Although maps of intracellular interactions are increasingly well characterized, little is known about large-scale maps of host-pathogen protein interactions. The investigation of host-pathogen interactions can reveal features of pathogenesis and provide a foundation for the development of drugs and disease prevention strategies. A compilation of experimentally verified interactions between HIV-1 and human proteins and a set of HIV-dependency factors (HDF) allowed insights into the topology and intricate interplay between viral and host proteins on a large scale. We found that targeted and HDF proteins appear predominantly in rich-clubs, groups of human proteins that are strongly intertwined among each other. These assemblies of proteins may serve as an infection gateway, allowing the virus to take control of the human host by reaching protein pathways and diversified cellular functions in a pronounced and focused way. Particular transcription factors and protein kinases facilitate indirect interactions between HDFs and viral proteins. Discerning the entanglement of directly targeted and indirectly interacting proteins may uncover molecular and functional sites that can provide novel perspectives on the progression of HIV infection and highlight new avenues to fight this virus. PMID:20827298

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

NASA Astrophysics Data System (ADS)

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

2012-12-01

The Barrow area of northern Alaska is one of the most intensely researched locations in the Arctic. The Barrow Area Information Database (BAID, www.baidims.org) is a cyberinfrastructure (CI) that details much of the historic and extant research undertaken within in the Barrow region in a suite of interactive web-based mapping and information portals (geobrowsers). The BAID user community and target audience for BAID is diverse and includes research scientists, science logisticians, land managers, educators, students, and the general public. BAID contains information on more than 9,600 Barrow area research sites that extend back to the 1940's and more than 640 remote sensing images and geospatial datasets. In a web-based setting, users can zoom, pan, query, measure distance, and save or print maps and query results. Data are described with metadata that meet Federal Geographic Data Committee standards and are archived at the University Corporation for Atmospheric Research Earth Observing Laboratory (EOL) where non-proprietary BAID data can be freely downloaded. BAID has been used to: Optimize research site choice; Reduce duplication of science effort; Discover complementary and potentially detrimental research activities in an area of scientific interest; Re-establish historical research sites for resampling efforts assessing change in ecosystem structure and function over time; Exchange knowledge across disciplines and generations; Facilitate communication between western science and traditional ecological knowledge; Provide local residents access to science data that facilitates adaptation to arctic change; (and) Educate the next generation of environmental and computer scientists. This poster describes key activities that will be undertaken over the next three years to provide BAID users with novel software tools to interact with a current and diverse selection of information and data about the Barrow area. Key activities include: 1. Collecting data on research activities, generating geospatial data, and providing mapping support. 2. Maintaining, updating and innovating the existing suite of BAID geobrowsers. 3. Maintaining and updating aging server hardware supporting BAID. 4. Adding interoperability with other CI using workflows, controlled vocabularies and web services. 5. Linking BAID to data archives at the National Snow and Ice Data Center (NSIDC). 6. Developing a wireless sensor network that provides web based interaction with near-real time climate and other data. 7. Training next generation of environmental and computer scientists and conducting outreach.

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

NASA Astrophysics Data System (ADS)

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

2013-12-01

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

Arctic Research Mapping Application (ARMAP): 2D Maps and 3D Globes Support Arctic Science

NASA Astrophysics Data System (ADS)

Johnson, G.; Gaylord, A. G.; Brady, J. J.; Cody, R. P.; Aguilar, J. A.; Dover, M.; Garcia-Lavigne, D.; Manley, W.; Score, R.; Tweedie, C. E.

2007-12-01

The Arctic Research Mapping Application (ARMAP) is a suite of online services to provide support of Arctic science. These services include: a text based online search utility, 2D Internet Map Server (IMS); 3D globes and Open Geospatial Consortium (OGC) Web Map Services (WMS). With ARMAP's 2D maps and 3D globes, users can navigate to areas of interest, view a variety of map layers, and explore U.S. Federally funded research projects. Projects can be queried by location, year, funding program, discipline, and keyword. Links take you to specific information and other web sites associated with a particular research project. The Arctic Research Logistics Support Service (ARLSS) database is the foundation of ARMAP including US research funded by the National Science Foundation, National Aeronautics and Space Administration, National Oceanic and Atmospheric Administration, and the United States Geological Survey. Avoiding a duplication of effort has been a primary objective of the ARMAP project which incorporates best practices (e.g. Spatial Data Infrastructure and OGC standard web services and metadata) and off the shelf technologies where appropriate. The ARMAP suite provides tools for users of various levels of technical ability to interact with the data by importing the web services directly into their own GIS applications and virtual globes; performing advanced GIS queries; simply printing maps from a set of predefined images in the map gallery; browsing the layers in an IMS; or by choosing to "fly to" sites using a 3D globe. With special emphasis on the International Polar Year (IPY), ARMAP has targeted science planners, scientists, educators, and the general public. In sum, ARMAP goes beyond a simple map display to enable analysis, synthesis, and coordination of Arctic research. ARMAP may be accessed via the gateway web site at http://www.armap.org.

Elucidating the druggable interface of protein-protein interactions using fragment docking and coevolutionary analysis.

PubMed

Bai, Fang; Morcos, Faruck; Cheng, Ryan R; Jiang, Hualiang; Onuchic, José N

2016-12-13

Protein-protein interactions play a central role in cellular function. Improving the understanding of complex formation has many practical applications, including the rational design of new therapeutic agents and the mechanisms governing signal transduction networks. The generally large, flat, and relatively featureless binding sites of protein complexes pose many challenges for drug design. Fragment docking and direct coupling analysis are used in an integrated computational method to estimate druggable protein-protein interfaces. (i) This method explores the binding of fragment-sized molecular probes on the protein surface using a molecular docking-based screen. (ii) The energetically favorable binding sites of the probes, called hot spots, are spatially clustered to map out candidate binding sites on the protein surface. (iii) A coevolution-based interface interaction score is used to discriminate between different candidate binding sites, yielding potential interfacial targets for therapeutic drug design. This approach is validated for important, well-studied disease-related proteins with known pharmaceutical targets, and also identifies targets that have yet to be studied. Moreover, therapeutic agents are proposed by chemically connecting the fragments that are strongly bound to the hot spots.

Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development

PubMed Central

Kazemian, Majid; Pham, Hannah; Wolfe, Scot A.; Brodsky, Michael H.; Sinha, Saurabh

2013-01-01

Regulation of eukaryotic gene transcription is often combinatorial in nature, with multiple transcription factors (TFs) regulating common target genes, often through direct or indirect mutual interactions. Many individual examples of cooperative binding by directly interacting TFs have been identified, but it remains unclear how pervasive this mechanism is during animal development. Cooperative TF binding should be manifest in genomic sequences as biased arrangements of TF-binding sites. Here, we explore the extent and diversity of such arrangements related to gene regulation during Drosophila embryogenesis. We used the DNA-binding specificities of 322 TFs along with chromatin accessibility information to identify enriched spacing and orientation patterns of TF-binding site pairs. We developed a new statistical approach for this task, specifically designed to accurately assess inter-site spacing biases while accounting for the phenomenon of homotypic site clustering commonly observed in developmental regulatory regions. We observed a large number of short-range distance preferences between TF-binding site pairs, including examples where the preference depends on the relative orientation of the binding sites. To test whether these binding site patterns reflect physical interactions between the corresponding TFs, we analyzed 27 TF pairs whose binding sites exhibited short distance preferences. In vitro protein–protein binding experiments revealed that >65% of these TF pairs can directly interact with each other. For five pairs, we further demonstrate that they bind cooperatively to DNA if both sites are present with the preferred spacing. This study demonstrates how DNA-binding motifs can be used to produce a comprehensive map of sequence signatures for different mechanisms of combinatorial TF action. PMID:23847101

Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development.

PubMed

Kazemian, Majid; Pham, Hannah; Wolfe, Scot A; Brodsky, Michael H; Sinha, Saurabh

2013-09-01

Regulation of eukaryotic gene transcription is often combinatorial in nature, with multiple transcription factors (TFs) regulating common target genes, often through direct or indirect mutual interactions. Many individual examples of cooperative binding by directly interacting TFs have been identified, but it remains unclear how pervasive this mechanism is during animal development. Cooperative TF binding should be manifest in genomic sequences as biased arrangements of TF-binding sites. Here, we explore the extent and diversity of such arrangements related to gene regulation during Drosophila embryogenesis. We used the DNA-binding specificities of 322 TFs along with chromatin accessibility information to identify enriched spacing and orientation patterns of TF-binding site pairs. We developed a new statistical approach for this task, specifically designed to accurately assess inter-site spacing biases while accounting for the phenomenon of homotypic site clustering commonly observed in developmental regulatory regions. We observed a large number of short-range distance preferences between TF-binding site pairs, including examples where the preference depends on the relative orientation of the binding sites. To test whether these binding site patterns reflect physical interactions between the corresponding TFs, we analyzed 27 TF pairs whose binding sites exhibited short distance preferences. In vitro protein-protein binding experiments revealed that >65% of these TF pairs can directly interact with each other. For five pairs, we further demonstrate that they bind cooperatively to DNA if both sites are present with the preferred spacing. This study demonstrates how DNA-binding motifs can be used to produce a comprehensive map of sequence signatures for different mechanisms of combinatorial TF action.

Analysis of functional importance of binding sites in the Drosophila gap gene network model.

PubMed

Kozlov, Konstantin; Gursky, Vitaly V; Kulakovskiy, Ivan V; Dymova, Arina; Samsonova, Maria

2015-01-01

The statistical thermodynamics based approach provides a promising framework for construction of the genotype-phenotype map in many biological systems. Among important aspects of a good model connecting the DNA sequence information with that of a molecular phenotype (gene expression) is the selection of regulatory interactions and relevant transcription factor bindings sites. As the model may predict different levels of the functional importance of specific binding sites in different genomic and regulatory contexts, it is essential to formulate and study such models under different modeling assumptions. We elaborate a two-layer model for the Drosophila gap gene network and include in the model a combined set of transcription factor binding sites and concentration dependent regulatory interaction between gap genes hunchback and Kruppel. We show that the new variants of the model are more consistent in terms of gene expression predictions for various genetic constructs in comparison to previous work. We quantify the functional importance of binding sites by calculating their impact on gene expression in the model and calculate how these impacts correlate across all sites under different modeling assumptions. The assumption about the dual interaction between hb and Kr leads to the most consistent modeling results, but, on the other hand, may obscure existence of indirect interactions between binding sites in regulatory regions of distinct genes. The analysis confirms the previously formulated regulation concept of many weak binding sites working in concert. The model predicts a more or less uniform distribution of functionally important binding sites over the sets of experimentally characterized regulatory modules and other open chromatin domains.

Multigraph: Interactive Data Graphs on the Web

NASA Astrophysics Data System (ADS)

Phillips, M. B.

2010-12-01

Many aspects of geophysical science involve time dependent data that is often presented in the form of a graph. Considering that the web has become a primary means of communication, there are surprisingly few good tools and techniques available for presenting time-series data on the web. The most common solution is to use a desktop tool such as Excel or Matlab to create a graph which is saved as an image and then included in a web page like any other image. This technique is straightforward, but it limits the user to one particular view of the data, and disconnects the graph from the data in a way that makes updating a graph with new data an often cumbersome manual process. This situation is somewhat analogous to the state of mapping before the advent of GIS. Maps existed only in printed form, and creating a map was a laborious process. In the last several years, however, the world of mapping has experienced a revolution in the form of web-based and other interactive computer technologies, so that it is now commonplace for anyone to easily browse through gigabytes of geographic data. Multigraph seeks to bring a similar ease of access to time series data. Multigraph is a program for displaying interactive time-series data graphs in web pages that includes a simple way of configuring the appearance of the graph and the data to be included. It allows multiple data sources to be combined into a single graph, and allows the user to explore the data interactively. Multigraph lets users explore and visualize "data space" in the same way that interactive mapping applications such as Google Maps facilitate exploring and visualizing geography. Viewing a Multigraph graph is extremely simple and intuitive, and requires no instructions. Creating a new graph for inclusion in a web page involves writing a simple XML configuration file and requires no programming. Multigraph can read data in a variety of formats, and can display data from a web service, allowing users to "surf" through large data sets, downloading only those the parts of the data that are needed for display. Multigraph is currently in use on several web sites including the US Drought Portal (www.drought.gov), the NOAA Climate Services Portal (www.climate.gov), the Climate Reference Network (www.ncdc.noaa.gov/crn), NCDC's State of the Climate Report (www.ncdc.noaa.gov/sotc), and the US Forest Service's Forest Change Assessment Viewer (ews.forestthreats.org/NPDE/NPDE.html). More information about Multigraph is available from the web site www.multigraph.org. Interactive Graph of Global Temperature Anomalies from ClimateWatch Magazine (http://www.climatewatch.noaa.gov/2009/articles/climate-change-global-temperature)

Interaction between LSD and dopamine D2/3 binding sites in pig brain.

PubMed

Minuzzi, Luciano; Nomikos, George G; Wade, Mark R; Jensen, Svend B; Olsen, Aage K; Cumming, Paul

2005-06-15

The psychoactive properties of the hallucinogen LSD have frequently been attributed to high affinity interactions with serotonin 5HT2 receptors in brain. Possible effects of LSD on dopamine D2/3 receptor availability have not previously been investigated in living brain. Therefore, we used PET to map the binding potential (pB) of [11C]raclopride in brain of three pigs, first in a baseline condition, and again at 1 and 4 h after administration of LSD (2.5 microg/kg, i.v.). There was a progressive treatment effect in striatum, where the pB was significantly reduced by 19% at 4 h after LSD administration. Concomitant maps of cerebral blood flow did not reveal significant changes in perfusion during this interval. Subsequent in vitro studies showed that LSD displaced [3H]raclopride (2 nM) from pig brain cryostat sections with an IC50 of 275 nM according to a one-site model. Fitting of a two-site model to the data suggested the presence of a component of the displacement curves with a subnanomolar IC50, comprising 20% of the total [3H]raclopride binding. In microdialysis experiments, LSD at similar and higher doses did not evoke changes in the interstitial concentration of dopamine or its acidic metabolites in rat striatum. Together, these results are consistent with a direct interaction between LSD and a portion of dopamine D2/3 receptors in pig brain, possibly contributing to the psychopharmacology of LSD. (c) 2005 Wiley-Liss, Inc.

A Global Map of Lipid-Binding Proteins and Their Ligandability in Cells.

PubMed

Niphakis, Micah J; Lum, Kenneth M; Cognetta, Armand B; Correia, Bruno E; Ichu, Taka-Aki; Olucha, Jose; Brown, Steven J; Kundu, Soumajit; Piscitelli, Fabiana; Rosen, Hugh; Cravatt, Benjamin F

2015-06-18

Lipids play central roles in physiology and disease, where their structural, metabolic, and signaling functions often arise from interactions with proteins. Here, we describe a set of lipid-based chemical proteomic probes and their global interaction map in mammalian cells. These interactions involve hundreds of proteins from diverse functional classes and frequently occur at sites of drug action. We determine the target profiles for several drugs across the lipid-interaction proteome, revealing that its ligandable content extends far beyond traditionally defined categories of druggable proteins. In further support of this finding, we describe a selective ligand for the lipid-binding protein nucleobindin-1 (NUCB1) and show that this compound perturbs the hydrolytic and oxidative metabolism of endocannabinoids in cells. The described chemical proteomic platform thus provides an integrated path to both discover and pharmacologically characterize a wide range of proteins that participate in lipid pathways in cells. Copyright © 2015 Elsevier Inc. All rights reserved.

Thermodynamic Characterization of Hydration Sites from Integral Equation-Derived Free Energy Densities: Application to Protein Binding Sites and Ligand Series.

PubMed

Güssregen, Stefan; Matter, Hans; Hessler, Gerhard; Lionta, Evanthia; Heil, Jochen; Kast, Stefan M

2017-07-24

Water molecules play an essential role for mediating interactions between ligands and protein binding sites. Displacement of specific water molecules can favorably modulate the free energy of binding of protein-ligand complexes. Here, the nature of water interactions in protein binding sites is investigated by 3D RISM (three-dimensional reference interaction site model) integral equation theory to understand and exploit local thermodynamic features of water molecules by ranking their possible displacement in structure-based design. Unlike molecular dynamics-based approaches, 3D RISM theory allows for fast and noise-free calculations using the same detailed level of solute-solvent interaction description. Here we correlate molecular water entities instead of mere site density maxima with local contributions to the solvation free energy using novel algorithms. Distinct water molecules and hydration sites are investigated in multiple protein-ligand X-ray structures, namely streptavidin, factor Xa, and factor VIIa, based on 3D RISM-derived free energy density fields. Our approach allows the semiquantitative assessment of whether a given structural water molecule can potentially be targeted for replacement in structure-based design. Finally, PLS-based regression models from free energy density fields used within a 3D-QSAR approach (CARMa - comparative analysis of 3D RISM Maps) are shown to be able to extract relevant information for the interpretation of structure-activity relationship (SAR) trends, as demonstrated for a series of serine protease inhibitors.

Prediction of Protein-Protein Interaction Sites Using Electrostatic Desolvation Profiles

PubMed Central

Fiorucci, Sébastien; Zacharias, Martin

2010-01-01

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

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

PubMed Central

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

2013-01-01

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

Signatures of pleiotropy, economy and convergent evolution in a domain-resolved map of human-virus protein-protein interaction networks.

PubMed

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

2013-01-01

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

Interactive map communication: pilot study of the visual perceptions and preferences of public health practitioners.

PubMed

Koenig, A; Samarasundera, E; Cheng, T

2011-08-01

To conduct a pilot study into the comprehension and visualisation preferences of geographic information by public health practitioners (PHPs), particularly in the context of interactive, Internet-based atlases. Structured human-computer interaction interviews. Seven academia-based PHPs were interviewed as information service users based on a structured questionnaire to assess their understanding of geographic representations of morbidity data, and identify their visualisation preferences in a geographic information systems environment. Awareness of area-based deprivation indices and the Index of Multiple Deprivation 2007 health and disability domain was near-universal. However, novice users of disease maps had difficulties in interpreting data classifications, in understanding supplementary information in the form of box plots and histograms, and in making use of links between interactive tabular and cartographic information. Choices for colour plans when viewing maps showed little agreement between users, although pre-viewing comments showed preferences for red-blue diverging schema. PHPs new to geographic information would benefit from enhanced interpretive support documentation to meet their needs when using Internet-based, interactive public health atlases, which are rarely provided at such sites. Technical, software-related support alone is insufficient. Increased interaction between PHPs and mapmakers would be beneficial to maximise the potential of the current growth in interactive, electronic atlases, and improve geographic information support for public health decision-making and informing the wider public. Copyright © 2011 The Royal Society for Public Health. Published by Elsevier Ltd. All rights reserved.

Biochemical investigations and mapping of the calcium-binding sites of heparinase I from Flavobacterium heparinum.

PubMed

Shriver, Z; Liu, D; Hu, Y; Sasisekharan, R

1999-02-12

The heparinases from Flavobacterium heparinum are lyases that specifically cleave heparin-like glycosaminoglycans. Previously, amino acids located in the active site of heparinase I have been identified and mapped. In an effort to further understand the mechanism by which heparinase I cleaves its polymer substrate, we sought to understand the role of calcium, as a necessary cofactor, in the enzymatic activity of heparinase I. Specifically, we undertook a series of biochemical and biophysical experiments to answer the question of whether heparinase I binds to calcium and, if so, which regions of the protein are involved in calcium binding. Using the fluorescent calcium analog terbium, we found that heparinase I tightly bound divalent and trivalent cations. Furthermore, we established that this interaction was specific for ions that closely approximate the ionic radius of calcium. Through the use of the modification reagents N-ethyl-5-phenylisoxazolium-3'-sulfonate (Woodward's reagent K) and 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride, we showed that the interaction between heparinase I and calcium was essential for proper functioning of the enzyme. Preincubation with either calcium alone or calcium in the presence of heparin was able to protect the enzyme from inactivation by these modifying reagents. In addition, through mapping studies of Woodward's reagent K-modified heparinase I, we identified two putative calcium-binding sites, CB-1 (Glu207-Ala219) and CB-2 (Thr373-Arg384), in heparinase I that not only are specifically modified by Woodward's reagent K, leading to loss of enzymatic activity, but also conform to the calcium-coordinating consensus motif.

#WomenInSTEM: Making a Cleaner Future

ScienceCinema

Lindgren, Mallory

2018-01-16

Mallory Lindgren uses geographic information systems or GIS - a mapping software that she compares to "a real-life videogame" - to assess how various constraints, such as wetlands or an airport, may interact with potential renewable energy projects. Her aim is to site and design projects that can effectively co-exist with the surrounding environment.

Investigating Groundwater/Surface Water Interaction at the Diversion Dam Site: Report Documentary 2007-2008

DTIC Science & Technology

2011-05-01

operations, and soil properties. Key findings of this study indicate that soils within the study reach are conductive, with groundwater responding...16 3 Develop Detailed Map of Soils and Their Properties in Bosque Adjacent to...27 4 Evaluate Ecological Impact of River Levels, Soil Types, and Dam

#WomenInSTEM: Making a Cleaner Future

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lindgren, Mallory

2014-09-09

Mallory Lindgren uses geographic information systems or GIS - a mapping software that she compares to "a real-life videogame" - to assess how various constraints, such as wetlands or an airport, may interact with potential renewable energy projects. Her aim is to site and design projects that can effectively co-exist with the surrounding environment.

Learning about Palau. [CD-ROM].

ERIC Educational Resources Information Center

Pacific Resources for Education and Learning, Honolulu, HI.

This CD-ROM contains information about the Republic of Palau, a sovereign state in the Pacific Ocean. The CD-ROM contains full-color photos and video clips of selected sites and events on Palau; interactive maps of Palau, including land forms, places of cultural significance, and public schools; and a glossary of geographic, geological, and…

Protein protein interactions: organization, cooperativity and mapping in a bottom-up Systems Biology approach

NASA Astrophysics Data System (ADS)

Keskin, Ozlem; Ma, Buyong; Rogale, Kristina; Gunasekaran, K.; Nussinov, Ruth

2005-06-01

Understanding and ultimately predicting protein associations is immensely important for functional genomics and drug design. Here, we propose that binding sites have preferred organizations. First, the hot spots cluster within densely packed 'hot regions'. Within these regions, they form networks of interactions. Thus, hot spots located within a hot region contribute cooperatively to the stability of the complex. However, the contributions of separate, independent hot regions are additive. Moreover, hot spots are often already pre-organized in the unbound (free) protein states. Describing a binding site through independent local hot regions has implications for binding site definition, design and parametrization for prediction. The compactness and cooperativity emphasize the similarity between binding and folding. This proposition is grounded in computation and experiment. It explains why summation of the interactions may over-estimate the stability of the complex. Furthermore, statistically, charge-charge coupling of the hot spots is disfavored. However, since within the highly packed regions the solvent is screened, the electrostatic contributions are strengthened. Thus, we propose a new description of protein binding sites: a site consists of (one or a few) self-contained cooperative regions. Since the residue hot spots are those conserved by evolution, proteins binding multiple partners at the same sites are expected to use all or some combination of these regions.

Memory matters: influence from a cognitive map on animal space use.

PubMed

Gautestad, Arild O

2011-10-21

A vertebrate individual's cognitive map provides a capacity for site fidelity and long-distance returns to favorable patches. Fractal-geometrical analysis of individual space use based on collection of telemetry fixes makes it possible to verify the influence of a cognitive map on the spatial scatter of habitat use and also to what extent space use has been of a scale-specific versus a scale-free kind. This approach rests on a statistical mechanical level of system abstraction, where micro-scale details of behavioral interactions are coarse-grained to macro-scale observables like the fractal dimension of space use. In this manner, the magnitude of the fractal dimension becomes a proxy variable for distinguishing between main classes of habitat exploration and site fidelity, like memory-less (Markovian) Brownian motion and Levy walk and memory-enhanced space use like Multi-scaled Random Walk (MRW). In this paper previous analyses are extended by exploring MRW simulations under three scenarios: (1) central place foraging, (2) behavioral adaptation to resource depletion (avoidance of latest visited locations) and (3) transition from MRW towards Levy walk by narrowing memory capacity to a trailing time window. A generalized statistical-mechanical theory with the power to model cognitive map influence on individual space use will be important for statistical analyses of animal habitat preferences and the mechanics behind site fidelity and home ranges. Copyright © 2011 Elsevier Ltd. All rights reserved.

The GLIMS Glacier Database

NASA Astrophysics Data System (ADS)

Raup, B. H.; Khalsa, S. S.; Armstrong, R.

2007-12-01

The Global Land Ice Measurements from Space (GLIMS) project has built a geospatial and temporal database of glacier data, composed of glacier outlines and various scalar attributes. These data are being derived primarily from satellite imagery, such as from ASTER and Landsat. Each "snapshot" of a glacier is from a specific time, and the database is designed to store multiple snapshots representative of different times. We have implemented two web-based interfaces to the database; one enables exploration of the data via interactive maps (web map server), while the other allows searches based on text-field constraints. The web map server is an Open Geospatial Consortium (OGC) compliant Web Map Server (WMS) and Web Feature Server (WFS). This means that other web sites can display glacier layers from our site over the Internet, or retrieve glacier features in vector format. All components of the system are implemented using Open Source software: Linux, PostgreSQL, PostGIS (geospatial extensions to the database), MapServer (WMS and WFS), and several supporting components such as Proj.4 (a geographic projection library) and PHP. These tools are robust and provide a flexible and powerful framework for web mapping applications. As a service to the GLIMS community, the database contains metadata on all ASTER imagery acquired over glacierized terrain. Reduced-resolution of the images (browse imagery) can be viewed either as a layer in the MapServer application, or overlaid on the virtual globe within Google Earth. The interactive map application allows the user to constrain by time what data appear on the map. For example, ASTER or glacier outlines from 2002 only, or from Autumn in any year, can be displayed. The system allows users to download their selected glacier data in a choice of formats. The results of a query based on spatial selection (using a mouse) or text-field constraints can be downloaded in any of these formats: ESRI shapefiles, KML (Google Earth), MapInfo, GML (Geography Markup Language) and GMT (Generic Mapping Tools). This "clip-and-ship" function allows users to download only the data they are interested in. Our flexible web interfaces to the database, which includes various support layers (e.g. a layer to help collaborators identify satellite imagery over their region of expertise) will facilitate enhanced analysis to be undertaken on glacier systems, their distribution, and their impacts on other Earth systems.

Unmanned Aerial Vehicle (UAV) Data Acquisition for Archaeological Site Identification and Mapping

NASA Astrophysics Data System (ADS)

Handayani, W.; Ayuningtyas, E. A.; Candra R, F. S.; Arif S, B.; Argadyanto, B.

2017-12-01

Archaeological sites as part of human history and located around community are important to be preserved for connecting historical information from generation to generation. Mapping of archaeological sites can be done as one of preservation efforts. Yogyakarta has several archaeological sites such as Pleret Palace, the former royal palace of Mataram Islam in the 16th Century. Data limitations and the difficulty of reconstructing the site sketches into a map become obstacles in archaeological sites mapping. Unmanned Aerial Vehicle (UAV) can be an alternative of high-resolution spatial data acquisition for detail mapping, including archaeological sites mapping. This study aims to see how far the UAV acquisition results can be used for Archaeological Site mapping in Pleret Palace. Data acquisition using UAV generated to mosaic orthophoto, Digital Surface Model (DSM), and Digital Terrain Model (DTM). Archaeological sites identified using DTM and matched with site sketch made by Cultural Agency. From these data, it can be recognized some relics form, such as palace fortress, moats and canals, and also dikes of Segarayasa. This research is expected to be a reference in archaeological site mapping using detailed spatial data, especially UAV. Furthermore, it can be obtained archaeological site map close to real condition; as well as archaeological sites preservation in Indonesia.

Mapping hydration dynamics and coupled water-protein fluctuations around a protein surface

NASA Astrophysics Data System (ADS)

Zhang, Luyuan; Wang, Lijuan; Kao, Ya-Ting; Qiu, Weihong; Yang, Yi; Okobiah, Oghaghare; Zhong, Dongping

2009-03-01

Elucidation of the molecular mechanism of water-protein interactions is critical to understanding many fundamental aspects of protein science, such as protein folding and misfolding and enzyme catalysis. We recently carried out a global mapping of protein-surface hydration dynamics around a globular α-helical protein apomyoglobin. The intrinsic optical probe tryptophan was employed to scan the protein surface one at a time by site-specific mutagenesis. With femtosecond resolution, we mapped out the dynamics of water-protein interactions with more than 20 mutants and for two states, native and molten globular. A robust bimodal distribution of time scales was observed, representing two types of water motions: local relaxation and protein-coupled fluctuations. The time scales show a strong correlation with the local protein structural rigidity and chemical identity. We also resolved two distinct contributions to the overall Stokes-shifts from the two time scales. These results are significant to understanding the role of hydration water on protein structural stability, dynamics and function.

THREaD Mapper Studio: a novel, visual web server for the estimation of genetic linkage maps

PubMed Central

Cheema, Jitender; Ellis, T. H. Noel; Dicks, Jo

2010-01-01

The estimation of genetic linkage maps is a key component in plant and animal research, providing both an indication of the genetic structure of an organism and a mechanism for identifying candidate genes associated with traits of interest. Because of this importance, several computational solutions to genetic map estimation exist, mostly implemented as stand-alone software packages. However, the estimation process is often largely hidden from the user. Consequently, problems such as a program crashing may occur that leave a user baffled. THREaD Mapper Studio (http://cbr.jic.ac.uk/threadmapper) is a new web site that implements a novel, visual and interactive method for the estimation of genetic linkage maps from DNA markers. The rationale behind the web site is to make the estimation process as transparent and robust as possible, while also allowing users to use their expert knowledge during analysis. Indeed, the 3D visual nature of the tool allows users to spot features in a data set, such as outlying markers and potential structural rearrangements that could cause problems with the estimation procedure and to account for them in their analysis. Furthermore, THREaD Mapper Studio facilitates the visual comparison of genetic map solutions from third party software, aiding users in developing robust solutions for their data sets. PMID:20494977

Experimental mapping of DNA duplex shape enabled by global lineshape analyses of a nucleotide-independent nitroxide probe

PubMed Central

Ding, Yuan; Zhang, Xiaojun; Tham, Kenneth W.; Qin, Peter Z.

2014-01-01

Sequence-dependent variation in structure and dynamics of a DNA duplex, collectively referred to as ‘DNA shape’, critically impacts interactions between DNA and proteins. Here, a method based on the technique of site-directed spin labeling was developed to experimentally map shapes of two DNA duplexes that contain response elements of the p53 tumor suppressor. An R5a nitroxide spin label, which was covalently attached at a specific phosphate group, was scanned consecutively through the DNA duplex. X-band continuous-wave electron paramagnetic resonance spectroscopy was used to monitor rotational motions of R5a, which report on DNA structure and dynamics at the labeling site. An approach based on Pearson's coefficient analysis was developed to collectively examine the degree of similarity among the ensemble of R5a spectra. The resulting Pearson's coefficients were used to generate maps representing variation of R5a mobility along the DNA duplex. The R5a mobility maps were found to correlate with maps of certain DNA helical parameters, and were capable of revealing similarity and deviation in the shape of the two closely related DNA duplexes. Collectively, the R5a probe and the Pearson's coefficient-based lineshape analysis scheme yielded a generalizable method for examining sequence-dependent DNA shapes. PMID:25092920

Magnetic properties and energy-mapping analysis.

PubMed

Xiang, Hongjun; Lee, Changhoon; Koo, Hyun-Joo; Gong, Xingao; Whangbo, Myung-Hwan

2013-01-28

The magnetic energy levels of a given magnetic solid are closely packed in energy because the interactions between magnetic ions are weak. Thus, in describing its magnetic properties, one needs to generate its magnetic energy spectrum by employing an appropriate spin Hamiltonian. In this review article we discuss how to determine and specify a necessary spin Hamiltonian in terms of first principles electronic structure calculations on the basis of energy-mapping analysis and briefly survey important concepts and phenomena that one encounters in reading the current literature on magnetic solids. Our discussion is given on a qualitative level from the perspective of magnetic energy levels and electronic structures. The spin Hamiltonian appropriate for a magnetic system should be based on its spin lattice, i.e., the repeat pattern of its strong magnetic bonds (strong spin exchange paths), which requires one to evaluate its Heisenberg spin exchanges on the basis of energy-mapping analysis. Other weaker energy terms such as Dzyaloshinskii-Moriya (DM) spin exchange and magnetocrystalline anisotropy energies, which a spin Hamiltonian must include in certain cases, can also be evaluated by performing energy-mapping analysis. We show that the spin orientation of a transition-metal magnetic ion can be easily explained by considering its split d-block levels as unperturbed states with the spin-orbit coupling (SOC) as perturbation, that the DM exchange between adjacent spin sites can become comparable in strength to the Heisenberg spin exchange when the two spin sites are not chemically equivalent, and that the DM interaction between rare-earth and transition-metal cations is governed largely by the magnetic orbitals of the rare-earth cation.

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

PubMed Central

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

2012-01-01

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

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

PubMed

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

2007-05-22

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 K(m) 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.

New Near-Real Time Monitoring of the Ionosphere over Europe Available On-line

NASA Astrophysics Data System (ADS)

Chevalier, J. M.; Bergeot, N.; Bruyninx, C.; Pottiaux, E.; Aerts, W.; Baire, Q.; Legrand, J.; Defraigne, P.

2012-04-01

With the beginning of the 24th Solar cycle, the increased Solar activity requires having a close eye on the ionosphere for better understanding Space Weather physics and its effects on radio communications. In that frame, near-real time ionospheric models over Europe are now routinely generated at the Royal Observatory of Belgium (ROB). These models are made available to the public through new interactive web pages at the web site of the GNSS team (www.gnss.be) and the Solar Influences Data Analysis Center (www.sidc.be) of ROB. The models are ionospheric Vertical Total Electron Content (VTEC) maps estimated every 15 minutes on a 0.5°x0.5° grid. They use the high-rate GPS observations of the real-time stations in the EUREF Permanent Network (EPN) provided by the ROB NTRIP broadcaster. The maps are published on the ROB web site with a latency of 7-15 minutes with respect to the last GPS measurement included in the 15-minute observation files. In a first step, this paper presents the processing strategy used to generate the VTEC maps: input data, parameter estimation, data cleaning and interpolation method. In addition, the tools developed to further exploit the product are introduced, e.g. on-demand animated VTEC maps. In a second step, the VTEC maps are compared with external ionospheric products and models such as Global Ionospheric Maps and IRI 2011. These new near-real time VTEC maps will allow any user within the geographical scope of the maps to estimate in near-real time the ionospheric delay induced along the signal of any observed satellite. In the future, the web site will continuously be updated in response to evolving user needs. This paper opens doors to discussions with the user community to target their needs.

Structural analyses of EBER1 and EBER2 ribonucleoprotein particles present in Epstein-Barr virus-infected cells.

PubMed Central

Glickman, J N; Howe, J G; Steitz, J A

1988-01-01

The ribonucleoprotein (RNP) particles containing the Epstein-Barr virus-associated small RNAs EBER1 and EBER2 were analyzed to determine their RNA secondary structures and sites of RNA-protein interaction. The secondary structures were probed with nucleases and by chemical modification with single-strand-specific reagents, and the sites of modification or cleavage were mapped by primer extension. These data were used to develop secondary structures for the two RNAs, and likely sites of close RNA-protein contact were identified by comparing modification patterns for naked RNA and RNA in RNP particles. In addition, sites of interaction between each Epstein-Barr virus-encoded RNA (EBER) and the La antigen were identified by analyzing RNA fragments resistant to digestion by RNase A or T1 after immunoprecipitation by an anti-La serum sample from a lupus patient. Our results confirm earlier findings that the La protein binds to the 3' terminus of each molecule. Possible functions for the EBER RNPs are discussed. Images PMID:2828685

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

PubMed

Fiorucci, Sébastien; Zacharias, Martin

2010-05-19

Protein-protein complex formation involves removal of water from the interface region. Surface regions with a small free energy penalty for water removal or desolvation may correspond to preferred interaction sites. A method to calculate the electrostatic free energy of placing a neutral low-dielectric probe at various protein surface positions has been designed and applied to characterize putative interaction sites. Based on solutions of the finite-difference Poisson equation, this method also includes long-range electrostatic contributions and the protein solvent boundary shape in contrast to accessible-surface-area-based solvation energies. Calculations on a large set of proteins indicate that in many cases (>90%), the known binding site overlaps with one of the six regions of lowest electrostatic desolvation penalty (overlap with the lowest desolvation region for 48% of proteins). Since the onset of electrostatic desolvation occurs even before direct protein-protein contact formation, it may help guide proteins toward the binding region in the final stage of complex formation. It is interesting that the probe desolvation properties associated with residue types were found to depend to some degree on whether the residue was outside of or part of a binding site. The probe desolvation penalty was on average smaller if the residue was part of a binding site compared to other surface locations. Applications to several antigen-antibody complexes demonstrated that the approach might be useful not only to predict protein interaction sites in general but to map potential antigenic epitopes on protein surfaces. Copyright (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Lysine Methylation of Nuclear Co-repressor Receptor Interacting Protein 140

PubMed Central

Huq, MD Mostaqul; Ha, Sung Gil; Barcelona, Helene; Wei, Li-Na

2009-01-01

Receptor interacting protein 140 (RIP140) undergoes extensive posttranslational modifications (PTMs), including phosphorylation, acetylation, arginine methylation, and pyridoxylation. PTMs affect its sub-cellular distribution, protein-protein interaction, and biological activity in adipocyte differentiation. Arginine methylation on Arg240, Arg650, and Arg948 suppresses the repressive activity of RIP140. Here we find that endogenous RIP140 in differentiated 3T3-L1 cells is also modified by lysine methylation. Three lysine residues, Lys591, Lys653, and Lys757 are mapped as potential methylation sites by mass spectrometry. Site-directed mutagenesis study shows that lysine methylation enhances its gene repressive activity. Mutation of lysine methylation sites enhances arginine methylation, while mutation on arginine methylation sites has little effect on its lysine methylation, suggesting a relationship between lysine methylation and arginine methylation. Kinetic analysis of PTMs of endogenous RIP140 in differentiated 3T3-L1 cells demonstrates sequential modifications on RIP140, initiated from constitutive lysine methylation, followed by increased arginine methylation later in differentiation. This study reveals a potential hierarchy of modifications, at least for lysine and arginine methylation, which bi-directionally regulate the functionality of a non-histone protein. PMID:19216533

Agricultural Census 2012: Publishing Mashable GIS Big Data Services

NASA Astrophysics Data System (ADS)

Mueller, R.

2014-12-01

The 2012 Agricultural Census was released by the US Department of Agriculture (USDA) on May 2nd 2014; published on a quinquennial basis covering all facets of American production agriculture. The Agricultural Census is a comprehensive source of uniform published agricultural data for every state and county in the US. This is the first Agricultural Census that is disseminated with web mapping services using REST APIs. USDA developed an open GIS mashable web portal that depicts over 250 maps on Crops and Plants, Economics, Farms, Livestock and Animals, and Operators. These mapping services written in JavaScript replace the traditional static maps published as the Ag Atlas. Web users can now visualize, interact, query, and download the Agricultural Census data in a means not previously discoverable. Stakeholders will now be able to leverage this data for activities such as community planning, agribusiness location suitability analytics, availability of loans/funds, service center locations and staffing, and farm programs and policies. Additional sites serving compatible mashable USDA Big Data web services are as follows: The Food Environment Atlas, The Atlas of Rural and Small-Town America, The Farm Program Atlas, SNAP Data System, CropScape, and VegScape. All portals use a similar data organization scheme of "Categories" and "Maps" providing interactive mashable web services for agricultural stakeholders to exploit.

Binding site exploration of CCR5 using in silico methodologies: a 3D-QSAR approach.

PubMed

Gadhe, Changdev G; Kothandan, Gugan; Cho, Seung Joo

2013-01-01

Chemokine receptor 5 (CCR5) is an important receptor used by human immunodeficiency virus type 1 (HIV-1) to gain viral entry into host cell. In this study, we used a combined approach of comparative modeling, molecular docking, and three dimensional quantitative structure activity relationship (3D-QSAR) analyses to elucidate detailed interaction of CCR5 with their inhibitors. Docking study of the most potent inhibitor from a series of compounds was done to derive the bioactive conformation. Parameters such as random selection, rational selection, different charges and grid spacing were utilized in the model development to check their performance on the model predictivity. Final comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) models were chosen based on the rational selection method, Gasteiger-Hückel charges and a grid spacing of 0.5 Å. Rational model for CoMFA (q(2) = 0.722, r(2) = 0.884, Q(2) = 0.669) and CoMSIA (q(2) = 0.712, r(2) = 0.825, Q(2) = 0.522) was obtained with good statistics. Mapping of contour maps onto CCR5 interface led us to better understand of the ligand-protein interaction. Docking analysis revealed that the Glu283 is crucial for interaction. Two new amino acid residues, Tyr89 and Thr167 were identified as important in ligand-protein interaction. No site directed mutagenesis studies on these residues have been reported.

Mapping the miRNA interactome by crosslinking ligation and sequencing of hybrids (CLASH)

PubMed Central

Helwak, Aleksandra; Tollervey, David

2014-01-01

RNA-RNA interactions play critical roles in many cellular processes but studying them is difficult and laborious. Here, we describe an experimental procedure, termed crosslinking ligation and sequencing of hybrids (CLASH), which allows high-throughput identification of sites of RNA-RNA interaction. During CLASH, a tagged bait protein is UV crosslinked in vivo to stabilise RNA interactions and purified under denaturing conditions. RNAs associated with the bait protein are partially truncated, and the ends of RNA-duplexes are ligated together. Following linker addition, cDNA library preparation and high-throughput sequencing, the ligated duplexes give rise to chimeric cDNAs, which unambiguously identify RNA-RNA interaction sites independent of bioinformatic predictions. This protocol is optimized for studying miRNA targets bound by Argonaute proteins, but should be easily adapted for other RNA-binding proteins and classes of RNA. The protocol requires around 5 days to complete, excluding the time required for high-throughput sequencing and bioinformatic analyses. PMID:24577361

Survey of protein–DNA interactions in Aspergillus oryzae on a genomic scale

PubMed Central

Wang, Chao; Lv, Yangyong; Wang, Bin; Yin, Chao; Lin, Ying; Pan, Li

2015-01-01

The genome-scale delineation of in vivo protein–DNA interactions is key to understanding genome function. Only ∼5% of transcription factors (TFs) in the Aspergillus genus have been identified using traditional methods. Although the Aspergillus oryzae genome contains >600 TFs, knowledge of the in vivo genome-wide TF-binding sites (TFBSs) in aspergilli remains limited because of the lack of high-quality antibodies. We investigated the landscape of in vivo protein–DNA interactions across the A. oryzae genome through coupling the DNase I digestion of intact nuclei with massively parallel sequencing and the analysis of cleavage patterns in protein–DNA interactions at single-nucleotide resolution. The resulting map identified overrepresented de novo TF-binding motifs from genomic footprints, and provided the detailed chromatin remodeling patterns and the distribution of digital footprints near transcription start sites. The TFBSs of 19 known Aspergillus TFs were also identified based on DNase I digestion data surrounding potential binding sites in conjunction with TF binding specificity information. We observed that the cleavage patterns of TFBSs were dependent on the orientation of TF motifs and independent of strand orientation, consistent with the DNA shape features of binding motifs with flanking sequences. PMID:25883143

Interplay of signal recognition particle and trigger factor at L23 near the nascent chain exit site on the Escherichia coli ribosome

PubMed Central

Ullers, Ronald S.; Houben, Edith N.G.; Raine, Amanda; ten Hagen-Jongman, Corinne M.; Ehrenberg, Måns; Brunner, Joseph; Oudega, Bauke; Harms, Nellie; Luirink, Joen

2003-01-01

As newly synthesized polypeptides emerge from the ribosome, they interact with chaperones and targeting factors that assist in folding and targeting to the proper location in the cell. In Escherichia coli, the chaperone trigger factor (TF) binds to nascent polypeptides early in biosynthesis facilitated by its affinity for the ribosomal proteins L23 and L29 that are situated around the nascent chain exit site on the ribosome. The targeting factor signal recognition particle (SRP) interacts specifically with the signal anchor (SA) sequence in nascent inner membrane proteins (IMPs). Here, we have used photocross-linking to map interactions of the SA sequence in a short, in vitro–synthesized, nascent IMP. Both TF and SRP were found to interact with the SA with partially overlapping binding specificity. In addition, extensive contacts with L23 and L29 were detected. Both purified TF and SRP could be cross-linked to L23 on nontranslating ribosomes with a competitive advantage for SRP. The results suggest a role for L23 in the targeting of IMPs as an attachment site for TF and SRP that is close to the emerging nascent chain. PMID:12756233

Multiple Antigenic Sites Are Involved in Blocking the Interaction of GII.4 Norovirus Capsid with ABH Histo-Blood Group Antigens

PubMed Central

Parra, Gabriel I.; Abente, Eugenio J.; Sandoval-Jaime, Carlos; Sosnovtsev, Stanislav V.; Bok, Karin

2012-01-01

Noroviruses are major etiological agents of acute viral gastroenteritis. In 2002, a GII.4 variant (Farmington Hills cluster) spread so rapidly in the human population that it predominated worldwide and displaced previous GII.4 strains. We developed and characterized a panel of six monoclonal antibodies (MAbs) directed against the capsid protein of a Farmington Hills-like GII.4 norovirus strain that was associated with a large hospital outbreak in Maryland in 2004. The six MAbs reacted with high titers against homologous virus-like particles (VLPs) by enzyme-linked immunoassay but did not react with denatured capsid protein in immunoblots. The expression and self-assembly of newly developed genogroup I/II chimeric VLPs showed that five MAbs bound to the GII.4 protruding (P) domain of the capsid protein, while one recognized the GII.4 shell (S) domain. Cross-competition assays and mutational analyses showed evidence for at least three distinct antigenic sites in the P domain and one in the S domain. MAbs that mapped to the P domain but not the S domain were able to block the interaction of VLPs with ABH histo-blood group antigens (HBGA), suggesting that multiple antigenic sites of the P domain are involved in HBGA blocking. Further analysis showed that two MAbs mapped to regions of the capsid that had been associated with the emergence of new GII.4 variants. Taken together, our data map antibody and HBGA carbohydrate binding to proximal regions of the norovirus capsid, showing that evolutionary pressures on the norovirus capsid protein may affect both antigenic and carbohydrate recognition phenotypes. PMID:22532688

The N-terminus of the human copper transporter 1 (hCTR1) is localized extracellularly, and interacts with itself.

PubMed Central

Klomp, Adriana E M; Juijn, Jenneke A; van der Gun, Linda T M; van den Berg, Inge E T; Berger, Ruud; Klomp, Leo W J

2003-01-01

We have used indirect immunofluorescense studies and glycosylation-site insertion and deletion mapping to characterize the topology of human copper transporter 1 (hCTR1), the putative human high-affinity copper-import protein. Both approaches indicated that hCTR1 contains three transmembrane domains and that the N-terminus of hCTR1, which contains several putative copper-binding sites, is localized extracellularly, whereas the C-terminus is exposed to the cytosol. Based on previous observations that CTR1 proteins form high-molecular-mass complexes, we investigated directly whether CTR1 proteins interact with themselves. Yeast two-hybrid studies showed that interaction of yeast, mouse, rat and human CTR1 occurs at the sites of their N-terminal domains, and is not dependent on the copper concentration in the growth media. Analysis of deletion constructs indicated that multiple regions in the N-terminus are essential for this self-interaction. In contrast, the N-terminal tail of the presumed low-affinity copper transporter, hCTR2, does not interact with itself. Taken together, these results suggest that CTR1 spans the membrane at least six times, permitting formation of a channel, which is consistent with its proposed role as a copper transporter. PMID:12466020

Cross-neutralizing human anti-poliovirus antibodies bind the recognition site for cellular receptor

PubMed Central

Chen, Zhaochun; Fischer, Elizabeth R.; Kouiavskaia, Diana; Hansen, Bryan T.; Ludtke, Steven J.; Bidzhieva, Bella; Makiya, Michelle; Agulto, Liane; Purcell, Robert H.; Chumakov, Konstantin

2013-01-01

Most structural information about poliovirus interaction with neutralizing antibodies was obtained in the 1980s in studies of mouse monoclonal antibodies. Recently we have isolated a number of human/chimpanzee anti-poliovirus antibodies and demonstrated that one of them, MAb A12, could neutralize polioviruses of both serotypes 1 and 2. This communication presents data on isolation of an additional cross-neutralizing antibody (F12) and identification of a previously unknown epitope on the surface of poliovirus virions. Epitope mapping was performed by sequencing of antibody-resistant mutants and by cryo-EM of complexes of virions with Fab fragments. The results have demonstrated that both cross-neutralizing antibodies bind the site located at the bottom of the canyon surrounding the fivefold axis of symmetry that was previously shown to interact with cellular poliovirus receptor CD155. However, the same antibody binds to serotypes 1 and 2 through different specific interactions. It was also shown to interact with type 3 poliovirus, albeit with about 10-fold lower affinity, insufficient for effective neutralization. Antibody interaction with the binding site of the cellular receptor may explain its broad reactivity and suggest that further screening or antibody engineering could lead to a universal antibody capable of neutralizing all three serotypes of poliovirus. PMID:24277851

High-Resolution Coarse-Grained Modeling Using Oriented Coarse-Grained Sites.

PubMed

Haxton, Thomas K

2015-03-10

We introduce a method to bring nearly atomistic resolution to coarse-grained models, and we apply the method to proteins. Using a small number of coarse-grained sites (about one per eight atoms) but assigning an independent three-dimensional orientation to each site, we preferentially integrate out stiff degrees of freedom (bond lengths and angles, as well as dihedral angles in rings) that are accurately approximated by their average values, while retaining soft degrees of freedom (unconstrained dihedral angles) mostly responsible for conformational variability. We demonstrate that our scheme retains nearly atomistic resolution by mapping all experimental protein configurations in the Protein Data Bank onto coarse-grained configurations and then analytically backmapping those configurations back to all-atom configurations. This roundtrip mapping throws away all information associated with the eliminated (stiff) degrees of freedom except for their average values, which we use to construct optimal backmapping functions. Despite the 4:1 reduction in the number of degrees of freedom, we find that heavy atoms move only 0.051 Å on average during the roundtrip mapping, while hydrogens move 0.179 Å on average, an unprecedented combination of efficiency and accuracy among coarse-grained protein models. We discuss the advantages of such a high-resolution model for parametrizing effective interactions and accurately calculating observables through direct or multiscale simulations.

iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions

PubMed Central

Briese, Michael; Zarnack, Kathi; Luscombe, Nicholas M.; Rot, Gregor; Zupan, Blaž; Curk, Tomaž; Ule, Jernej

2010-01-01

The regulation of alternative splicing involves interactions between RNA-binding proteins and pre-mRNA positions close to the splice sites. T-cell intracellular antigen 1 (TIA1) and TIA1-like 1 (TIAL1) locally enhance exon inclusion by recruiting U1 snRNP to 5′ splice sites. However, effects of TIA proteins on splicing of distal exons have not yet been explored. We used UV-crosslinking and immunoprecipitation (iCLIP) to find that TIA1 and TIAL1 bind at the same positions on human RNAs. Binding downstream of 5′ splice sites was used to predict the effects of TIA proteins in enhancing inclusion of proximal exons and silencing inclusion of distal exons. The predictions were validated in an unbiased manner using splice-junction microarrays, RT-PCR, and minigene constructs, which showed that TIA proteins maintain splicing fidelity and regulate alternative splicing by binding exclusively downstream of 5′ splice sites. Surprisingly, TIA binding at 5′ splice sites silenced distal cassette and variable-length exons without binding in proximity to the regulated alternative 3′ splice sites. Using transcriptome-wide high-resolution mapping of TIA-RNA interactions we evaluated the distal splicing effects of TIA proteins. These data are consistent with a model where TIA proteins shorten the time available for definition of an alternative exon by enhancing recognition of the preceding 5′ splice site. Thus, our findings indicate that changes in splicing kinetics could mediate the distal regulation of alternative splicing. PMID:21048981

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

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

O-GlcNAc site-mapping of liver X receptor-α and O-GlcNAc transferase.

PubMed

Fan, Qiong; Moen, Anders; Anonsen, Jan Haug; Bindesbøll, Christian; Sæther, Thomas; Carlson, Cathrine Rein; Grønning-Wang, Line M

2018-05-05

The Liver X Receptor α (LXRα) belongs to the nuclear receptor superfamily and plays an essential role in regulating cholesterol, lipid and glucose metabolism and inflammatory responses. We have previously shown that LXRα is post-translationally modified by O-linked β-N-acetyl-glucosamine (O-GlcNAc) with increased transcriptional activity. Moreover, we showed that LXRα associates with O-GlcNAc transferase (OGT) in vitro and in vivo in mouse liver. In this study, we report that human LXRα is O-GlcNAc modified in its N-terminal domain (NTD) by identifying a specific O-GlcNAc site S49 and a novel O-GlcNAc modified peptide 20 LWKPGAQDASSQAQGGSSCILRE 42 . However, O-GlcNAc site-mutations did not modulate LXRα transactivation of selected target gene promoters in vitro. Peptide array and co-immunoprecipitation assays demonstrate that LXRα interacts with OGT in its NTD and ligand-binding domain (LBD) in a ligand-independent fashion. Moreover, we map two new O-GlcNAc sites in the longest OGT isoform (ncOGT): S437 in the tetratricopeptide repeat (TPR) 13 domain and T1043 in the far C-terminus, and a new O-GlcNAc modified peptide (amino acids 826-832) in the intervening region (Int-D) within the catalytic domain. We also map four new O-GlcNAc sites in the short isoform sOGT: S391, T393, S399 and S437 in the TPRs 11-13 domain. Future studies will reveal the biological role of identified O-GlcNAc sites in LXRα and OGT. Copyright © 2018 Elsevier Inc. All rights reserved.

Geovisualization in the HydroProg web map service

NASA Astrophysics Data System (ADS)

Spallek, Waldemar; Wieczorek, Malgorzata; Szymanowski, Mariusz; Niedzielski, Tomasz; Swierczynska, Malgorzata

2016-04-01

The HydroProg system, built at the University of Wroclaw (Poland) in frame of the research project no. 2011/01/D/ST10/04171 financed by the National Science Centre of Poland, has been designed for computing predictions of river stages in real time on a basis of multimodelling. This experimental system works on the upper Nysa Klodzka basin (SW Poland) above the gauge in the town of Bardo, with the catchment area of 1744 square kilometres. The system operates in association with the Local System for Flood Monitoring of Klodzko County (LSOP), and produces hydrograph prognoses as well as inundation predictions. For presenting the up-to-date predictions and their statistics in the online mode, the dedicated real-time web map service has been designed. Geovisualisation in the HydroProg map service concerns: interactive maps of study area, interactive spaghetti hydrograms of water level forecasts along with observed river stages, animated images of inundation. The LSOP network offers a high spatial and temporal resolution of observations, as the length of the sampling interval is equal to 15 minutes. The main environmental elements related to hydrological modelling are shown on the main map. This includes elevation data (hillshading and hypsometric tints), rivers and reservoirs as well as catchment boundaries. Furthermore, we added main towns, roads as well as political and administrative boundaries for better map understanding. The web map was designed as a multi-scale representation, with levels of detail and zooming according to scales: 1:100 000, 1:250 000 and 1:500 000. Observations of water level in LSOP are shown on interactive hydrographs for each gauge. Additionally, predictions and some of their statistical characteristics (like prediction errors and Nash-Sutcliffe efficiency) are shown for selected gauges. Finally, predictions of inundation are presented on animated maps which have been added for four experimental sites. The HydroProg system is a strictly scientific project, but the web map service has been designed for all web users. The main objective of the paper is to present the design process of the web map service, following the cartographic and graphic principles.

Hybrid incompatibility arises in a sequence-based bioenergetic model of transcription factor binding.

PubMed

Tulchinsky, Alexander Y; Johnson, Norman A; Watt, Ward B; Porter, Adam H

2014-11-01

Postzygotic isolation between incipient species results from the accumulation of incompatibilities that arise as a consequence of genetic divergence. When phenotypes are determined by regulatory interactions, hybrid incompatibility can evolve even as a consequence of parallel adaptation in parental populations because interacting genes can produce the same phenotype through incompatible allelic combinations. We explore the evolutionary conditions that promote and constrain hybrid incompatibility in regulatory networks using a bioenergetic model (combining thermodynamics and kinetics) of transcriptional regulation, considering the bioenergetic basis of molecular interactions between transcription factors (TFs) and their binding sites. The bioenergetic parameters consider the free energy of formation of the bond between the TF and its binding site and the availability of TFs in the intracellular environment. Together these determine fractional occupancy of the TF on the promoter site, the degree of subsequent gene expression and in diploids, and the degree of dominance among allelic interactions. This results in a sigmoid genotype-phenotype map and fitness landscape, with the details of the shape determining the degree of bioenergetic evolutionary constraint on hybrid incompatibility. Using individual-based simulations, we subjected two allopatric populations to parallel directional or stabilizing selection. Misregulation of hybrid gene expression occurred under either type of selection, although it evolved faster under directional selection. Under directional selection, the extent of hybrid incompatibility increased with the slope of the genotype-phenotype map near the derived parental expression level. Under stabilizing selection, hybrid incompatibility arose from compensatory mutations and was greater when the bioenergetic properties of the interaction caused the space of nearly neutral genotypes around the stable expression level to be wide. F2's showed higher hybrid incompatibility than F1's to the extent that the bioenergetic properties favored dominant regulatory interactions. The present model is a mechanistically explicit case of the Bateson-Dobzhansky-Muller model, connecting environmental selective pressure to hybrid incompatibility through the molecular mechanism of regulatory divergence. The bioenergetic parameters that determine expression represent measurable properties of transcriptional regulation, providing a predictive framework for empirical studies of how phenotypic evolution results in epistatic incompatibility at the molecular level in hybrids. Copyright © 2014 by the Genetics Society of America.

In silico evolution of the Drosophila gap gene regulatory sequence under elevated mutational pressure.

PubMed

Chertkova, Aleksandra A; Schiffman, Joshua S; Nuzhdin, Sergey V; Kozlov, Konstantin N; Samsonova, Maria G; Gursky, Vitaly V

2017-02-07

Cis-regulatory sequences are often composed of many low-affinity transcription factor binding sites (TFBSs). Determining the evolutionary and functional importance of regulatory sequence composition is impeded without a detailed knowledge of the genotype-phenotype map. We simulate the evolution of regulatory sequences involved in Drosophila melanogaster embryo segmentation during early development. Natural selection evaluates gene expression dynamics produced by a computational model of the developmental network. We observe a dramatic decrease in the total number of transcription factor binding sites through the course of evolution. Despite a decrease in average sequence binding energies through time, the regulatory sequences tend towards organisations containing increased high affinity transcription factor binding sites. Additionally, the binding energies of separate sequence segments demonstrate ubiquitous mutual correlations through time. Fewer than 10% of initial TFBSs are maintained throughout the entire simulation, deemed 'core' sites. These sites have increased functional importance as assessed under wild-type conditions and their binding energy distributions are highly conserved. Furthermore, TFBSs within close proximity of core sites exhibit increased longevity, reflecting functional regulatory interactions with core sites. In response to elevated mutational pressure, evolution tends to sample regulatory sequence organisations with fewer, albeit on average, stronger functional transcription factor binding sites. These organisations are also shaped by the regulatory interactions among core binding sites with sites in their local vicinity.

Electrostatic interaction map reveals a new binding position for tropomyosin on F-actin.

PubMed

Rynkiewicz, Michael J; Schott, Veronika; Orzechowski, Marek; Lehman, William; Fischer, Stefan

2015-12-01

Azimuthal movement of tropomyosin around the F-actin thin filament is responsible for muscle activation and relaxation. Recently a model of αα-tropomyosin, derived from molecular-mechanics and electron microscopy of different contractile states, showed that tropomyosin is rather stiff and pre-bent to present one specific face to F-actin during azimuthal transitions. However, a new model based on cryo-EM of troponin- and myosin-free filaments proposes that the interacting-face of tropomyosin can differ significantly from that in the original model. Because resolution was insufficient to assign tropomyosin side-chains, the interacting-face could not be unambiguously determined. Here, we use structural analysis and energy landscapes to further examine the proposed models. The observed bend in seven crystal structures of tropomyosin is much closer in direction and extent to the original model than to the new model. Additionally, we computed the interaction map for repositioning tropomyosin over the F-actin surface, but now extended over a much larger surface than previously (using the original interacting-face). This map shows two energy minima-one corresponding to the "blocked-state" as in the original model, and the other related by a simple 24 Å translation of tropomyosin parallel to the F-actin axis. The tropomyosin-actin complex defined by the second minimum fits perfectly into the recent cryo-EM density, without requiring any change in the interacting-face. Together, these data suggest that movement of tropomyosin between regulatory states does not require interacting-face rotation. Further, they imply that thin filament assembly may involve an interplay between initially seeded tropomyosin molecules growing from distinct binding-site regions on actin.

Metallofullerenol Gd@C82(OH)22 distracts the proline-rich-motif from putative binding on the SH3 domain

NASA Astrophysics Data System (ADS)

Kang, Seung-Gu; Huynh, Tien; Zhou, Ruhong

2013-03-01

Biocompatibility is often regarded as one important aspect of de novo designed nanomaterials for biosafety. However, the toxicological effect, appearing along with its latency, is much more difficult to address by linearly mapping physicochemical properties of related nanomaterials with biological effects such as immune or cellular regulatory responses due to the complicated protein-protein interactions. Here, we investigate a potential interference of a metallofullerenol, Gd@C82(OH)22, on the function of SH3 domain, a highly promiscuous protein-protein interaction mediator involved in signaling and regulatory pathways through its binding with the proline-rich motif (PRM) peptides, using the atomistic molecular dynamics simulation. Our study shows that when only Gd@C82(OH)22 and the SH3 domain are present (without the PRM ligand), Gd@C82(OH)22 can interact with the SH3 domain by either directly blocking the hydrophobic active site or binding with a hydrophilic off-site with almost equal probability, which can be understood from its intrinsic amphiphilic nature. In a binding competition with the PRM onto the SH3 domain, however, the on-site binding mode is depleted while Gd@C82(OH)22 effectively intercepts the PRM from the putative binding site of the SH3 domain, implying that Gd@C82(OH)22 can disturb protein-protein interactions mediated by the SH3 domain. Despite a successful surface modification in an aqueous biological medium and a more recent demonstration as potential de novo cancer therapeutics, our study indicates that greater attention is needed in assessing the potential cytotoxicity of these nanomaterials.Biocompatibility is often regarded as one important aspect of de novo designed nanomaterials for biosafety. However, the toxicological effect, appearing along with its latency, is much more difficult to address by linearly mapping physicochemical properties of related nanomaterials with biological effects such as immune or cellular regulatory responses due to the complicated protein-protein interactions. Here, we investigate a potential interference of a metallofullerenol, Gd@C82(OH)22, on the function of SH3 domain, a highly promiscuous protein-protein interaction mediator involved in signaling and regulatory pathways through its binding with the proline-rich motif (PRM) peptides, using the atomistic molecular dynamics simulation. Our study shows that when only Gd@C82(OH)22 and the SH3 domain are present (without the PRM ligand), Gd@C82(OH)22 can interact with the SH3 domain by either directly blocking the hydrophobic active site or binding with a hydrophilic off-site with almost equal probability, which can be understood from its intrinsic amphiphilic nature. In a binding competition with the PRM onto the SH3 domain, however, the on-site binding mode is depleted while Gd@C82(OH)22 effectively intercepts the PRM from the putative binding site of the SH3 domain, implying that Gd@C82(OH)22 can disturb protein-protein interactions mediated by the SH3 domain. Despite a successful surface modification in an aqueous biological medium and a more recent demonstration as potential de novo cancer therapeutics, our study indicates that greater attention is needed in assessing the potential cytotoxicity of these nanomaterials. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr33756a

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

PubMed Central

Li, Xiaoyu; Song, Jinghui; Yi, Chengqi

2014-01-01

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

Charge-patterning phase transition on a surface lattice of titratable sites adjacent to an electrolyte solution

NASA Astrophysics Data System (ADS)

Shore, Joel; Thurston, George

We discuss a model for a charge-patterning phase transition on a two-dimensional square lattice of titratable sites, here regarded as protonation sites, placed on a square lattice in a dielectric medium just below the planar interface between this medium and an aqueous salt solution. Within Debye-Huckel theory, the analytical form of the electrostatic repulsion between protonated sites exhibits an approximate inverse cubic power-law decrease beyond short distances. The problem can thus be mapped onto the two-dimensional antiferromagnetic Ising model with this longer-range interaction, which we study with Monte Carlo simulations. As we increase pH, the occupation probability of a site decreases from 1 at low pH to 0 at high pH. For sufficiently-strong interaction strengths, a phase transition occurs as the occupation probability of 1/2 is approached: the charges arrange themselves into a checkerboard pattern. This ordered phase persists over a range of pH until a transition occurs back to a disordered state. This state is the analogue of the Neel state in the antiferromagnetic Ising spin model. More complicated ordered phases are expected for sufficiently strong interactions (with occupation probabilities of 1/4 and 3/4) and if the lattice is triangular rather than square. This work was supported by NIH EY018249 (GMT).

NASA Lunar and Planetary Mapping and Modeling

NASA Astrophysics Data System (ADS)

Day, B. H.; Law, E.

2016-12-01

NASA's Lunar and Planetary Mapping and Modeling Portals provide web-based suites of interactive visualization and analysis tools to enable mission planners, planetary scientists, students, and the general public to access mapped lunar data products from past and current missions for the Moon, Mars, and Vesta. New portals for additional planetary bodies are being planned. This presentation will recap significant enhancements to these toolsets during the past year and look forward to the results of the exciting work currently being undertaken. Additional data products and tools continue to be added to the Lunar Mapping and Modeling Portal (LMMP). These include both generalized products as well as polar data products specifically targeting potential sites for the Resource Prospector mission. Current development work on LMMP also includes facilitating mission planning and data management for lunar CubeSat missions, and working with the NASA Astromaterials Acquisition and Curation Office's Lunar Apollo Sample database in order to help better visualize the geographic contexts from which samples were retrieved. A new user interface provides, among other improvements, significantly enhanced 3D visualizations and navigation. Mars Trek, the project's Mars portal, has now been assigned by NASA's Planetary Science Division to support site selection and analysis for the Mars 2020 Rover mission as well as for the Mars Human Landing Exploration Zone Sites. This effort is concentrating on enhancing Mars Trek with data products and analysis tools specifically requested by the proposing teams for the various sites. Also being given very high priority by NASA Headquarters is Mars Trek's use as a means to directly involve the public in these upcoming missions, letting them explore the areas the agency is focusing upon, understand what makes these sites so fascinating, follow the selection process, and get caught up in the excitement of exploring Mars. The portals also serve as outstanding resources for education and outreach. As such, they have been designated by NASA's Science Mission Directorate as key supporting infrastructure for the new education programs selected through the division's recent CAN.

Predicting Ligand Binding Sites on Protein Surfaces by 3-Dimensional Probability Density Distributions of Interacting Atoms

PubMed Central

Jian, Jhih-Wei; Elumalai, Pavadai; Pitti, Thejkiran; Wu, Chih Yuan; Tsai, Keng-Chang; Chang, Jeng-Yih; Peng, Hung-Pin; Yang, An-Suei

2016-01-01

Predicting ligand binding sites (LBSs) on protein structures, which are obtained either from experimental or computational methods, is a useful first step in functional annotation or structure-based drug design for the protein structures. In this work, the structure-based machine learning algorithm ISMBLab-LIG was developed to predict LBSs on protein surfaces with input attributes derived from the three-dimensional probability density maps of interacting atoms, which were reconstructed on the query protein surfaces and were relatively insensitive to local conformational variations of the tentative ligand binding sites. The prediction accuracy of the ISMBLab-LIG predictors is comparable to that of the best LBS predictors benchmarked on several well-established testing datasets. More importantly, the ISMBLab-LIG algorithm has substantial tolerance to the prediction uncertainties of computationally derived protein structure models. As such, the method is particularly useful for predicting LBSs not only on experimental protein structures without known LBS templates in the database but also on computationally predicted model protein structures with structural uncertainties in the tentative ligand binding sites. PMID:27513851

Site-occupation embedding theory using Bethe ansatz local density approximations

NASA Astrophysics Data System (ADS)

Senjean, Bruno; Nakatani, Naoki; Tsuchiizu, Masahisa; Fromager, Emmanuel

2018-06-01

Site-occupation embedding theory (SOET) is an alternative formulation of density functional theory (DFT) for model Hamiltonians where the fully interacting Hubbard problem is mapped, in principle exactly, onto an impurity-interacting (rather than a noninteracting) one. It provides a rigorous framework for combining wave-function (or Green function)-based methods with DFT. In this work, exact expressions for the per-site energy and double occupation of the uniform Hubbard model are derived in the context of SOET. As readily seen from these derivations, the so-called bath contribution to the per-site correlation energy is, in addition to the latter, the key density functional quantity to model in SOET. Various approximations based on Bethe ansatz and perturbative solutions to the Hubbard and single-impurity Anderson models are constructed and tested on a one-dimensional ring. The self-consistent calculation of the embedded impurity wave function has been performed with the density-matrix renormalization group method. It has been shown that promising results are obtained in specific regimes of correlation and density. Possible further developments have been proposed in order to provide reliable embedding functionals and potentials.

Interactions of the GM2 activator protein with phosphatidylcholine bilayers: a site-directed spin-labeling power saturation study.

PubMed

Mathias, Jordan D; Ran, Yong; Carter, Jeffery D; Fanucci, Gail E

2009-09-02

The GM2 activator protein (GM2AP) is an accessory protein that is an essential component in the catabolism of the ganglioside GM2. A function of GM2AP is to bind and extract GM2 from intralysosomal vesicles, forming a soluble protein-lipid complex, which interacts with the hydrolase Hexosaminidase A, the enzyme that cleaves the terminal sugar group of GM2. Here, we used site-directed spin labeling with power saturation electron paramagnetic resonance to determine the surface-bound orientation of GM2AP upon phosphatidylcholine vesicles. Because GM2AP extracts lipid ligands from the vesicle and is undergoing exchange on and off the vesicle surface, we utilized a nickel-chelating lipid to localize the paramagnetic metal collider to the lipid bilayer-aqueous interface. Spin-labeled sites that collide with the lipid-bound metal relaxing agent provide a means for mapping sites of the protein that interact with the lipid bilayer interface. Results show that GM2AP binds to lipid bilayers such that the residues lining the lipid-binding cavity lie on the vesicle surface. This orientation creates a favorable microenvironment that can allow for the lipid tails to flip out of the bilayer directly into the hydrophobic pocket of GM2AP.

www.fallasdechile.cl, the First Online Repository for Neotectonic Faults in the Chilean Andes

NASA Astrophysics Data System (ADS)

Aron, F.; Salas, V.; Bugueño, C. J.; Hernández, C.; Leiva, L.; Santibanez, I.; Cembrano, J. M.

2016-12-01

We introduce the site www.fallasdechile.cl, created and maintained by undergraduate students and researchers at the Catholic University of Chile. Though the web page seeks to inform and educate the general public about potentially seismogenic faults of the country, layers of increasing content complexity allow students, researchers and educators to consult the site as a scientific tool as well. This is the first comprehensive, open access database on Chilean geologic faults; we envision that it may grow organically with contributions from peer scientists, resembling the SCEC community fault model for southern California. Our website aims at filling a gap between science and society providing users the opportunity to get involved by self-driven learning through interactive education modules. The main page highlights recent developments and open questions in Chilean earthquake science. Front pages show first level information of general concepts in earthquake topics such as tectonic settings, definition of geologic faults, and space-time constraints of faults. Users can navigate interactive modules to explore, with real data, different earthquake scenarios and compute values of seismic moment and magnitude. A second level covers Chilean/Andean faults classified according to their geographic location containing at least one of the following parameters: mapped trace, 3D geometry, sense of slip, recurrence times and date of last event. Fault traces are displayed on an interactive map using a Google Maps API. The material is compiled and curated in an effort to present, up to our knowledge, accurate and up to date information. If interested, the user can navigate to a third layer containing more advanced technical details including primary sources of the data, a brief structural description, published scientific articles, and links to other online content complementing our site. Also, geographically referenced fault traces with attributes (kml, shapefiles) and fault 3D surfaces (contours, tsurf files) will be available to download. Given its potential for becoming a referential database for active faults in Chile, this project evidences that undergrads can go beyond the classroom, be of service to the scientific community, and make contributions with broader impacts.

Engaging Students through Mapping Local History

PubMed Central

Mitchell, Katharyne; Elwood, Sarah

2015-01-01

This article argues that the integration of local history and geography through collaborative digital mapping can lead to greater interest in civic participation by early adolescent learners. In the study, twenty-nine middle school students were asked to research, represent, and discuss local urban sites of historical significance on an interactive Web platform. As students learned more about local community events, people, and historical forces, they became increasingly engaged with the material and enthusiastic about making connections to larger issues and processes. In the final session, students expressed interest in participating in their own communities through joining nonprofit organizations and educating others about community history and daily life. PMID:25635145

Engaging Students through Mapping Local History.

PubMed

Mitchell, Katharyne; Elwood, Sarah

2012-07-01

This article argues that the integration of local history and geography through collaborative digital mapping can lead to greater interest in civic participation by early adolescent learners. In the study, twenty-nine middle school students were asked to research, represent, and discuss local urban sites of historical significance on an interactive Web platform. As students learned more about local community events, people, and historical forces, they became increasingly engaged with the material and enthusiastic about making connections to larger issues and processes. In the final session, students expressed interest in participating in their own communities through joining nonprofit organizations and educating others about community history and daily life.

Mapping jet-ISM interactions in X-ray binaries with ALMA: a GRS 1915+105 case study

NASA Astrophysics Data System (ADS)

Tetarenko, A. J.; Freeman, P.; Rosolowsky, E. W.; Miller-Jones, J. C. A.; Sivakoff, G. R.

2018-03-01

We present Atacama Large Millimetre/Sub-Millimetre Array (ALMA) observations of IRAS 19132+1035, a candidate jet-interstellar medium (ISM) interaction zone near the black hole X-ray binary (BHXB) GRS 1915+105. With these ALMA observations (combining data from the 12 m array and the Atacama Compact Array), we map the molecular line emission across the IRAS 19132+1035 region. We detect emission from the 12CO [J = 2 - 1], 13CO [ν = 0, J = 2 - 1], C18O [J = 2 - 1], H2CO [J = 30, 3 - 20, 2], H2CO [J = 32, 2 - 22, 1], H2CO [J = 32, 1 - 22, 0], SiO [ν = 0, J = 5 - 4], CH3OH [J = 42, 2 - 31, 2], and CS [ν = 0, J = 5 - 4] transitions. Given the morphological, spectral, and kinematic properties of this molecular emission, we present several lines of evidence that support the presence of a jet-ISM interaction at this site, including a jet-blown cavity in the molecular gas. This compelling new evidence identifies this site as a jet-ISM interaction zone, making GRS 1915+105, the third Galactic BHXB with at least one conclusive jet-ISM interaction zone. However, we find that this interaction occurs on much smaller scales than was postulated by previous work, where the BHXB jet does not appear to be dominantly powering the entire IRAS 19132+1035 region. Using estimates of the ISM conditions in the region, we utilize the detected cavity as a calorimeter to estimate the time-averaged power carried in the GRS 1915+105 jets of (8.4^{+7.7}_{-8.1})× 10^{32} erg s^{-1}. Overall, our analysis demonstrates that molecular lines are excellent diagnostic tools to identify and probe jet-ISM interaction zones near Galactic BHXBs.

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

NASA Astrophysics Data System (ADS)

Kang, S.; Kim, K.

2013-12-01

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

Chemical and isotopic data collected from groundwater, surface-water, and atmospheric precipitation sites in Upper Kittitas County, Washington, 2010-12

USGS Publications Warehouse

Hinkle, Stephen R.; Ely, D. Matthew

2013-01-01

As part of a multidisciplinary U.S. Geological Survey study of water resources in Upper Kittitas County, Washington, chemical and isotopic data were collected from groundwater, surface-water, and atmospheric precipitation sites from 2010 to 2012. These data are documented here so that interested parties can quickly and easily find those chemical and isotopic data related to this study. The locations of the samples are shown on an interactive map of the study area. This report is dynamic; additional data will be added to it as they become available.

Carbohydrate binding specificity of pea lectin studied by NMR spectroscopy and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Cheong, Youngjoo; Shim, Gyuchang; Kang, Dongil; Kim, Yangmee

1999-02-01

The conformational details of Man( α1,6)Man( α)OMe are investigated through NMR spectroscopy in conjunction with molecular modeling. The lowest energy structure (M1) in the adiabatic energy map calculated with a dielectric constant of 50 has glycosidic dihedral angles of φ=-60°, ψ=180° and ω=180°. The other low energy structure (M2) has glycosidic dihedral angles of φ=-60°, ψ=180° and ω=-60°. Molecular dynamics simulations and NMR experiments prove that Man( α1,6)Man( α)OMe in the free form exists with conformational averaging of M1 and M2 conformers predominantly. Molecular dynamics simulations of the pea lectin-carbohydrate complex with explicit water molecules starting from the X-ray crystallographic structure of pea lectin show that the protein-carbohydrate interaction centers mainly on the hydrogen bonds and van der Waals interactions between protein and carbohydrate. From the molecular dynamics simulation, it is found that the M1 structure can bind to pea lectin better than the M2 structure. The origin of this selectivity is the water- mediated hydrogen bond interactions between the remote mannose and the binding site of pea lectin as well as the direct hydrogen bond interaction between the terminal mannose and pea lectin. Extensive networks of interactions in the carbohydrate binding site and the metal binding site are important in maintaining the carbohydrate binding properties of pea lectin. Especially, the predominant factors of mannose binding specificity of pea lectin are the hydrogen bond interactions between the 4th hydroxyl groups of the terminal sugar ring and the side chains of Asp-81 and Asn-125 in the carbohydrate binding site, and the additional interactions between these side chains of Asp-81 and Asn-125 and the calcium ion in the metal binding site of pea lectin.

Visualization of Host-Polerovirus Interaction Topologies Using Protein Interaction Reporter Technology.

PubMed

DeBlasio, Stacy L; Chavez, Juan D; Alexander, Mariko M; Ramsey, John; Eng, Jimmy K; Mahoney, Jaclyn; Gray, Stewart M; Bruce, James E; Cilia, Michelle

2016-02-15

Demonstrating direct interactions between host and virus proteins during infection is a major goal and challenge for the field of virology. Most protein interactions are not binary or easily amenable to structural determination. Using infectious preparations of a polerovirus (Potato leafroll virus [PLRV]) and protein interaction reporter (PIR), a revolutionary technology that couples a mass spectrometric-cleavable chemical cross-linker with high-resolution mass spectrometry, we provide the first report of a host-pathogen protein interaction network that includes data-derived, topological features for every cross-linked site that was identified. We show that PLRV virions have hot spots of protein interaction and multifunctional surface topologies, revealing how these plant viruses maximize their use of binding interfaces. Modeling data, guided by cross-linking constraints, suggest asymmetric packing of the major capsid protein in the virion, which supports previous epitope mapping studies. Protein interaction topologies are conserved with other species in the Luteoviridae and with unrelated viruses in the Herpesviridae and Adenoviridae. Functional analysis of three PLRV-interacting host proteins in planta using a reverse-genetics approach revealed a complex, molecular tug-of-war between host and virus. Structural mimicry and diversifying selection-hallmarks of host-pathogen interactions-were identified within host and viral binding interfaces predicted by our models. These results illuminate the functional diversity of the PLRV-host protein interaction network and demonstrate the usefulness of PIR technology for precision mapping of functional host-pathogen protein interaction topologies. The exterior shape of a plant virus and its interacting host and insect vector proteins determine whether a virus will be transmitted by an insect or infect a specific host. Gaining this information is difficult and requires years of experimentation. We used protein interaction reporter (PIR) technology to illustrate how viruses exploit host proteins during plant infection. PIR technology enabled our team to precisely describe the sites of functional virus-virus, virus-host, and host-host protein interactions using a mass spectrometry analysis that takes just a few hours. Applications of PIR technology in host-pathogen interactions will enable researchers studying recalcitrant pathogens, such as animal pathogens where host proteins are incorporated directly into the infectious agents, to investigate how proteins interact during infection and transmission as well as develop new tools for interdiction and therapy. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

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

PubMed Central

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

2011-01-01

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. PMID:21963238

Quantum simulation of the Hubbard model with dopant atoms in silicon

PubMed Central

Salfi, J.; Mol, J. A.; Rahman, R.; Klimeck, G.; Simmons, M. Y.; Hollenberg, L. C. L.; Rogge, S.

2016-01-01

In quantum simulation, many-body phenomena are probed in controllable quantum systems. Recently, simulation of Bose–Hubbard Hamiltonians using cold atoms revealed previously hidden local correlations. However, fermionic many-body Hubbard phenomena such as unconventional superconductivity and spin liquids are more difficult to simulate using cold atoms. To date the required single-site measurements and cooling remain problematic, while only ensemble measurements have been achieved. Here we simulate a two-site Hubbard Hamiltonian at low effective temperatures with single-site resolution using subsurface dopants in silicon. We measure quasi-particle tunnelling maps of spin-resolved states with atomic resolution, finding interference processes from which the entanglement entropy and Hubbard interactions are quantified. Entanglement, determined by spin and orbital degrees of freedom, increases with increasing valence bond length. We find separation-tunable Hubbard interaction strengths that are suitable for simulating strongly correlated phenomena in larger arrays of dopants, establishing dopants as a platform for quantum simulation of the Hubbard model. PMID:27094205

Special-Status Plant Species Surveys and Vegetation Mapping at Lawrence Livermore National Laboratory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Preston, R E

This report presents the results of Jones & Stokes special-status plant surveys and vegetation mapping for the University of California, Lawrence Livermore National Laboratory (LLNL). Special-status plant surveys were conducted at Site 300 in April to May 1997 and in March to April 2002. Eight special-status plants were identified at Site 300: large-flowered fiddleneck, big tarplant, diamond-petaled poppy, round-leaved filaree, gypsum-loving larkspur, California androsace, stinkbells, and hogwallow starfish. Maps identifying the locations of these species, a discussion of the occurrence of these species at Site 300, and a checklist of the flora of Site 300 are presented. A reconnaissance surveymore » of the LLNL Livermore Site was conducted in June 2002. This survey concluded that no special-status plants occur at the Livermore Site. Vegetation mapping was conducted in 2001 at Site 300 to update a previous vegetation study done in 1986. The purpose of the vegetation mapping was to update and to delineate more precisely the boundaries between vegetation types and to map vegetation types that previously were not mapped. The vegetation map is presented with a discussion of the vegetation classification used.« less

Host-Primed Ebola Virus GP Exposes a Hydrophobic NPC1 Receptor-Binding Pocket, Revealing a Target for Broadly Neutralizing Antibodies.

PubMed

Bornholdt, Zachary A; Ndungo, Esther; Fusco, Marnie L; Bale, Shridhar; Flyak, Andrew I; Crowe, James E; Chandran, Kartik; Saphire, Erica Ollmann

2016-02-23

The filovirus surface glycoprotein (GP) mediates viral entry into host cells. Following viral internalization into endosomes, GP is cleaved by host cysteine proteases to expose a receptor-binding site (RBS) that is otherwise hidden from immune surveillance. Here, we present the crystal structure of proteolytically cleaved Ebola virus GP to a resolution of 3.3 Å. We use this structure in conjunction with functional analysis of a large panel of pseudotyped viruses bearing mutant GP proteins to map the Ebola virus GP endosomal RBS at molecular resolution. Our studies indicate that binding of GP to its endosomal receptor Niemann-Pick C1 occurs in two distinct stages: the initial electrostatic interactions are followed by specific interactions with a hydrophobic trough that is exposed on the endosomally cleaved GP1 subunit. Finally, we demonstrate that monoclonal antibodies targeting the filovirus RBS neutralize all known filovirus GPs, making this conserved pocket a promising target for the development of panfilovirus therapeutics. Ebola virus uses its glycoprotein (GP) to enter new host cells. During entry, GP must be cleaved by human enzymes in order for receptor binding to occur. Here, we provide the crystal structure of the cleaved form of Ebola virus GP. We demonstrate that cleavage exposes a site at the top of GP and that this site binds the critical domain C of the receptor, termed Niemann-Pick C1 (NPC1). We perform mutagenesis to find parts of the site essential for binding NPC1 and map distinct roles for an upper, charged crest and lower, hydrophobic trough in cleaved GP. We find that this 3-dimensional site is conserved across the filovirus family and that antibody directed against this site is able to bind cleaved GP from every filovirus tested and neutralize viruses bearing those GPs. Copyright © 2016 Bornholdt et al.

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

PubMed Central

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

2013-01-01

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

Spatial resolution of pace mapping of idiopathic ventricular tachycardia/ectopy originating in the right ventricular outflow tract.

PubMed

Bogun, Frank; Taj, Majid; Ting, Michael; Kim, Hyungjin Myra; Reich, Stephen; Good, Eric; Jongnarangsin, Krit; Chugh, Aman; Pelosi, Frank; Oral, Hakan; Morady, Fred

2008-03-01

Pace mapping has been used to identify the site of origin of focal ventricular arrhythmias. The spatial resolution of pace mapping has not been adequately quantified using currently available three-dimensional mapping systems. The purpose of this study was to determine the spatial resolution of pace mapping in patients with idiopathic ventricular tachycardia or premature ventricular contractions originating in the right ventricular outflow tract. In 16 patients with idiopathic ventricular tachycardia/ectopy from the right ventricular outflow tract, comparisons and classifications of pace maps were performed by two observers (good pace map: match >10/12 leads; inadequate pace map: match < or =10/12 leads) and a customized MATLAB 6.0 program (assessing correlation coefficient and normalized root mean square of the difference (nRMSd) between test and template signals). With an electroanatomic mapping system, the correlation coefficient of each pace map was correlated with the distance between the pacing site and the effective ablation site. The endocardial area within the 10-ms activation isochrone was measured. The ablation procedure was effective in all patients. Sites with good pace maps had a higher correlation coefficient and lower nRMSd than sites with inadequate pace maps (correlation coefficient: 0.96 +/- 0.03 vs 0.76 +/- 0.18, P <.0001; nRMSd: 0.41 +/- 0.16 vs 0.89 +/- 0.39, P <.0001). Using receiver operating characteristic curves, appropriate cutoff values were >0.94 for correlation coefficient (sensitivity 81%, specificity 89%) and < or =0.54 for nRMSd (sensitivity 76%, specificity 80%). Good pace maps were located a mean of 7.3 +/- 5.0 mm from the effective ablation site and had a mean activation time of -24 +/- 7 ms. However, in 3 (18%) of 16 patients, the best pace map was inadequate at the effective ablation site, with an endocardial activation time at these sites of -25 +/- 12 ms. Pace maps with correlation coefficient > or =0.94 were confined to an area of 1.8 +/- 0.6 cm2. The 10-ms isochrone measured 1.2 +/- 0.7 cm2. The spatial resolution of a good pace map for targeting ventricular tachycardia/ectopy is 1.8 cm2 in the right ventricular outflow tract and therefore is inferior to the spatial resolution of activation mapping as assessed by isochronal activation. In approximately 20% of patients, pace mapping is unreliable in identifying the site of origin, possibly due a deeper site of origin and preferential conduction via fibers connecting the focus to the endocardial surface.

The Rock Engineering System (RES) applied to landslide susceptibility zonation of the northeastern flank of Etna: methodological approach and results

NASA Astrophysics Data System (ADS)

Apuani, Tiziana; Corazzato, Claudia

2015-04-01

Ground deformations in the northeastern flank of Etna are well known. Despite only a few landslide events have been documented, these have significantly involved and damaged lifelines and buildings. These events are mainly related to the activity of the volcano-tectonic structures and associated seismicity, as in the case of the 2002 reactivation of the Presa landslide during an increased activity of the Pernicana fault system. In order to highlight the areal distribution of potentially unstable slopes based on a detailed, site-specific study of the factors responsible for landslide, and to ultimately contribute to risk management, a landslide susceptibility analysis of the northeastern flank of Etna in the Pernicana area was carried out, and a susceptibility map at 1:10.000 scale was produced, extending over an area of 168 km2. Different methods are proposed in the literature to obtain the regional distribution of potentially unstable slopes, depending on the problem scale, the slope dynamic evolution in the geological context, and the availability of data. Among semi-quantitative approaches, the present research combines the Rock Engineering System (RES) methodology with parameter zonation mapping in a GIS environment. The RES method represents a structured approach to manage a high number of interacting factors involved in the instability problem. A numerically coded, site-specific interaction matrix (IM) analyzes the cause-effect relationship in these factors, and calculates the degree of interactivity of each parameter, normalized by the overall interactivity of the system (weight factor). In the specific Etna case, the considered parameters are: slope attitude, lithotechnical properties (lithology, structural complexity, soil and rock mass quality), land use, tectonic structures, seismic activity (horizontal acceleration) and hydrogeological conditions (groundwater and drainage). Thematic maps are prepared at 1:10.000 scale for each of these parameters, and instability-related numerical ratings are assigned to classes. An instability index map is then produced by assigning, to each areal elementary cell (in our case a 10 m pixel), the sum of the products of each weight factor to the normalized parameter rating coming from each input zonation map. This map is then opportunely classified in landslide susceptibility classes (expressed as a percentage), enabling to discriminate areas prone to instability. Overall, the study area is characterized by a low propensity to slope instability. Few areas have an instability index of more than 45% of the theoretical maximum imposed by the matrix. These are located in the few steep slopes associated with active faults, and strongly depending on the seismic activity. Some other areas correspond to limited outcrops characterized by significantly reduced lithotechnical properties (low shear strength). The produced susceptibility map combines the application of the RES with the parameter zonation, following methodology which had never been applied up to now in in active volcanic environments. The comparison of the results with the ground deformation evidence coming from monitoring networks suggests the validity of the approach.

Visualization of Host-Polerovirus Interaction Topologies Using Protein Interaction Reporter Technology

PubMed Central

DeBlasio, Stacy L.; Chavez, Juan D.; Alexander, Mariko M.; Ramsey, John; Eng, Jimmy K.; Mahoney, Jaclyn; Gray, Stewart M.; Bruce, James E.

2015-01-01

ABSTRACT Demonstrating direct interactions between host and virus proteins during infection is a major goal and challenge for the field of virology. Most protein interactions are not binary or easily amenable to structural determination. Using infectious preparations of a polerovirus (Potato leafroll virus [PLRV]) and protein interaction reporter (PIR), a revolutionary technology that couples a mass spectrometric-cleavable chemical cross-linker with high-resolution mass spectrometry, we provide the first report of a host-pathogen protein interaction network that includes data-derived, topological features for every cross-linked site that was identified. We show that PLRV virions have hot spots of protein interaction and multifunctional surface topologies, revealing how these plant viruses maximize their use of binding interfaces. Modeling data, guided by cross-linking constraints, suggest asymmetric packing of the major capsid protein in the virion, which supports previous epitope mapping studies. Protein interaction topologies are conserved with other species in the Luteoviridae and with unrelated viruses in the Herpesviridae and Adenoviridae. Functional analysis of three PLRV-interacting host proteins in planta using a reverse-genetics approach revealed a complex, molecular tug-of-war between host and virus. Structural mimicry and diversifying selection—hallmarks of host-pathogen interactions—were identified within host and viral binding interfaces predicted by our models. These results illuminate the functional diversity of the PLRV-host protein interaction network and demonstrate the usefulness of PIR technology for precision mapping of functional host-pathogen protein interaction topologies. IMPORTANCE The exterior shape of a plant virus and its interacting host and insect vector proteins determine whether a virus will be transmitted by an insect or infect a specific host. Gaining this information is difficult and requires years of experimentation. We used protein interaction reporter (PIR) technology to illustrate how viruses exploit host proteins during plant infection. PIR technology enabled our team to precisely describe the sites of functional virus-virus, virus-host, and host-host protein interactions using a mass spectrometry analysis that takes just a few hours. Applications of PIR technology in host-pathogen interactions will enable researchers studying recalcitrant pathogens, such as animal pathogens where host proteins are incorporated directly into the infectious agents, to investigate how proteins interact during infection and transmission as well as develop new tools for interdiction and therapy. PMID:26656710

MapApp: A Java(TM) Applet for Accessing Geographic Databases

NASA Astrophysics Data System (ADS)

Haxby, W.; Carbotte, S.; Ryan, W. B.; OHara, S.

2001-12-01

MapApp (http://coast.ldeo.columbia.edu/help/MapApp.html) is a prototype Java(TM) applet that is intended to give easy and versatile access to geographic data sets through a web browser. It was developed initially to interface with the RIDGE Multibeam Synthesis. Subsequently, interfaces with other geophysical databases were added. At present, multibeam bathymetry grids, underway geophysics along ship tracks, and the LDEO Borehole Research Group's ODP well logging database are accessible through MapApp. We plan to add an interface with the Ridge Petrology Database in the near future. The central component of MapApp is a world physiographic map. Users may navigate around the map (zoom/pan) without waiting for HTTP requests to a remote server to be processed. A focus request loads image tiles from the server to compose a new map at the current viewing resolution. Areas in which multibeam grids are available may be focused to a pixel resolution of about 200 m. These areas may be identified by toggling a mask. Databases may be accessed through menus, and selected data objects may be loaded into MapApp by selecting items from tables. Once loaded, a bathymetry grid may be contoured or used to create bathymetric profiles; ship tracks and ODP sites may be overlain on the map and their geophysical data plotted in X-Y graphs. The advantage of applets over traditional web pages is that they permit dynamic interaction with data sets, while limiting time consuming interaction with a remote server. Users may customize the graphics display by modifying the scale, or the symbol or line characteristics of rendered data, contour interval, etc. The ease with which users can select areas, view the physiography of areas, and preview data sets and evaluate them for quality and applicability, makes MapApp a valuable tool for education and research.

Mapping NEHRP VS30 site classes

USGS Publications Warehouse

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

2005-01-01

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

BAID: The Barrow Area Information Database - An Interactive Web Mapping Portal and Cyberinfrastructure Showcasing Scientific Activities in the Vicinity of Barrow, Arctic Alaska.

NASA Astrophysics Data System (ADS)

Escarzaga, S. M.; Cody, R. P.; Kassin, A.; Barba, M.; Gaylord, A. G.; Manley, W. F.; Mazza Ramsay, F. D.; Vargas, S. A., Jr.; Tarin, G.; Laney, C. M.; Villarreal, S.; Aiken, Q.; Collins, J. A.; Green, E.; Nelson, L.; Tweedie, C. E.

2015-12-01

The Barrow area of northern Alaska is one of the most intensely researched locations in the Arctic and the Barrow Area Information Database (BAID, www.barrowmapped.org) tracks and facilitates a gamut of research, management, and educational activities in the area. BAID is a cyberinfrastructure (CI) that details much of the historic and extant research undertaken within in the Barrow region in a suite of interactive web-based mapping and information portals (geobrowsers). The BAID user community and target audience for BAID is diverse and includes research scientists, science logisticians, land managers, educators, students, and the general public. BAID contains information on more than 12,000 Barrow area research sites that extend back to the 1940's and more than 640 remote sensing images and geospatial datasets. In a web-based setting, users can zoom, pan, query, measure distance, save or print maps and query results, and filter or view information by space, time, and/or other tags. Additionally, data are described with metadata that meet Federal Geographic Data Committee standards. Recent advances include the addition of more than 2000 new research sites, the addition of a query builder user interface allowing rich and complex queries, and provision of differential global position system (dGPS) and high-resolution aerial imagery support to visiting scientists. Recent field surveys include over 80 miles of coastline to document rates of erosion and the collection of high-resolution sonar data for bathymetric mapping of Elson Lagoon and near shore region of the Chukchi Sea. A network of five climate stations has been deployed across the peninsula to serve as a wireless net for the research community and to deliver near real time climatic data to the user community. Local GIS personal have also been trained to better make use of scientific data for local decision making. Links to Barrow area datasets are housed at national data archives and substantial upgrades have been made to the BAID website and web mapping applications to include the public release of a new multi-temporal Imagery Viewer that allow users to interact with and compare imagery of the Barrow area from 1949 to present.

Structural and biochemical characterization of Xylella fastidiosa DsbA family members: new insights into the enzyme-substrate interaction.

PubMed

Rinaldi, Fábio C; Meza, Andréia N; Guimarães, Beatriz G

2009-04-21

Disulfide oxidoreductase DsbA catalyzes disulfide bond formation in proteins secreted to the periplasm and has been related to the folding process of virulence factors in many organisms. It is among the most oxidizing of the thioredoxin-like proteins, and DsbA redox power is understood in terms of the electrostatic interactions involving the active site motif CPHC. The plant pathogen Xylella fastidiosa has two chromosomal genes encoding two oxidoreductases belonging to the DsbA family, and in one of them, the canonical motif CPHC is replaced by CPAC. Biochemical assays showed that both X. fastidiosa homologues have similar redox properties and the determination of the crystal structure of XfDsbA revealed substitutions in the active site of X. fastidiosa enzymes, which are proposed to compensate for the lack of the conserved histidine in XfDsbA2. In addition, electron density maps showed a ligand bound to the XfDsbA active site, allowing the characterization of the enzyme interaction with an 8-mer peptide. Finally, surface analysis of XfDsbA and XfDsbA2 suggests that X. fastidiosa enzymes may have different substrate specificities.

Structural and Biochemical Characterization of Xylella fastidiosa DsbA Family Members: New insightsinto the Enzyme-Substrate Interaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rinaldi, F.; Meza, A; Gulmarges, B

2009-01-01

Disulfide oxidoreductase DsbA catalyzes disulfide bond formation in proteins secreted to the periplasm and has been related to the folding process of virulence factors in many organisms. It is among the most oxidizing of the thioredoxin-like proteins, and DsbA redox power is understood in terms of the electrostatic interactions involving the active site motif CPHC. The plant pathogen Xylella fastidiosa has two chromosomal genes encoding two oxidoreductases belonging to the DsbA family, and in one of them, the canonical motif CPHC is replaced by CPAC. Biochemical assays showed that both X. fastidiosa homologues have similar redox properties and the determinationmore » of the crystal structure of XfDsbA revealed substitutions in the active site of X. fastidiosa enzymes, which are proposed to compensate for the lack of the conserved histidine in XfDsbA2. In addition, electron density maps showed a ligand bound to the XfDsbA active site, allowing the characterization of the enzyme interaction with an 8-mer peptide. Finally, surface analysis of XfDsbA and XfDsbA2 suggests that X. fastidiosa enzymes may have different substrate specificities.« less

Tampa Bay Study Data and Information Management System (DIMS)

NASA Astrophysics Data System (ADS)

Edgar, N. T.; Johnston, J. B.; Yates, K.; Smith, K. E.

2005-05-01

Providing easy access to data and information is an essential component of both science and management. The Tampa Bay Data and Information Management System (DIMS) catalogs and publicizes data and products which are generated through the Tampa Bay Integrated Science Study. The publicly accessible interface consists of a Web site (http://gulfsci.usgs.gov), a digital library, and an interactive map server (IMS). The Tampa Bay Study Web site contains information from scientists involved in the study, and is also the portal site for the digital library and IMS. Study information is highlighted on the Web site according to the estuarine component: geology and geomorphology, water and sediment quality, ecosystem structure and function, and hydrodynamics. The Tampa Bay Digital Library is a web-based clearinghouse for digital products on Tampa Bay, including documents, maps, spatial and tabular data sets, presentations, etc. New developments to the digital library include new search features, 150 new products over the past year, and partnerships to expand the offering of science products. The IMS is a Web-based geographic information system (GIS) used to store, analyze and display data pertaining to Tampa Bay. Upgrades to the IMS have improved performance and speed, as well as increased the number of data sets available for mapping. The Tampa Bay DIMS is a dynamic entity and will continue to evolve with the study. Beginning in 2005, the Tampa Bay Integrated Coastal Model will have a more prominent presence within the DIMS. The Web site will feature model projects and plans; the digital library will host model products and data sets; the IMS will display spatial model data sets and analyses. These tools will be used to increase communication of USGS efforts in Tampa Bay to the public, local managers, and scientists.

SH2 Binding Site Protection Assay: A Method for Identification of SH2 Domain Interaction Partners by Exploiting SH2 Mediated Phosphosite Protection.

PubMed

Jadwin, Joshua A

2017-01-01

Over the last two decades there has been a significant effort in the field to characterize the phosphosite binding specificities of SH2 domains with the goal of deciphering the pY signaling code. Although high throughput studies in various formats using most SH2 domains have collectively provided a rich resource of in vitro SH2-pTyr site specificity maps, this data can only be used approximate what is happening in the cell where protein concentrations and localization are not homogenous, as they are for in vitro experiments. Here we describe an in vivo approach, SH2 site protection assay, which can capture the pTyr binding specificity of SH2 domains in the cell. The basis of this approach is SH2-pY site protection, the ability of SH2 domains to prevent the PTP-dependent dephosphorylation of their pY site binding partners. We overexpress a tracer SH2 domain in cells and quantify the change in abundance of tyrosine phosphorylated sites using MS. Since the method is performed in vivo, it has the advantage of identifying SH2-pY interactions as they occur within in the cell.

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

NASA Astrophysics Data System (ADS)

Hren, Rok

1998-06-01

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

Mapping multiple potential ATP binding sites on the matrix side of the bovine ADP/ATP carrier by the combined use of MD simulation and docking.

PubMed

Di Marino, Daniele; Oteri, Francesco; della Rocca, Blasco Morozzo; D'Annessa, Ilda; Falconi, Mattia

2012-06-01

The mitochondrial adenosine diphosphate/adenosine triphosphate (ADP/ATP) carrier-AAC-was crystallized in complex with its specific inhibitor carboxyatractyloside (CATR). The protein consists of a six-transmembrane helix bundle that defines the nucleotide translocation pathway, which is closed towards the matrix side due to sharp kinks in the odd-numbered helices. In this paper, we describe the interaction between the matrix side of the AAC transporter and the ATP(4-) molecule using carrier structures obtained through classical molecular dynamics simulation (MD) and a protein-ligand docking procedure. Fifteen structures were extracted from a previously published MD trajectory through clustering analysis, and 50 docking runs were carried out for each carrier conformation, for a total of 750 runs ("MD docking"). The results were compared to those from 750 docking runs performed on the X-ray structure ("X docking"). The docking procedure indicated the presence of a single interaction site in the X-ray structure that was conserved in the structures extracted from the MD trajectory. MD docking showed the presence of a second binding site that was not found in the X docking. The interaction strategy between the AAC transporter and the ATP(4-) molecule was analyzed by investigating the composition and 3D arrangement of the interaction pockets, together with the orientations of the substrate inside them. A relationship between sequence repeats and the ATP(4-) binding sites in the AAC carrier structure is proposed.

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

PubMed Central

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

2015-01-01

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

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

PubMed Central

Cai, Kewen; Itoh, Yoshiki; Khorana, H. Gobind

2001-01-01

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 λ >495 nm. Subsequent irradiation of the complex at λ310 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 Tα. For identification of the sites of crosslinks in Tα, 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 Tα 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 Tα derivatives and isolation of Tα 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 Tα containing the amino acid sequences 310–313 and 342–345. PMID:11320237

Groundwater levels for selected wells in Upper Kittitas County, Washington

USGS Publications Warehouse

Fasser, E.T.; Julich, R.J.

2011-01-01

Groundwater levels for selected wells in Upper Kittitas County, Washington, are presented on an interactive, web-based map to document the spatial distribution of groundwater levels in the study area measured during spring 2011. Groundwater-level data and well information were collected by the U.S. Geological Survey using standard techniques and are stored in the U.S. Geological Survey National Water Information System, Groundwater Site-Inventory database.

POLYVIEW-MM: web-based platform for animation and analysis of molecular simulations

PubMed Central

Porollo, Aleksey; Meller, Jaroslaw

2010-01-01

Molecular simulations offer important mechanistic and functional clues in studies of proteins and other macromolecules. However, interpreting the results of such simulations increasingly requires tools that can combine information from multiple structural databases and other web resources, and provide highly integrated and versatile analysis tools. Here, we present a new web server that integrates high-quality animation of molecular motion (MM) with structural and functional analysis of macromolecules. The new tool, dubbed POLYVIEW-MM, enables animation of trajectories generated by molecular dynamics and related simulation techniques, as well as visualization of alternative conformers, e.g. obtained as a result of protein structure prediction methods or small molecule docking. To facilitate structural analysis, POLYVIEW-MM combines interactive view and analysis of conformational changes using Jmol and its tailored extensions, publication quality animation using PyMol, and customizable 2D summary plots that provide an overview of MM, e.g. in terms of changes in secondary structure states and relative solvent accessibility of individual residues in proteins. Furthermore, POLYVIEW-MM integrates visualization with various structural annotations, including automated mapping of known inter-action sites from structural homologs, mapping of cavities and ligand binding sites, transmembrane regions and protein domains. URL: http://polyview.cchmc.org/conform.html. PMID:20504857

Fluvial and Lacustrine Processes in Meridiani Planum and the Origin of the Hematite by Aqueous Alteration

NASA Technical Reports Server (NTRS)

Newsom, H. E.; Barber, C. A.; Schelble, R. T.; Hare, T. M.; Feldman, W. C.; Sutherland, V.; Livingston, A.; Lewis, K.

2003-01-01

The prime MER landing site in Meridiani Planum is located on layered materials, including hematite, whose origin as lacustrine or aeolian sediments, or volcanic materials is uncertain. Our detailed mapping of the region provides important constraints on the history of the region. Our mapping of the location of fluvial and lacustrine land forms in the region relative to the layered deposits provides new evidence of a long history of erosion and deposition as has long been noted . In addition, our detailed mapping of the southern boundary of the hematite deposit strongly supports an association between longlived fluvial channels and lacustrine basins and the strongest hematite signatures. This evidence supports an origin of the hematite deposits by interaction with water under ambient conditions in contrast to suggestions of hydrothermal processes due to volcanic or impact crater processes. An important part of the story is the evidence for the localization of the layered deposits due to topographic control induce by the presence of a large early basin we have identified that extends to the north-east of the landing site. Distribution of current channel networks, drainages,

Bottom-up derivation of conservative and dissipative interactions for coarse-grained molecular liquids with the conditional reversible work method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deichmann, Gregor; Marcon, Valentina; Vegt, Nico F. A. van der, E-mail: vandervegt@csi.tu-darmstadt.de

Molecular simulations of soft matter systems have been performed in recent years using a variety of systematically coarse-grained models. With these models, structural or thermodynamic properties can be quite accurately represented while the prediction of dynamic properties remains difficult, especially for multi-component systems. In this work, we use constraint molecular dynamics simulations for calculating dissipative pair forces which are used together with conditional reversible work (CRW) conservative forces in dissipative particle dynamics (DPD) simulations. The combined CRW-DPD approach aims to extend the representability of CRW models to dynamic properties and uses a bottom-up approach. Dissipative pair forces are derived frommore » fluctuations of the direct atomistic forces between mapped groups. The conservative CRW potential is obtained from a similar series of constraint dynamics simulations and represents the reversible work performed to couple the direct atomistic interactions between the mapped atom groups. Neopentane, tetrachloromethane, cyclohexane, and n-hexane have been considered as model systems. These molecular liquids are simulated with atomistic molecular dynamics, coarse-grained molecular dynamics, and DPD. We find that the CRW-DPD models reproduce the liquid structure and diffusive dynamics of the liquid systems in reasonable agreement with the atomistic models when using single-site mapping schemes with beads containing five or six heavy atoms. For a two-site representation of n-hexane (3 carbons per bead), time scale separation can no longer be assumed and the DPD approach consequently fails to reproduce the atomistic dynamics.« less

Interactions between geomorphology and vegetation in the Western Swiss Alps: first investigations

NASA Astrophysics Data System (ADS)

Giaccone, Elisa; Mariéthoz, Grégoire; Lambiel, Christophe

2017-04-01

The influence of earth surface processes can modify the microhabitat conditions and the species richness, composition and distribution patterns of plant communities. It is therefore important to understand how geomorphology affects the distribution of plant species to predict future vegetation evolution in a context of climate change. To better analyse the influence of geomorphology on vegetation growth in the alpine periglacial belt, we are studying various geomorphological processes (e.g. cryoturbation and solifluction), permafrost, nivation and ground surface characteristics at three focus sites of the Vaud Alps (Western Swiss Alps). The sites are located at an altitude range comprised between 2000 and 2600 m a.s.l. The geomorphology is characterized mainly by the presence of small glaciers, large moraine deposits, rock glaciers and debris slopes. Monitoring of the ground surface temperatures, permafrost mapping, vegetation survey and drone flights have been carried out to investigate in detail the environmental variables. Initial results show a heterogeneous vegetation cover depending on time since deglaciation, debris size, ground stability and soil age. Debris pioneer species are present on moraines, rock glaciers and debris slope; grassland are developed in zones not affected by LIA glacier advances or other interfering processes such as avalanches. The high-resolution images obtained from drone flights (5 cm/pixel) allow a detailed study of the granulometry. In order to use such geomorphological information on a wider area of interest, the local data acquired on focus sites have to be spatialized to a regional scale. This is accomplished by developing an approach based on remote sensing and multiple-point geostatistics that performs a semi-automated geomorphological mapping (SAGM). The SAGM is based on a training image composed by a geomorphological map yet existent, an orthophoto, the slope, the aspect, the curvature, the granulometry classification and the NDVI. The SAGM will be first elaborated for the focus sites and will then be extended to the entire Vaud Alps above 2000 m a.s.l. This information will be used to better understand the geomorphology-vegetation interactions and their spatialization.

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

PubMed Central

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

2012-01-01

First-generation interaction maps of Src homology 2 (SH2) domains with receptor tyrosine kinase (RTK) phosphosites have previously been generated using protein microarray (PM) technologies. Here, we developed a large-scale fluorescence polarization (FP) methodology that was able to characterize interactions between SH2 domains and ErbB receptor phosphosites with higher fidelity and sensitivity than was previously achieved with PMs. We used the FP assay to query the interaction of synthetic phosphopeptides corresponding to 89 ErbB receptor intracellular tyrosine sites against 93 human SH2 domains and 2 phosphotyrosine binding (PTB) domains. From 358,944 polarization measurements, the affinities for 1,405 unique biological interactions were determined, 83% of which are novel. In contrast to data from previous reports, our analyses suggested that ErbB2 was not more promiscuous than the other ErbB receptors. Our results showed that each receptor displays unique preferences in the affinity and location of recruited SH2 domains that may contribute to differences in downstream signaling potential. ErbB1 was enriched versus the other receptors for recruitment of domains from RAS GEFs whereas ErbB2 was enriched for recruitment of domains from tyrosine and phosphatidyl inositol phosphatases. ErbB3, the kinase inactive ErbB receptor family member, was predictably enriched for recruitment of domains from phosphatidyl inositol kinases and surprisingly, was enriched for recruitment of domains from tyrosine kinases, cytoskeletal regulatory proteins, and RHO GEFs but depleted for recruitment of domains from phosphatidyl inositol phosphatases. Many novel interactions were also observed with phosphopeptides corresponding to ErbB receptor tyrosines not previously reported to be phosphorylated by mass spectrometry, suggesting the existence of many biologically relevant RTK sites that may be phosphorylated but below the detection threshold of standard mass spectrometry procedures. This dataset represents a rich source of testable hypotheses regarding the biological mechanisms of ErbB receptors. PMID:22973453

Spitzer Space Telescope IRS Spectral Mapping of Photoionized Columns in M16 and the Carina HII Regions

NASA Astrophysics Data System (ADS)

Cotera, Angela; Simpson, J. P.; Sellgren, K.; Stolovy, S. R.

2013-01-01

Photoevaporated columns of dust and gas - also called elephant trunks, pillars or fingers - are found in the periphery of many H II regions. They have been observed within the Galaxy, the SMC and the LMC. These features are thought to be sites of current star formation, but the question remains whether the columns persist because stars formed in the denser regions prior to interactions with the UV radiation and stellar winds of nearby massive stars, or because of core collapse resulting from these interactions. We have obtained Spitzer IRS spectral maps of three columns within M 16 and three columns within the Carina nebula, to test our understanding of the impact on these transitory features of differing stellar populations and initial conditions. We use the wealth of molecular, atomic and PAH emission lines located within the spectral range of the high resolution IRS modes (9.9-37.2 micron) to determine the excitation state, dust and gas temperatures, and probe the shock characteristics within the columns as a function of location. Using the IRS spectral mapping mode, in conjunction with the CUBISM tool and the CLOUDY H II region model code, we have constructed detailed maps of the accessible emission lines and derived parameters for each column. Mapping the distribution of the physical states of the dust and gas in these columns is enhancing our understanding of the competing processes within these dynamic objects. The data presented here represent the only IRS spectral maps of photoionized pillars.

LiDAR Mapping of Earthquake Uplifted Paleo-shorelines, Southern Wairarapa Coast, North Island, New Zealand

NASA Astrophysics Data System (ADS)

Valenciano, J.; Angenent, J.; Marshall, J. S.; Clark, K.; Litchfield, N. J.

2017-12-01

The Hikurangi subduction margin along the east coast of the North Island, New Zealand accommodates oblique convergence of the Pacific Plate westward beneath the Australian plate at 45 mm/yr. Pronounced forearc uplift occurs at the southern end of the margin along the Wairarapa coast, onshore of the subducting Hikurangi plateau. Along a narrow coastal lowland, a series of uplifted Holocene marine terraces and beach ridges preserve a geologic record of prehistoric coseismic uplift events. In January 2017, we participated in the Research Experience for Undergraduates (REU) program of the NSF SHIRE Project (Subduction at Hikurangi Integrated Research Experiment). We visited multiple coastal sites for reconnaissance fieldwork to select locations for future in-depth study. For the coastline between Flat Point and Te Kaukau Point, we used airborne LiDAR data provided by Land Information New Zealand (LINZ) to create ArcGIS digital terrain models for mapping and correlating uplifted paleo-shorelines. Terrace elevations derived from the LiDAR data were calibrated through the use of Real Time Kinematic (RTK) GPS surveying at one field site (Glenburn Station). Prior field mapping and radiocarbon dating results (Berryman et al., 2001; Litchfield and Clark, 2015) were used to guide our LiDAR mapping efforts. The resultant maps show between four and seven uplifted terraces and associated beach ridges along this coastal segment. At some sites, terrace mapping and lateral correlation are impeded by discontinuous exposures and the presence of landslide debris, alluvial fan deposits, and sand dunes. Tectonic uplift along the southern Hikurangi margin is generated by a complex interaction between deep megathrust slip and shallow upper-plate faulting. Each uplifted Holocene paleo-shoreline is interpreted to represent a single coseismic uplift event. Continued mapping, surveying, and age dating may help differentiate between very large margin-wide megathrust earthquakes (M8.0-9.0+) and smaller, more localized upper-plate thrust events (M7.0-8.0). Both of these earthquake types pose a significant seismic and tsunami hazard for New Zealand residents.

CosmoQuest Year 1.5: Citizen Scientist Behaviors and Site Usage Across Multiple Projects

NASA Astrophysics Data System (ADS)

Gugliucci, Nicole E.; Gay, P. L.; Bracey, G.; CosmoQuest Team

2013-06-01

CosmoQuest launched as a citizen science portal in January 2012 and has since expanded to include three projects in planetary surface mapping, one completed project searching for KBOs, and several more on the way with various astrophysical science goals. We take a close look at how our users move through the site, how much time they spend on various tasks, project retention rate, and how many use multiple projects on the site. We are also piloting a citizen science motivation survey given to random site users to find out why citizen scientists join new projects and continue to participate. This is part of a larger project using online and real-life interactions to study citizen scientist behaviors, motivations, and learning with a goal of building better community with researchers, volunteers, educators, and developers.

Language Mapping with Navigated Repetitive TMS: Proof of Technique and Validation

PubMed Central

Tarapore, Phiroz E.; Findlay, Anne M.; Honma, Susanne M.; Mizuiri, Danielle; Houde, John F.; Berger, Mitchel S.; Nagarajan, Srikantan S.

2013-01-01

Objective Lesion-based mapping of speech pathways has been possible only during invasive neurosurgical procedures using direct cortical stimulation (DCS). However, navigated transcranial magnetic stimulation (nTMS) may allow for lesion-based interrogation of language pathways noninvasively. Although not lesion-based, magnetoencephalographic imaging (MEGI) is another noninvasive modality for language mapping. In this study, we compare the accuracy of nTMS and MEGI with DCS. Methods Subjects with lesions around cortical language areas underwent preoperative nTMS and MEGI for language mapping. nTMS maps were generated using a repetitive TMS protocol to deliver trains of stimulations during a picture naming task. MEGI activation maps were derived from adaptive spatial filtering of beta-band power decreases prior to overt speech during picture naming and verb generation tasks. The subjects subsequently underwent awake language mapping via intraoperative DCS. The language maps obtained from each of the 3 modalities were recorded and compared. Results nTMS and MEGI were performed on 12 subjects. nTMS yielded 21 positive language disruption sites (11 speech arrest, 5 anomia, and 5 other) while DCS yielded 10 positive sites (2 speech arrest, 5 anomia, and 3 other). MEGI isolated 32 sites of peak activation with language tasks. Positive language sites were most commonly found in the pars opercularis for all three modalities. In 9 instances the positive DCS site corresponded to a positive nTMS site, while in 1 instance it did not. In 4 instances, a positive nTMS site corresponded to a negative DCS site, while 169 instances of negative nTMS and DCS were recorded. The sensitivity of nTMS was therefore 90%, specificity was 98%, the positive predictive value was 69% and the negative predictive value was 99% as compared with intraoperative DCS. MEGI language sites for verb generation and object naming correlated with nTMS sites in 5 subjects, and with DCS sites in 2 subjects. Conclusion Maps of language function generated with nTMS correlate well with those generated by DCS. Negative nTMS mapping also correlates with negative DCS mapping. In our study, MEGI lacks the same level of correlation with intraoperative mapping; nevertheless it provides useful adjunct information in some cases. nTMS may offer a lesion-based method for noninvasively interrogating language pathways and be valuable in managing patients with peri-eloquent lesions. PMID:23702420

SfiI genomic cleavage map of Escherichia coli K-12 strain MG1655.

PubMed Central

Perkins, J D; Heath, J D; Sharma, B R; Weinstock, G M

1992-01-01

An SfiI restriction map of Escherichia coli K-12 strain MG1655 is presented. The map contains thirty-one cleavage sites separating fragments ranging in size from 407 kb to 3.7 kb. Several techniques were used in the construction of this map, including CHEF pulsed field gel electrophoresis; physical analysis of a set of twenty-six auxotrophic transposon insertions; correlation with the restriction map of Kohara and coworkers using the commercially available E. coli Gene Mapping Membranes; analysis of publicly available sequence information; and correlation of the above data with the combined genetic and physical map developed by Rudd, et al. The combination of these techniques has yielded a map in which all but one site can be localized within a range of +/- 2 kb, and over half the sites can be localized precisely by sequence data. Two sites present in the EcoSeq5 sequence database are not cleaved in MG1655 and four sites are noted to be sensitive to methylation by the dcm methylase. This map, combined with the NotI physical map of MG1655, can aid in the rapid, precise mapping of several different types of genetic alterations, including transposon mediated mutations and other insertions, inversions, deletions and duplications. Images PMID:1312707

Investigation and identification of functional post-translational modification sites associated with drug binding and protein-protein interactions.

PubMed

Su, Min-Gang; Weng, Julia Tzu-Ya; Hsu, Justin Bo-Kai; Huang, Kai-Yao; Chi, Yu-Hsiang; Lee, Tzong-Yi

2017-12-21

Protein post-translational modification (PTM) plays an essential role in various cellular processes that modulates the physical and chemical properties, folding, conformation, stability and activity of proteins, thereby modifying the functions of proteins. The improved throughput of mass spectrometry (MS) or MS/MS technology has not only brought about a surge in proteome-scale studies, but also contributed to a fruitful list of identified PTMs. However, with the increase in the number of identified PTMs, perhaps the more crucial question is what kind of biological mechanisms these PTMs are involved in. This is particularly important in light of the fact that most protein-based pharmaceuticals deliver their therapeutic effects through some form of PTM. Yet, our understanding is still limited with respect to the local effects and frequency of PTM sites near pharmaceutical binding sites and the interfaces of protein-protein interaction (PPI). Understanding PTM's function is critical to our ability to manipulate the biological mechanisms of protein. In this study, to understand the regulation of protein functions by PTMs, we mapped 25,835 PTM sites to proteins with available three-dimensional (3D) structural information in the Protein Data Bank (PDB), including 1785 modified PTM sites on the 3D structure. Based on the acquired structural PTM sites, we proposed to use five properties for the structural characterization of PTM substrate sites: the spatial composition of amino acids, residues and side-chain orientations surrounding the PTM substrate sites, as well as the secondary structure, division of acidity and alkaline residues, and solvent-accessible surface area. We further mapped the structural PTM sites to the structures of drug binding and PPI sites, identifying a total of 1917 PTM sites that may affect PPI and 3951 PTM sites associated with drug-target binding. An integrated analytical platform (CruxPTM), with a variety of methods and online molecular docking tools for exploring the structural characteristics of PTMs, is presented. In addition, all tertiary structures of PTM sites on proteins can be visualized using the JSmol program. Resolving the function of PTM sites is important for understanding the role that proteins play in biological mechanisms. Our work attempted to delineate the structural correlation between PTM sites and PPI or drug-target binding. CurxPTM could help scientists narrow the scope of their PTM research and enhance the efficiency of PTM identification in the face of big proteome data. CruxPTM is now available at http://csb.cse.yzu.edu.tw/CruxPTM/ .

Computational and Biochemical Docking of the Irreversible Cocaine Analog RTI 82 Directly Demonstrates Ligand Positioning in the Dopamine Transporter Central Substrate-binding Site*

PubMed Central

Dahal, Rejwi Acharya; Pramod, Akula Bala; Sharma, Babita; Krout, Danielle; Foster, James D.; Cha, Joo Hwan; Cao, Jianjing; Newman, Amy Hauck; Lever, John R.; Vaughan, Roxanne A.; Henry, L. Keith

2014-01-01

The dopamine transporter (DAT) functions as a key regulator of dopaminergic neurotransmission via re-uptake of synaptic dopamine (DA). Cocaine binding to DAT blocks this activity and elevates extracellular DA, leading to psychomotor stimulation and addiction, but the mechanisms by which cocaine interacts with DAT and inhibits transport remain incompletely understood. Here, we addressed these questions using computational and biochemical methodologies to localize the binding and adduction sites of the photoactivatable irreversible cocaine analog 3β-(p-chlorophenyl)tropane-2β-carboxylic acid, 4′-azido-3′-iodophenylethyl ester ([125I]RTI 82). Comparative modeling and small molecule docking indicated that the tropane pharmacophore of RTI 82 was positioned in the central DA active site with an orientation that juxtaposed the aryliodoazide group for cross-linking to rat DAT Phe-319. This prediction was verified by focused methionine substitution of residues flanking this site followed by cyanogen bromide mapping of the [125I]RTI 82-labeled mutants and by the substituted cysteine accessibility method protection analyses. These findings provide positive functional evidence linking tropane pharmacophore interaction with the core substrate-binding site and support a competitive mechanism for transport inhibition. This synergistic application of computational and biochemical methodologies overcomes many uncertainties inherent in other approaches and furnishes a schematic framework for elucidating the ligand-protein interactions of other classes of DA transport inhibitors. PMID:25179220

47 CFR 73.4108 - FM transmitter site map submissions.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 47 Telecommunication 4 2011-10-01 2011-10-01 false FM transmitter site map submissions. 73.4108 Section 73.4108 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) BROADCAST RADIO SERVICES RADIO BROADCAST SERVICES Rules Applicable to All Broadcast Stations § 73.4108 FM transmitter site map...

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

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

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

Molecular Features of Phosphatase and Tensin Homolog (PTEN) Regulation by C-terminal Phosphorylation*

PubMed Central

Chen, Zan; Dempsey, Daniel R.; Thomas, Stefani N.; Hayward, Dawn; Bolduc, David M.; Cole, Philip A.

2016-01-01

PTEN is a tumor suppressor that functions to negatively regulate the PI3K/AKT pathway as the lipid phosphatase for phosphatidylinositol 3,4,5-triphosphate. Phosphorylation of a cluster of Ser/Thr residues (amino acids 380–385) on the C-terminal tail serves to alter the conformational state of PTEN from an open active state to a closed inhibited state, resulting in a reduction of plasma membrane localization and inhibition of enzyme activity. The relative contribution of each phosphorylation site to PTEN autoinhibition and the structural basis for the conformational closure is still unclear. To further the structural understanding of PTEN regulation by C-terminal tail phosphorylation, we used protein semisynthesis to insert stoichiometric and site-specific phospho-Ser/Thr(s) in the C-terminal tail of PTEN. Additionally, we employed photo-cross-linking to map the intramolecular PTEN interactions of the phospho-tail. Systematic evaluation of the PTEN C-tail phospho-cluster showed autoinhibition, and conformational closure was influenced by the aggregate effect of multiple phospho-sites rather than dominated by a single phosphorylation site. Moreover, photo-cross-linking suggested a direct interaction between the PTEN C-tail and a segment in the N-terminal region of the catalytic domain. Mutagenesis experiments provided additional insights into how the PTEN phospho-tail interacts with both the C2 and catalytic domains. PMID:27226612

Human-Robot Site Survey and Sampling for Space Exploration

NASA Technical Reports Server (NTRS)

Fong, Terrence; Bualat, Maria; Edwards, Laurence; Flueckiger, Lorenzo; Kunz, Clayton; Lee, Susan Y.; Park, Eric; To, Vinh; Utz, Hans; Ackner, Nir

2006-01-01

NASA is planning to send humans and robots back to the Moon before 2020. In order for extended missions to be productive, high quality maps of lunar terrain and resources are required. Although orbital images can provide much information, many features (local topography, resources, etc) will have to be characterized directly on the surface. To address this need, we are developing a system to perform site survey and sampling. The system includes multiple robots and humans operating in a variety of team configurations, coordinated via peer-to-peer human-robot interaction. In this paper, we present our system design and describe planned field tests.

phiGENOME: an integrative navigation throughout bacteriophage genomes.

PubMed

Stano, Matej; Klucar, Lubos

2011-11-01

phiGENOME is a web-based genome browser generating dynamic and interactive graphical representation of phage genomes stored in the phiSITE, database of gene regulation in bacteriophages. phiGENOME is an integral part of the phiSITE web portal (http://www.phisite.org/phigenome) and it was optimised for visualisation of phage genomes with the emphasis on the gene regulatory elements. phiGENOME consists of three components: (i) genome map viewer built using Adobe Flash technology, providing dynamic and interactive graphical display of phage genomes; (ii) sequence browser based on precisely formatted HTML tags, providing detailed exploration of genome features on the sequence level and (iii) regulation illustrator, based on Scalable Vector Graphics (SVG) and designed for graphical representation of gene regulations. Bringing 542 complete genome sequences accompanied with their rich annotations and references, makes phiGENOME a unique information resource in the field of phage genomics. Copyright © 2011 Elsevier Inc. All rights reserved.

Amicoumacin A inhibits translation by stabilizing mRNA interaction with the ribosome

PubMed Central

Polikanov, Yury S.; Osterman, Ilya A.; Szal, Teresa; Tashlitsky, Vadim N.; Serebryakova, Marina V.; Kusochek, Pavel; Bulkley, David; Malanicheva, Irina A.; Efimenko, Tatyana A.; Efremenkova, Olga V.; Konevega, Andrey L.; Shaw, Karen J.; Bogdanov, Alexey A.; Rodnina, Marina V.; Dontsova, Olga A.; Mankin, Alexander S.; Steitz, Thomas A.; Sergiev, Petr V.

2014-01-01

SUMMARY We demonstrate that the antibiotic amicoumacin A (AMI) whose cellular target was unknown, is a potent inhibitor of protein synthesis. Resistance mutations in helix 24 of the 16S rRNA mapped the AMI binding site to the small ribosomal subunit. The crystal structure of bacterial ribosome in complex with AMI solved at 2.4 Å resolution revealed that the antibiotic makes contacts with universally conserved nucleotides of 16S rRNA in the E site and the mRNA backbone. Simultaneous interactions of AMI with 16S rRNA and mRNA and the in vivo experimental evidence suggest that it may inhibit the progression of the ribosome along mRNA. Consistent with this proposal, binding of AMI interferes with translocation in vitro. The inhibitory action of AMI can be partly compensated by mutations in the translation elongation factor G. PMID:25306919

Intrinsic disorder in scaffold proteins: Getting more from less

PubMed Central

Cortese, Marc S.; Uversky, Vladimir N.; Dunker, A. Keith

2008-01-01

Regulation, recognition and cell signaling involve the coordinated actions of many players. Signaling scaffolds, with their ability to bring together proteins belonging to common and/or interlinked pathways, play crucial roles in orchestrating numerous events by coordinating specific interactions among signaling proteins. This review examines the roles of intrinsic disorder (ID) in signaling scaffold protein function. Several well-characterized scaffold proteins with structurally and functionally characterized ID regions are used here to illustrate the importance of ID for scaffolding function. These examples include scaffolds that are mostly disordered, only partially disordered or those in which the ID resides in a scaffold partner. Specific scaffolds discussed include RNase, voltage-activated potassium channels, axin, BRCA1, GSK-3β, p53, Ste5, titin, Fus3, BRCA1, Titin, MAP2, D-AKAP2 and AKAP250. Among the mechanisms discussed are: molecular recognition features, fly-casting, ease of encounter complex formation, structural isolation of partners, modulation of interactions between bound partners, masking of intramolecular interaction sites, maximized interaction surface per residue, toleration of high evolutionary rates, binding site overlap, allosteric modification, palindromic binding, reduced constraints for alternative splicing, efficient regulation via posttranslational modification, efficient regulation via rapid degradation, protection of normally solvent-exposed sites, enhancing the plasticity of interaction and molecular crowding. We conclude that ID can enhance scaffold function by a diverse array of mechanisms. In other words, scaffold proteins utilize several ID-facilitated mechanisms to enhance function, and by doing so, get more functionality from less structure. PMID:18619997

Investigation of an "alternate water supply system" in enzymatic hydrolysis in the processive endocellulase Cel7A from Rasamsonia emersonii by molecular dynamics simulation.

PubMed

Sun, Xun; Qian, Meng-Dan; Guan, Shan-Shan; Shan, Ya-Ming; Dong, Ying; Zhang, Hao; Wang, Song; Han, Wei-Wei

2017-02-01

Cel7A from Rasamsonia emersonii is one of the processive endocellulases classified under family 7 glycoside hydrolase. Molecular dynamics simulations were carried out to obtain the optimized sliding and hydrolyzing conformations, in which the reducing ends of sugar chains are located on different sites. Hydrogen bonds are investigated to clarify the interactions between protein and substrate in either conformation. Nine hydrogen bonding interactions are identified in the sliding conformation, and six similar interactions are also found correspondingly in the hydrolyzing conformation. In addition, four strong hydrophobic interactions are also determined. The domain cross-correlation map analysis shows movement correlation of protein including autocorrelation between residues. The root mean square fluctuations analysis represents the various flexibilities of different fragment in the two conformations. Comparing the two conformations reveals the water-supply mechanism of selective hydrolysis of cellulose in Cel7A. The mechanism can be described as follow. When the reducing end of substrate slides from the unhydrolyzing site (sliding conformation) to the hydrolyzing site (hydrolyzing conformation), His225 is pushed down and rotated, the rotation leads to the movement of Glu209 with the interstrand hydrogen bonding in β-sheet. It further makes Asp211 close to the hydrolysis center and provides a water molecule bounding on its carboxyl in the previous unhydrolyzing site. After the hydrolysis takes place and the product is excluded from the enzyme, the Asp211 comes back to its initial position. In summary, Asp211 acts as an elevator to transport outer water molecules into the hydrolysis site for every other glycosidic bond. © 2016 Wiley Periodicals, Inc.

Influence of substrate modification and C-terminal truncation on the active site structure of substrate-bound heme oxygenase from Neisseriae meningitidis; A 1H NMR study†

PubMed Central

Peng, Dungeng; Satterlee, James D.; Ma, Li-Hua; Dallas, Jerry L.; Smith, Kevin M.; Zhang, Xuhong; Sato, Michihiko; La Mar, Gerd N.

2011-01-01

Heme oxygenase, HO, from the pathogenic bacterium N. meningitidis, NmHO, which secures host iron, shares many properties with mammalian HOs, but also exhibits some key differences. The crystal structure appears more compact and the crystal-undetected C-terminus interacts with substrate in solution. The unique nature of substrate-protein, specifically pyrrole-I/II-helix-2, peripheral interactions in NmHO are probed by 2D 1H NMR to reveal unique structural features controlling substrate orientation. The thermodynamics of substrate orientational isomerism are mapped for substrates with individual vinyl → methyl → hydrogen substitutions and with enzyme C-terminal deletions. NmHO exhibits significantly stronger orientational preference, reflecting much stronger and selective pyrrole-I/II interactions with the protein matrix, than in mammalian HOs. Thus, replacing bulky vinyls with hydrogens results in a 180° rotation of substrate about the α,γ-meso axis in the active site. A "collapse" of the substrate pocket as substrate size decreases is reflected in movement of helix-2 toward the substrate as indicated by significant and selective increased NOESY cross peak intensity, increase in steric Fe-CN tilt reflected in the orientation of the major magnetic axis, and decrease in steric constraints controlling the rate of aromatic ring reorientation. The active site of NmHO appears "stressed" for native protohemin and its "collapse" upon replacing vinyls by hydrogen leads to a factor ~102 increase in substrate affinity. Interaction of the C-terminus with the active site destabilizes the crystallographic protohemin orientation by ~0.7 kcal/mol, which is consistent with optimizing the His207-Asp27 H-bond. Implications of the active site "stress" for product release are discussed. PMID:21870860

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

PubMed

Haider, Kamran; Huggins, David J

2013-10-28

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

MAP kinase-independent signaling in angiotensin II regulation of neuromodulation in SHR neurons.

PubMed

Yang, H; Raizada, M K

1998-09-01

Angiotensin II (Ang II), via its interaction with the angiotensin type 1 (AT1) receptor subtype, causes enhanced stimulation of norepinephrine (NE) neuromodulation. This involves increased transcription of NE transporter, tyrosine hydroxylase, and dopamine ss-hydroxylase genes in Wistar-Kyoto rat (WKY) brain neurons. AT1 receptor-mediated regulation of certain signaling events (such as activation of the Ras-Raf-1-mitogen activated protein (MAP) kinase signaling pathway, nuclear translocation of transcription factors such as Fos and Jun, and the interactions of these factors with AP-1 binding sites) is involved in this NE neuromodulation (Lu et al. J Cell Biol. 1996;135:1609-1617). The aim of this study was to compare the signal transduction mechanism of Ang II regulation of NE neuromodulation in WKY and spontaneously hypertensive rat (SHR) brain neurons, in view of the fact that AT1 receptor expression and Ang II stimulation of NE neuromodulation are higher in SHR neurons compared with WKY neurons. Despite this hyperactivity, Ang II stimulation of Ras, Raf-1, and MAP kinase activities was comparable between the neurons from WKY and SHR. Similarly, central injections of Ang II caused a comparable stimulation of MAP kinase in the hypothalamic and brain stem areas of adult WKY and SHR. Inhibition of MAP kinase by either an MAP kinase kinase inhibitor (PD98059) or an MAP kinase antisense oligonucleotide completely attenuated the stimulatory effects of Ang II on [3H]-NE uptake, NE transporter mRNA, and tyrosine hydroxylase mRNA levels in WKY neurons. These treatments resulted in only 43% to 50% inhibition of [3H]-NE uptake and NE transporter and tyrosine hydroxylase mRNAs in SHR neurons. Thus, Ang II stimulation of NE neuromodulation was completely blocked by MAP kinase inhibition in WKY neurons and only partially blocked in the SHR neurons. These observations suggest the presence of an additional signal transduction pathway involved in NE neuromodulation in SHR neurons that is independent of the MAP kinase pathway.

Sitewise manipulations and Mott insulator-superfluid transition of interacting photons using superconducting circuit simulators

DOE PAGES

Deng, Xiuhao; Jia, Chunjing; Chien, Chih-Chun

2015-02-23

We report that the Bose Hubbard model (BHM) of interacting bosons in a lattice has been a paradigm in many-body physics, and it exhibits a Mott insulator (MI)-superfluid (SF) transition at integer filling. Here a quantum simulator of the BHM using a superconducting circuit is proposed. Specifically, a superconducting transmission line resonator supporting microwave photons is coupled to a charge qubit to form one site of the BHM, and adjacent sites are connected by a tunable coupler. To obtain a mapping from the superconducting circuit to the BHM, we focus on the dispersive regime where the excitations remain photonlike. Standardmore » perturbation theory is implemented to locate the parameter range where the MI-SF transition may be simulated. This simulator allows single-site manipulations and we illustrate this feature by considering two scenarios where a single-site manipulation can drive a MI-SF transition. The transition can be analyzed by mean-field analyses, and the exact diagonalization was implemented to provide accurate results. The variance of the photon density and the fidelity metric clearly show signatures of the transition. Lastly, experimental realizations and other possible applications of this simulator are also discussed.« less

Groundwater Levels for Selected Wells in the Chehalis River Basin, Washington

USGS Publications Warehouse

Fasser, E.T.; Julich, R.J.

2010-01-01

Groundwater levels for selected wells in the Chehalis River basin, Washington, are presented on an interactive web-based map to document the spatial distribution of groundwater levels in the study area during late summer 2009. Groundwater level data and well information were collected by the U.S. Geological Survey using standard techniques. The data are stored in the USGS National Water Information System (NWIS), Ground-Water Site-Inventory (GWSI) System.

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

PubMed Central

2015-01-01

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

Rhodopsin TM6 can interact with two separate and distinct sites on arrestin: evidence for structural plasticity and multiple docking modes in arrestin-rhodopsin binding.

PubMed

Sinha, Abhinav; Jones Brunette, Amber M; Fay, Jonathan F; Schafer, Christopher T; Farrens, David L

2014-05-27

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

Mapping alpha-helical induced folding within the intrinsically disordered C-terminal domain of the measles virus nucleoprotein by site-directed spin-labeling EPR spectroscopy.

PubMed

Belle, Valérie; Rouger, Sabrina; Costanzo, Stéphanie; Liquière, Elodie; Strancar, Janez; Guigliarelli, Bruno; Fournel, André; Longhi, Sonia

2008-12-01

Using site-directed spin-labeling EPR spectroscopy, we mapped the region of the intrinsically disordered C-terminal domain of measles virus nucleoprotein (N(TAIL)) that undergoes induced folding. In addition to four spin-labeled N(TAIL) variants (S407C, S488C, L496C, and V517C) (Morin et al. (2006), J Phys Chem 110: 20596-20608), 10 new single-site cysteine variants were designed, purified from E. coli, and spin-labeled. These 14 spin-labeled variants enabled us to map in detail the gain of rigidity of N(TAIL) in the presence of either the secondary structure stabilizer 2,2,2-trifluoroethanol or the C-terminal domain X (XD) of the viral phosphoprotein. Different regions of N(TAIL) were shown to contribute to a different extent to the binding to XD, while the mobility of the spin labels grafted at positions 407 and 460 was unaffected upon addition of XD; that of the spin labels grafted within the 488-502 and the 505-522 regions was severely and moderately reduced, respectively. Furthermore, EPR experiments in the presence of 30% sucrose allowed us to precisely map to residues 488-502, the N(TAIL) region undergoing alpha-helical folding. The mobility of the 488-502 region was found to be restrained even in the absence of the partner, a behavior that could be accounted for by the existence of a transiently populated folded state. Finally, we show that the restrained motion of the 505-522 region upon binding to XD is due to the alpha-helical transition occurring within the 488-502 region and not to a direct interaction with XD.

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

USGS Publications Warehouse

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

2007-01-01

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

Developing a novel comprehensive framework for the investigation of cellular and whole heart electrophysiology in the in situ human heart: historical perspectives, current progress and future prospects.

PubMed

Taggart, Peter; Orini, Michele; Hanson, Ben; Hayward, Martin; Clayton, Richard; Dobrzynski, Halina; Yanni, Joseph; Boyett, Mark; Lambiase, Pier D

2014-08-01

Understanding the mechanisms of fatal ventricular arrhythmias is of great importance. In view of the many electrophysiological differences that exist between animal species and humans, the acquisition of basic electrophysiological data in the intact human heart is essential to drive and complement experimental work in animal and in-silico models. Over the years techniques have been developed to obtain basic electrophysiological signals directly from the patients by incorporating these measurements into routine clinical procedures which access the heart such as cardiac catheterisation and cardiac surgery. Early recordings with monophasic action potentials provided valuable information including normal values for the in vivo human heart, cycle length dependent properties, the effect of ischaemia, autonomic nervous system activity, and mechano-electric interaction. Transmural recordings addressed the controversial issue of the mid myocardial "M" cell. More recently, the technique of multielectrode mapping (256 electrodes) developed in animal models has been extended to humans, enabling mapping of activation and repolarisation on the entire left and right ventricular epicardium in patients during cardiac surgery. Studies have examined the issue of whether ventricular fibrillation was driven by a "mother" rotor with inhomogeneous and fragmented conduction as in some animal models, or by multiple wavelets as in other animal studies; results showed that both mechanisms are operative in humans. The simpler spatial organisation of human VF has important implications for treatment and prevention. To link in-vivo human electrophysiological mapping with cellular biophysics, multielectrode mapping is now being combined with myocardial biopsies. This technique enables region-specific electrophysiology changes to be related to underlying cellular biology, for example: APD alternans, which is a precursor of VF and sudden death. The mechanism is incompletely understood but related to calcium cycling and APD restitution. Multielectrode sock mapping during incremental pacing enables epicardial sites to be identified which exhibit marked APD alternans and sites where APD alternans is absent. Whole heart electrophysiology is assessed by activation repolarisation mapping and analysis is performed immediately on-site in order to guide biopsies to specific myocardial sites. Samples are analysed for ion channel expression, Ca(2+)-handling proteins, gap junctions and extracellular matrix. This new comprehensive approach to bridge cellular and whole heart electrophysiology allowed to identify 20 significant changes in mRNA for ion channels Ca(2+)-handling proteins, a gap junction channel, a Na(+)-K(+) pump subunit and receptors (particularly Kir 2.1) between the positive and negative alternans sites. Copyright © 2014 Elsevier Ltd. All rights reserved.

Candidate Cell and Matrix Interaction Domains on the Collagen Fibril, the Predominant Protein of Vertebrates*S⃞

PubMed Central

Sweeney, Shawn M.; Orgel, Joseph P.; Fertala, Andrzej; McAuliffe, Jon D.; Turner, Kevin R.; Di Lullo, Gloria A.; Chen, Steven; Antipova, Olga; Perumal, Shiamalee; Ala-Kokko, Leena; Forlino, Antonella; Cabral, Wayne A.; Barnes, Aileen M.; Marini, Joan C.; Antonio, James D. San

2008-01-01

Type I collagen, the predominant protein of vertebrates, polymerizes with type III and V collagens and non-collagenous molecules into large cable-like fibrils, yet how the fibril interacts with cells and other binding partners remains poorly understood. To help reveal insights into the collagen structure-function relationship, a data base was assembled including hundreds of type I collagen ligand binding sites and mutations on a two-dimensional model of the fibril. Visual examination of the distribution of functional sites, and statistical analysis of mutation distributions on the fibril suggest it is organized into two domains. The “cell interaction domain” is proposed to regulate dynamic aspects of collagen biology, including integrin-mediated cell interactions and fibril remodeling. The “matrix interaction domain” may assume a structural role, mediating collagen cross-linking, proteoglycan interactions, and tissue mineralization. Molecular modeling was used to superimpose the positions of functional sites and mutations from the two-dimensional fibril map onto a three-dimensional x-ray diffraction structure of the collagen microfibril in situ, indicating the existence of domains in the native fibril. Sequence searches revealed that major fibril domain elements are conserved in type I collagens through evolution and in the type II/XI collagen fibril predominant in cartilage. Moreover, the fibril domain model provides potential insights into the genotype-phenotype relationship for several classes of human connective tissue diseases, mechanisms of integrin clustering by fibrils, the polarity of fibril assembly, heterotypic fibril function, and connective tissue pathology in diabetes and aging. PMID:18487200

Candidate Cell and Matrix Interaction Domains on the Collagen Fibril, the Predominant Protein of Vertebrates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sweeney, Shawn M.; Orgel, Joseph P.; Fertala, Andrzej

Type I collagen, the predominant protein of vertebrates, polymerizes with type III and V collagens and non-collagenous molecules into large cable-like fibrils, yet how the fibril interacts with cells and other binding partners remains poorly understood. To help reveal insights into the collagen structure-function relationship, a data base was assembled including hundreds of type I collagen ligand binding sites and mutations on a two-dimensional model of the fibril. Visual examination of the distribution of functional sites, and statistical analysis of mutation distributions on the fibril suggest it is organized into two domains. The 'cell interaction domain' is proposed to regulatemore » dynamic aspects of collagen biology, including integrin-mediated cell interactions and fibril remodeling. The 'matrix interaction domain' may assume a structural role, mediating collagen cross-linking, proteoglycan interactions, and tissue mineralization. Molecular modeling was used to superimpose the positions of functional sites and mutations from the two-dimensional fibril map onto a three-dimensional x-ray diffraction structure of the collagen microfibril in situ, indicating the existence of domains in the native fibril. Sequence searches revealed that major fibril domain elements are conserved in type I collagens through evolution and in the type II/XI collagen fibril predominant in cartilage. Moreover, the fibril domain model provides potential insights into the genotype-phenotype relationship for several classes of human connective tissue diseases, mechanisms of integrin clustering by fibrils, the polarity of fibril assembly, heterotypic fibril function, and connective tissue pathology in diabetes and aging.« less

GIS Tool for Real-time Decision Making and Analysis of Multidisciplinary Cryosphere Datasets.

NASA Astrophysics Data System (ADS)

Roberts, S. D.; Moore, J. A.

2004-12-01

In support of the Western Arctic Shelf-Basin Interaction Project(SBI) a web-based interactive mapping server was installed on the USCGC Healy's on-board science computer network during its 2004 spring(HLY-04-02) and summer cruises (HLY-04-03) in the Chukchi and Beaufort Seas. SBI is a National Science Foundation sponsored multi-year and multidisciplinary project studying the biological productivity in the region. The mapping server was developed by the UCAR Joint Office of Science Support(JOSS) using OpenSource GIS tools(University of Minnesota Mapserver and USGS MapSurfer). Additional OpenSource tools such as GMT and MB-Systems were also utilized. The key layers in this system are the current ship track, station locations, multibeam bottom bathymetry, IBCAO bathymetry, DMSP satellite imagery , NOAA AVHRR Sea Surface temperature and all past SBI Project ship tracks and station locations. The ship track and multibeam layers are updated in real-time and the satellite layers are updated daily only during clear weather. In addition to using current high resolution multibeam bathymetry data, a composite high resolution bathymetry layer was created using multibeam data from past cruises in the SBI region. The server provides click-and-drag zooms, pan, feature query, distance measure and lat/lon/depth querys on a polar projection map of the arctic ocean. The main use of the system on the ship was for cruise track and station position planning by the scientists utilizing all available historical data and high resolution bathymetry. It was also the main source of information to all the scientist on board as to the cruise progress and plans. The system permitted on-board scientists to integrate historical cruise information for comparative purposes. A mirror web site was set up on land and the current ship track/station information was copied once a day to this site via a satellite link so people interested SBI research could follow the cruise progress.

EnviroAtlas - Austin, TX - Historic Places by Census Block Group

EPA Pesticide Factsheets

This EnviroAtlas dataset portrays the total number of historic places located within each Census Block Group (CBG). The historic places data were compiled from the National Register of Historic Places, which provides official federal lists of districts, sites, buildings, structures and objects significant to American history, architecture, archeology, engineering, and culture.This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

Direct integrin alphavbeta6-ERK binding: implications for tumour growth.

PubMed

Ahmed, Nuzhat; Niu, Jun; Dorahy, Douglas J; Gu, Xinhua; Andrews, Sarah; Meldrum, Cliff J; Scott, Rodney J; Baker, Mark S; Macreadie, Ian G; Agrez, Michael V

2002-02-21

Blockade of the mitogen-activated protein (MAP) kinase pathway suppresses growth of colon cancer in vivo. Here we demonstrate a direct link between the extracellular signal-regulated kinase ERK2 and the growth-promoting cell adhesion molecule, integrin alphavbeta6, in colon cancer cells. Down-regulation of beta6 integrin subunit expression inhibits tumour growth in vivo and MAP kinase activity in response to serum stimulation. In alphavbeta6-expressing cells ERK2 is bound only to the beta6 subunit. The increase in cytosolic MAP kinase activity upon epidermal growth factor stimulation is all accounted for by beta6-bound ERK. Deletion of the ERK2 binding site on the beta6 cytoplasmic domain inhibits tumour growth and leads to an association between ERK and the beta5 subunit. The physical interaction between integrin alphavbeta6 and ERK2 defines a novel paradigm of integrin-mediated signalling and provides a therapeutic target for cancer treatment.

Apparent Resistivity and Estimated Interaction Potential of Surface Water and Groundwater along Selected Canals and Streams in the Elkhorn-Loup Model Study Area, North-Central Nebraska, 2006-07

USGS Publications Warehouse

Teeple, Andrew; Vrabel, Joseph; Kress, Wade H.; Cannia, James C.

2009-01-01

In 2005, the State of Nebraska adopted new legislation that in part requires local Natural Resources Districts to include the effect of groundwater use on surface-water systems in their groundwater management plan. In response the U.S. Geological Survey, in cooperation with the Upper Elkhorn, Lower Elkhorn, Upper Loup, Lower Loup, Middle Niobrara, Lower Niobrara, Lewis and Clark, and Lower Platte North Natural Resources Districts, did a study during 2006-07 to investigate the surface-water and groundwater interaction within a 79,800-square-kilometer area in north-central Nebraska. To determine how streambed materials affect surface-water and groundwater interaction, surface geophysical and lithologic data were integrated at four sites to characterize the hydrogeologic conditions within the study area. Frequency-domain electromagnetic and waterborne direct- current resistivity profiles were collected to map the near-surface hydrogeologic conditions along sections of Ainsworth Canal near Ainsworth, Nebraska; Mirdan and Geranium Canals near Ord, Nebraska; North Loup River near Ord, Nebraska; and Middle Loup River near Thedford, Nebraska. Lithologic data were collected from test holes at each site to aid interpretation of the geophysical data. Geostatistical analysis incorporating the spatial variability of resistivity was used to account for the effect of lithologic heterogeneity on effective hydraulic permeability. The geostatistical analysis and lithologic data descriptions were used to make an interpretation of the hydrogeologic system and derive estimates of surface-water/groundwater interaction potential within the canals and streambeds. The estimated interaction potential at the Ainsworth Canal site and the Mirdan and Geranium Canal site is generally low to moderately low. The sediment textures at nearby test holes typically were silt and clay and fine-to-medium sand. The apparent resistivity values for these sites ranged from 2 to 120 ohm-meters. The vertical and horizontal variability of the apparent resistivity data were consistently low. Low resistive variability indicates little lithologic heterogeneity for either canal site. The surface-water/groundwater interaction-potential estimates are in agreement with the narrow frequency distribution of resistivity, low apparent resistivities, low spatial heterogeneity, and test-hole grain-size ranges. The estimated surface-water/groundwater interaction potential at the North Loup and Middle Loup River sites is moderate to moderately high. The sediment textures at nearby test holes were predominantly fine, medium, and coarse sand with some silt and silty to sandy clay. The apparent resistivity values for these sites ranged from 34 to 1,338 ohm-meters. The vertical variability of the resistivity data was moderately high. The horizontal variability at these sites is low to moderately low. The higher resistive variability at these sites indicates generally greater lithologic heterogeneity than at either the Ainsworth Canal site or the Mirdan and Geranium Canal site. The surface-water/groundwater interaction-potential estimates are in agreement with the generally moderate to high apparent resistivity, the greater spatial heterogeneity, and the variable lithologic texture. A higher interaction potential as compared to the canal sites is expected because of the higher subsurface resistivity and greater lithologic heterogeneity.

Interactive computer programs for the graphic analysis of nucleotide sequence data.

PubMed Central

Luckow, V A; Littlewood, R K; Rownd, R H

1984-01-01

A group of interactive computer programs have been developed which aid in the collection and graphical analysis of nucleotide and protein sequence data. The programs perform the following basic functions: a) enter, edit, list, and rearrange sequence data; b) permit automatic entry of nucleotide sequence data directly from an autoradiograph into the computer; c) search for restriction sites or other specified patterns and plot a linear or circular restriction map, or print their locations; d) plot base composition; e) analyze homology between sequences by plotting a two-dimensional graphic matrix; and f) aid in plotting predicted secondary structures of RNA molecules. PMID:6546437

Mars Trek: An Interactive Web Portal for Current and Future Missions to Mars

NASA Technical Reports Server (NTRS)

Law, E.; Day, B.

2017-01-01

NASA's Mars Trek (https://marstrek.jpl.nasa.gov) provides a web-based Portal and a suite of interactive visualization and analysis tools to enable mission planners, lunar scientists, and engineers to access mapped data products from past and current missions to Mars. During the past year, the capabilities and data served by Mars Trek have been significantly expanded beyond its original design as a public outreach tool. At the request of NASA's Science Mission Directorate and Human Exploration Operations Mission Directorate, Mars Trek's technology and capabilities are now being extended to support site selection and analysis activities for the first human missions to Mars.

GRAPHICS MANAGER (GFXMGR): An interactive graphics software program for the Advanced Electronics Design (AED) graphics controller, Model 767

DOE Office of Scientific and Technical Information (OSTI.GOV)

Faculjak, D.A.

1988-03-01

Graphics Manager (GFXMGR) is menu-driven, user-friendly software designed to interactively create, edit, and delete graphics displays on the Advanced Electronics Design (AED) graphics controller, Model 767. The software runs on the VAX family of computers and has been used successfully in security applications to create and change site layouts (maps) of specific facilities. GFXMGR greatly benefits graphics development by minimizing display-development time, reducing tedium on the part of the user, and improving system performance. It is anticipated that GFXMGR can be used to create graphics displays for many types of applications. 8 figs., 2 tabs.

Mars Trek: An Interactive Web Portal for Current and Future Missions to Mars

NASA Astrophysics Data System (ADS)

Law, E.; Day, B.

2017-09-01

NASA's Mars Trek (https://marstrek.jpl.nasa.gov) provides a web-based Portal and a suite of interactive visualization and analysis tools to enable mission planners, lunar scientists, and engineers to access mapped data products from past and current missions to Mars. During the past year, the capabilities and data served by Mars Trek have been significantly expanded beyond its original design as a public outreach tool. At the request of NASA's Science Mission Directorate and Human Exploration Operations Mission Directorate, Mars Trek's technology and capabilities are now being extended to support site selection and analysis activities for the first human missions to Mars.

A global interaction network maps a wiring diagram of cellular function

PubMed Central

Costanzo, Michael; VanderSluis, Benjamin; Koch, Elizabeth N.; Baryshnikova, Anastasia; Pons, Carles; Tan, Guihong; Wang, Wen; Usaj, Matej; Hanchard, Julia; Lee, Susan D.; Pelechano, Vicent; Styles, Erin B.; Billmann, Maximilian; van Leeuwen, Jolanda; van Dyk, Nydia; Lin, Zhen-Yuan; Kuzmin, Elena; Nelson, Justin; Piotrowski, Jeff S.; Srikumar, Tharan; Bahr, Sondra; Chen, Yiqun; Deshpande, Raamesh; Kurat, Christoph F.; Li, Sheena C.; Li, Zhijian; Usaj, Mojca Mattiazzi; Okada, Hiroki; Pascoe, Natasha; Luis, Bryan-Joseph San; Sharifpoor, Sara; Shuteriqi, Emira; Simpkins, Scott W.; Snider, Jamie; Suresh, Harsha Garadi; Tan, Yizhao; Zhu, Hongwei; Malod-Dognin, Noel; Janjic, Vuk; Przulj, Natasa; Troyanskaya, Olga G.; Stagljar, Igor; Xia, Tian; Ohya, Yoshikazu; Gingras, Anne-Claude; Raught, Brian; Boutros, Michael; Steinmetz, Lars M.; Moore, Claire L.; Rosebrock, Adam P.; Caudy, Amy A.; Myers, Chad L.; Andrews, Brenda; Boone, Charles

2017-01-01

We generated a global genetic interaction network for Saccharomyces cerevisiae, constructing over 23 million double mutants, identifying ~550,000 negative and ~350,000 positive genetic interactions. This comprehensive network maps genetic interactions for essential gene pairs, highlighting essential genes as densely connected hubs. Genetic interaction profiles enabled assembly of a hierarchical model of cell function, including modules corresponding to protein complexes and pathways, biological processes, and cellular compartments. Negative interactions connected functionally related genes, mapped core bioprocesses, and identified pleiotropic genes, whereas positive interactions often mapped general regulatory connections among gene pairs, rather than shared functionality. The global network illustrates how coherent sets of genetic interactions connect protein complex and pathway modules to map a functional wiring diagram of the cell. PMID:27708008

Coastal system mapping: a new approach to formalising and conceptualising the connectivity of large-scale coastal systems

NASA Astrophysics Data System (ADS)

French, J.; Burningham, H.; Whitehouse, R.

2010-12-01

The concept of the coastal sediment cell has proved invaluable as a basis for estimating sediment budgets and as a framework for coastal management. However, whilst coastal sediment cells are readily identified on compartmentalised coastlines dominated by beach-grade material, the cell concept is less suited to handling broader linkages between estuarine, coastal and offshore systems, and for incorporating longer-range suspended sediment transport. We present a new approach to the conceptualisation of large-scale coastal geomorphic systems based on a hierarchical classification of component landforms and management interventions and mapping of the interactions between them. Coastal system mapping is founded on a classification that identifies high-level landform features, low-level landform elements and engineering interventions. Geomorphic features define the large-scale organisation of a system and include landforms that define gross coastal configuration (e.g. headland, bay) as well as fluvial, estuarine and offshore sub-systems that exchange sediment with and influence the open coast. Detailed system structure is mapped out with reference to a larger set of geomorphic elements (e.g. cliff, dune, beach ridge). Element-element interactions define cross-shore linkages (conceptualised as hinterland, backshore and foreshore zones) and alongshore system structure. Both structural and non-structural engineering interventions are also represented at this level. Element-level mapping is rationalised to represent alongshore variation using as few elements as possible. System linkages include both sediment transfer pathways and influences not associated with direct mass transfer (e.g. effect of a jetty at an inlet). A formal procedure for capturing and graphically representing coastal system structure has been developed around free concept mapping software, CmapTools (http://cmap.ihmc.us). Appended meta-data allow geographic coordinates, data, images and literature pertaining to specific locations to be embedded in system maps. Exported maps can be analysed separately to quantify abundance of system components and their scales of interaction. Our approach is demonstrated for different scales and geomorphic contexts in the UK, including Alnmouth Bay (NE England; 15km), Lowestoft to Felixstowe (E England; 73km) and Cardigan Bay (Wales; 267km). Aerial imagery provides the primary basis for identifying features and elements and likely modes of interaction. This interpretation is then checked against relevant research literature and site data. Coastal system mapping is a kind of knowledge formalisation that generalises disparate sources of information (‘plain data’) into usable knowledge. Consensus-derived system maps are highly effective as a catalyst for structured discussion of geomorphic system behaviour and its implications for coastal management. They also function as a repository for results from quantitative analyses and modelling.

Exploiting Uniformly 13C-Labeled Carbohydrates for Probing Carbohydrate-Protein Interactions by NMR Spectroscopy.

PubMed

Nestor, Gustav; Anderson, Taigh; Oscarson, Stefan; Gronenborn, Angela M

2017-05-03

NMR of a uniformly 13 C-labeled carbohydrate was used to elucidate the atomic details of a sugar-protein complex. The structure of the 13 C-labeled Manα(1-2)Manα(1-2)ManαOMe trisaccharide ligand, when bound to cyanovirin-N (CV-N), was characterized and revealed that in the complex the glycosidic linkage torsion angles between the two reducing-end mannoses are different from the free trisaccharide. Distances within the carbohydrate were employed for conformational analysis, and NOE-based distance mapping between sugar and protein revealed that Manα(1-2)Manα(1-2)ManαOMe is bound more intimately with its two reducing-end mannoses into the domain A binding site of CV-N than with the nonreducing end unit. Taking advantage of the 13 C spectral dispersion of 13 C-labeled carbohydrates in isotope-filtered experiments is a versatile means for a simultaneous mapping of the binding interactions on both, the carbohydrate and the protein.

GEBCO-NF Alumni Team's entry for Shell Ocean Discovery XPRIZE. An innovative seafloor mapping system of an AUV integrated with the newly designed USV SEA-KIT.

NASA Astrophysics Data System (ADS)

Wigley, R. A.; Anderson, R.; Bazhenova, E.; Falconer, R. K. H.; Kearns, T.; Martin, T.; Minami, H.; Roperez, J.; Rosedee, A.; Ryzhov, I.; Sade, H.; Seeboruth, S.; Simpson, B.; Sumiyoshi, M.; Tinmouth, N.; Zarayskaya, Y.; Zwolak, K.

2017-12-01

The international team of Nippon Foundation/GEBCO Alumni was formed to compete in the Shell Ocean Discovery XPRIZE competition. The aim of the Team is to build an innovative seafloor mapping system, not only to successfully compete in the XPRIZE challenge, but also to make a step towards autonomously mapping the complex global seafloor at resolutions not achievable by standard surface mapping systems. This new technology is linked to goals of the recently announced Nippon Foundation-GEBCO Seabed 2030 Project, aiming in highest possible resolution bathymetric mapping of global World Ocean floor by 2030. The mapping system is composed of three main elements: an Unmanned Surface Vessel (USV), an Autonomous Underwater Vehicle (AUV) and an on-shore control station. A newly designed, USV, called SEA-KIT, was be built to interact with any AUV, acting as remote surface access to the deep ocean. The major function of the SEA-KIT in the system design is 1) the potential transportation of a commercially available AUV to and from the launch site to the survey site and 2) the deployment and recovery of the AUV. In further development stages, options for AUV charging and data transfer are considered. Additionally, the SEA-KIT will offer a positioning solution during AUV operations, utilizing an Ultra Short Base Line (USBL) acoustic system. The data acquisition platform (AUV) is equipped with a high-end technology interferometric sonar with synthetic aperture options, providing the possibility of collecting bathymetric data co-registered with seafloor object imagery. An automated data processing workflow is highly desirable due to the large amount of data collected during each mission. The processing workflow is being designed to be as autonomous as possible and an algorithm for automated data processing onboard are being considered to reduce the time of data processing and make a final products available as soon as possible after the completion of data collection. No human intervention on site is required for the operation of data collection using the integrated USV and AUV mapping system. The on-shore control station only plays a supervision role and is able to assess the USV performance, while AUV works autonomously, according to a previously set survey plan. This leads to lower-risk, less-effort deep ocean mapping.

NASA Lunar and Planetary Mapping and Modeling

NASA Astrophysics Data System (ADS)

Day, Brian; Law, Emily

2016-10-01

NASA's Lunar and Planetary Mapping and Modeling Portals provide web-based suites of interactive visualization and analysis tools to enable mission planners, planetary scientists, students, and the general public to access mapped lunar data products from past and current missions for the Moon, Mars, and Vesta. New portals for additional planetary bodies are being planned. This presentation will recap some of the enhancements to these products during the past year and preview work currently being undertaken.New data products added to the Lunar Mapping and Modeling Portal (LMMP) include both generalized products as well as polar data products specifically targeting potential sites for the Resource Prospector mission. New tools being developed include traverse planning and surface potential analysis. Current development work on LMMP also includes facilitating mission planning and data management for lunar CubeSat missions. Looking ahead, LMMP is working with the NASA Astromaterials Office to integrate with their Lunar Apollo Sample database to help better visualize the geographic contexts of retrieved samples. All of this will be done within the framework of a new user interface which, among other improvements, will provide significantly enhanced 3D visualizations and navigation.Mars Trek, the project's Mars portal, has now been assigned by NASA's Planetary Science Division to support site selection and analysis for the Mars 2020 Rover mission as well as for the Mars Human Landing Exploration Zone Sites, and is being enhanced with data products and analysis tools specifically requested by the proposing teams for the various sites. NASA Headquarters is giving high priority to Mars Trek's use as a means to directly involve the public in these upcoming missions, letting them explore the areas the agency is focusing upon, understand what makes these sites so fascinating, follow the selection process, and get caught up in the excitement of exploring Mars.The portals also serve as outstanding resources for education and outreach. As such, they have been designated by NASA's Science Mission Directorate as key supporting infrastructure for the new education programs selected through the division's recent CAN.

Efficient implementation of three-dimensional reference interaction site model self-consistent-field method: Application to solvatochromic shift calculations

NASA Astrophysics Data System (ADS)

Minezawa, Noriyuki; Kato, Shigeki

2007-02-01

The authors present an implementation of the three-dimensional reference interaction site model self-consistent-field (3D-RISM-SCF) method. First, they introduce a robust and efficient algorithm for solving the 3D-RISM equation. The algorithm is a hybrid of the Newton-Raphson and Picard methods. The Jacobian matrix is analytically expressed in a computationally useful form. Second, they discuss the solute-solvent electrostatic interaction. For the solute to solvent route, the electrostatic potential (ESP) map on a 3D grid is constructed directly from the electron density. The charge fitting procedure is not required to determine the ESP. For the solvent to solute route, the ESP acting on the solute molecule is derived from the solvent charge distribution obtained by solving the 3D-RISM equation. Matrix elements of the solute-solvent interaction are evaluated by the direct numerical integration. A remarkable reduction in the computational time is observed in both routes. Finally, the authors implement the first derivatives of the free energy with respect to the solute nuclear coordinates. They apply the present method to "solute" water and formaldehyde in aqueous solvent using the simple point charge model, and the results are compared with those from other methods: the six-dimensional molecular Ornstein-Zernike SCF, the one-dimensional site-site RISM-SCF, and the polarizable continuum model. The authors also calculate the solvatochromic shifts of acetone, benzonitrile, and nitrobenzene using the present method and compare them with the experimental and other theoretical results.

Efficient implementation of three-dimensional reference interaction site model self-consistent-field method: application to solvatochromic shift calculations.

PubMed

Minezawa, Noriyuki; Kato, Shigeki

2007-02-07

The authors present an implementation of the three-dimensional reference interaction site model self-consistent-field (3D-RISM-SCF) method. First, they introduce a robust and efficient algorithm for solving the 3D-RISM equation. The algorithm is a hybrid of the Newton-Raphson and Picard methods. The Jacobian matrix is analytically expressed in a computationally useful form. Second, they discuss the solute-solvent electrostatic interaction. For the solute to solvent route, the electrostatic potential (ESP) map on a 3D grid is constructed directly from the electron density. The charge fitting procedure is not required to determine the ESP. For the solvent to solute route, the ESP acting on the solute molecule is derived from the solvent charge distribution obtained by solving the 3D-RISM equation. Matrix elements of the solute-solvent interaction are evaluated by the direct numerical integration. A remarkable reduction in the computational time is observed in both routes. Finally, the authors implement the first derivatives of the free energy with respect to the solute nuclear coordinates. They apply the present method to "solute" water and formaldehyde in aqueous solvent using the simple point charge model, and the results are compared with those from other methods: the six-dimensional molecular Ornstein-Zernike SCF, the one-dimensional site-site RISM-SCF, and the polarizable continuum model. The authors also calculate the solvatochromic shifts of acetone, benzonitrile, and nitrobenzene using the present method and compare them with the experimental and other theoretical results.

The interaction of E. coli integration host factor and lambda cos DNA: multiple complex formation and protein-induced bending.

PubMed Central

Kosturko, L D; Daub, E; Murialdo, H

1989-01-01

The interaction of E. coli's integration Host Factor (IHF) with fragments of lambda DNA containing the cos site has been studied by gel-mobility retardation and electron microscopy. The cos fragment used in the mobility assays is 398 bp and spans a region from 48,298 to 194 on the lambda chromosome. Several different complexes of IHF with this fragment can be distinguished by their differential mobility on polyacrylamide gels. Relative band intensities indicate that the formation of a complex between IHF and this DNA fragment has an equilibrium binding constant of the same magnitude as DNA fragments containing lambda's attP site. Gel-mobility retardation and electron microscopy have been employed to show that IHF sharply bends DNA near cos and to map the bending site. The protein-induced bend is near an intrinsic bend due to DNA sequence. The position of the bend suggests that IHF's role in lambda DNA packaging may be the enhancement of terminase binding/cos cutting by manipulating DNA structure. Images PMID:2521383

MAPS of Cancer

NASA Technical Reports Server (NTRS)

Gray, Lincoln

1998-01-01

Our goal was to produce an interactive visualization from a mathematical model that successfully predicts metastases from head and neck cancer. We met this goal early in the project. The visualization is available for the public to view. Our work appears to fill a need for more information about this deadly disease. The idea of this project was to make an easily interpretable visualization based on what we call "functional maps" of disease. A functional map is a graphic summary of medical data, where distances between parts of the body are determined by the probability of disease, not by anatomical distances. Functional maps often beat little resemblance to anatomical maps, but they can be used to predict the spread of disease. The idea of modeling the spread of disease in an abstract multidimensional space is difficult for many people. Our goal was to make the important predictions easy to see. NASA must face this problem frequently: how to help laypersons and professionals see important trends in abstract, complex data. We took advantage of concepts perfected in NASA's graphics libraries. As an analogy, consider a functional map of early America. Suppose we choose travel times, rather than miles, as our measures of inter-city distances. For Abraham Lincoln, travel times would have been the more meaningful measure of separation between cities. In such a map New Orleans would be close to Memphis because of the Mississippi River. St. Louis would be close to Portland because of the Oregon Trail. Oklahoma City would be far from Little Rock because of the Cheyenne. Such a map would look puzzling to those of us who have always seen physical maps, but the functional map would be more useful in predicting the probabilities of inter-site transit. Continuing the analogy, we could predict the spread of social diseases such as gambling along the rivers and cattle rustling along the trails. We could simply print the functional map of America, but it would be more interesting to show meaningful patterns of dispersal. We had previously published the functional map of the head and neck, but it was difficult to explain to either patients or surgeons because that view of our body did not resemble anatomy. This discrepancy between functional and physical maps is just a mathematical restatement of the well-known fact that some diseases, such as head and neck cancer, spread in complex patterns, not always to the next nearest site. We had discovered that a computer could re-arrange anatomy so that this particular disease spreads to the next nearest site. The functional map explains over 95% of the metastases in 1400 patients. In a sense, we had graphed what our body "looks like" to a tumor. The tumor readily travels between adjacent areas in the functional map. The functional map is a succinct visual display of trends that are not easily appreciated in tables of probabilities.

Mapping and analysis of phosphorylation sites: a quick guide for cell biologists

PubMed Central

Dephoure, Noah; Gould, Kathleen L.; Gygi, Steven P.; Kellogg, Douglas R.

2013-01-01

A mechanistic understanding of signaling networks requires identification and analysis of phosphorylation sites. Mass spectrometry offers a rapid and highly sensitive approach to mapping phosphorylation sites. However, mass spectrometry has significant limitations that must be considered when planning to carry out phosphorylation-site mapping. Here we provide an overview of key information that should be taken into consideration before beginning phosphorylation-site analysis, as well as a step-by-step guide for carrying out successful experiments. PMID:23447708

Global Profiling of hnRNP A2/B1-RNA Binding on Chromatin Highlights LncRNA Interactions.

PubMed

Nguyen, Eric D; Balas, Maggie M; Griffin, April M; Roberts, Justin T; Johnson, Aaron M

2018-06-23

Long noncoding RNAs (lncRNAs) often carry out their functions through associations with adaptor proteins. We recently identified heterogeneous ribonucleoprotein (hnRNP) A2/B1 as an adaptor of the human HOTAIR lncRNA. hnRNP A2 and B1 are splice isoforms of the same gene. The spliced version of HOTAIR preferentially associates with the B1 isoform, which we hypothesize contributes to RNA-RNA matching between HOTAIR and transcripts of target genes in breast cancer. Here we used enhanced cross-linking immunoprecipitation (eCLIP) to map the direct interactions between A2/B1 and RNA in breast cancer cells. Despite differing by only twelve amino acids, the A2 and B1 splice isoforms associate preferentially with distinct populations of RNA in vivo. Through cellular fractionation experiments we characterize the pattern of RNA association in chromatin, nucleoplasm, and cytoplasm. We find that a majority of interactions occur on chromatin, even those that do not contribute to co-transcriptional splicing. A2/B1 binding site locations on multiple RNAs hint at a contribution to the regulation and function of lncRNAs. Surprisingly, the strongest A2/B1 binding site occurs in a retained intron of HOTAIR, which interrupts an RNA-RNA interaction hotspot. In vitro eCLIP experiments highlight additional exonic B1 binding sites in HOTAIR which also surround the RNA-RNA interaction hotspot. Interestingly, a version of HOTAIR with the intron retained is still capable of making RNA-RNA interactions in vitro through the hotspot region. Our data further characterize the multiple functions of a repurposed splicing factor with isoform-biased interactions, and highlight that the majority of these functions occur on chromatin-associated RNA.

47 CFR 73.4108 - FM transmitter site map submissions.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 47 Telecommunication 4 2010-10-01 2010-10-01 false FM transmitter site map submissions. 73.4108... RADIO BROADCAST SERVICES Rules Applicable to All Broadcast Stations § 73.4108 FM transmitter site map submissions. See Memorandum Opinion and Order and Public Notice, adopted October 24, 1986. 1 FCC Rcd 381 (1986...

Histological evidence for muscle insertion in extant amniote femora: implications for muscle reconstruction in fossils.

PubMed

Petermann, Holger; Sander, Martin

2013-04-01

Since the 19th century, identification of muscle attachment sites on bones has been important for muscle reconstructions, especially in fossil tetrapods, and therefore has been the subject of numerous biological and paleontological studies. At the microscopic level, in histological thin sections, the only features that can be used reliably for identifying tendon-bone or muscle-tendon-bone interactions are Sharpey's fibers. Muscles, however, do not only attach to the bone indirectly with tendons, but also directly. Previous studies failed to provide new indicators for muscle attachment, or to address the question of whether muscles with direct attachment can be identified histologically. However, histological identification of direct muscle attachments is important because these attachments do not leave visible marks (e.g. scars and rugosities) on the bone surface. We dissected the right hind limb and mapped the muscle attachment sites on the femur of one rabbit (Oryctolagus cuniculus), one Alligator mississippiensis, and one turkey (Meleagris cuniculus). We then extracted the femur and prepared four histological thin sections for the rabbit and the turkey and five histological thin sections for the alligator. Sharpey's fibers, vascular canal orientation, and a frayed periosteal margin can be indicators for indirect but also direct muscle attachment. Sharpey's fibers can be oriented to the cutting plane of the thin section at high angles, and two Sharpey's fibers orientations can occur in one area, possibly indicating a secondary force axis. However, only about 60% of mapped muscle attachment sites could be detected in thin sections, and frequently histological features suggestive of muscle attachment occurred outside mapped sites. While these insights should improve our ability to successfully identify and reconstruct muscles in extinct species, they also show the limitations of this approach. © 2013 The Authors Journal of Anatomy © 2013 Anatomical Society.

Histological evidence for muscle insertion in extant amniote femora: implications for muscle reconstruction in fossils

PubMed Central

Petermann, Holger; Sander, Martin

2013-01-01

Since the 19th century, identification of muscle attachment sites on bones has been important for muscle reconstructions, especially in fossil tetrapods, and therefore has been the subject of numerous biological and paleontological studies. At the microscopic level, in histological thin sections, the only features that can be used reliably for identifying tendon–bone or muscle–tendon-bone interactions are Sharpey's fibers. Muscles, however, do not only attach to the bone indirectly with tendons, but also directly. Previous studies failed to provide new indicators for muscle attachment, or to address the question of whether muscles with direct attachment can be identified histologically. However, histological identification of direct muscle attachments is important because these attachments do not leave visible marks (e.g. scars and rugosities) on the bone surface. We dissected the right hind limb and mapped the muscle attachment sites on the femur of one rabbit (Oryctolagus cuniculus), one Alligator mississippiensis, and one turkey (Meleagris cuniculus). We then extracted the femur and prepared four histological thin sections for the rabbit and the turkey and five histological thin sections for the alligator. Sharpey's fibers, vascular canal orientation, and a frayed periosteal margin can be indicators for indirect but also direct muscle attachment. Sharpey's fibers can be oriented to the cutting plane of the thin section at high angles, and two Sharpey's fibers orientations can occur in one area, possibly indicating a secondary force axis. However, only about 60% of mapped muscle attachment sites could be detected in thin sections, and frequently histological features suggestive of muscle attachment occurred outside mapped sites. While these insights should improve our ability to successfully identify and reconstruct muscles in extinct species, they also show the limitations of this approach. PMID:23439026

Mapping of chloroplast mutations conferring resistance to antibiotics in Chlamydomonas: evidence for a novel site of streptomycin resistance in the small subunit rRNA.

PubMed

Gauthier, A; Turmel, M; Lemieux, C

1988-10-01

A major obstacle to our understanding of the mechanisms governing the inheritance, recombination and segregation of chloroplast genes in Chlamydomonas is that the majority of antibiotic resistance mutations that have been used to gain insights into such mechanisms have not been physically localized on the chloroplast genome. We report here the physical mapping of two chloroplast antibiotic resistance mutations: one conferring cross-resistance to erythromycin and spiramycin in Chlamydomonas moewusii (er-nM1) and the other conferring resistance to streptomycin in the interfertile species C. eugametos (sr-2). The er-nM1 mutation results from a C to G transversion at a well-known site of macrolide resistance within the peptidyl transferase loop region of the large subunit rRNA gene. This locus, designated rib-2 in yeast mitochondrial DNA, corresponds to residue C-2611 in the 23 S rRNA of Escherichia coli. The sr-2 locus maps within the small subunit (SSU) rRNA gene at a site that has not been described previously. The mutation results from an A to C transversion at a position equivalent to residue A-523 in the E. coli 16 S rRNA. Although this region of the E. coli SSU rRNA has no binding affinity for streptomycin, it binds to ribosomal protein S4, a protein that has long been associated with the response of bacterial cells to this antibiotic. We propose that the sr-2 mutation indirectly affects the nearest streptomycin binding site through an altered interaction between a ribosomal protein and the SSU rRNA.

Climate-Smart Seedlot Selection Tool: Reforestation and Restoration for the 21st Century

NASA Astrophysics Data System (ADS)

Stevenson-Molnar, N.; Howe, G.; St Clair, B.; Bachelet, D. M.; Ward, B. C.

2017-12-01

Local populations of trees are generally adapted to their local climates. Historically, this has meant that local seed zones based on geography and elevation have been used to guide restoration and reforestation. In the face of climate change, seeds from local sources will likely be subjected to climates significantly different from those to which they are currently adapted. The Seedlot Selection Tool (SST) offers a new approach for matching seed sources with planting sites based on future climate scenarios. The SST is a mapping program designed for forest managers and researchers. Users can use the tool to to find seedlots for a given planting site, or to find potential planting sites for a given seedlot. Users select a location (seedlot or planting site), climate scenarios (a climate to which seeds are adapted, and a current or future climate scenario), climate variables, and transfer limits (the maximum climatic distance that is considered a suitable match). Transfer limits are provided by the user, or derived from the range of values within a geographically defined seed zone. The tool calculates scores across the landscape based on an area's similarity, in a multivariate climate space, to the input. Users can explore results on an interactive map, and export PDF and PowerPoint reports, including a map of the results along with the inputs used. Planned future improvements include support for non-forest use cases and ability to download results as GeoTIFF data. The Seedlot Selection Tool and its source code are available online at https://seedlotselectiontool.org. It is co-developed by the United States Forest Service, Oregon State University, and the Conservation Biology Institute.

Tissue-Specific Chromatin Modifications at a Multigene Locus Generate Asymmetric Transcriptional Interactions

PubMed Central

Yoo, Eung Jae; Cajiao, Isabela; Kim, Jeong-Seon; Kimura, Atsushi P.; Zhang, Aiwen; Cooke, Nancy E.; Liebhaber, Stephen A.

2006-01-01

Random assortment within mammalian genomes juxtaposes genes with distinct expression profiles. This organization, along with the prevalence of long-range regulatory controls, generates a potential for aberrant transcriptional interactions. The human CD79b/GH locus contains six tightly linked genes with three mutually exclusive tissue specificities and interdigitated control elements. One consequence of this compact organization is that the pituitarycell-specific transcriptional events that activate hGH-N also trigger ectopic activation of CD79b. However, the B-cell-specific events that activate CD79b do not trigger reciprocal activation of hGH-N. Here we utilized DNase I hypersensitive site mapping, chromatin immunoprecipitation, and transgenic models to explore the basis for this asymmetric relationship. The results reveal tissue-specific patterns of chromatin structures and transcriptional controls at the CD79b/GH locus in B cells distinct from those in the pituitary gland and placenta. These three unique transcriptional environments suggest a set of corresponding gene expression pathways and transcriptional interactions that are likely to be found juxtaposed at multiple sites within the eukaryotic genome. PMID:16847312

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

PubMed Central

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

2012-01-01

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

Comparing measured and modelled soil carbon: which site-specific variables are linked to high stability?

NASA Astrophysics Data System (ADS)

Robertson, Andy; Schipanski, Meagan; Ma, Liwang; Ahuja, Lajpat; McNamara, Niall; Smith, Pete; Davies, Christian

2016-04-01

Changes in soil carbon (C) stocks have been studied in depth over the last two decades, as net greenhouse gas (GHG) sinks are highlighted to be a partial solution to the causes of climate change. However, the stability of this soil C is often overlooked when measuring these changes. Ultimately a net sequestration in soils is far less beneficial if labile C is replacing more stable forms. To date there is no accepted framework for measuring soil C stability, and as a result there is considerable uncertainty associated with the simulated impacts of land management and land use change when using process-based systems models. However, a recent effort to equate measurable soil C fractions to model pools has generated data that help to assess the impacts of land management, and can ultimately help to reduce the uncertainty of model predictions. Our research compiles this existing fractionation data along with site metadata to create a simplistic statistical model able to quantify the relative importance of different site-specific conditions. Data was mined from 23 published studies and combined with original data to generate a dataset of 100+ land use change sites across Europe. For sites to be included they required soil C fractions isolated using the Zimmermann et al. (2007) method and specific site metadata (mean annual precipitation, MAP; mean annual temperature, MAT; soil pH; land use; altitude). Of the sites, 75% were used to develop a generalized linear mixed model (GLMM) to create coefficients where site parameters can be used to predict influence on the measured soil fraction C stocks. The remaining 25% of sites were used to evaluate uncertainty and validate this empirical model. Further, four of the aforementioned sites were used to simulate soil C dynamics using the RothC, DayCent and RZWQM2 models. A sensitivity analysis (4096 model runs for each variable applying Latin hypercube random sampling techniques) was then used to observe whether these models place as much weight on the same site parameters as the GLMM. Sites were spread across an extensive geographic area and encompassed a wide range of conditions (2% to 44% clay content; 0.9° C to 18° C MAT; 300mm to 1400mm MAP). Topsoil (30 cm) C stocks also varied considerably (29.0 to 115.9 t/ha) but the proportion deemed stable (mean residence time >10 years) was relatively consistent (72 ± 2 %). The GLMM approach suggested that an interaction of soil pH and historic land use explained the largest amount of variation seen in stable fraction C stocks, closely followed by MAT and MAP interactions. For all three systems models, the stable soil C pools were most sensitive to climatic variables and land use. However, RZWQM2 did indicate that soil characteristics (texture, pH) also had an influence on stable C pool dynamics. References 1 - Zimmermann et al., 2007. Measured soil organic matter fractions can be related to pools in the RothC model. European Journal of Soil Science, 58:658-667.

Transcription factor profiling reveals molecular choreography and key regulators of human retrotransposon expression

PubMed Central

Sun, Xiaoji; Wang, Xuya; Tang, Zuojian; Grivainis, Mark; Kahler, David; Yun, Chi; Mita, Paolo; Fenyö, David

2018-01-01

Transposable elements (TEs) represent a substantial fraction of many eukaryotic genomes, and transcriptional regulation of these factors is important to determine TE activities in human cells. However, due to the repetitive nature of TEs, identifying transcription factor (TF)-binding sites from ChIP-sequencing (ChIP-seq) datasets is challenging. Current algorithms are focused on subtle differences between TE copies and thus bias the analysis to relatively old and inactive TEs. Here we describe an approach termed “MapRRCon” (mapping repeat reads to a consensus) which allows us to identify proteins binding to TE DNA sequences by mapping ChIP-seq reads to the TE consensus sequence after whole-genome alignment. Although this method does not assign binding sites to individual insertions in the genome, it provides a landscape of interacting TFs by capturing factors that bind to TEs under various conditions. We applied this method to screen TFs’ interaction with L1 in human cells/tissues using ENCODE ChIP-seq datasets and identified 178 of the 512 TFs tested as bound to L1 in at least one biological condition with most of them (138) localized to the promoter. Among these L1-binding factors, we focused on Myc and CTCF, as they play important roles in cancer progression and 3D chromatin structure formation. Furthermore, we explored the transcriptomes of The Cancer Genome Atlas breast and ovarian tumor samples in which a consistent anti-/correlation between L1 and Myc/CTCF expression was observed, suggesting that these two factors may play roles in regulating L1 transcription during the development of such tumors. PMID:29802231

IRS Spectral Maps of Photoevaporative Columns in M16, Carina, and the Galactic Center

NASA Astrophysics Data System (ADS)

Cotera, Angela; Healy, Kevin; Hester, Jeff; Sellgren, Kris; Simpson, Janet; Stolovy, Susan

2008-03-01

Photoevaporated columns of dust and gas - also called elephant trunks, pillars or fingers - are found in the periphery of H II regions, and have been observed within the Galaxy, the SMC and the LMC. These features are sites of current star formation, but the question remains whether the columns persist because stars formed in the denser regions prior to interactions with the UV radiation and stellar winds of nearby massive stars, or because of core collapse resulting from these interactions. Mapping the distribution of the physical states of the dust and gas in these columns is a necessary step towards understanding the possible star formation mechanisms within these dynamic objects. We propose to obtain IRS spectral maps of columns within M 16, the Carina nebula, and the Galactic center (GC) to understand the effects on these pillars from different stellar populations and initial conditions, and to better understand star formation in the GC. Within the spectral range of the high resolution IRS modes (9.9-37.2 micron) there are a wealth of molecular, atomic and PAH emission lines that will enable us to determine the excitation state, dust and gas temperatures, and probe the shock characteristics within the columns. Using the IRS spectral mapping mode, in conjunction with the CUBISM tool and the CLOUDY H II region model code, we will be able to construct detailed maps of the accessible emission lines and derived parameters for each column. IRS mapping of elephant trunks has not been done to date, yet provides a wealth of information unobtainable for the foreseeable future once Cycle 5 is completed.

Developing nurses' intercultural/intraprofessional communication skills using the EXCELLence in Cultural Experiential Learning and Leadership Social Interaction Maps.

PubMed

Henderson, Saras; Barker, Michelle

2017-09-27

To examine how the use of Social Interaction Maps, a tool in the EXCELLence in Cultural Experiential Learning and Leadership Program, can enhance the development of nurses' intercultural/intraprofessional communication skills. Nurses face communication challenges when interacting with others from similar background as well as those from a culturally and linguistically diverse background. We used the EXCELLence in Cultural Experiential Learning and Leadership Program's Social Interaction Maps tool to foster intercultural/intraprofessional communication skills in nurses. Social Interaction Maps describe verbal and nonverbal communication behaviours that model ways of communicating in a culturally appropriate manner. The maps include four stages of an interaction, namely Approach, Bridging, Communicating and Departing using the acronym ABCD. Qualitative approach was used with a purposeful sample of nurses enrolled in a postgraduate course. Fifteen participants were recruited. The Social Interaction Map tool was taught to participants in a workshop where they engaged in sociocultural communication activities using scenarios. Participants were asked to apply Social Interaction Maps in their workplaces. Six weeks later, participants completed a semistructured open-ended questionnaire and participated in a discussion forum on their experience of using Social Interaction Maps. Data were content-analysed. Four themes identified in the use of the Social Interaction Maps were (i) enhancing self-awareness of communication skills; (ii) promoting skills in being nonconfrontational during difficult interactions; (iii) highlighting the importance of A (Approach) and B (Bridging) in interaction with others; and (iv) awareness of how others interpret what is said C (Communicating) and discussing to resolve issues before closure D (Departing). Application of the EXCELLence in Cultural Experiential Learning and Leadership Social Interaction Mapping tool was shown to be useful in developing intercultural/intraprofessional communication skills in nurses. Professional development programmes that incorporate EXCELLence in Cultural Experiential Learning and Leadership Social Interaction Maps can enhance nurses' intercultural/intraprofessional communication competencies when engaging with others from culturally and linguistically diverse backgrounds and improve the way nurses communicate with each other. © 2017 John Wiley & Sons Ltd.

Hydrographs Showing Ground-Water Level Changes for Selected Wells in the Lower Skagit River Basin, Washington

USGS Publications Warehouse

Fasser, E.T.; Julich, R.J.

2009-01-01

Hydrographs for selected wells in the Lower Skagit River basin, Washington, are presented in an interactive web-based map to illustrate monthly and seasonal changes in ground-water levels in the study area. Ground-water level data and well information were collected by the U.S. Geological Survey using standard techniques and were stored in the USGS National Water Information System (NWIS), Ground-Water Site-Inventory (GWSI) System.

Site-specific microtubule-associated protein 4 dephosphorylation causes microtubule network densification in pressure overload cardiac hypertrophy.

PubMed

Chinnakkannu, Panneerselvam; Samanna, Venkatesababa; Cheng, Guangmao; Ablonczy, Zsolt; Baicu, Catalin F; Bethard, Jennifer R; Menick, Donald R; Kuppuswamy, Dhandapani; Cooper, George

2010-07-09

In severe pressure overload-induced cardiac hypertrophy, a dense, stabilized microtubule network forms that interferes with cardiocyte contraction and microtubule-based transport. This is associated with persistent transcriptional up-regulation of cardiac alpha- and beta-tubulin and microtubule-stabilizing microtubule-associated protein 4 (MAP4). There is also extensive microtubule decoration by MAP4, suggesting greater MAP4 affinity for microtubules. Because the major determinant of this affinity is site-specific MAP4 dephosphorylation, we characterized this in hypertrophied myocardium and then assessed the functional significance of each dephosphorylation site found by mimicking it in normal cardiocytes. We first isolated MAP4 from normal and pressure overload-hypertrophied feline myocardium; volume-overloaded myocardium, which has an equal degree and duration of hypertrophy but normal functional and cytoskeletal properties, served as a control for any nonspecific growth-related effects. After cloning cDNA-encoding feline MAP4 and obtaining its deduced amino acid sequence, we characterized by mass spectrometry any site-specific MAP4 dephosphorylation. Solely in pressure overload-hypertrophied myocardium, we identified striking MAP4 dephosphorylation at Ser-472 in the MAP4 N-terminal projection domain and at Ser-924 and Ser-1056 in the assembly-promoting region of the C-terminal microtubule-binding domain. Site-directed mutagenesis of MAP4 cDNA was then used to switch each serine to non-phosphorylatable alanine. Wild-type and mutated cDNAs were used to construct adenoviruses; microtubule network density, stability, and MAP4 decoration were assessed in normal cardiocytes following an equivalent level of MAP4 expression. The Ser-924 --> Ala MAP4 mutant produced a microtubule phenotype indistinguishable from that seen in pressure overload hypertrophy, such that Ser-924 MAP4 dephosphorylation during pressure overload hypertrophy may be central to this cytoskeletal abnormality.

Mapping hydration dynamics around a protein surface

PubMed Central

Zhang, Luyuan; Wang, Lijuan; Kao, Ya-Ting; Qiu, Weihong; Yang, Yi; Okobiah, Oghaghare; Zhong, Dongping

2007-01-01

Protein surface hydration is fundamental to its structure and activity. We report here the direct mapping of global hydration dynamics around a protein in its native and molten globular states, using a tryptophan scan by site-specific mutations. With 16 tryptophan mutants and in 29 different positions and states, we observed two robust, distinct water dynamics in the hydration layer on a few (≈1–8 ps) and tens to hundreds of picoseconds (≈20–200 ps), representing the initial local relaxation and subsequent collective network restructuring, respectively. Both time scales are strongly correlated with protein's structural and chemical properties. These results reveal the intimate relationship between hydration dynamics and protein fluctuations and such biologically relevant water–protein interactions fluctuate on picosecond time scales. PMID:18003912

Updating the Geologic Maps of the Apollo 15, 16, and 17 Landing Sites

NASA Astrophysics Data System (ADS)

Garry, W. B.; Mest, S. C.; Yingst, R. A.; Ostrach, L. R.; Petro, N. E.; Cohen, B. A.

2018-06-01

Our team is funded through NASA's Planetary Data Archiving, Restoration, and Tools (PDART) program to produce two new USGS Special Investigation Maps (SIM) for the Apollo 15, 16, and 17 missions: a regional map (1:200K) and a landing-site map (1:24K).

27 CFR 9.192 - Wahluke Slope.

Code of Federal Regulations, 2011 CFR

2011-04-01

... boundary line of section 15, which forms a portion of the boundary line of the Hanford Site, T15N/R26E, Wahatis Peak map; then (4) Proceed generally southwest along the Hanford Site boundary in a series of 90... Bridge map, and continue onto the Priest Rapids NE map to the intersection of the Hanford Site boundary...

27 CFR 9.192 - Wahluke Slope.

Code of Federal Regulations, 2010 CFR

2010-04-01

... boundary line of section 15, which forms a portion of the boundary line of the Hanford Site, T15N/R26E, Wahatis Peak map; then (4) Proceed generally southwest along the Hanford Site boundary in a series of 90... Bridge map, and continue onto the Priest Rapids NE map to the intersection of the Hanford Site boundary...

27 CFR 9.192 - Wahluke Slope.

Code of Federal Regulations, 2012 CFR

2012-04-01

... boundary line of section 15, which forms a portion of the boundary line of the Hanford Site, T15N/R26E, Wahatis Peak map; then (4) Proceed generally southwest along the Hanford Site boundary in a series of 90... Bridge map, and continue onto the Priest Rapids NE map to the intersection of the Hanford Site boundary...

27 CFR 9.192 - Wahluke Slope.

Code of Federal Regulations, 2013 CFR

2013-04-01

... boundary line of section 15, which forms a portion of the boundary line of the Hanford Site, T15N/R26E, Wahatis Peak map; then (4) Proceed generally southwest along the Hanford Site boundary in a series of 90... Bridge map, and continue onto the Priest Rapids NE map to the intersection of the Hanford Site boundary...

27 CFR 9.192 - Wahluke Slope.

Code of Federal Regulations, 2014 CFR

2014-04-01

... boundary line of section 15, which forms a portion of the boundary line of the Hanford Site, T15N/R26E, Wahatis Peak map; then (4) Proceed generally southwest along the Hanford Site boundary in a series of 90... Bridge map, and continue onto the Priest Rapids NE map to the intersection of the Hanford Site boundary...

Across-site patterns of modulation detection: Relation to speech recognitiona)

PubMed Central

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

2012-01-01

The aim of this study was to identify across-site patterns of modulation detection thresholds (MDTs) in subjects with cochlear implants and to determine if removal of sites with the poorest MDTs from speech processor programs would result in improved speech recognition. Five hundred millisecond trains of symmetric-biphasic pulses were modulated sinusoidally at 10 Hz and presented at a rate of 900 pps using monopolar stimulation. Subjects were asked to discriminate a modulated pulse train from an unmodulated pulse train for all electrodes in quiet and in the presence of an interleaved unmodulated masker presented on the adjacent site. Across-site patterns of masked MDTs were then used to construct two 10-channel MAPs such that one MAP consisted of sites with the best masked MDTs and the other MAP consisted of sites with the worst masked MDTs. Subjects’ speech recognition skills were compared when they used these two different MAPs. Results showed that MDTs were variable across sites and were elevated in the presence of a masker by various amounts across sites. Better speech recognition was observed when the processor MAP consisted of sites with best masked MDTs, suggesting that temporal modulation sensitivity has important contributions to speech recognition with a cochlear implant. PMID:22559376

Selection of Inhibitor-Resistant Viral Potassium Channels Identifies a Selectivity Filter Site that Affects Barium and Amantadine Block

PubMed Central

Fujiwara, Yuichiro; Arrigoni, Cristina; Domigan, Courtney; Ferrara, Giuseppina; Pantoja, Carlos; Thiel, Gerhard; Moroni, Anna; Minor, Daniel L.

2009-01-01

Background Understanding the interactions between ion channels and blockers remains an important goal that has implications for delineating the basic mechanisms of ion channel function and for the discovery and development of ion channel directed drugs. Methodology/Principal Findings We used genetic selection methods to probe the interaction of two ion channel blockers, barium and amantadine, with the miniature viral potassium channel Kcv. Selection for Kcv mutants that were resistant to either blocker identified a mutant bearing multiple changes that was resistant to both. Implementation of a PCR shuffling and backcrossing procedure uncovered that the blocker resistance could be attributed to a single change, T63S, at a position that is likely to form the binding site for the inner ion in the selectivity filter (site 4). A combination of electrophysiological and biochemical assays revealed a distinct difference in the ability of the mutant channel to interact with the blockers. Studies of the analogous mutation in the mammalian inward rectifier Kir2.1 show that the T→S mutation affects barium block as well as the stability of the conductive state. Comparison of the effects of similar barium resistant mutations in Kcv and Kir2.1 shows that neighboring amino acids in the Kcv selectivity filter affect blocker binding. Conclusions/Significance The data support the idea that permeant ions have an integral role in stabilizing potassium channel structure, suggest that both barium and amantadine act at a similar site, and demonstrate how genetic selections can be used to map blocker binding sites and reveal mechanistic features. PMID:19834614

Condensin-driven remodelling of X chromosome topology during dosage compensation

NASA Astrophysics Data System (ADS)

Crane, Emily; Bian, Qian; McCord, Rachel Patton; Lajoie, Bryan R.; Wheeler, Bayly S.; Ralston, Edward J.; Uzawa, Satoru; Dekker, Job; Meyer, Barbara J.

2015-07-01

The three-dimensional organization of a genome plays a critical role in regulating gene expression, yet little is known about the machinery and mechanisms that determine higher-order chromosome structure. Here we perform genome-wide chromosome conformation capture analysis, fluorescent in situ hybridization (FISH), and RNA-seq to obtain comprehensive three-dimensional (3D) maps of the Caenorhabditis elegans genome and to dissect X chromosome dosage compensation, which balances gene expression between XX hermaphrodites and XO males. The dosage compensation complex (DCC), a condensin complex, binds to both hermaphrodite X chromosomes via sequence-specific recruitment elements on X (rex sites) to reduce chromosome-wide gene expression by half. Most DCC condensin subunits also act in other condensin complexes to control the compaction and resolution of all mitotic and meiotic chromosomes. By comparing chromosome structure in wild-type and DCC-defective embryos, we show that the DCC remodels hermaphrodite X chromosomes into a sex-specific spatial conformation distinct from autosomes. Dosage-compensated X chromosomes consist of self-interacting domains (~1 Mb) resembling mammalian topologically associating domains (TADs). TADs on X chromosomes have stronger boundaries and more regular spacing than on autosomes. Many TAD boundaries on X chromosomes coincide with the highest-affinity rex sites and become diminished or lost in DCC-defective mutants, thereby converting the topology of X to a conformation resembling autosomes. rex sites engage in DCC-dependent long-range interactions, with the most frequent interactions occurring between rex sites at DCC-dependent TAD boundaries. These results imply that the DCC reshapes the topology of X chromosomes by forming new TAD boundaries and reinforcing weak boundaries through interactions between its highest-affinity binding sites. As this model predicts, deletion of an endogenous rex site at a DCC-dependent TAD boundary using CRISPR/Cas9 greatly diminished the boundary. Thus, the DCC imposes a distinct higher-order structure onto X chromosomes while regulating gene expression chromosome-wide.

Condensin-Driven Remodeling of X-Chromosome Topology during Dosage Compensation

PubMed Central

Crane, Emily; Bian, Qian; McCord, Rachel Patton; Lajoie, Bryan R.; Wheeler, Bayly S.; Ralston, Edward J.; Uzawa, Satoru; Dekker, Job; Meyer, Barbara J.

2015-01-01

The three-dimensional organization of a genome plays a critical role in regulating gene expression, yet little is known about the machinery and mechanisms that determine higher-order chromosome structure1,2. Here we perform genome-wide chromosome conformation capture analysis, FISH, and RNA-seq to obtain comprehensive 3D maps of the Caenorhabditis elegans genome and to dissect X-chromosome dosage compensation, which balances gene expression between XX hermaphrodites and XO males. The dosage compensation complex (DCC), a condensin complex, binds to both hermaphrodite X chromosomes via sequence-specific recruitment elements on X (rex sites) to reduce chromosome-wide gene expression by half3–7. Most DCC condensin subunits also act in other condensin complexes to control the compaction and resolution of all mitotic and meiotic chromosomes5,6. By comparing chromosome structure in wild-type and DCC-defective embryos, we show that the DCC remodels hermaphrodite X chromosomes into a sex-specific spatial conformation distinct from autosomes. Dosage-compensated X chromosomes consist of self-interacting domains (~1 Mb) resembling mammalian Topologically Associating Domains (TADs)8,9. TADs on X have stronger boundaries and more regular spacing than on autosomes. Many TAD boundaries on X coincide with the highest-affinity rex sites and become diminished or lost in DCC-defective mutants, thereby converting the topology of X to a conformation resembling autosomes. rex sites engage in DCC-dependent long-range interactions, with the most frequent interactions occurring between rex sites at DCC-dependent TAD boundaries. These results imply that the DCC reshapes the topology of X by forming new TAD boundaries and reinforcing weak boundaries through interactions between its highest-affinity binding sites. As this model predicts, deletion of an endogenous rex site at a DCC-dependent TAD boundary using CRISPR/Cas9 greatly diminished the boundary. Thus, the DCC imposes a distinct higher-order structure onto X while regulating gene expression chromosome wide. PMID:26030525

The calcium-binding protein ALG-2 regulates protein secretion and trafficking via interactions with MISSL and MAP1B proteins.

PubMed

Takahara, Terunao; Inoue, Kuniko; Arai, Yumika; Kuwata, Keiko; Shibata, Hideki; Maki, Masatoshi

2017-10-13

Mobilization of intracellular calcium is essential for a wide range of cellular processes, including signal transduction, apoptosis, and vesicular trafficking. Several lines of evidence have suggested that apoptosis-linked gene 2 (ALG-2, also known as PDCD6 ), a calcium-binding protein, acts as a calcium sensor linking calcium levels with efficient vesicular trafficking, especially at the endoplasmic reticulum (ER)-to-Golgi transport step. However, how ALG-2 regulates these processes remains largely unclear. Here, we report that M APK1- i nteracting and s pindle- s tabilizing (MISS)- l ike (MISSL), a previously uncharacterized protein, interacts with ALG-2 in a calcium-dependent manner. Live-cell imaging revealed that upon a rise in intracellular calcium levels, GFP-tagged MISSL (GFP-MISSL) dynamically relocalizes in a punctate pattern and colocalizes with ALG-2. MISSL knockdown caused disorganization of the components of the ER exit site, the ER-Golgi intermediate compartment, and Golgi. Importantly, knockdown of either MISSL or ALG-2 attenuated the secretion of se creted a lkaline p hosphatase (SEAP), a model secreted cargo protein, with similar reductions in secretion by single- and double-protein knockdowns, suggesting that MISSL and ALG-2 act in the same pathway to regulate the secretion process. Furthermore, ALG-2 or MISSL knockdown delayed ER-to-Golgi transport of procollagen type I. We also found that ALG-2 and MISSL interact with microtubule-associated protein 1B (MAP1B) and that MAP1B knockdown reverts the reduced secretion of SEAP caused by MISSL or ALG-2 depletion. These results suggest that a change in the intracellular calcium level plays a role in regulation of the secretory pathway via interaction of ALG-2 with MISSL and MAP1B. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Surface-material maps of Viking landing sites on Mars

NASA Technical Reports Server (NTRS)

Moore, H. J.; Keller, J. M.

1991-01-01

Researchers mapped the surface materials at the Viking landing sites on Mars to gain a better understanding of the materials and rock populations at the sites and to provide information for future exploration. The maps extent to about 9 m in front of each lander and are about 15 m wide - an area comparable to the area of a pixel in high resolution Viking Orbiter images. The maps are divided into the near and far fields. Data for the near fields are from 1/10 scale maps, umpublished maps, and lander images. Data for the far fields are from 1/20 scale contour maps, contoured lander camera mosaics, and lander images. Rocks are located on these maps using stereometric measurements and the contour maps. Frequency size distribution of rocks and the responses of soil-like materials to erosion by engine exhausts during landings are discussed.

Gemstones and geosciences in space and time. Digital maps to the "Chessboard classification scheme of mineral deposits"

NASA Astrophysics Data System (ADS)

Dill, Harald G.; Weber, Berthold

2013-12-01

The gemstones, covering the spectrum from jeweler's to showcase quality, have been presented in a tripartite subdivision, by country, geology and geomorphology realized in 99 digital maps with more than 2600 mineralized sites. The various maps were designed based on the "Chessboard classification scheme of mineral deposits" proposed by Dill (2010a, 2010b) to reveal the interrelations between gemstone deposits and mineral deposits of other commodities and direct our thoughts to potential new target areas for exploration. A number of 33 categories were used for these digital maps: chromium, nickel, titanium, iron, manganese, copper, tin-tungsten, beryllium, lithium, zinc, calcium, boron, fluorine, strontium, phosphorus, zirconium, silica, feldspar, feldspathoids, zeolite, amphibole (tiger's eye), olivine, pyroxenoid, garnet, epidote, sillimanite-andalusite, corundum-spinel - diaspore, diamond, vermiculite-pagodite, prehnite, sepiolite, jet, and amber. Besides the political base map (gems by country) the mineral deposit is drawn on a geological map, illustrating the main lithologies, stratigraphic units and tectonic structure to unravel the evolution of primary gemstone deposits in time and space. The geomorphological map is to show the control of climate and subaerial and submarine hydrography on the deposition of secondary gemstone deposits. The digital maps are designed so as to be plotted as a paper version of different scale and to upgrade them for an interactive use and link them to gemological databases.

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

USGS Publications Warehouse

Torresan, Michael E.; Gardner, James V.

2000-01-01

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

Normalization of a chromosomal contact map.

PubMed

Cournac, Axel; Marie-Nelly, Hervé; Marbouty, Martial; Koszul, Romain; Mozziconacci, Julien

2012-08-30

Chromatin organization has been increasingly studied in relation with its important influence on DNA-related metabolic processes such as replication or regulation of gene expression. Since its original design ten years ago, capture of chromosome conformation (3C) has become an essential tool to investigate the overall conformation of chromosomes. It relies on the capture of long-range trans and cis interactions of chromosomal segments whose relative proportions in the final bank reflect their frequencies of interactions, hence their spatial proximity in a population of cells. The recent coupling of 3C with deep sequencing approaches now allows the generation of high resolution genome-wide chromosomal contact maps. Different protocols have been used to generate such maps in various organisms. This includes mammals, drosophila and yeast. The massive amount of raw data generated by the genomic 3C has to be carefully processed to alleviate the various biases and byproducts generated by the experiments. Our study aims at proposing a simple normalization procedure to minimize the influence of these unwanted but inevitable events on the final results. Careful analysis of the raw data generated previously for budding yeast S. cerevisiae led to the identification of three main biases affecting the final datasets, including a previously unknown bias resulting from the circularization of DNA molecules. We then developed a simple normalization procedure to process the data and allow the generation of a normalized, highly contrasted, chromosomal contact map for S. cerevisiae. The same method was then extended to the first human genome contact map. Using the normalized data, we revisited the preferential interactions originally described between subsets of discrete chromosomal features. Notably, the detection of preferential interactions between tRNA in yeast and CTCF, PolII binding sites in human can vary with the normalization procedure used. We quantitatively reanalyzed the genomic 3C data obtained for S. cerevisiae, identified some of the biases inherent to the technique and proposed a simple normalization procedure to analyse them. Such an approach can be easily generalized for genomic 3C experiments in other organisms. More experiments and analysis will be necessary to reach optimal resolution and accuracies of the maps generated through these approaches. Working with cell population presenting highest levels of homogeneity will prove useful in this regards.

Molecular simulations of multimodal ligand-protein binding: elucidation of binding sites and correlation with experiments.

PubMed

Freed, Alexander S; Garde, Shekhar; Cramer, Steven M

2011-11-17

Multimodal chromatography, which employs more than one mode of interaction between ligands and proteins, has been shown to have unique selectivity and high efficacy for protein purification. To test the ability of free solution molecular dynamics (MD) simulations in explicit water to identify binding regions on the protein surface and to shed light on the "pseudo affinity" nature of multimodal interactions, we performed MD simulations of a model protein ubiquitin in aqueous solution of free ligands. Comparisons of MD with NMR spectroscopy of ubiquitin mutants in solutions of free ligands show a good agreement between the two with regard to the preferred binding region on the surface of the protein and several binding sites. MD simulations also identify additional binding sites that were not observed in the NMR experiments. "Bound" ligands were found to be sufficiently flexible and to access a number of favorable conformations, suggesting only a moderate loss of ligand entropy in the "pseudo affinity" binding of these multimodal ligands. Analysis of locations of chemical subunits of the ligand on the protein surface indicated that electrostatic interaction units were located on the periphery of the preferred binding region on the protein. The analysis of the electrostatic potential, the hydrophobicity maps, and the binding of both acetate and benzene probes were used to further study the localization of individual ligand moieties. These results suggest that water-mediated electrostatic interactions help the localization and orientation of the MM ligand to the binding region with additional stability provided by nonspecific hydrophobic interactions.

Characterization of N-palmitoylated human growth hormone by in situ liquid-liquid extraction and MALDI tandem mass spectrometry.

PubMed

Sachon, Emmanuelle; Nielsen, Per Franklin; Jensen, Ole Nørregaard

2007-06-01

Acylation is a common post-translational modification found in secreted proteins and membrane-associated proteins, including signal transducing and regulatory proteins. Acylation is also explored in the pharmaceutical and biotechnology industry to increase the stability and lifetime of protein-based products. The presence of acyl moieties in proteins and peptides affects the physico-chemical properties of these species, thereby modulating protein stability, function, localization and molecular interactions. Characterization of protein acylation is a challenging analytical task, which includes the precise definition of the acylation sites in proteins and determination of the identity and molecular heterogeneity of the acyl moiety at each individual site. In this study, we generated a chemically modified human growth hormone (hGH) by incorporation of a palmitoyl moiety on the N(epsilon) group of a lysine residue. Monoacylation of the hGH protein was confirmed by determination of the intact molecular weight by mass spectrometry. Detailed analysis of protein acylation was achieved by analysis of peptides derived from hGH by protease treatment. However, peptide mass mapping by MALDI MS using trypsin and AspN proteases and standard sample preparation methods did not reveal any palmitoylated peptides. In contrast, in situ liquid-liquid extraction (LLE) performed directly on the MALDI MS metal target enabled detection of acylated peptide candidates by MALDI MS and demonstrated that hGH was N-palmitoylated at multiple lysine residues. MALDI MS and MS/MS analysis of the modified peptides mapped the N-palmitoylation sites to Lys158, Lys172 and Lys140 or Lys145. This study demonstrates the utility of LLE/MALDI MS/MS for mapping and characterization of acylation sites in proteins and peptides and the importance of optimizing sample preparation methods for mass spectrometry-based determination of substoichiometric, multi-site protein modifications.

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

PubMed Central

2013-01-01

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

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

PubMed

Kuperstein, Inna; Cohen, David P A; Pook, Stuart; Viara, Eric; Calzone, Laurence; Barillot, Emmanuel; Zinovyev, Andrei

2013-10-07

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

Structure- and Modeling-based Identification of the Adenovirus E4orf4 Binding Site in the Protein Phosphatase 2A B55α Subunit*

PubMed Central

Horowitz, Ben; Sharf, Rakefet; Avital-Shacham, Meirav; Pechkovsky, Antonina; Kleinberger, Tamar

2013-01-01

The adenovirus E4orf4 protein regulates the progression of viral infection and when expressed outside the context of the virus it induces nonclassical, cancer cell-specific apoptosis. All E4orf4 functions known to date require an interaction between E4orf4 and protein phosphatase 2A (PP2A), which is mediated through PP2A regulatory B subunits. Specifically, an interaction with the B55α subunit is required for induction of cell death by E4orf4. To gain a better insight into the E4orf4-PP2A interaction, mapping of the E4orf4 interaction site in PP2A-B55α has been undertaken. To this end we used a combination of bioinformatics analyses of PP2A-B55α and of E4orf4, which led to the prediction of E4orf4 binding sites on the surface of PP2A-B55α. Mutation analysis, immunoprecipitation, and GST pulldown assays based on the theoretical predictions revealed that the E4orf4 binding site included the α1 and α2 helices described in the B55α structure and involved at least three residues located in these helices facing each other. Loss of E4orf4 binding was accompanied by reduced contribution of the B55α mutants to E4orf4-induced cell death. The identified E4orf4 binding domain lies above the previously described substrate binding site and does not overlap it, although its location could be consistent with direct or indirect effects on substrate binding. This work assigns for the first time a functional significance to the α1,α2 helices of B55α, and we suggest that the binding site defined by these helices could also contribute to interactions between PP2A and some of its cellular regulators. PMID:23530045

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

PubMed Central

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

2007-01-01

Yeast two-hybrid screens are an important method for mapping pairwise physical interactions between proteins. The fraction of interactions detected in independent screens can be very small, and an outstanding challenge is to determine the reason for the low overlap. Low overlap can arise from either a high false-discovery rate (interaction sets have low overlap because each set is contaminated by a large number of stochastic false-positive interactions) or a high false-negative rate (interaction sets have low overlap because each misses many true interactions). We extend capture–recapture theory to provide the first unified model for false-positive and false-negative rates for two-hybrid screens. Analysis of yeast, worm, and fly data indicates that 25% to 45% of the reported interactions are likely false positives. Membrane proteins have higher false-discovery rates on average, and signal transduction proteins have lower rates. The overall false-negative rate ranges from 75% for worm to 90% for fly, which arises from a roughly 50% false-negative rate due to statistical undersampling and a 55% to 85% false-negative rate due to proteins that appear to be systematically lost from the assays. Finally, statistical model selection conclusively rejects the Erdös-Rényi network model in favor of the power law model for yeast and the truncated power law for worm and fly degree distributions. Much as genome sequencing coverage estimates were essential for planning the human genome sequencing project, the coverage estimates developed here will be valuable for guiding future proteomic screens. All software and datasets are available in Datasets S1 and S2, Figures S1–S5, and Tables S1−S6, and are also available from our Web site, http://www.baderzone.org. PMID:18039026

A simultaneous multichannel monophasic action potential electrode array for in vivo epicardial repolarization mapping.

PubMed

Sahakian, A V; Peterson, M S; Shkurovich, S; Hamer, M; Votapka, T; Ji, T; Swiryn, S

2001-03-01

While the recording of extracellular monophasic action potentials (MAPs) from single epicardial or endocardial sites has been performed for over a century, we are unaware of any previous successful attempt to record MAPs simultaneously from a large number of sites in vivo. We report here the design and validation of an array of MAP electrodes which records both depolarization and repolarization simultaneously at up to 16 epicardial sites in a square array on the heart in vivo. The array consists of 16 sintered Ag-AgCl electrodes mounted in a common housing with individual suspensions allowing each electrode to exert a controlled pressure on the epicardial surface. The electrodes are arranged in a square array, with each quadrant of four having an additional recessed sintered Ag-AgCl reference electrode at its center. A saline-soaked sponge establishes ionic contact between the reference electrodes and the tissue. The array was tested on six anesthetized open-chested pigs. Simultaneous diagnostic-quality MAP recordings were obtained from up to 13 out of 16 ventricular sites. Ventricular MAPs had amplitudes of 10-40 mV with uniform morphologies and stable baselines for up to 30 min. MAP duration at 90% repolarization was measured and shown to vary as expected with cycle length during sustained pacing. The relationship between MAP duration and effective refractory period was also confirmed. The ability of the array to detect local differences in repolarization was tested in two ways. Placement of the array straddling the atrioventricular (AV) junction yielded simultaneous atrial or ventricular recordings at corresponding sites during 1:1 and 2:1 AV conduction. Localized ischemia via constriction of a coronary artery branch resulted in shortening of the repolarization phase at the ischemic, but not the nonischemic, sites. In conclusion, these results indicate that the simultaneous multichannel MAP electrode array is a viable method for in vivo epicardial repolarization mapping. The array has the potential to be expanded to increase the number of sites and spatial resolution.

Whole Sky Imager Characterization of Sky Obscuration by Clouds for the Starfire Optical Range

DTIC Science & Technology

2010-01-11

9.3 Further Algorithm Development and Evaluation 58 9.4 Analysis of the Data Base 58 10.0 DISCUSSION OF CONTRACT REQUIREMENTS 59 10.1...clouds, Site 5 Feb 14 2008 0900 28 21 Transmittance map, Moonlight , clear sky, Site 5 Feb 3 2008 0700 28 22 Transmittance map, Moonlight , thin...clouds, Site 5 Feb 8 2008 1200 29 23 Transmittance map, Moonlight , broken clouds, Site 5 Feb 2 2008 0800 29 24 Cloud Algorithm Results, Moonlight

Candidate Mars Surveyor Landing Sites Near Apollinaris Patera

NASA Astrophysics Data System (ADS)

Gulick, Virginia C.

1999-06-01

Regions near Apollinaris Patera are proposed for consideration as Mars Surveyor landing sites. Gulick (1998) proposed this region at the First Mars Surveyor Landing Site workshop; Bulmer and Gregg (1998) provided additional support. Apollinaris Patera is situated on the highlands/lowlands boundary at 8.5S, 186W. The volcano itself has been mapped as Hesperian in age. The regions surrounding Apollinaris show evidence for volcanism, volcano-ice interactions, and erosion by water. Numerous valleys modified by fluvial processes dissect a large fan structure emanating from the southern flank of the volcano. Sapping valleys have formed along the southern terminus of the fan structure. Regions near Apollinaris Patera provide a unique opportunity to sample outcrop lithologies ranging from highland Noachian basement rocks, to Hesperian aged lava flows, channel and flood plain materials, to Amazonian volcanic, ash and channel deposits.

Candidate Mars Surveyor Landing Sites Near Apollinaris Patera

NASA Technical Reports Server (NTRS)

Gulick, Virginia C.

1999-01-01

Regions near Apollinaris Patera are proposed for consideration as Mars Surveyor landing sites. Gulick (1998) proposed this region at the First Mars Surveyor Landing Site workshop; Bulmer and Gregg (1998) provided additional support. Apollinaris Patera is situated on the highlands/lowlands boundary at 8.5S, 186W. The volcano itself has been mapped as Hesperian in age. The regions surrounding Apollinaris show evidence for volcanism, volcano-ice interactions, and erosion by water. Numerous valleys modified by fluvial processes dissect a large fan structure emanating from the southern flank of the volcano. Sapping valleys have formed along the southern terminus of the fan structure. Regions near Apollinaris Patera provide a unique opportunity to sample outcrop lithologies ranging from highland Noachian basement rocks, to Hesperian aged lava flows, channel and flood plain materials, to Amazonian volcanic, ash and channel deposits.

Design of a High Resolution Open Access Global Snow Cover Web Map Service Using Ground and Satellite Observations

NASA Astrophysics Data System (ADS)

Kadlec, J.; Ames, D. P.

2014-12-01

The aim of the presented work is creating a freely accessible, dynamic and re-usable snow cover map of the world by combining snow extent and snow depth datasets from multiple sources. The examined data sources are: remote sensing datasets (MODIS, CryoLand), weather forecasting model outputs (OpenWeatherMap, forecast.io), ground observation networks (CUAHSI HIS, GSOD, GHCN, and selected national networks), and user-contributed snow reports on social networks (cross-country and backcountry skiing trip reports). For adding each type of dataset, an interface and an adapter is created. Each adapter supports queries by area, time range, or combination of area and time range. The combined dataset is published as an online snow cover mapping service. This web service lowers the learning curve that is required to view, access, and analyze snow depth maps and snow time-series. All data published by this service are licensed as open data; encouraging the re-use of the data in customized applications in climatology, hydrology, sports and other disciplines. The initial version of the interactive snow map is on the website snow.hydrodata.org. This website supports the view by time and view by site. In view by time, the spatial distribution of snow for a selected area and time period is shown. In view by site, the time-series charts of snow depth at a selected location is displayed. All snow extent and snow depth map layers and time series are accessible and discoverable through internationally approved protocols including WMS, WFS, WCS, WaterOneFlow and WaterML. Therefore they can also be easily added to GIS software or 3rd-party web map applications. The central hypothesis driving this research is that the integration of user contributed data and/or social-network derived snow data together with other open access data sources will result in more accurate and higher resolution - and hence more useful snow cover maps than satellite data or government agency produced data by itself.

Quantitative susceptibility mapping of human brain at 3T: a multisite reproducibility study.

PubMed

Lin, P-Y; Chao, T-C; Wu, M-L

2015-03-01

Quantitative susceptibility mapping of the human brain has demonstrated strong potential in examining iron deposition, which may help in investigating possible brain pathology. This study assesses the reproducibility of quantitative susceptibility mapping across different imaging sites. In this study, the susceptibility values of 5 regions of interest in the human brain were measured on 9 healthy subjects following calibration by using phantom experiments. Each of the subjects was imaged 5 times on 1 scanner with the same procedure repeated on 3 different 3T systems so that both within-site and cross-site quantitative susceptibility mapping precision levels could be assessed. Two quantitative susceptibility mapping algorithms, similar in principle, one by using iterative regularization (iterative quantitative susceptibility mapping) and the other with analytic optimal solutions (deterministic quantitative susceptibility mapping), were implemented, and their performances were compared. Results show that while deterministic quantitative susceptibility mapping had nearly 700 times faster computation speed, residual streaking artifacts seem to be more prominent compared with iterative quantitative susceptibility mapping. With quantitative susceptibility mapping, the putamen, globus pallidus, and caudate nucleus showed smaller imprecision on the order of 0.005 ppm, whereas the red nucleus and substantia nigra, closer to the skull base, had a somewhat larger imprecision of approximately 0.01 ppm. Cross-site errors were not significantly larger than within-site errors. Possible sources of estimation errors are discussed. The reproducibility of quantitative susceptibility mapping in the human brain in vivo is regionally dependent, and the precision levels achieved with quantitative susceptibility mapping should allow longitudinal and multisite studies such as aging-related changes in brain tissue magnetic susceptibility. © 2015 by American Journal of Neuroradiology.

Anomalous critical behavior in the polymer collapse transition of three-dimensional lattice trails.

PubMed

Bedini, Andrea; Owczarek, Aleksander L; Prellberg, Thomas

2012-07-01

Trails (bond-avoiding walks) provide an alternative lattice model of polymers to self-avoiding walks, and adding self-interaction at multiply visited sites gives a model of polymer collapse. Recently a two-dimensional model (triangular lattice) where doubly and triply visited sites are given different weights was shown to display a rich phase diagram with first- and second-order collapse separated by a multicritical point. A kinetic growth process of trails (KGTs) was conjectured to map precisely to this multicritical point. Two types of low-temperature phases, a globule phase and a maximally dense phase, were encountered. Here we investigate the collapse properties of a similar extended model of interacting lattice trails on the simple cubic lattice with separate weights for doubly and triply visited sites. Again we find first- and second-order collapse transitions dependent on the relative sizes of the doubly and triply visited energies. However, we find no evidence of a low-temperature maximally dense phase with only the globular phase in existence. Intriguingly, when the ratio of the energies is precisely that which separates the first-order from the second-order regions anomalous finite-size scaling appears. At the finite-size location of the rounded transition clear evidence exists for a first-order transition that persists in the thermodynamic limit. This location moves as the length increases, with its limit apparently at the point that maps to a KGT. However, if one fixes the temperature to sit at exactly this KGT point, then only a critical point can be deduced from the data. The resolution of this apparent contradiction lies in the breaking of crossover scaling and the difference in the shift and transition width (crossover) exponents.

Mutation of mapped TIA-1/TIAR binding sites in the 3' terminal stem-loop of West Nile virus minus-strand RNA in an infectious clone negatively affects genomic RNA amplification.

PubMed

Emara, Mohamed M; Liu, Hsuan; Davis, William G; Brinton, Margo A

2008-11-01

Previous data showed that the cellular proteins TIA-1 and TIAR bound specifically to the West Nile virus 3' minus-strand stem-loop [WNV3'(-)SL] RNA (37) and colocalized with flavivirus replication complexes in WNV- and dengue virus-infected cells (21). In the present study, the sites on the WNV3'(-)SL RNA required for efficient in vitro T-cell intracellular antigen-related (TIAR) and T-cell intracellular antigen-1 (TIA-1) protein binding were mapped to short AU sequences (UAAUU) located in two internal loops of the WNV3'(-)SL RNA structure. Infectious clone RNAs with all or most of the binding site nucleotides in one of the 3' (-)SL loops deleted or substituted did not produce detectable virus after transfection or subsequent passage. With one exception, deletion/mutation of a single terminal nucleotide in one of the binding sequences had little effect on the efficiency of protein binding or virus production, but mutation of a nucleotide in the middle of a binding sequence reduced both the in vitro protein binding efficiency and virus production. Plaque size, intracellular genomic RNA levels, and virus production progressively decreased with decreasing in vitro TIAR/TIA-1 binding activity, but the translation efficiency of the various mutant RNAs was similar to that of the parental RNA. Several of the mutant RNAs that inefficiently interacted with TIAR/TIA-1 in vitro rapidly reverted in vivo, indicating that they could replicate at a low level and suggesting that an interaction between TIAR/TIA-1 and the viral 3'(-)SL RNA is not required for initial low-level symmetric RNA replication but instead facilitates the subsequent asymmetric amplification of genome RNA from the minus-strand template.

Mapping intermolecular interactions and active site conformations: from human MMP-1 crystal structure to molecular dynamics free energy calculations.

PubMed

Nash, Anthony; Birch, Helen L; de Leeuw, Nora H

2017-02-01

The zinc-dependent Matrix Metalloproteinases (MMPs) found within the extracellular matrix (ECM) of vertebrates are linked to pathological processes such as arthritis, skin ulceration and cancer. Although a general backbone proteolytic mechanism is understood, crystallographic data continue to suggest an active site that is too narrow to encompass the respective substrate. We present a fully parameterised Molecular Dynamics (MD) study of the structural properties of an MMP-1-collagen crystallographic structure (Protein Data Bank - 4AUO), followed by an exploration of the free energy surface of a collagen polypeptide chain entering the active site, using a combined meta-dynamics and umbrella sampling (MDUS) approach. We conclude that the interactions between MMP-1 and the collagen substrate are in good agreement with a number of experimental studies. As such, our unrestrained MD simulations and our MDUS results, which indicate an energetic barrier for a local uncoiling and insertion event, can inform future investigations of the collagen-peptide non-bonded association steps with the active site prior to proteolytic mechanisms. The elucidation of such free energy barriers provides a better understanding of the role of the enzyme in the ECM and is important in the design of future MMP inhibitors.

γ-Adducin Stimulates the Thiazide-sensitive NaCl Cotransporter

PubMed Central

Dimke, Henrik; San-Cristobal, Pedro; de Graaf, Mark; Lenders, Jacques W.; Deinum, Jaap; Hoenderop, Joost G.J.

2011-01-01

The thiazide-sensitive NaCl cotransporter (NCC) plays a key role in renal salt reabsorption and the determination of systemic BP, but the molecular mechanisms governing the regulation of NCC are not completely understood. Here, through pull-down experiments coupled to mass spectrometry, we found that γ-adducin interacts with the NCC transporter. γ-Adducin colocalized with NCC to the distal convoluted tubule. 22Na+ uptake experiments in the Xenopus laevis oocyte showed that γ-adducin stimulated NCC activity in a dose-dependent manner, an effect that occurred upstream from With No Lysine (WNK) 4 kinase. The binding site of γ-adducin mapped to the N terminus of NCC and encompassed three previously reported phosphorylation sites. Supporting this site of interaction, competition with the N-terminal domain of NCC abolished the stimulatory effect of γ-adducin on the transporter. γ-Adducin failed to increase NCC activity when these phosphorylation sites were constitutively inactive or active. In addition, γ-adducin bound only to the dephosphorylated N terminus of NCC. Taken together, our observations suggest that γ-adducin dynamically regulates NCC, likely by amending the phosphorylation state, and consequently the activity, of the transporter. These data suggest that γ-adducin may influence BP homeostasis by modulating renal NaCl transport. PMID:21164023

Allosteric binding sites in Rab11 for potential drug candidates

PubMed Central

2018-01-01

Rab11 is an important protein subfamily in the RabGTPase family. These proteins physiologically function as key regulators of intracellular membrane trafficking processes. Pathologically, Rab11 proteins are implicated in many diseases including cancers, neurodegenerative diseases and type 2 diabetes. Although they are medically important, no previous study has found Rab11 allosteric binding sites where potential drug candidates can bind to. In this study, by employing multiple clustering approaches integrating principal component analysis, independent component analysis and locally linear embedding, we performed structural analyses of Rab11 and identified eight representative structures. Using these representatives to perform binding site mapping and virtual screening, we identified two novel binding sites in Rab11 and small molecules that can preferentially bind to different conformations of these sites with high affinities. After identifying the binding sites and the residue interaction networks in the representatives, we computationally showed that these binding sites may allosterically regulate Rab11, as these sites communicate with switch 2 region that binds to GTP/GDP. These two allosteric binding sites in Rab11 are also similar to two allosteric pockets in Ras that we discovered previously. PMID:29874286

Magnetic Measurements and Heavy Metal Concentrations at Formosa Mine Superfund Site, Douglas County, OR

NASA Astrophysics Data System (ADS)

Upton, T. L.

2015-12-01

Advances in the field of environmental magnetism have led to exciting new applications for this field. Magnetic minerals are ubiquitous in the environment and tend to have an affinity for heavy metals. It has been demonstrated that magnetic properties are often significantly related to concentrations of heavy metals and/or pollution loading index (PLI). As a result, magnetic techniques have been used as proxy for determining hot spots of several types of pollution produced from a diversity of anthropogenic sources. Magnetic measurements are non-destructive and relatively inexpensive compared to geochemical analyses. The utility of environmental magnetic methods varies widely depending on biological, chemical and physical processes that create and transform soils and sediments. Applications in the direction of mapping heavy metals have been studied and shown to be quite useful in countries such as China and India but to date, little research has been done in the US. As such, there is need to expand the scope of research to a wider range of soil types and land uses, especially within the US. This study investigates the application of environmental magnetic techniques to mapping of heavy metal concentrations and PLI at the Formosa Mine Superfund Site, an abandoned mine about 25 miles southwest of Roseburg, OR. Using hotspot analysis, correlation and cluster analyses, interactions between metals and magnetic parameters are examined in relation to environmental factors such as proximity to seeps and adits. Preliminary results suggest significant correlation of magnetic susceptibility with certain heavy metals, signifying that magnetic methods may be useful in mapping heavy metal hotspots at this site.

Site-specific Microtubule-associated Protein 4 Dephosphorylation Causes Microtubule Network Densification in Pressure Overload Cardiac Hypertrophy*

PubMed Central

Chinnakkannu, Panneerselvam; Samanna, Venkatesababa; Cheng, Guangmao; Ablonczy, Zsolt; Baicu, Catalin F.; Bethard, Jennifer R.; Menick, Donald R.; Kuppuswamy, Dhandapani; Cooper, George

2010-01-01

In severe pressure overload-induced cardiac hypertrophy, a dense, stabilized microtubule network forms that interferes with cardiocyte contraction and microtubule-based transport. This is associated with persistent transcriptional up-regulation of cardiac α- and β-tubulin and microtubule-stabilizing microtubule-associated protein 4 (MAP4). There is also extensive microtubule decoration by MAP4, suggesting greater MAP4 affinity for microtubules. Because the major determinant of this affinity is site-specific MAP4 dephosphorylation, we characterized this in hypertrophied myocardium and then assessed the functional significance of each dephosphorylation site found by mimicking it in normal cardiocytes. We first isolated MAP4 from normal and pressure overload-hypertrophied feline myocardium; volume-overloaded myocardium, which has an equal degree and duration of hypertrophy but normal functional and cytoskeletal properties, served as a control for any nonspecific growth-related effects. After cloning cDNA-encoding feline MAP4 and obtaining its deduced amino acid sequence, we characterized by mass spectrometry any site-specific MAP4 dephosphorylation. Solely in pressure overload-hypertrophied myocardium, we identified striking MAP4 dephosphorylation at Ser-472 in the MAP4 N-terminal projection domain and at Ser-924 and Ser-1056 in the assembly-promoting region of the C-terminal microtubule-binding domain. Site-directed mutagenesis of MAP4 cDNA was then used to switch each serine to non-phosphorylatable alanine. Wild-type and mutated cDNAs were used to construct adenoviruses; microtubule network density, stability, and MAP4 decoration were assessed in normal cardiocytes following an equivalent level of MAP4 expression. The Ser-924 → Ala MAP4 mutant produced a microtubule phenotype indistinguishable from that seen in pressure overload hypertrophy, such that Ser-924 MAP4 dephosphorylation during pressure overload hypertrophy may be central to this cytoskeletal abnormality. PMID:20436166

mTOR kinase structure, mechanism and regulation by the rapamycin-binding domain

PubMed Central

Yang, Haijuan; Rudge, Derek G.; Koos, Joseph D.; Vaidialingam, Bhamini; Yang, Hyo J.; Pavletich, Nikola P.

2015-01-01

The mammalian target of rapamycin (mTOR), a phosphoinositide 3-kinase related protein kinase, controls cell growth in response to nutrients and growth factors and is frequently deregulated in cancer. Here we report co-crystal structures of a truncated mTOR-mLST8 complex with an ATP transition state mimic and with ATP-site inhibitors. The structures reveal an intrinsically active kinase conformation, with catalytic residues and mechanism remarkably similar to canonical protein kinases. The active site is highly recessed due to the FKBP12-Rapamycin binding (FRB) domain and an inhibitory helix protruding from the catalytic cleft. mTOR activating mutations map to the structural framework that holds these elements in place, indicating the kinase is controlled by restricted access. In vitro biochemistry indicates that the FRB domain acts as a gatekeeper, with its rapamycin-binding site interacting with substrates to grant them access to the restricted active site. FKBP12-rapamycin inhibits by directly blocking substrate recruitment and by further restricting active site access. The structures also reveal active site residues and conformational changes that underlie inhibitor potency and specificity. PMID:23636326

Six independent fucose-binding sites in the crystal structure of Aspergillus oryzae lectin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Makyio, Hisayoshi; Shimabukuro, Junpei; Suzuki, Tatsuya

The crystal structure of AOL (a fucose-specific lectin of Aspergillus oryzae) has been solved by SAD (single-wavelength anomalous diffraction) and MAD (multi-wavelength anomalous diffraction) phasing of seleno-fucosides. The overall structure is a six-bladed β-propeller similar to that of other fucose-specific lectins. The fucose moieties of the seleno-fucosides are located in six fucose-binding sites. Although the Arg and Glu/Gln residues bound to the fucose moiety are common to all fucose-binding sites, the amino-acid residues involved in fucose binding at each site are not identical. The varying peak heights of the seleniums in the electron density map suggest that each fucose-binding sitemore » has a different carbohydrate binding affinity. - Highlights: • The six-bladed β-propeller structure of AOL was solved by seleno-sugar phasing. • The mode of fucose binding is essentially conserved at all six binding sites. • The seleno-fucosides exhibit slightly different interactions and electron densities. • These findings suggest that the affinity for fucose is not identical at each site.« less

Voyager Interactive Web Interface to EarthScope

NASA Astrophysics Data System (ADS)

Eriksson, S. C.; Meertens, C. M.; Estey, L.; Weingroff, M.; Hamburger, M. W.; Holt, W. E.; Richard, G. A.

2004-12-01

Visualization of data is essential in helping scientists and students develop a conceptual understanding of relationships among many complex types of data and keep track of large amounts of information. Developed initially by UNAVCO for study of global-scale geodynamic processes, the Voyager map visualization tools have evolved into interactive, web-based map utilities that can make scientific results accessible to a large number and variety of educators and students as well as the originally targeted scientists. A portal to these map tools can be found at: http://jules.unavco.org. The Voyager tools provide on-line interactive data visualization through pre-determined map regions via a simple HTML/JavaScript interface (for large numbers of students using the tools simultaneously) or through student-selectable areas using a Java interface to a Generic Mapping Tools (GMT) engine. Students can access a variety of maps, satellite images, and geophysical data at a range of spatial scales for the earth and other planets of the solar system. Students can also choose from a variety of base maps (satellite mosaics, global topography, geoid, sea-floor age, strain rate and seismic hazard maps, and others) and can then add a number of geographic and geophysical overlays, for example coastlines, political boundaries, rivers and lakes, earthquake and volcano locations, stress axes, and observed and model plate motion, as well as deformation velocity vectors representing a compilation of over 5000 geodetic measurements from around the world. The related educational website, "Exploring our Dynamic Planet", (http://www.dpc.ucar.edu/VoyagerJr/jvvjrtool.html) incorporates background materials and curricular activities that encourage students to explore Earth processes. One of the present curricular modules is designed for high school students or introductory-level undergraduate non-science majors. The purpose of the module is for students to examine real data to investigate how plate tectonic processes are reflected in observed geophysical phenomena. Constructing maps by controlling map parameters and answering open-ended questions which describe, compare relationships, and work with both observed and model data, promote conceptual understanding of plate tectonics and related processes. The goals of curricular development emphasize inquiry, development of critical thinking skills, and student-centered interests. Custom editions of the map utility have been made as the "Jules Verne Voyager" and "Voyager Junior", for the International Lithosphere Project's "Global Strain Rate Map", and for EarthScope Education and Outreach as "EarthScope Voyager Jr.". For the latter, a number of EarthScope-specific features have been added, including locations of proposed USArray (seismic), Plate Boundary Observatory (geodetic), and San Andreas Fault Observatory at Depth sites, plus detailed maps and geographically referenced examples of EarthScope-related scientific investigations. As EarthScope develops, maps will be updated in `real time' so that students of all ages can use the data in formal and informal educational settings.

Modeling forest site productivity using mapped geospatial attributes within a South Carolina landscape, USA

Treesearch

B.R. Parresol; D.A. Scott; S.J. Zarnoch; L.A. Edwards; J.I. Blake

2017-01-01

Spatially explicit mapping of forest productivity is important to assess many forest management alternatives. We assessed the relationship between mapped variables and site index of forests ranging from southern pine plantations to natural hardwoods on a 74,000-ha landscape in South Carolina, USA. Mapped features used in the analysis were soil association, land use...

ChiPPI: a novel method for mapping chimeric protein-protein interactions uncovers selection principles of protein fusion events in cancer.

PubMed

Frenkel-Morgenstern, Milana; Gorohovski, Alessandro; Tagore, Somnath; Sekar, Vaishnovi; Vazquez, Miguel; Valencia, Alfonso

2017-07-07

Fusion proteins, comprising peptides deriving from the translation of two parental genes, are produced in cancer by chromosomal aberrations. The expressed fusion protein incorporates domains of both parental proteins. Using a methodology that treats discrete protein domains as binding sites for specific domains of interacting proteins, we have cataloged the protein interaction networks for 11 528 cancer fusions (ChiTaRS-3.1). Here, we present our novel method, chimeric protein-protein interactions (ChiPPI) that uses the domain-domain co-occurrence scores in order to identify preserved interactors of chimeric proteins. Mapping the influence of fusion proteins on cell metabolism and pathways reveals that ChiPPI networks often lose tumor suppressor proteins and gain oncoproteins. Furthermore, fusions often induce novel connections between non-interactors skewing interaction networks and signaling pathways. We compared fusion protein PPI networks in leukemia/lymphoma, sarcoma and solid tumors finding distinct enrichment patterns for each disease type. While certain pathways are enriched in all three diseases (Wnt, Notch and TGF β), there are distinct patterns for leukemia (EGFR signaling, DNA replication and CCKR signaling), for sarcoma (p53 pathway and CCKR signaling) and solid tumors (FGFR and EGFR signaling). Thus, the ChiPPI method represents a comprehensive tool for studying the anomaly of skewed cellular networks produced by fusion proteins in cancer. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Near surface geophysics techniques and geomorphological approach to reconstruct the hazard cave map in historical and urban areas

NASA Astrophysics Data System (ADS)

Lazzari, M.; Loperte, A.; Perrone, A.

2010-03-01

This work, carried out with an integrated methodological approach, focuses on the use of near surface geophysics techniques, such as ground penetrating radar and electrical resistivity tomography (ERT), and geomorphological analysis, in order to reconstruct the cave distribution and geometry in a urban context and, in particular, in historical centres. The interaction during recent centuries between human activity (caves excavation, birth and growth of an urban area) and the characters of the natural environment were the reasons of a progressive increase in hazard and vulnerability levels of several sites. The reconstruction of a detailed cave map distribution is the first step to define the anthropic and geomorphological hazard in urban areas, fundamental basis for planning and assessing the risk.

Ridge 2000 Data Management System

NASA Astrophysics Data System (ADS)

Goodwillie, A. M.; Carbotte, S. M.; Arko, R. A.; Haxby, W. F.; Ryan, W. B.; Chayes, D. N.; Lehnert, K. A.; Shank, T. M.

2005-12-01

Hosted at Lamont by the marine geoscience Data Management group, mgDMS, the NSF-funded Ridge 2000 electronic database, http://www.marine-geo.org/ridge2000/, is a key component of the Ridge 2000 multi-disciplinary program. The database covers each of the three Ridge 2000 Integrated Study Sites: Endeavour Segment, Lau Basin, and 8-11N Segment. It promotes the sharing of information to the broader community, facilitates integration of the suite of information collected at each study site, and enables comparisons between sites. The Ridge 2000 data system provides easy web access to a relational database that is built around a catalogue of cruise metadata. Any web browser can be used to perform a versatile text-based search which returns basic cruise and submersible dive information, sample and data inventories, navigation, and other relevant metadata such as shipboard personnel and links to NSF program awards. In addition, non-proprietary data files, images, and derived products which are hosted locally or in national repositories, as well as science and technical reports, can be freely downloaded. On the Ridge 2000 database page, our Data Link allows users to search the database using a broad range of parameters including data type, cruise ID, chief scientist, geographical location. The first Ridge 2000 field programs sailed in 2004 and, in addition to numerous data sets collected prior to the Ridge 2000 program, the database currently contains information on fifteen Ridge 2000-funded cruises and almost sixty Alvin dives. Track lines can be viewed using a recently- implemented Web Map Service button labelled Map View. The Ridge 2000 database is fully integrated with databases hosted by the mgDMS group for MARGINS and the Antarctic multibeam and seismic reflection data initiatives. Links are provided to partner databases including PetDB, SIOExplorer, and the ODP Janus system. Improved inter-operability with existing and new partner repositories continues to be strengthened. One major effort involves the gradual unification of the metadata across these partner databases. Standardised electronic metadata forms that can be filled in at sea are available from our web site. Interactive map-based exploration and visualisation of the Ridge 2000 database is provided by GeoMapApp, a freely-available Java(tm) application being developed within the mgDMS group. GeoMapApp includes high-resolution bathymetric grids for the 8-11N EPR segment and allows customised maps and grids for any of the Ridge 2000 ISS to be created. Vent and instrument locations can be plotted and saved as images, and Alvin dive photos are also available.

Mapping the interactions of the single-stranded DNA binding protein of bacteriophage T4 (gp32) with DNA lattices at single nucleotide resolution: polynucleotide binding and cooperativity

PubMed Central

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

2015-01-01

We here use our site-specific base analog mapping approach to study the interactions and binding equilibria of cooperatively-bound clusters of the single-stranded DNA binding protein (gp32) of the T4 DNA replication complex with longer ssDNA (and dsDNA) lattices. We show that in cooperatively bound clusters the binding free energy appears to be equi-partitioned between the gp32 monomers of the cluster, so that all bind to the ssDNA lattice with comparable affinity, but also that the outer domains of the gp32 monomers at the ends of the cluster can fluctuate on and off the lattice and that the clusters of gp32 monomers can slide along the ssDNA. We also show that at very low binding densities gp32 monomers bind to the ssDNA lattice at random, but that cooperatively bound gp32 clusters bind preferentially at the 5′-end of the ssDNA lattice. We use these results and the gp32 monomer-binding results of the companion paper to propose a detailed model for how gp32 might bind to and interact with ssDNA lattices in its various binding modes, and also consider how these clusters might interact with other components of the T4 DNA replication complex. PMID:26275774

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

ERIC Educational Resources Information Center

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

2008-01-01

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

Replication Cycle and Molecular Biology of the West Nile Virus

PubMed Central

Brinton, Margo A.

2013-01-01

West Nile virus (WNV) is a member of the genus Flavivirus in the family Flaviviridae. Flaviviruses replicate in the cytoplasm of infected cells and modify the host cell environment. Although much has been learned about virion structure and virion-endosomal membrane fusion, the cell receptor(s) used have not been definitively identified and little is known about the early stages of the virus replication cycle. Members of the genus Flavivirus differ from members of the two other genera of the family by the lack of a genomic internal ribosomal entry sequence and the creation of invaginations in the ER membrane rather than double-membrane vesicles that are used as the sites of exponential genome synthesis. The WNV genome 3' and 5' sequences that form the long distance RNA-RNA interaction required for minus strand initiation have been identified and contact sites on the 5' RNA stem loop for NS5 have been mapped. Structures obtained for many of the viral proteins have provided information relevant to their functions. Viral nonstructural protein interactions are complex and some may occur only in infected cells. Although interactions between many cellular proteins and virus components have been identified, the functions of most of these interactions have not been delineated. PMID:24378320

The impact of active site mutations of South African HIV PR on drug resistance: Insight from molecular dynamics simulations, binding free energy and per-residue footprints.

PubMed

Ahmed, Shaimaa M; Maguire, Glenn E M; Kruger, Hendrik G; Govender, Thirumala

2014-04-01

Molecular dynamics simulations and binding free energy calculations were used to provide an understanding of the impact of active site drug-resistant mutations of the South African HIV protease subtype C (C-SA HIV PR), V82A and V82F/I84V on drug resistance. Unique per-residue interaction energy 'footprints' were developed to map the overall drug-binding profiles for the wild type and mutants. Results confirmed that these mutations altered the overall binding landscape of the amino acid residues not only in the active site region but also in the flaps as well. Four FDA-approved drugs were investigated in this study; these include ritonavir (RTV), saquinavir (SQV), indinavir (IDV), and nelfinavir (NFV). Computational results compared against experimental findings were found to be complementary. Against the V82F/I84V variant, saquinavir, indinavir, and nelfinavir lose remarkable entropic contributions relative to both wild-type and V82A C-SA HIV PRs. The per-residue energy 'footprints' and the analysis of ligand-receptor interactions for the drug complexes with the wild type and mutants have also highlighted the nature of drug interactions. The data presented in this study will prove useful in the design of more potent inhibitors effective against drug-resistant HIV strains. © 2013 John Wiley & Sons A/S.

Minimal invasive epicardial lead implantation: optimizing cardiac resynchronization with a new mapping device for epicardial lead placement.

PubMed

Maessen, J G; Phelps, B; Dekker, A L A J; Dijkman, B

2004-05-01

To optimize resynchronization in biventricular pacing with epicardial leads, mapping to determine the best pacing site, is a prerequisite. A port access surgical mapping technique was developed that allowed multiple pace site selection and reproducible lead evaluation and implantation. Pressure-volume loops analysis was used for real time guidance in targeting epicardial lead placement. Even the smallest changes in lead position revealed significantly different functional results. Optimizing the pacing site with this technique allowed functional improvement up to 40% versus random pace site selection.

Trail Orienteering: An Effective Way To Practice Map Interpretation.

ERIC Educational Resources Information Center

Horizons, 1999

1999-01-01

Discusses a type of orienteering developed in Great Britain to allow people with physical disabilities to compete on equal terms. Sites are viewed from a wheelchair-accessible main route. The main skill is interpreting the maps at each site, not finding the sites. Describes differences from standard orienteering, how sites work, and essential…

Perceived usefulness, perceived ease of use, and perceived enjoyment as drivers for the user acceptance of interactive mobile maps

NASA Astrophysics Data System (ADS)

Hussain, Azham; Mkpojiogu, Emmanuel O. C.; Yusof, Muhammad Mat

2016-08-01

This study examines the user perception of usefulness, ease of use and enjoyment as drivers for the users' complex interaction with map on mobile devices. TAM model was used to evaluate users' intention to use and their acceptance of interactive mobile map using the above three beliefs as antecedents. Quantitative research (survey) methodology was employed and the analysis and findings showed that all the three explanatory variables used in this study, explain the variability in the user acceptance of interactive mobile map technology. Perceived usefulness, perceived ease of use, and perceived enjoyment each have significant positive influence on user acceptance of interactive mobile maps. This study further validates the TAM model.

Genomic structure and chromosomal mapping of the human CD22 gene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilson, G.L.; Kozlow, E.; Kehrl, J.H.

1993-06-01

The human CD22 gene is expressed specifically in B lymphocytes and likely has an important function in cell-cell interactions. A nearly full length human CD22 cDNA clone was used to isolate genomic clones that span the CD22 gene. The CD22 gene is spread over 22 kb of DNA and is composed of 15 exons. The first exon contains the major transcriptional start sites. The translation initiation codon is located in exon 3, which also encodes a portion of the signal peptide. Exons 4 to 10 encode the seven Ig domains of CD22, exon 11 encodes the transmembrane domain, exons 12more » to 15 encode the intracytoplasmic domain of CD22, and exon 15 also contains the 3' untranslated region. A minor form of CD22 mRNA likely results from splicing of exon 5 to exon 8, skipping exons 6 and 7. A 4.6-kb Xbal fragment of the CD22 gene was used to map the chromosomal location of CD22 by fluorescence in situ hybridization. The hybridization locus was identified by combining fluorescent images of the probe with the chromosomal banding pattern generated by an Alu probe. The results demonstrate the CD22 is located within the band region q13.1 of chromosome 19. Two closely clustered major transcription start sites and several minor start sites were mapped by primer extension. Similarly to many other lymphoid-specific genes, the CD22 promoter lacks an obvious TATA box. Approximately 4 kb of DNA 5' of the transcription start sites were sequenced and found to contain multiple Alu elements. Potential binding sites for the transcriptional factors NF-kB, AP-1, and Oct-2 are located within 300 bp 5' of the major transcription start sites. A 400-bp fragment (bp -339 through +71) of the CD22 promoter region was subcloned into a pGEM-chloramphenicol acetyltransferase vector and after transfection into B and T cells was found to be active in both B and T cells. 45 refs., 7 figs., 2 tabs.« less

National Park Service Vegetation Inventory Program, Cuyahoga Valley National Park, Ohio

USGS Publications Warehouse

Hop, Kevin D.; Drake, J.; Strassman, Andrew C.; Hoy, Erin E.; Menard, Shannon; Jakusz, J.W.; Dieck, J.J.

2013-01-01

The National Park Service (NPS) Vegetation Inventory Program (VIP) is an effort to classify, describe, and map existing vegetation of national park units for the NPS Natural Resource Inventory and Monitoring (I&M) Program. The NPS VIP is managed by the NPS Biological Resources Management Division and provides baseline vegetation information to the NPS Natural Resource I&M Program. The U.S. Geological Survey (USGS) Vegetation Characterization Program lends a cooperative role in the NPS VIP. The USGS Upper Midwest Environmental Sciences Center, NatureServe, and NPS Cuyahoga Valley National Park (CUVA) have completed vegetation classification and mapping of CUVA.Mappers, ecologists, and botanists collaborated to identify and describe vegetation types within the National Vegetation Classification Standard (NVCS) and to determine how best to map them by using aerial imagery. The team collected data from 221 vegetation plots within CUVA to develop detailed descriptions of vegetation types. Data from 50 verification sites were also collected to test both the key to vegetation types and the application of vegetation types to a sample set of map polygons. Furthermore, data from 647 accuracy assessment (AA) sites were collected (of which 643 were used to test accuracy of the vegetation map layer). These data sets led to the identification of 45 vegetation types at the association level in the NVCS at CUVA.A total of 44 map classes were developed to map the vegetation and general land cover of CUVA, including the following: 29 map classes represent natural/semi-natural vegetation types in the NVCS, 12 map classes represent cultural vegetation (agricultural and developed) in the NVCS, and 3 map classes represent non-vegetation features (open-water bodies). Features were interpreted from viewing color-infrared digital aerial imagery dated October 2010 (during peak leaf-phenology change of trees) via digital onscreen three-dimensional stereoscopic workflow systems in geographic information systems (GIS). The interpreted data were digitally and spatially referenced, thus making the spatial database layers usable in GIS. Polygon units were mapped to either a 0.5 ha or 0.25 ha minimum mapping unit, depending on vegetation type.A geodatabase containing various feature-class layers and tables shows the locations of vegetation types and general land cover (vegetation map), vegetation plot samples, verification sites, AA sites, project boundary extent, and aerial photographic centers. The feature-class layer and relate tables for the CUVA vegetation map provides 4,640 polygons of detailed attribute data covering 13,288.4 ha, with an average polygon size of 2.9 ha.Summary reports generated from the vegetation map layer show map classes representing natural/semi-natural types in the NVCS apply to 4,151 polygons (89.4% of polygons) and cover 11,225.0 ha (84.5%) of the map extent. Of these polygons, the map layer shows CUVA to be 74.4% forest (9,888.8 ha), 2.5% shrubland (329.7 ha), and 7.6% herbaceous vegetation cover (1,006.5 ha). Map classes representing cultural types in the NVCS apply to 435 polygons (9.4% of polygons) and cover 1,825.7 ha (13.7%) of the map extent. Map classes representing non-NVCS units (open water) apply to 54 polygons (1.2% of polygons) and cover 237.7 ha (1.8%) of the map extent.A thematic AA study was conducted of map classes representing natural/semi-natural types in the NVCS. Results present an overall accuracy of 80.7% (kappa index of 79.5%) based on data from 643 of the 647 AA sites. Most individual map-class themes exceed the NPS VIP standard of 80% with a 90% confidence interval.The CUVA vegetation mapping project delivers many geospatial and vegetation data products in hardcopy and/or digital formats. These products consist of an in-depth project report discussing methods and results, which include descriptions and a dichotomous key to vegetation types, map classification and map-class descriptions, and a contingency table showing AA results. The suite of products also includes a database of vegetation plots, verification sites, and AA sites; digital pictures of field sites; field data sheets; aerial photographic imagery; hardcopy and digital maps; and a geodatabase of vegetation types and land cover (map layer), fieldwork locations (vegetation plots, verification sites, and AA sites), aerial photographic index, project boundary, and metadata. All geospatial products are projected in Universal Transverse Mercator, Zone 17, by using the North American Datum of 1983. Information on the NPS VIP and completed park mapping projects are located on the Internet at and .

EnviroAtlas - Historic Places by 12-digit HUC for the Conterminous United States

EPA Pesticide Factsheets

This EnviroAtlas dataset portrays the total number of historic places located within each 12-digit Hydrologic Unit (HUC). The historic places data were compiled from the National Park Service's National Register of Historic Places (NRHP), which provides official federal lists of districts, sites, buildings, structures and objects significant to American history, architecture, archeology, engineering, and culture. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

Interdomain allosteric regulation of Polo kinase by Aurora B and Map205 is required for cytokinesis

PubMed Central

Kachaner, David; Pinson, Xavier; El Kadhi, Khaled Ben; Normandin, Karine; Talje, Lama; Lavoie, Hugo; Lépine, Guillaume; Carréno, Sébastien; Kwok, Benjamin H.; Hickson, Gilles R.

2014-01-01

Drosophila melanogaster Polo and its human orthologue Polo-like kinase 1 fulfill essential roles during cell division. Members of the Polo-like kinase (Plk) family contain an N-terminal kinase domain (KD) and a C-terminal Polo-Box domain (PBD), which mediates protein interactions. How Plks are regulated in cytokinesis is poorly understood. Here we show that phosphorylation of Polo by Aurora B is required for cytokinesis. This phosphorylation in the activation loop of the KD promotes the dissociation of Polo from the PBD-bound microtubule-associated protein Map205, which acts as an allosteric inhibitor of Polo kinase activity. This mechanism allows the release of active Polo from microtubules of the central spindle and its recruitment to the site of cytokinesis. Failure in Polo phosphorylation results in both early and late cytokinesis defects. Importantly, the antagonistic regulation of Polo by Aurora B and Map205 in cytokinesis reveals that interdomain allosteric mechanisms can play important roles in controlling the cellular functions of Plks. PMID:25332165

In Silico Design of Human IMPDH Inhibitors Using Pharmacophore Mapping and Molecular Docking Approaches

PubMed Central

Li, Rui-Juan; Wang, Ya-Li; Wang, Qing-He; Wang, Jian; Cheng, Mao-Sheng

2015-01-01

Inosine 5′-monophosphate dehydrogenase (IMPDH) is one of the crucial enzymes in the de novo biosynthesis of guanosine nucleotides. It has served as an attractive target in immunosuppressive, anticancer, antiviral, and antiparasitic therapeutic strategies. In this study, pharmacophore mapping and molecular docking approaches were employed to discover novel Homo sapiens IMPDH (hIMPDH) inhibitors. The Güner-Henry (GH) scoring method was used to evaluate the quality of generated pharmacophore hypotheses. One of the generated pharmacophore hypotheses was found to possess a GH score of 0.67. Ten potential compounds were selected from the ZINC database using a pharmacophore mapping approach and docked into the IMPDH active site. We find two hits (i.e., ZINC02090792 and ZINC00048033) that match well the optimal pharmacophore features used in this investigation, and it is found that they form interactions with key residues of IMPDH. We propose that these two hits are lead compounds for the development of novel hIMPDH inhibitors. PMID:25784957

Hyperspectral remote sensing and GIS techniques application for the evaluation and monitoring of interactions between natural risks and industrial hazards

NASA Astrophysics Data System (ADS)

Marino, Alessandra; Ludovisi, Giancarlo; Moccaldi, Antonio; Damiani, Fiorenzo

2001-02-01

The aim of this paper is to outline the potential of imaging spectroscopy and GIS techniques as tool for the management of data rich environments, as complex fluvial areas, exposed to geological, geomorphological, and hydrogeological risks. The area of study, the Pescara River Basin is characterized by the presence of important industrial sites and by the occurrence of floods, landslides and seismic events. Data were collected, during a specific flight, using an hyperspectral MIVIS sensor. Images have been processed in order to obtain updated and accurate land-cover and land-use maps that have been inserted in a specific GIS database and integrated with further information like lithology, geological structure, geomorphology, hydrogeological features, productive plants location and characters. The processing of data layers was performed, using a dedicated software, through typical GIS operators like indexing, recording, matrix analysis, proximity analysis. The interactions between natural risks, industrial installations, agricultural areas, water resources and urban settlements have been analyzed. This allowed the creation and processing of thematic layers like vulnerability, risk and impact maps.

Synchrotron-based X-ray Fluorescence Microscopy in Conjunction with Nanoindentation to Study Molecular-Scale Interactions of Phenol-Formaldehyde in Wood Cell Walls

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jakes, Joseph E.; Hunt, Chris G.; Yelle, Daniel J.

Understanding and controlling molecular-scale interactions between adhesives and wood polymers are critical to accelerate the development of improved adhesives for advanced wood-based materials. The submicrometer resolution of synchrotron-based X-ray fluorescence microscopy (XFM) was found capable of mapping and quantifying infiltration of Br-labeled phenolformaldehyde (BrPF) into wood cell walls. Cell wall infiltration of five BrPF adhesives with different average molecular weights (MWs) was mapped. Nanoindentation on the same cell walls was performed to assess the effects of BrPF infiltration on cell wall hygromechanical properties. For the same amount of weight uptake, lower MW BrPF adhesives were found to be more effectivemore » at decreasing moisture-induced mechanical softening. This greater effectiveness of lower MW phenolic adhesives likely resulted from their ability to more intimately associate with water sorption sites in the wood polymers. Evidence also suggests that a BrPF interpenetrating polymer network (IPN) formed within the wood polymers, which might also decrease moisture sorption by mechanically restraining wood polymers during swelling.« less

Roles of Fog and Topography in Redwood Forest Hydrology

NASA Astrophysics Data System (ADS)

Francis, E. J.; Asner, G. P.

2017-12-01

Spatial variability of water in forests is a function of both climatic gradients that control water inputs and topo-edaphic variation that determines the flows of water belowground, as well as interactions of climate with topography. Coastal redwood forests are hydrologically unique because they are influenced by coastal low clouds, or fog, that is advected onto land by a strong coastal-to-inland temperature difference. Where fog intersects the land surface, annual water inputs from summer fog drip can be greater than that of winter rainfall. In this study, we take advantage of mapped spatial gradients in forest canopy water storage, topography, and fog cover in California to better understand the roles and interactions of fog and topography in the hydrology of redwood forests. We test a conceptual model of redwood forest hydrology with measurements of canopy water content derived from high-resolution airborne imaging spectroscopy, topographic variables derived from high-resolution LiDAR data, and fog cover maps derived from NASA MODIS data. Landscape-level results provide insight into hydrological processes within redwood forests, and cross-site analyses shed light on their generality.

Atmospheric propagation modeling indicates homing pigeons use loft-specific infrasonic 'map' cues.

PubMed

Hagstrum, Jonathan T

2013-02-15

Results from an acoustic ray-tracing program using daily meteorological profiles are presented to explain 'release-site biases' for homing pigeons at three experimental sites in upstate New York where W. T. Keeton and his co-workers at Cornell University conducted extensive releases between 1968 and 1987 in their investigations of the avian navigational 'map'. The sites are the Jersey Hill and Castor Hill fire towers, and another near Weedsport, where control pigeons from the Cornell loft vanished in random directions, in directions consistently >50 deg clockwise and in directions ∼15 deg clockwise from the homeward bearing, respectively. Because Cornell pigeons were disoriented at Jersey Hill whereas birds from other lofts were not, it is inferred that Jersey Hill lies within an acoustic 'shadow' zone relative to infrasonic signals originating from the Cornell loft's vicinity. Such signals could arise from ground-to-air coupling of near-continuous microseisms, or from scattering of direct microbaroms off terrain features, both of which are initially generated by wave-wave interactions in the deep ocean. HARPA runs show that little or no infrasound from the loft area arrived at Jersey Hill on days when Cornell pigeons were disoriented there, and that homeward infrasonic signals could have arrived at all three sites from directions consistent with pigeon departure bearings, especially on days when these bearings were unusual. The general stability of release-site biases might be due to influences of terrain on transmission of the homeward signals under prevailing weather patterns, whereas short-term changes in biases might be caused by rapid shifts in atmospheric conditions.

Isolation of a High Affinity Neutralizing Monoclonal Antibody against 2009 Pandemic H1N1 Virus That Binds at the ‘Sa’ Antigenic Site

PubMed Central

Mishra, Arpita; Yeolekar, Leena; Dhere, Rajeev; Kapre, Subhash; Varadarajan, Raghavan; Gupta, Satish Kumar

2013-01-01

Influenza virus evades host immunity through antigenic drift and shift, and continues to circulate in the human population causing periodic outbreaks including the recent 2009 pandemic. A large segment of the population was potentially susceptible to this novel strain of virus. Historically, monoclonal antibodies (MAbs) have been fundamental tools for diagnosis and epitope mapping of influenza viruses and their importance as an alternate treatment option is also being realized. The current study describes isolation of a high affinity (K D = 2.1±0.4 pM) murine MAb, MA2077 that binds specifically to the hemagglutinin (HA) surface glycoprotein of the pandemic virus. The antibody neutralized the 2009 pandemic H1N1 virus in an in vitro microneutralization assay (IC50 = 0.08 µg/ml). MA2077 also showed hemagglutination inhibition activity (HI titre of 0.50 µg/ml) against the pandemic virus. In a competition ELISA, MA2077 competed with the binding site of the human MAb, 2D1 (isolated from a survivor of the 1918 Spanish flu pandemic) on pandemic H1N1 HA. Epitope mapping studies using yeast cell-surface display of a stable HA1 fragment, wherein ‘Sa’ and ‘Sb’ sites were independently mutated, localized the binding site of MA2077 within the ‘Sa’ antigenic site. These studies will facilitate our understanding of antigen antibody interaction in the context of neutralization of the pandemic influenza virus. PMID:23383214

The Zamama-Thor region of Io: Insights from a synthesis of mapping, topography, and Galileo spacecraft data

USGS Publications Warehouse

Williams, D.A.; Keszthelyi, L.P.; Schenk, P.M.; Milazzo, M.P.; Lopes, R.M.C.; Rathbun, J.A.; Greeley, R.

2005-01-01

We have studied data from the Galileo spacecraft's three remote sensing instruments (Solid-State Imager (SSI), Near-Infrared Mapping Spectrometer (NIMS), and Photopolarimeter-Radiometer (PPR)) covering the Zamama - Thor region of Io's antijovian hemisphere, and produced a geomorphological map of this region. This is the third of three regional maps we are producing from the Galileo spacecraft data. Our goal is to assess the variety of volcanic and tectonic materials and their interrelationships on Io using planetary mapping techniques, supplemented with all available Galileo remote sensing data. Based on the Galileo data analysis and our mapping, we have determined that the most recent geologic activity in the Zamama - Thor region has been dominated by two sites of large-scale volcanic surface changes. The Zamama Eruptive Center is a site of both explosive and effusive eruptions, which emanate from two relatively steep edifices (Zamama Tholi A and B) that appear to be built by both silicate and sulfur volcanism. A ???100-km long flow field formed sometime after the 1979 Voyager flybys, which appears to be a site of promethean-style compound flows, flow-front SO2 plumes, and adjacent sulfur flows. Larger, possibly stealthy, plumes have on at least one occasion during the Galileo mission tapped a source that probably includes S and/or Cl to produce a red pyroclastic deposit from the same vent from which silicate lavas were erupted. The Thor Eruptive Center, which may have been active prior to Voyager, became active again during the Galileo mission between May and August 2001. A pillanian-style eruption at Thor included the tallest plume observed to date on Io (at least 500 km high) and new dark lava flows. The plume produced a central dark pyroclastic deposit (probably silicate-rich) and an outlying white diffuse ring that is SO2-rich. Mapping shows that several of th000e new dark lava flows around the plume vent have reoccupied sites of earlier flows. Unlike most of the other pillanian eruptions observed during the Galileo mission, the 2001 Thor eruption did not produce a large red ring deposit, indicating a relative lack of S and/or Cl gases interacting with the magma during that eruption. Between these two eruptive centers are two paterae, Thomagata and Reshef. Thomagata Patera is located on a large shield-like mesa and shows no signs of activity. In contrast, Reshef Patera is located on a large, irregular mesa that is apparently undergoing degradation through erosion (perhaps from SO2 -sapping or chemical decomposition of sulfur-rich material) from multiple secondary volcanic centers. ?? 2005 Elsevier Inc. All rights reserved.

In vitro phosphorylation of insulin receptor substrate 1 by protein kinase C-zeta: functional analysis and identification of novel phosphorylation sites.

PubMed

Sommerfeld, Mark R; Metzger, Sabine; Stosik, Magdalene; Tennagels, Norbert; Eckel, Jürgen

2004-05-18

Protein kinase C-zeta (PKC-zeta) participates both in downstream insulin signaling and in the negative feedback control of insulin action. Here we used an in vitro approach to identify PKC-zeta phosphorylation sites within insulin receptor substrate 1 (IRS-1) and to characterize the functional implications. A recombinant IRS-1 fragment (rIRS-1(449)(-)(664)) containing major tyrosine motifs for interaction with phosphatidylinositol (PI) 3-kinase strongly associated to the p85alpha subunit of PI 3-kinase after Tyr phosphorylation by the insulin receptor. Phosphorylation of rIRS-1(449)(-)(664) by PKC-zeta induced a prominent inhibition of this process with a mixture of classical PKC isoforms being less effective. Both PKC-zeta and the classical isoforms phosphorylated rIRS-1(449)(-)(664) on Ser(612). However, modification of this residue did not reduce the affinity of p85alpha binding to pTyr-containing peptides (amino acids 605-615 of rat IRS-1), as determined by surface plasmon resonance. rIRS-1(449)(-)(664) was then phosphorylated by PKC-zeta using [(32)P]ATP and subjected to tryptic phosphopeptide mapping based on two-dimensional HPLC coupled to mass spectrometry. Ser(498) and Ser(570) were identified as novel phosphoserine sites targeted by PKC-zeta. Both sites were additionally confirmed by phosphopeptide mapping of the corresponding Ser --> Ala mutants of rIRS-1(449)(-)(664). Ser(570) was specifically targeted by PKC-zeta, as shown by immunoblotting with a phosphospecific antiserum against Ser(570) of IRS-1. Binding of p85alpha to the S570A mutant was less susceptible to inhibition by PKC-zeta, when compared to the S612A mutant. In conclusion, our in vitro data demonstrate a strong inhibitory action of PKC-zeta at the level of IRS-1/PI 3-kinase interaction involving multiple serine phosphorylation sites. Whereas Ser(612) appears not to participate in the negative control of insulin signaling, Ser(570) may at least partly contribute to this process.

QuickMap: a public tool for large-scale gene therapy vector insertion site mapping and analysis.

PubMed

Appelt, J-U; Giordano, F A; Ecker, M; Roeder, I; Grund, N; Hotz-Wagenblatt, A; Opelz, G; Zeller, W J; Allgayer, H; Fruehauf, S; Laufs, S

2009-07-01

Several events of insertional mutagenesis in pre-clinical and clinical gene therapy studies have created intense interest in assessing the genomic insertion profiles of gene therapy vectors. For the construction of such profiles, vector-flanking sequences detected by inverse PCR, linear amplification-mediated-PCR or ligation-mediated-PCR need to be mapped to the host cell's genome and compared to a reference set. Although remarkable progress has been achieved in mapping gene therapy vector insertion sites, public reference sets are lacking, as are the possibilities to quickly detect non-random patterns in experimental data. We developed a tool termed QuickMap, which uniformly maps and analyzes human and murine vector-flanking sequences within seconds (available at www.gtsg.org). Besides information about hits in chromosomes and fragile sites, QuickMap automatically determines insertion frequencies in +/- 250 kb adjacency to genes, cancer genes, pseudogenes, transcription factor and (post-transcriptional) miRNA binding sites, CpG islands and repetitive elements (short interspersed nuclear elements (SINE), long interspersed nuclear elements (LINE), Type II elements and LTR elements). Additionally, all experimental frequencies are compared with the data obtained from a reference set, containing 1 000 000 random integrations ('random set'). Thus, for the first time a tool allowing high-throughput profiling of gene therapy vector insertion sites is available. It provides a basis for large-scale insertion site analyses, which is now urgently needed to discover novel gene therapy vectors with 'safe' insertion profiles.

A mammalian germ cell-specific RNA-binding protein interacts with ubiquitously expressed proteins involved in splice site selection

NASA Astrophysics Data System (ADS)

Elliott, David J.; Bourgeois, Cyril F.; Klink, Albrecht; Stévenin, James; Cooke, Howard J.

2000-05-01

RNA-binding motif (RBM) genes are found on all mammalian Y chromosomes and are implicated in spermatogenesis. Within human germ cells, RBM protein shows a similar nuclear distribution to components of the pre-mRNA splicing machinery. To address the function of RBM, we have used protein-protein interaction assays to test for possible physical interactions between these proteins. We find that RBM protein directly interacts with members of the SR family of splicing factors and, in addition, strongly interacts with itself. We have mapped the protein domains responsible for mediating these interactions and expressed the mouse RBM interaction region as a bacterial fusion protein. This fusion protein can pull-down several functionally active SR protein species from cell extracts. Depletion and add-back experiments indicate that these SR proteins are the only splicing factors bound by RBM which are required for the splicing of a panel of pre-mRNAs. Our results suggest that RBM protein is an evolutionarily conserved mammalian splicing regulator which operates as a germ cell-specific cofactor for more ubiquitously expressed pre-mRNA splicing activators.

PRMT7 Interacts with ASS1 and Citrullinemia Mutations Disrupt the Interaction.

PubMed

Verma, Mamta; Charles, Ramya Chandar M; Chakrapani, Baskar; Coumar, Mohane Selvaraj; Govindaraju, Gayathri; Rajavelu, Arumugam; Chavali, Sreenivas; Dhayalan, Arunkumar

2017-07-21

Protein arginine methyltransferase 7 (PRMT7) catalyzes the introduction of monomethylation marks at the arginine residues of substrate proteins. PRMT7 plays important roles in the regulation of gene expression, splicing, DNA damage, paternal imprinting, cancer and metastasis. However, little is known about the interaction partners of PRMT7. To address this, we performed yeast two-hybrid screening of PRMT7 and identified argininosuccinate synthetase (ASS1) as a potential interaction partner of PRMT7. We confirmed that PRMT7 directly interacts with ASS1 using pull-down studies. ASS1 catalyzes the rate-limiting step of arginine synthesis in urea cycle and citrulline-nitric oxide cycle. We mapped the interface of PRMT7-ASS1 complex through computational approaches and validated the predicted interface in vivo by site-directed mutagenesis. Evolutionary analysis revealed that the ASS1 residues important for PRMT7-ASS1 interaction have co-evolved with PRMT7. We showed that ASS1 mutations linked to type I citrullinemia disrupt the ASS1-PRMT7 interaction, which might explain the molecular pathogenesis of the disease. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

PubMed Central

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

2015-01-01

The prokaryotic Type ISP restriction-modification enzymes are single-chain proteins comprising an Mrr-family nuclease, a superfamily 2 helicase-like ATPase, a coupler domain, a methyltransferase, and a DNA-recognition domain. Upon recognising an unmodified DNA target site, the helicase-like domain hydrolyzes ATP to cause site release (remodeling activity) and to then drive downstream translocation consuming 1–2 ATP per base pair (motor activity). On an invading foreign DNA, double-strand breaks are introduced at random wherever two translocating enzymes form a so-called collision complex following long-range communication between a pair of target sites in inverted (head-to-head) repeat. Paradoxically, structural models for collision suggest that the nuclease domains are too far apart (>30 bp) to dimerise and produce a double-strand DNA break using just two strand-cleavage events. Here, we examined the organisation of different collision complexes and how these lead to nuclease activation. We mapped DNA cleavage when a translocating enzyme collides with a static enzyme bound to its site. By following communication between sites in both head-to-head and head-to-tail orientations, we could show that motor activity leads to activation of the nuclease domains via distant interactions of the helicase or MTase-TRD. Direct nuclease dimerization is not required. To help explain the observed cleavage patterns, we also used exonuclease footprinting to demonstrate that individual Type ISP domains can swing off the DNA. This study lends further support to a model where DNA breaks are generated by multiple random nicks due to mobility of a collision complex with an overall DNA-binding footprint of ∼30 bp. PMID:26507855

A Mobile, Map-Based Tasking Interface for Human-Robot Interaction

DTIC Science & Technology

2010-12-01

A MOBILE, MAP-BASED TASKING INTERFACE FOR HUMAN-ROBOT INTERACTION By Eli R. Hooten Thesis Submitted to the Faculty of the Graduate School of...SUBTITLE A Mobile, Map-Based Tasking Interface for Human-Robot Interaction 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6...3 II.1 Interactive Modalities and Multi-Touch . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 II.2

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Interfering with the neural activity of mirror-related frontal areas impairs mentalistic inferences.

PubMed

Herbet, Guillaume; Lafargue, Gilles; Moritz-Gasser, Sylvie; Bonnetblanc, François; Duffau, Hugues

2015-07-01

According to recently proposed interactive dual-process theories, mentalizing abilities emerge from the coherent interaction between two physically distinct neural systems: (1) the mirror network, coding for the low-level embodied representations involved in pre-reflective sociocognitive processes and (2) the mentalizing network per se, which codes for higher level representations subtending the reflective attribution of psychological states. However, although the latest studies have shown that the core areas forming these two neurocognitive systems do indeed maintain effective connectivity during mentalizing, it is unclear whether an intact mirror system (and, more specifically, its anterior node, namely the posterior inferior frontal cortex) is a prerequisite for accurate mentalistic inferences. Intraoperative brain mapping via direct electrical stimulation offers a unique opportunity to address this issue. Electrical stimulation of the brain creates a "virtual" lesion, which provides functional information on well-defined parts of the cerebral cortex. In the present study, five patients were mapped in real time while they performed a mentalizing task. We found six responsive sites: four in the lateral part of the right pars opercularis and two in the dorsal part of the right pars triangularis. On the subcortical level, two additional sites were located within the white matter connectivity of the pars opercularis. Taken as a whole, our results suggest that the right inferior frontal cortex and its underlying axonal connectivity have a key role in mentalizing. Specifically, our findings support the hypothesis whereby transient, functional disruption of the mirror network influences higher order mentalistic inferences.

77 FR 74266 - Review of National Environmental Policy Act Categorical Exclusion Survey Posted on DOT/FHWA Web Site

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-13

... of National Environmental Policy Act Categorical Exclusion Survey Posted on DOT/FHWA Web Site AGENCY... review is now available on the FHWA Web site, http://www.fhwa.dot.gov/map21 , and FTA Web site, http://www.fta.dot.gov/map21 . DATES: These reports were posted on the Web site on December 7, 2012...

Crystal Structure of the Extracellular Cholinesterase-Like Domain from Neuroligin-2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koehnke,J.; Jin, X.; Budreck, E.

Neuroligins (NLs) are catalytically inactive members of a family of cholinesterase-like transmembrane proteins that mediate cell adhesion at neuronal synapses. Postsynaptic neuroligins engage in Ca2+-dependent transsynaptic interactions via their extracellular cholinesterase domain with presynaptic neurexins (NRXs). These interactions may be regulated by two short splice insertions (termed A and B) in the NL cholinesterase domain. Here, we present the 3.3- Angstroms crystal structure of the ectodomain from NL2 containing splice insertion A (NL2A). The overall structure of NL2A resembles that of cholinesterases, but several structural features are unique to the NL proteins. First, structural elements surrounding the esterase active-site regionmore » differ significantly between active esterases and NL2A. On the opposite surface of the NL2A molecule, the positions of the A and B splice insertions identify a candidate NRX interaction site of the NL protein. Finally, sequence comparisons of NL isoforms allow for mapping the location of residues of previously identified mutations in NL3 and NL4 found in patients with autism spectrum disorders. Overall, the NL2 structure promises to provide a valuable model for dissecting NL isoform- and synapse-specific functions.« less

Domain Architecture of the Catalytic Subunit in the ISW2-Nucleosome Complex▿

PubMed Central

Dang, Weiwei; Bartholomew, Blaine

2007-01-01

ATP-dependent chromatin remodeling has an important role in the regulation of cellular differentiation and development. For the first time, a topological view of one of these complexes has been revealed, by mapping the interactions of the catalytic subunit Isw2 with nucleosomal and extranucleosomal DNA in the complex with all four subunits of ISW2 bound to nucleosomes. Different domains of Isw2 were shown to interact with the nucleosome near the dyad axis, another near the entry site of the nucleosome, and another with extranucleosomal DNA. The conserved DEXD or ATPase domain was found to contact the superhelical location 2 (SHL2) of the nucleosome, providing a direct physical connection of ATP hydrolysis with this region of nucleosomes. The C terminus of Isw2, comprising the SLIDE (SANT-like domain) and HAND domains, was found to be associated with extranucleosomal DNA and the entry site of nucleosomes. It is thus proposed that the C-terminal domains of Isw2 are involved in anchoring the complex to nucleosomes through their interactions with linker DNA and that they facilitate the movement of DNA along the surface of nucleosomes. PMID:17908792

Crystal structure of the extracellular cholinesterase-like domain from neuroligin-2

PubMed Central

Koehnke, Jesko; Jin, Xiangshu; Budreck, Elaine C.; Posy, Shoshana; Scheiffele, Peter; Honig, Barry; Shapiro, Lawrence

2008-01-01

Neuroligins (NLs) are catalytically inactive members of a family of cholinesterase-like transmembrane proteins that mediate cell adhesion at neuronal synapses. Postsynaptic neuroligins engage in Ca2+-dependent transsynaptic interactions via their extracellular cholinesterase domain with presynaptic neurexins (NRXs). These interactions may be regulated by two short splice insertions (termed A and B) in the NL cholinesterase domain. Here, we present the 3.3-Å crystal structure of the ectodomain from NL2 containing splice insertion A (NL2A). The overall structure of NL2A resembles that of cholinesterases, but several structural features are unique to the NL proteins. First, structural elements surrounding the esterase active-site region differ significantly between active esterases and NL2A. On the opposite surface of the NL2A molecule, the positions of the A and B splice insertions identify a candidate NRX interaction site of the NL protein. Finally, sequence comparisons of NL isoforms allow for mapping the location of residues of previously identified mutations in NL3 and NL4 found in patients with autism spectrum disorders. Overall, the NL2 structure promises to provide a valuable model for dissecting NL isoform- and synapse-specific functions. PMID:18250328

Self-organization in irregular landscapes: Detecting autogenic interactions from field data using descriptive statistics and dynamical systems theory

NASA Astrophysics Data System (ADS)

Larsen, L.; Watts, D.; Khurana, A.; Anderson, J. L.; Xu, C.; Merritts, D. J.

2015-12-01

The classic signal of self-organization in nature is pattern formation. However, the interactions and feedbacks that organize depositional landscapes do not always result in regular or fractal patterns. How might we detect their existence and effects in these "irregular" landscapes? Emergent landscapes such as newly forming deltaic marshes or some restoration sites provide opportunities to study the autogenic processes that organize landscapes and their physical signatures. Here we describe a quest to understand autogenic vs. allogenic controls on landscape evolution in Big Spring Run, PA, a landscape undergoing restoration from bare-soil conditions to a target wet meadow landscape. The contemporary motivation for asking questions about autogenic vs. allogenic controls is to evaluate how important initial conditions or environmental controls may be for the attainment of management objectives. However, these questions can also inform interpretation of the sedimentary record by enabling researchers to separate signals that may have arisen through self-organization processes from those resulting from environmental perturbations. Over three years at Big Spring Run, we mapped the dynamic evolution of floodplain vegetation communities and distributions of abiotic variables and topography. We used principal component analysis and transition probability analysis to detect associative interactions between vegetation and geomorphic variables and convergent cross-mapping on lidar data to detect causal interactions between biomass and topography. Exploratory statistics revealed that plant communities with distinct morphologies exerted control on landscape evolution through stress divergence (i.e., channel initiation) and promoting the accumulation of fine sediment in channels. Together, these communities participated in a negative feedback that maintains low energy and multiple channels. Because of the spatially explicit nature of this feedback, causal interactions could not be uncovered from convergent cross-mapping with this limited dataset, serving as a reminder that spatially explicit approaches for revealing causality are needed to reconstruct self-organizing mechanisms from data.

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

NASA Astrophysics Data System (ADS)

Giroux, D.; Bélanger, R.

2003-04-01

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

Cruise report: RV Ocean Alert Cruise A2-98-SC: mapping the southern California continental margin; March 26 through April 11, 1998; San Diego to Long Beach, California

USGS Publications Warehouse

Gardner, James V.; Mayer, Larry A.

1998-01-01

The major objective of cruise A2-98 was to map portions of the southern California continental margin, including mapping in detail US Environmental Protection Agency (USEPA) ocean dumping sites. Mapping was accomplished using a high-resolution multibeam mapping system. The cruise was a jointly funded project between the USEPA and the US Geological Survey (USGS). The USEPA is specifically interested in a series of ocean dump sites off San Diego, Newport Beach, and Long Beach (see Fig. 1 in report) that require high-resolution base maps for site monitoring purposes. The USGS Coastal and Marine Geology Program has several on-going projects off southern California that lack high-precision base maps for a variety of ongoing geological studies. The cruise was conducted under a Cooperative Agreement between the USGS and the Ocean Mapping Group, University of New Brunswick, Canada.

NMR and Bioinformatics Discovery of Exosites That Tune Metalloelastase Specificity for Solubilized Elastin and Collagen Triple Helices*

PubMed Central

Palmier, Mark O.; Fulcher, Yan G.; Bhaskaran, Rajagopalan; Duong, Vinh Q.; Fields, Gregg B.; Van Doren, Steven R.

2010-01-01

The catalytic domain of metalloelastase (matrix metalloproteinase-12 or MMP-12) is unique among MMPs in exerting high proteolytic activity upon fibrils that resist hydrolysis, especially elastin from lungs afflicted with chronic obstructive pulmonary disease or arteries with aneurysms. How does the MMP-12 catalytic domain achieve this specificity? NMR interface mapping suggests that α-elastin species cover the primed subsites, a strip across the β-sheet from β-strand IV to the II–III loop, and a broad bowl from helix A to helix C. The many contacts may account for the comparatively high affinity, as well as embedding of MMP-12 in damaged elastin fibrils in vivo. We developed a strategy called BINDSIght, for bioinformatics and NMR discovery of specificity of interactions, to evaluate MMP-12 specificity without a structure of a complex. BINDSIght integration of the interface mapping with other ambiguous information from sequences guided choice mutations in binding regions nearer the active site. Single substitutions at each of ten locations impair specific activity toward solubilized elastin. Five of them impair release of peptides from intact elastin fibrils. Eight lesions also impair specific activity toward triple helices from collagen IV or V. Eight sites map to the “primed” side in the III–IV, V–B, and S1′ specificity loops. Two map to the “unprimed” side in the IV–V and B–C loops. The ten key residues circumscribe the catalytic cleft, form an exosite, and are distinctive features available for targeting by new diagnostics or therapeutics. PMID:20663866

Using Landsat time series for characterizing forest disturbance dynamics in the coupled human and natural systems of Central Europe.

PubMed

Senf, Cornelius; Pflugmacher, Dirk; Hostert, Patrick; Seidl, Rupert

2017-08-01

Remote sensing is a key information source for improving the spatiotemporal understanding of forest ecosystem dynamics. Yet, the mapping and attribution of forest change remains challenging, particularly in areas where a number of interacting disturbance agents simultaneously affect forest development. The forest ecosystems of Central Europe are coupled human and natural systems, with natural and human disturbances affecting forests both individually and in combination. To better understand the complex forest disturbance dynamics in such systems, we utilize 32-year Landsat time series to map forest disturbances in five sites across Austria, the Czech Republic, Germany, Poland, and Slovakia. All sites consisted of a National Park and the surrounding forests, reflecting three management zones of different levels of human influence (managed, protected, strictly protected). This allowed for a comparison of spectral, temporal, and spatial disturbance patterns across a gradient from natural to coupled human and natural disturbances. Disturbance maps achieved overall accuracies ranging from 81% to 93%. Disturbance patches were generally small, with 95% of the disturbances being smaller than 10 ha. Disturbance rates ranged from 0.29% yr -1 to 0.95% yr -1 , and differed substantially among management zones and study sites. Natural disturbances in strictly protected areas were longer in duration (median of 8 years) and slightly less variable in magnitude compared to human-dominated disturbances in managed forests (median duration of 1 year). However, temporal dynamics between natural and human-dominated disturbances showed strong synchrony, suggesting that disturbance peaks are driven by natural events affecting managed and unmanaged areas simultaneously. Our study demonstrates the potential of remote sensing for mapping forest disturbances in coupled human and natural systems, such as the forests of Central Europe. Yet, we also highlight the complexity of such systems in terms of agent attribution, as many natural disturbances are modified by management responding to them outside protected areas.

Using Landsat time series for characterizing forest disturbance dynamics in the coupled human and natural systems of Central Europe

NASA Astrophysics Data System (ADS)

Senf, Cornelius; Pflugmacher, Dirk; Hostert, Patrick; Seidl, Rupert

2017-08-01

Remote sensing is a key information source for improving the spatiotemporal understanding of forest ecosystem dynamics. Yet, the mapping and attribution of forest change remains challenging, particularly in areas where a number of interacting disturbance agents simultaneously affect forest development. The forest ecosystems of Central Europe are coupled human and natural systems, with natural and human disturbances affecting forests both individually and in combination. To better understand the complex forest disturbance dynamics in such systems, we utilize 32-year Landsat time series to map forest disturbances in five sites across Austria, the Czech Republic, Germany, Poland, and Slovakia. All sites consisted of a National Park and the surrounding forests, reflecting three management zones of different levels of human influence (managed, protected, strictly protected). This allowed for a comparison of spectral, temporal, and spatial disturbance patterns across a gradient from natural to coupled human and natural disturbances. Disturbance maps achieved overall accuracies ranging from 81% to 93%. Disturbance patches were generally small, with 95% of the disturbances being smaller than 10 ha. Disturbance rates ranged from 0.29% yr-1 to 0.95% yr-1, and differed substantially among management zones and study sites. Natural disturbances in strictly protected areas were longer in duration (median of 8 years) and slightly less variable in magnitude compared to human-dominated disturbances in managed forests (median duration of 1 year). However, temporal dynamics between natural and human-dominated disturbances showed strong synchrony, suggesting that disturbance peaks are driven by natural events affecting managed and unmanaged areas simultaneously. Our study demonstrates the potential of remote sensing for mapping forest disturbances in coupled human and natural systems, such as the forests of Central Europe. Yet, we also highlight the complexity of such systems in terms of agent attribution, as many natural disturbances are modified by management responding to them outside protected areas.

Geospatial Analysis and Remote Sensing from Airplanes and Satellites for Cultural Resources Management

NASA Technical Reports Server (NTRS)

Giardino, Marco J.; Haley, Bryan S.

2005-01-01

Cultural resource management consists of research to identify, evaluate, document and assess cultural resources, planning to assist in decision-making, and stewardship to implement the preservation, protection and interpretation of these decisions and plans. One technique that may be useful in cultural resource management archaeology is remote sensing. It is the acquisition of data and derivative information about objects or materials (targets) located on the Earth's surface or in its atmosphere by using sensor mounted on platforms located at a distance from the targets to make measurements on interactions between the targets and electromagnetic radiation. Included in this definition are systems that acquire imagery by photographic methods and digital multispectral sensors. Data collected by digital multispectral sensors on aircraft and satellite platforms play a prominent role in many earth science applications, including land cover mapping, geology, soil science, agriculture, forestry, water resource management, urban and regional planning, and environmental assessments. Inherent in the analysis of remotely sensed data is the use of computer-based image processing techniques. Geographical information systems (GIS), designed for collecting, managing, and analyzing spatial information, are also useful in the analysis of remotely sensed data. A GIS can be used to integrate diverse types of spatially referenced digital data, including remotely sensed and map data. In archaeology, these tools have been used in various ways to aid in cultural resource projects. For example, they have been used to predict the presence of archaeological resources using modern environmental indicators. Remote sensing techniques have also been used to directly detect the presence of unknown sites based on the impact of past occupation on the Earth's surface. Additionally, remote sensing has been used as a mapping tool aimed at delineating the boundaries of a site or mapping previously unknown features. All of these applications are pertinent to the goals of site discovery and assessment in cultural resource management.

Interaction of Plasmodium falciparum knob-associated histidine-rich protein (KAHRP) with erythrocyte ankyrin R is required for its attachment to the erythrocyte membrane.

PubMed

Weng, Haibo; Guo, Xinhua; Papoin, Julien; Wang, Jie; Coppel, Ross; Mohandas, Narla; An, Xiuli

2014-01-01

The malaria parasite Plasmodium falciparum exports a large number of proteins into the erythrocyte cytoplasm during the asexual intraerythrocytic stage of its life cycle. A subset of these proteins interacts with erythrocyte membrane skeletal proteins and grossly alters the structure and function of the membrane. Several of the exported proteins, such as PfEMP1, PfEMP3, RESA and KAHRP, interact with the preponderant erythrocyte skeleton protein, spectrin. Here we have searched for possible interaction of these four malaria proteins with another major erythrocyte skeleton protein, ankyrin R. We have shown that KAHRP, but none of the other three, binds to ankyrin R. We have mapped the binding site for ankyrin R to a 79-residue segment of the KAHRP sequence, and the reciprocal binding site for KAHRP in ankyrin R to a subdomain (D3) of the 89kDa ankyrin R membrane-binding domain. Interaction of intact ankyrin R with KAHRP was inhibited by the free D3 subdomain. When, moreover, red cells loaded with the soluble D3 subdomain were infected with P. falciparum, KAHRP secreted by the intraerythrocytic parasite no longer migrated to the host cell membrane, but remained diffusely distributed throughout the cytosol. Our findings suggest a potentially important role for interaction of KAHRP with red cell membrane skeleton in promoting the adhesion of malaria-infected red cells to endothelial surfaces, a central element in the pathophysiology of malaria. © 2013.

Systematic analysis of transcription start sites in avian development.

PubMed

Lizio, Marina; Deviatiiarov, Ruslan; Nagai, Hiroki; Galan, Laura; Arner, Erik; Itoh, Masayoshi; Lassmann, Timo; Kasukawa, Takeya; Hasegawa, Akira; Ros, Marian A; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R R; Kawaji, Hideya; Gusev, Oleg; Sheng, Guojun

2017-09-01

Cap Analysis of Gene Expression (CAGE) in combination with single-molecule sequencing technology allows precision mapping of transcription start sites (TSSs) and genome-wide capture of promoter activities in differentiated and steady state cell populations. Much less is known about whether TSS profiling can characterize diverse and non-steady state cell populations, such as the approximately 400 transitory and heterogeneous cell types that arise during ontogeny of vertebrate animals. To gain such insight, we used the chick model and performed CAGE-based TSS analysis on embryonic samples covering the full 3-week developmental period. In total, 31,863 robust TSS peaks (>1 tag per million [TPM]) were mapped to the latest chicken genome assembly, of which 34% to 46% were active in any given developmental stage. ZENBU, a web-based, open-source platform, was used for interactive data exploration. TSSs of genes critical for lineage differentiation could be precisely mapped and their activities tracked throughout development, suggesting that non-steady state and heterogeneous cell populations are amenable to CAGE-based transcriptional analysis. Our study also uncovered a large set of extremely stable housekeeping TSSs and many novel stage-specific ones. We furthermore demonstrated that TSS mapping could expedite motif-based promoter analysis for regulatory modules associated with stage-specific and housekeeping genes. Finally, using Brachyury as an example, we provide evidence that precise TSS mapping in combination with Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-on technology enables us, for the first time, to efficiently target endogenous avian genes for transcriptional activation. Taken together, our results represent the first report of genome-wide TSS mapping in birds and the first systematic developmental TSS analysis in any amniote species (birds and mammals). By facilitating promoter-based molecular analysis and genetic manipulation, our work also underscores the value of avian models in unravelling the complex regulatory mechanism of cell lineage specification during amniote development.

Mapping of the immunophilin-immunosuppressant site of interaction on calcineurin.

PubMed

Husi, H; Luyten, M A; Zurini, M G

1994-05-13

The interaction of the immunosuppressive complexes cyclosporin A-cyclophilin A and FK506 binding protein-FK506 with the Ca(2+)- and calmodulin-dependent protein phosphatase calcineurin has been investigated by means of photoaffinity labeling and chemical cross-linking. Photolabeling of purified bovine brain calcineurin with the affinity label [O-[4-[4-(1-diazo-2,2,2-trifluoroethyl)benzoyl]aminobutanoyl]-D- serine8]cyclosporin in the presence of cyclophilin A results, in addition to the labeling of cyclophilin itself, in the transfer of some of the chemical probe to both the catalytic subunit A and the regulatory subunit B of calcineurin. Chemical cross-linking studies with disuccinimidyl suberate in the presence of either cyclophilin A, B, or C in complex with cyclosporin A or FK506 binding protein-FK506 result on the other hand in the apparently exclusive and strictly immunosuppressant-dependent formation of covalent immunophilin-calcineurin B subunit products. Cross-linking of immunophilins to calcineurin B subunit requires the presence of subunit A. In the present study, using a set of recombinant maltose-binding protein fusion products representing different stretches of the catalytic subunit A, we were able to map the minimal calcineurin A sequence necessary for immunophilin-ligand-calcineurin B interaction to occur.

An integrated remote sensing approach for identifying ecological range sites. [parker mountain

NASA Technical Reports Server (NTRS)

Jaynes, R. A.

1983-01-01

A model approach for identifying ecological range sites was applied to high elevation sagebrush-dominated rangelands on Parker Mountain, in south-central Utah. The approach utilizes map information derived from both high altitude color infrared photography and LANDSAT digital data, integrated with soils, geological, and precipitation maps. Identification of the ecological range site for a given area requires an evaluation of all relevant environmental factors which combine to give that site the potential to produce characteristic types and amounts of vegetation. A table is presented which allows the user to determine ecological range site based upon an integrated use of the maps which were prepared. The advantages of identifying ecological range sites through an integrated photo interpretation/LANDSAT analysis are discussed.

Multi-level assessment protocol (MAP) for adoption in multi-site clinical trials

PubMed Central

Guydish, J.; Manser, S.T.; Jessup, M.; Tajima, B.; Sears, C.; Montini, T.

2010-01-01

The National Institute on Drug Abuse (NIDA) Clinical Trials Network (CTN) is intended to test promising drug abuse treatment models in multi-site clinical trials, and to support adoption of new interventions into clinical practice. Using qualitative research methods we asked: How might the technology of multi-site clinical trials be modified to better support adoption of tested interventions? A total of 42 participants, representing 8 organizational levels ranging from clinic staff to clinical trial leaders, were interviewed about their role in the clinical trial, its interactions with clinics, and intervention adoption. Among eight clinics participating in the clinical trial, we found adoption of the tested intervention in one clinic only. In analysis of interview data we identified four conceptual themes which are likely to affect adoption and may be informative in future multi-site clinical trials. We offer the conclusion that planning for adoption in the early stages of protocol development will better serve the aim of integrating new interventions into practice. PMID:20890376

Cloud Computing for Protein-Ligand Binding Site Comparison

PubMed Central

2013-01-01

The proteome-wide analysis of protein-ligand binding sites and their interactions with ligands is important in structure-based drug design and in understanding ligand cross reactivity and toxicity. The well-known and commonly used software, SMAP, has been designed for 3D ligand binding site comparison and similarity searching of a structural proteome. SMAP can also predict drug side effects and reassign existing drugs to new indications. However, the computing scale of SMAP is limited. We have developed a high availability, high performance system that expands the comparison scale of SMAP. This cloud computing service, called Cloud-PLBS, combines the SMAP and Hadoop frameworks and is deployed on a virtual cloud computing platform. To handle the vast amount of experimental data on protein-ligand binding site pairs, Cloud-PLBS exploits the MapReduce paradigm as a management and parallelizing tool. Cloud-PLBS provides a web portal and scalability through which biologists can address a wide range of computer-intensive questions in biology and drug discovery. PMID:23762824

Cloud computing for protein-ligand binding site comparison.

PubMed

Hung, Che-Lun; Hua, Guan-Jie

2013-01-01

The proteome-wide analysis of protein-ligand binding sites and their interactions with ligands is important in structure-based drug design and in understanding ligand cross reactivity and toxicity. The well-known and commonly used software, SMAP, has been designed for 3D ligand binding site comparison and similarity searching of a structural proteome. SMAP can also predict drug side effects and reassign existing drugs to new indications. However, the computing scale of SMAP is limited. We have developed a high availability, high performance system that expands the comparison scale of SMAP. This cloud computing service, called Cloud-PLBS, combines the SMAP and Hadoop frameworks and is deployed on a virtual cloud computing platform. To handle the vast amount of experimental data on protein-ligand binding site pairs, Cloud-PLBS exploits the MapReduce paradigm as a management and parallelizing tool. Cloud-PLBS provides a web portal and scalability through which biologists can address a wide range of computer-intensive questions in biology and drug discovery.

Endoglucanase Peripheral Loops Facilitate Complexation of Glucan Chains on Cellulose via Adaptive Coupling to the Emergent Substrate Structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Yuchun; Beckham, Gregg T.; Himmel, Michael E.

We examine how the catalytic domain of a glycoside hydrolase family 7 endoglucanase catalytic domain (Cel7B CD) facilitates complexation of cellulose chains from a crystal surface. With direct relevance to the science of biofuel production, this problem also represents a model system of biopolymer processing by proteins in Nature. Interactions of Cel7B CD with a cellulose microfibril along different paths of complexation are characterized by mapping the atomistic fluctuations recorded in free-energy simulations onto the parameters of a coarse-grain model. The resulting patterns of protein-biopolymer couplings also uncover the sequence signatures of the enzyme in peeling off glucan chains frommore » the microfibril substrate. We show that the semiopen active site of Cel7B CD exhibits similar barriers and free energies of complexation over two distinct routes; namely, scooping of a chain into the active-site cleft and threading from the chain end into the channel. On the other hand, the complexation energetics strongly depends on the surface packing of the targeted chain and the resulting interaction sites with the enzyme. A revealed principle is that Cel7B CD facilitates cellulose deconstruction via adaptive coupling to the emergent substrate. The flexible, peripheral segments of the protein outside of the active-site cleft are able to accommodate the varying features of cellulose along the simulated paths of complexation. The general strategy of linking physics-based molecular interactions to protein sequence could also be helpful in elucidating how other protein machines process biopolymers.« less

The Future of Web Maps in Next Generation Textbooks

NASA Astrophysics Data System (ADS)

DiBiase, D.; Prasad, S.

2014-12-01

The reformation of the "Object Formerly Known as Textbook" (coined by the Chronicle of Higher Education) toward a digital future is underway. Emerging nextgen texts look less like electronic books ("ebooks") and more like online courseware. In addition to text and illustrations, nextgen textbooks for STEM subjects are likely to combine quizzes, grade management tools, support for social learning, and interactive media including web maps. Web maps are interactive, multi-scale, online maps that enable teachers and learners to explore, interrogate, and mash up the wide variety of map layers available in the cloud. This presentation will show how web maps coupled with interactive quizzes enable students' purposeful explorations and interpretations of spatial patterns related to humankind's interactions with the earth. Attendees will also learn about Esri's offer to donate ArcGIS Online web mapping subscriptions to every U.S. school as part of the President Obama's ConnectED initiative.

Interactive computer methods for generating mineral-resource maps

USGS Publications Warehouse

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

1980-01-01

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

Protein interactome analysis of 12 mitogen-activated protein kinase kinase kinase in rice using a yeast two-hybrid system.

PubMed

Singh, Raksha; Lee, Jae-Eun; Dangol, Sarmina; Choi, Jihyun; Yoo, Ran Hee; Moon, Jae Sun; Shim, Jae-Kyung; Rakwal, Randeep; Agrawal, Ganesh Kumar; Jwa, Nam-Soo

2014-01-01

The mitogen-activated protein kinase (MAPK) cascade is composed at least of MAP3K (for MAPK kinase kinase), MAP2K, and MAPK family modules. These components together play a central role in mediating extracellular signals to the cell and vice versa by interacting with their partner proteins. However, the MAP3K-interacting proteins remain poorly investigated in plants. Here, we utilized a yeast two-hybrid system and bimolecular fluorescence complementation in the model crop rice (Oryza sativa) to map MAP3K-interacting proteins. We identified 12 novel nonredundant interacting protein pairs (IPPs) representing 11 nonredundant interactors using 12 rice MAP3Ks (available as full-length cDNA in the rice KOME (http://cdna01.dna.affrc.go.jp/cDNA/) at the time of experimental design and execution) as bait and a rice seedling cDNA library as prey. Of the 12 MAP3Ks, only six had interacting protein partners. The established MAP3K interactome consisted of two kinases, three proteases, two forkhead-associated domain-containing proteins, two expressed proteins, one E3 ligase, one regulatory protein, and one retrotransposon protein. Notably, no MAP3K showed physical interaction with either MAP2K or MAPK. Seven IPPs (58.3%) were confirmed in vivo by bimolecular fluorescence complementation. Subcellular localization of 14 interactors, together involved in nine IPPs (75%) further provide prerequisite for biological significance of the IPPs. Furthermore, GO of identified interactors predicted their involvement in diverse physiological responses, which were supported by a literature survey. These findings increase our knowledge of the MAP3K-interacting proteins, help in proposing a model of MAPK modules, provide a valuable resource for developing a complete map of the rice MAPK interactome, and allow discussion for translating the interactome knowledge to rice crop improvement against environmental factors. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

AAPG-CSD geologic provinces code map

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meyer, R.F.; Wallace, L.G.; Wagner, F.J. Jr.

1991-10-01

This article provides the history of a revised geologic map which was drawn based on both surface geology and petroleum occurrence. The map includes offshore maps for California and the Gulf Coast of Texas and Louisiana. For onshore sites it provides geologic province boundaries which were drawn along county boundaries to approximate their position relative to oil and gas production. The offshore sites are drawn based on the universal transverse Mercator system.

Regional hydrogeological screening characteristics used for siting near-surface waste-disposal facilities in Oklahoma, U.S.A.

USGS Publications Warehouse

Johnson, K.S.

1991-01-01

The Oklahoma Geological Survey has developed several maps and reports for preliminary screening of the state of Oklahoma to identify areas that are generally acceptable or unacceptable for disposal of a wide variety of waste materials. These maps and reports focus on the geologic and hydrogeologic parameters that must be evaluated in the screening process. One map (and report) shows the outcrop distribution of 35 thick shale or clay units that are generally suitable for use as host rocks for surface disposal of wastes. A second map shows the distribution of unconsolidated alluvial and terrace-deposit aquifers, and a third map shows the distribution and hydrologic character of bedrock aquifers and their recharge areas. These latter two maps show the areas in the state where special attention must be exercised in permitting storage or disposal of waste materials that could degrade the quality of groundwater. State regulatory agencies and industry are using these maps and reports in preliminary screening of the state to identify potential disposal sites. These maps in no way replace the need for site-specific investigations to prove (or disprove) the adequacy of a site to safely contain waste materials. ?? 1991 Springer-Verlag New York Inc.

Predictive and comparative analysis of Ebolavirus proteins

PubMed Central

Cong, Qian; Pei, Jimin; Grishin, Nick V

2015-01-01

Ebolavirus is the pathogen for Ebola Hemorrhagic Fever (EHF). This disease exhibits a high fatality rate and has recently reached a historically epidemic proportion in West Africa. Out of the 5 known Ebolavirus species, only Reston ebolavirus has lost human pathogenicity, while retaining the ability to cause EHF in long-tailed macaque. Significant efforts have been spent to determine the three-dimensional (3D) structures of Ebolavirus proteins, to study their interaction with host proteins, and to identify the functional motifs in these viral proteins. Here, in light of these experimental results, we apply computational analysis to predict the 3D structures and functional sites for Ebolavirus protein domains with unknown structure, including a zinc-finger domain of VP30, the RNA-dependent RNA polymerase catalytic domain and a methyltransferase domain of protein L. In addition, we compare sequences of proteins that interact with Ebolavirus proteins from RESTV-resistant primates with those from RESTV-susceptible monkeys. The host proteins that interact with GP and VP35 show an elevated level of sequence divergence between the RESTV-resistant and RESTV-susceptible species, suggesting that they may be responsible for host specificity. Meanwhile, we detect variable positions in protein sequences that are likely associated with the loss of human pathogenicity in RESTV, map them onto the 3D structures and compare their positions to known functional sites. VP35 and VP30 are significantly enriched in these potential pathogenicity determinants and the clustering of such positions on the surfaces of VP35 and GP suggests possible uncharacterized interaction sites with host proteins that contribute to the virulence of Ebolavirus. PMID:26158395

Soil Organic Carbon and Its interaction with Minerals in Two Hillslopes with Different Climates and Erosion Processes

NASA Astrophysics Data System (ADS)

Wang, X.; Yoo, K.; Wackett, A. A.; Gutknecht, J.; Amundson, R.; Heimsath, A. M.

2017-12-01

Climate and topography have been widely recognized as important factors regulating soil organic carbon (SOC) dynamics but their interactive effects on SOC storage and its pools remain poorly constrained. Here we aimed to evaluate SOC storages and carbon-mineral interactions along two hillslope transects with moderately different climates (MAP: 549 mm vs. 816 mm) in Southeastern Australia. We sampled soil along the convex (eroding)-to-convergent (depositional) continuum at each hillslope transect and conducted size and density fractionation of these samples. In responses to the difference in climate factor, SOC inventories of eroding soils were twice as large at the wetter site compared with the drier site but showed little difference between two sites in depositional soils. These trends in SOC inventories were primarily controlled by SOC concentrations and secondarily by soil thicknesses. Similar patterns were observed for mineral associated organic carbon (MOC), and the abundances of MOC were controlled by the two independently operating processes affecting MOC concentration and fine-heavy fraction minerals. The contents and species of secondary clay and iron oxide minerals, abundances of particulate organic carbon, and bioturbation affected MOC concentrations. In contrast, the abundances of fine-heavy fraction minerals were impacted by erosion mechanisms that uniquely responded to regional- and micro- climate conditions. Consequently, topographic influences on SOC inventories and carbon-mineral interactions were more strongly pronounced in the drier climate where vegetation and erosion mechanisms were sensitive to microclimate. Our results highlight the significance of understanding topography and erosional processes in capturing climatic effects on soil carbon dynamics.

Predictive and comparative analysis of Ebolavirus proteins.

PubMed

Cong, Qian; Pei, Jimin; Grishin, Nick V

2015-01-01

Ebolavirus is the pathogen for Ebola Hemorrhagic Fever (EHF). This disease exhibits a high fatality rate and has recently reached a historically epidemic proportion in West Africa. Out of the 5 known Ebolavirus species, only Reston ebolavirus has lost human pathogenicity, while retaining the ability to cause EHF in long-tailed macaque. Significant efforts have been spent to determine the three-dimensional (3D) structures of Ebolavirus proteins, to study their interaction with host proteins, and to identify the functional motifs in these viral proteins. Here, in light of these experimental results, we apply computational analysis to predict the 3D structures and functional sites for Ebolavirus protein domains with unknown structure, including a zinc-finger domain of VP30, the RNA-dependent RNA polymerase catalytic domain and a methyltransferase domain of protein L. In addition, we compare sequences of proteins that interact with Ebolavirus proteins from RESTV-resistant primates with those from RESTV-susceptible monkeys. The host proteins that interact with GP and VP35 show an elevated level of sequence divergence between the RESTV-resistant and RESTV-susceptible species, suggesting that they may be responsible for host specificity. Meanwhile, we detect variable positions in protein sequences that are likely associated with the loss of human pathogenicity in RESTV, map them onto the 3D structures and compare their positions to known functional sites. VP35 and VP30 are significantly enriched in these potential pathogenicity determinants and the clustering of such positions on the surfaces of VP35 and GP suggests possible uncharacterized interaction sites with host proteins that contribute to the virulence of Ebolavirus.

IE1 and hr facilitate the localization of Bombyx mori nucleopolyhedrovirus ORF8 to specific nuclear sites.

PubMed

Kang, WonKyung; Imai, Noriko; Kawasaki, Yu; Nagamine, Toshihiro; Matsumoto, Shogo

2005-11-01

The Bombyx mori nucleopolyhedrovirus (BmNPV) ORF8 protein has previously been reported to colocalize with IE1 to specific nuclear sites during infection. Transient expression of green fluorescent protein (GFP)-fused ORF8 showed the protein to have cytoplasmic localization, but following BmNPV infection the protein formed foci, suggesting that ORF8 requires some other viral factor(s) for this. Therefore, interacting factors were looked for using the yeast two-hybrid system and IE1 was identified. We mapped the interacting region of ORF8 using a yeast two-hybrid assay. An N-terminal region (residues 1-110) containing a predicted coiled-coil domain interacted with IE1, while a truncated N-terminal region (residues 1-78) that lacks this domain did not. In addition, a protein with a complete deletion of the N-terminal region failed to interact with IE1. These results suggest that the ORF8 N-terminal region containing the coiled-coil domain is required for the interaction with IE1. Next, whether IE1 plays a role in ORF8 localization was investigated. In the presence of IE1, GFP-ORF8 localized to the nucleus. In addition, cotransfection with a plasmid expressing IE1 and a plasmid containing the hr3 element resulted in nuclear foci formation. A GFP-fused ORF8 mutant protein containing the coiled-coil domain, previously shown to interact with IE1, also formed nuclear foci in the presence of IE1 and hr3. However, ORF8 mutant proteins that did not interact with IE1 failed to form nuclear foci. In contrast to wild-type IE1, focus formation was not observed for an IE1 mutant protein that was deficient in hr binding. These results suggest that IE1 and hr facilitate the localization of BmNPV ORF8 to specific nuclear sites.

Teaching Plate Tectonic Concepts using GeoMapApp Learning Activities

NASA Astrophysics Data System (ADS)

Goodwillie, A. M.; Kluge, S.

2012-12-01

GeoMapApp Learning Activities ( http://serc.carleton.edu/geomapapp/collection.html ) can help educators to expose undergraduate students to a range of earth science concepts using high-quality data sets in an easy-to-use map-based interface called GeoMapApp. GeoMapApp Learning Activities require students to interact with and analyse research-quality geoscience data as a means to explore and enhance their understanding of underlying content and concepts. Each activity is freely available through the SERC-Carleton web site and offers step-by-step student instructions and answer sheets. Also provided are annotated educator versions of the worksheets that include teaching tips, additional content and suggestions for further work. The activities can be used "off-the-shelf". Or, since the educator may require flexibility to tailor the activities, the documents are provided in Word format for easy modification. Examples of activities include one on the concept of seafloor spreading that requires students to analyse global seafloor crustal age data to calculate spreading rates in different ocean basins. Another activity has students explore hot spots using radiometric age dating of rocks along the Hawaiian-Emperor seamount chain. A third focusses upon the interactive use of contours and profiles to help students visualise 3-D topography on 2-D computer screens. A fourth activity provides a study of mass wasting as revealed through geomorphological evidence. The step-by-step instructions and guided inquiry approach reduce the need for teacher intervention whilst boosting the time that students can spend on productive exploration and learning. The activities can be used, for example, in a classroom lab with the educator present and as self-paced assignments in an out-of-class setting. GeoMapApp Learning Activities are funded through the NSF GeoEd program and are aimed at students in the introductory undergraduate, community college and high school levels. The activities are based upon GeoMapApp (http://www.geomapapp.org), a free map-based data exploration and visualisation tool that allows students to access a wide range of geoscience data in a virtual lab-like environment.

Estimating forest species abundance through linear unmixing of CHRIS/PROBA imagery

NASA Astrophysics Data System (ADS)

Stagakis, Stavros; Vanikiotis, Theofilos; Sykioti, Olga

2016-09-01

The advancing technology of hyperspectral remote sensing offers the opportunity of accurate land cover characterization of complex natural environments. In this study, a linear spectral unmixing algorithm that incorporates a novel hierarchical Bayesian approach (BI-ICE) was applied on two spatially and temporally adjacent CHRIS/PROBA images over a forest in North Pindos National Park (Epirus, Greece). The scope is to investigate the potential of this algorithm to discriminate two different forest species (i.e. beech - Fagus sylvatica, pine - Pinus nigra) and produce accurate species-specific abundance maps. The unmixing results were evaluated in uniformly distributed plots across the test site using measured fractions of each species derived by very high resolution aerial orthophotos. Landsat-8 images were also used to produce a conventional discrete-type classification map of the test site. This map was used to define the exact borders of the test site and compare the thematic information of the two mapping approaches (discrete vs abundance mapping). The required ground truth information, regarding training and validation of the applied mapping methodologies, was collected during a field campaign across the study site. Abundance estimates reached very good overall accuracy (R2 = 0.98, RMSE = 0.06). The most significant source of error in our results was due to the shadowing effects that were very intense in some areas of the test site due to the low solar elevation during CHRIS acquisitions. It is also demonstrated that the two mapping approaches are in accordance across pure and dense forest areas, but the conventional classification map fails to describe the natural spatial gradients of each species and the actual species mixture across the test site. Overall, the BI-ICE algorithm presented increased potential to unmix challenging objects with high spectral similarity, such as different vegetation species, under real and not optimum acquisition conditions. Its full potential remains to be investigated in further and more complex study sites in view of the upcoming satellite hyperspectral missions.

Determinants of woody cover in African savannas

USGS Publications Warehouse

Sankaran, M.; Hanan, N.P.; Scholes, Robert J.; Ratnam, J.; Augustine, D.J.; Cade, B.S.; Gignoux, J.; Higgins, S.I.; Le, Roux X.; Ludwig, F.; Ardo, J.; Banyikwa, F.; Bronn, A.; Bucini, G.; Caylor, K.K.; Coughenour, M.B.; Diouf, A.; Ekaya, W.; Feral, C.J.; February, E.C.; Frost, P.G.H.; Hiernaux, P.; Hrabar, H.; Metzger, K.L.; Prins, H.H.T.; Ringrose, S.; Sea, W.; Tews, J.; Worden, J.; Zambatis, N.

2005-01-01

Savannas are globally important ecosystems of great significance to human economies. In these biomes, which are characterized by the co-dominance of trees and grasses, woody cover is a chief determinant of ecosystem properties 1-3. The availability of resources (water, nutrients) and disturbance regimes (fire, herbivory) are thought to be important in regulating woody cover1,2,4,5, but perceptions differ on which of these are the primary drivers of savanna structure. Here we show, using data from 854 sites across Africa, that maximum woody cover in savannas receiving a mean annual precipitation (MAP) of less than ???650 mm is constrained by, and increases linearly with, MAP. These arid and semi-arid savannas may be considered 'stable' systems in which water constrains woody cover and permits grasses to coexist, while fire, herbivory and soil properties interact to reduce woody cover below the MAP-controlled upper bound. Above a MAP of ???650 mm, savannas are 'unstable' systems in which MAP is sufficient for woody canopy closure, and disturbances (fire, herbivory) are required for the coexistence of trees and grass. These results provide insights into the nature of African savannas and suggest that future changes in precipitation 6 may considerably affect their distribution and dynamics. ?? 2005 Nature Publishing Group.

Linking hyporheic flow and nitrogen cycling near the Willamette River - A large river in Oregon, USA

USGS Publications Warehouse

Hinkle, S.R.; Duff, J.H.; Triska, F.J.; Laenen, A.; Gates, E.B.; Bencala, K.E.; Wentz, D.A.; Silva, S.R.

2001-01-01

Several approaches were used to characterize ground water/surface water interactions near the Willamette River - A large (ninth order) river in Oregon, USA. A series of potentiometric surface maps demonstrated the presence of highly dynamic hydraulic gradients between rivers and the adjacent aquifer. Hyporheic zone gradients extended on the order of hundreds of meters. River gains and losses at the river stretch scale (tens of kilometers) were consistent with fluxes implied by the potentiometric surface maps, and apparently reflect regional ground water/surface water interactions. Gains and losses of up to 5-10% of streamflow were observed at this scale. On the river reach scale (1-2 km), gains and losses on the order of 5% of streamflow were interpreted as representing primarily local hyporheic exchange. Isotopic and chemical data collected from shallow hyporheic zone wells demonstrated interaction between regional ground water and river water. The origin of sampled hyporheic zone water ranged from a mixture dominated by regional ground water to water containing 100% river water. The common assumption that ground and river water mix primarily in the river channel is not applicable in this system. Isotopic and chemical data also indicated that significant (nearly complete) vegetative nitrate uptake and/or nitrate reduction occurred in water from 4 of 12 hyporheic zone sites. In these cases, it was primarily nitrate transported to the hyporheic zone in regional ground water that was removed from solution. Isotopes of water and nitrate indicated that hyporheic zone water sampled at two sites was composed of water originating as river water and demonstrated that significant vegetative nitrate uptake and nitrate reduction occurred along these hyporheic zone flowpaths. Thus, the hyporheic zone may, in some instances, serve to remove nitrate from river water. Additional investigations with chemical tools and microbial enzyme assays were conducted at one hyporheic site. A strong vertical redox gradient was observed, with nitrate-limited denitrification potential in deeper sediment and both nitrification and denitrification potential in shallower sediment. Since nitrogen cycling is strongly affected by redox conditions, nitrogen cycling in the hyporheic zone of this large-river system likely is affected by dynamics of ground water/surface water interactions that control fluxes of nitrogen and other redox species to hyporheic zone sediment.

The Documentation of Historic Maps of World Heritage Site City Suzhou

NASA Astrophysics Data System (ADS)

Guangwei, Z.

2013-07-01

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

Validation of a novel mapping system and utility for mapping complex atrial tachycardias.

PubMed

Honarbakhsh, S; Hunter, R J; Dhillon, G; Ullah, W; Keating, E; Providencia, R; Chow, A; Earley, M J; Schilling, R J

2018-03-01

This study sought to validate a novel wavefront mapping system utilizing whole-chamber basket catheters (CARTOFINDER, Biosense Webster). The system was validated in terms of (1) mapping atrial-paced beats and (2) mapping complex wavefront patterns in atrial tachycardia (AT). Patients undergoing catheter ablation for AT and persistent AF were included. A 64-pole-basket catheter was used to acquire unipolar signals that were processed by CARTOFINDER mapping system to generate dynamic wavefront propagation maps. The left atrium was paced from four sites to demonstrate focal activation. ATs were mapped with the mechanism confirmed by conventional mapping, entrainment, and response to ablation. Twenty-two patients were included in the study (16 with AT and 6 with AF initially who terminated to AT during ablation). In total, 172 maps were created with the mapping system. It correctly identified atrial-pacing sites in all paced maps. It accurately mapped 9 focal/microreentrant and 18 macroreentrant ATs both in the left and right atrium. A third and fourth observer independently identified the sites of atrial pacing and the AT mechanism from the CARTOFINDER maps, while being blinded to the conventional activation maps. This novel mapping system was effectively validated by mapping focal activation patterns from atrial-paced beats. The system was also effective in mapping complex wavefront patterns in a range of ATs in patients with scarred atria. The system may therefore be of practical use in the mapping and ablation of AT and could have potential for mapping wavefront activations in AF. © 2018 Wiley Periodicals, Inc.

Hyperspectral mapping of alteration assemblages within a hydrothermal vug at the Haughton impact structure, Canada

NASA Astrophysics Data System (ADS)

Greenberger, Rebecca N.; Mustard, John F.; Osinski, Gordon R.; Tornabene, Livio L.; Pontefract, Alexandra J.; Marion, Cassandra L.; Flemming, Roberta L.; Wilson, Janette H.; Cloutis, Edward A.

2016-12-01

Meteorite impacts on Earth and Mars can generate hydrothermal systems that alter the primary mineralogies of rocks and provide suitable environments for microbial colonization. We investigate a calcite-marcasite-bearing vug at the 23 km diameter Haughton impact structure, Devon Island, Nunavut, Canada, using imaging spectroscopy of the outcrop in the field (0.65-1.1 μm) and samples in the laboratory (0.4-2.5 μm), point spectroscopy (0.35-2.5 μm), major element chemistry, and X-ray diffraction analyses. The mineral assemblages mapped at the outcrop include marcasite; marcasite with minor gypsum and jarosite; fibroferrite and copiapite with minor gypsum and melanterite; gypsum, Fe3+ oxides, and jarosite; and calcite, gypsum, clay, microcline, and quartz. Hyperspectral mapping of alteration phases shows spatial patterns that illuminate changes in alteration conditions and formation of specific mineral phases. Marcasite formed from the postimpact hydrothermal system under reducing conditions, while subsequent weathering oxidized the marcasite at low temperatures and water/rock ratios. The acidic fluids resulting from the oxidation collected on flat-lying portions of the outcrop, precipitating fibroferrite + copiapite. That assemblage then likely dissolved, and the changing chemistry and pH resulting from interaction with the calcite-rich host rock formed gypsum-bearing red coatings. These results have implications for understanding water-rock interactions and habitabilities at this site and on Mars.

A genetic linkage map of the Durum x Triticum dicoccoides backcross population based on SSRs and AFLP markers, and QTL analysis for milling traits.

PubMed

Elouafi, I; Nachit, M M

2004-02-01

Durum wheat ( Triticum turgidum L. var durum) is mainly produced and consumed in the Mediterranean region; it is used to produce several specific end-products; such as local pasta, couscous and burghul. To study the genetics of grain-milling quality traits, chromosomal locations, and interaction with the environment, a genetic linkage map of durum was constructed and the quantitative trait loci QTLs for the milling-related traits, test weight (TW) and thousand-kernel weight (TKW), were identified. The population constituted 114 recombinant inbred lines derived from the cross: Omrabi 5 /Triticum dicoccoides 600545// Omrabi 5. TW and TKW were analyzed over 18 environments (sites x years). Single-sequence-repeat markers (SSRs), Amplified-fragment-length-polymorphism markers (AFLPs), and seed storage proteins (SSPs) showed a high level of polymorphism (>60%). The map was constructed with 124 SSRs, 149 AFLPs and 6 SSPs; its length covered 2,288.8 cM (8.2 cM/marker). The map showed high synteny with previous wheat maps, and both SSRs and AFLPs mapped evenly across the genome, with more markers in the B genome. However, some rearrangements were observed. For TW, a high genotypic effect was detected and two QTLs with epistasic effect were identified on 7AS and 6BS, explaining 30% of the total variation. The TKW showed a significant transgressive inheritance and five QTLs were identified, explaining 32% of the total variation, out of which 25% was of a genetic nature, and showing QTLxE interaction. The major TKW-QTLs were around the centromere region of 6B. For both traits, Omrabi 5 alleles had a significant positive effect. This population will be used to determine other QTLs of interest, as its parents are likely to harbor different genes for diseases and drought tolerance.

BAID: The Barrow Area Information Database - an Interactive Web Mapping Portal and Cyberinfrastructure for Science and Land Management in the Vicinity of Barrow on the North Slope of Alaska.

NASA Astrophysics Data System (ADS)

Escarzaga, S. M.; Cody, R. P.; Gaylord, A. G.; Kassin, A.; Barba, M.; Aiken, Q.; Nelson, L.; Mazza Ramsay, F. D.; Tweedie, C. E.

2016-12-01

The Barrow area of northern Alaska is one of the most intensely researched locations in the Arctic and the Barrow Area Information Database (BAID, www.barrowmapped.org) tracks and facilitates a gamut of research, management, and educational activities in the area. BAID is a cyberinfrastructure (CI) that details much of the historic and extant research undertaken within in the Barrow region in a suite of interactive web-based mapping and information portals (geobrowsers). The BAID user community and target audience for BAID is diverse and includes research scientists, science logisticians, land managers, educators, students, and the general public. BAID contains information on more than 16,000 Barrow area research sites that extend back to the 1940's and more than 640 remote sensing images and geospatial datasets. In a web-based setting, users can zoom, pan, query, measure distance, save or print maps and query results, and filter or view information by space, time, and/or other tags. Recent advances include provision of differential global positioning (dGPS) system and high resolution aerial imagery support to visiting scientists, analysis and multitemporal mapping of over 120 km of coastline for erosion monitoring; maintenance of a wireless micrometeorological sensor network; links to Barrow area datasets housed at national data archives; and substantial upgrades to the BAID website. Web mapping applications that have launched to the public include: an Imagery Time Viewer that allows users to compare imagery of the Barrow area between 1949 and the present; a Coastal Erosion Viewer that allows users to view long-term (1955-2015) and recent (2013-2015) rates of erosion for the Barrow area; and a Community Planning Tool that allows users to view and print dynamic reports based on an array of basemaps including a new 0.5m resolution wetlands map designed to enhance decision making for development and land management.

Mapping Potential Amplification and Transmission Hotspots for MERS-CoV, Kenya.

PubMed

Gikonyo, Stephen; Kimani, Tabitha; Matere, Joseph; Kimutai, Joshua; Kiambi, Stella G; Bitek, Austine O; Juma Ngeiywa, K J Z; Makonnen, Yilma J; Tripodi, Astrid; Morzaria, Subhash; Lubroth, Juan; Rugalema, Gabriel; Fasina, Folorunso Oludayo

2018-03-16

Dromedary camels have been implicated consistently as the source of Middle East respiratory syndrome coronavirus (MERS-CoV) human infections and attention to prevent and control it has focused on camels. To understanding the epidemiological role of camels in the transmission of MERS-CoV, we utilized an iterative empirical process in Geographic Information System (GIS) to identify and qualify potential hotspots for maintenance and circulation of MERS-CoV, and produced risk-based surveillance sites in Kenya. Data on camel population and distribution were used to develop camel density map, while camel farming system was defined using multi-factorial criteria including the agro-ecological zones (AEZs), production and marketing practices. Primary and secondary MERS-CoV seroprevalence data from specific sites were analyzed, and location-based prevalence matching with camel densities was conducted. High-risk convergence points (migration zones, trade routes, camel markets, slaughter slabs) were profiled and frequent cross-border camel movement mapped. Results showed that high camel-dense areas and interaction (markets and migration zones) were potential hotspot for transmission and spread. Cross-border contacts occurred with in-migrated herds at hotspot locations. AEZ differential did not influence risk distribution and plausible risk factors for spatial MERS-CoV hotspots were camel densities, previous cases of MERS-CoV, high seroprevalence and points of camel convergences. Although Kenyan camels are predisposed to MERS-CoV, no shedding is documented to date. These potential hotspots, determined using anthropogenic, system and trade characterizations should guide selection of sampling/surveillance sites, high-risk locations, critical areas for interventions and policy development in Kenya, as well as instigate further virological examination of camels.

Intercomparison of clumping index estimates from POLDER, MODIS, and MISR satellite data over reference sites

NASA Astrophysics Data System (ADS)

Pisek, Jan; Govind, Ajit; Arndt, Stefan K.; Hocking, Darren; Wardlaw, Timothy J.; Fang, Hongliang; Matteucci, Giorgio; Longdoz, Bernard

2015-03-01

Clumping index is the measure of foliage grouping relative to a random distribution of leaves in space. It is a key structural parameter of plant canopies that influences canopy radiation regimes and controls canopy photosynthesis and other land-atmosphere interactions. The Normalized Difference between Hotspot and Darkspot (NDHD) index has been previously used to retrieve global clumping index maps from POLarization and Directionality of the Earth's Reflectances (POLDER) data at ˜6 km resolution and the Bidirectional Reflectance Distribution Function (BRDF) product from Moderate Resolution Imaging Spectroradiometer (MODIS) at 500 m resolution. Most recently the algorithm was also applied with Multi-angle Imaging SpectroRadiometer (MISR) data at 275 m resolution over selected areas. In this study for the first time we characterized and compared the three products over a set of sites representing diverse biomes and different canopy structures. The products were also directly validated with both in-situ vertical profiles and available seasonal trajectories of clumping index over several sites. We demonstrated that the vertical distribution of foliage and especially the effect of understory need to be taken into account while validating foliage clumping products from remote sensing products with values measured in the field. Satellite measurements responded to the structural effects near the top of canopies, while ground measurements may be biased by the lower vegetation layers. Additionally, caution should be taken regarding the misclassification in land cover maps as their errors can propagate into the foliage clumping maps. Our results indicate that MODIS data and MISR data, with 275 m in particular, can provide good quality clumping index estimates at spatial scales pertinent for modeling local carbon and energy fluxes.

Planning by Using Digital Technology in the Reconstruction of Cultural Heritage Sites - a Case Study of Qiong-Lin Settlement in Kinmen Area

NASA Astrophysics Data System (ADS)

Yang, W. B.; Ye, Y. N.

2017-08-01

ICOMOS Florence Declaration in 2014, encourages an in-depth reflection on human values through cultural heritage and landscapes, which emphasizes the importance of historical heritage sites, in order to achieve the application of cultural heritage records through the public participation, sharing new technology platform and facilitation tools for knowledge diffusion, for instance. Nikos adopted digitized intangible cultural heritage within i-Treasures project to create a novel digital platform in 2016. Nowadays, the display platform developed based on geographic information system has been gradually accepted and widely used to distribute cultural heritage information, aiming to combine geography, time, events, issues, trends with the interactive maps to show the context of data changes from the consideration of planarity; for example, Burnaby City in Canada has cooperated with the Columbia University to create a navigation platform for guidance of tangible cultural heritage based on story maps in order to provide public recognition function. In this study, Qiong-Lin Settlement in Kinmen Area was taken as an example to illustrate the developing process of an overall planning framework for reappearing the glory of historic settlements of cultural heritage sites with digital technology, which included tangible and intangible cultural heritage preservation and transmission planning, community participation and digital navigation programs. The digital technology with the GIS-based digital platform can provide more diverse and interesting information while using an intuitive, graphical user story mapping interface. So that tangible cultural heritage can be effectively understood, interpreted and preserved with the value-added methods, and also intangible cultural heritage can be continuously transmitted to establish a complete system of cultural heritage preservation. The main contents include several navigation technologies, such as 3D laser scanning, UAV images, photogrammetry, panorama, audio/video, geographic information systems etc.

Research Networks Map | Division of Cancer Prevention

Cancer.gov

The Division of Cancer Prevention supports major scientific collaborations and research networks at more than 100 sites across the United States. Seven Major Programs' sites are shown on this map. | The Division of Cancer Prevention supports major scientific collaborations and research networks at more than 100 sites across the United States.

Monopolar Detection Thresholds Predict Spatial Selectivity of Neural Excitation in Cochlear Implants: Implications for Speech Recognition

PubMed Central

2016-01-01

The objectives of the study were to (1) investigate the potential of using monopolar psychophysical detection thresholds for estimating spatial selectivity of neural excitation with cochlear implants and to (2) examine the effect of site removal on speech recognition based on the threshold measure. Detection thresholds were measured in Cochlear Nucleus® device users using monopolar stimulation for pulse trains that were of (a) low rate and long duration, (b) high rate and short duration, and (c) high rate and long duration. Spatial selectivity of neural excitation was estimated by a forward-masking paradigm, where the probe threshold elevation in the presence of a forward masker was measured as a function of masker-probe separation. The strength of the correlation between the monopolar thresholds and the slopes of the masking patterns systematically reduced as neural response of the threshold stimulus involved interpulse interactions (refractoriness and sub-threshold adaptation), and spike-rate adaptation. Detection threshold for the low-rate stimulus most strongly correlated with the spread of forward masking patterns and the correlation reduced for long and high rate pulse trains. The low-rate thresholds were then measured for all electrodes across the array for each subject. Subsequently, speech recognition was tested with experimental maps that deactivated five stimulation sites with the highest thresholds and five randomly chosen ones. Performance with deactivating the high-threshold sites was better than performance with the subjects’ clinical map used every day with all electrodes active, in both quiet and background noise. Performance with random deactivation was on average poorer than that with the clinical map but the difference was not significant. These results suggested that the monopolar low-rate thresholds are related to the spatial neural excitation patterns in cochlear implant users and can be used to select sites for more optimal speech recognition performance. PMID:27798658

Relating Magnetic Parameters to Heavy Metal Concentrations and Environmental Factors at Formosa Mine Superfund Site, Douglas County, OR

NASA Astrophysics Data System (ADS)

Upton, T. L.

2016-12-01

Advances in the field of environmental magnetism have led to exciting new applications for this field. Magnetic minerals are ubiquitous in the environment and tend to have an affinity for heavy metals. Hence, it has been demonstrated that magnetic properties are often significantly related to concentrations of heavy metals and other pollutants. As a result, magnetic techniques have been used as proxy for determining hot spots of several types of pollution produced from a diversity of anthropogenic sources. Magnetic measurements are non-destructive and relatively inexpensive compared to geochemical analyses. The utility of environmental magnetic methods varies widely depending on biological, chemical and physical processes that create and transform soils and sediments. Applications in the direction of mapping heavy metals have been studied and shown to be quite useful in countries such as China and India but to date, little research has been done in the US. As such, there is need to expand the scope of research to a wider range of soil types and land uses, especially within the US. This study investigates the application of environmental magnetic techniques to mapping of heavy metal concentrations at the Formosa Mine Superfund Site, an abandoned mine about 25 miles southwest of Roseburg, OR. The soils and sediment at this site are derived from pyrite-rich bedrock which is weak in terms of magnetic susceptibility. Using hotspot analysis, correlation and cluster analyses, interactions between metals and magnetic parameters are investigated in relation to environmental factors such as proximity to seeps and adits. Preliminary results suggest significant correlation of magnetic susceptibility with certain heavy metals, signifying that magnetic methods may be useful in mapping heavy metal hotspots at this site. Further analysis examines the relation of various land use differences in magnetic signatures obtained throughout the Cow Creek watershed.

BOREAS TE-23 Map Plot Data

NASA Technical Reports Server (NTRS)

Rich, Paul M.; Fournier, Robert; Hall, Forrest G. (Editor); Papagno, Andrea (Editor)

2000-01-01

The Boreal Ecosystem-Atmospheric Study (BOREAS) TE-23 (Terrestrial Ecology) team collected map plot data in support of its efforts to characterize and interpret information on canopy architecture and understory cover at the BOREAS tower flux sites and selected auxiliary sites from May to August 1994. Mapped plots (typical dimensions 50 m x 60 m) were set up and characterized at all BOREAS forested tower flux and selected auxiliary sites. Detailed measurement of the mapped plots included: (1) stand characteristics (location, density, basal area); (2) map locations diameter at breast height (DBH) of all trees; (3) detailed geometric measures of a subset of trees (height, crown dimensions); and (4) understory cover maps. The data are stored in tabular ASCII files. The data files are available on a CD-ROM (see document number 20010000884), or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).

Educational websites--Bioinformatics Tools II.

PubMed

Lomberk, Gwen

2009-01-01

In this issue, the highlighted websites are a continuation of a series of educational websites; this one in particular from a couple of years ago, Bioinformatics Tools [Pancreatology 2005;5:314-315]. These include sites that are valuable resources for many research needs in genomics and proteomics. Bioinformatics has become a laboratory tool to map sequences to databases, develop models of molecular interactions, evaluate structural compatibilities, describe differences between normal and disease-associated DNA, identify conserved motifs within proteins, and chart extensive signaling networks, all in silico. Copyright 2008 S. Karger AG, Basel and IAP.

The prototype HIV-1 maturation inhibitor, bevirimat, binds to the CA-SP1 cleavage site in immature Gag particles.

PubMed

Nguyen, Albert T; Feasley, Christa L; Jackson, Ken W; Nitz, Theodore J; Salzwedel, Karl; Air, Gillian M; Sakalian, Michael

2011-12-07

Bevirimat, the prototype Human Immunodeficiency Virus type 1 (HIV-1) maturation inhibitor, is highly potent in cell culture and efficacious in HIV-1 infected patients. In contrast to inhibitors that target the active site of the viral protease, bevirimat specifically inhibits a single cleavage event, the final processing step for the Gag precursor where p25 (CA-SP1) is cleaved to p24 (CA) and SP1. In this study, photoaffinity analogs of bevirimat and mass spectrometry were employed to map the binding site of bevirimat to Gag within immature virus-like particles. Bevirimat analogs were found to crosslink to sequences overlapping, or proximal to, the CA-SP1 cleavage site, consistent with previous biochemical data on the effect of bevirimat on Gag processing and with genetic data from resistance mutations, in a region predicted by NMR and mutational studies to have α-helical character. Unexpectedly, a second region of interaction was found within the Major Homology Region (MHR). Extensive prior genetic evidence suggests that the MHR is critical for virus assembly. This is the first demonstration of a direct interaction between the maturation inhibitor, bevirimat, and its target, Gag. Information gained from this study sheds light on the mechanisms by which the virus develops resistance to this class of drug and may aid in the design of next-generation maturation inhibitors.

Mapping specificity landscapes of RNA-protein interactions by high throughput sequencing.

PubMed

Jankowsky, Eckhard; Harris, Michael E

2017-04-15

To function in a biological setting, RNA binding proteins (RBPs) have to discriminate between alternative binding sites in RNAs. This discrimination can occur in the ground state of an RNA-protein binding reaction, in its transition state, or in both. The extent by which RBPs discriminate at these reaction states defines RBP specificity landscapes. Here, we describe the HiTS-Kin and HiTS-EQ techniques, which combine kinetic and equilibrium binding experiments with high throughput sequencing to quantitatively assess substrate discrimination for large numbers of substrate variants at ground and transition states of RNA-protein binding reactions. We discuss experimental design, practical considerations and data analysis and outline how a combination of HiTS-Kin and HiTS-EQ allows the mapping of RBP specificity landscapes. Copyright © 2017 Elsevier Inc. All rights reserved.

Lead identification and optimization of novel collagenase inhibitors; pharmacophore and structure based studies

PubMed Central

Kalva, Sukesh; Vadivelan, S; Sanam, Ramadevi; Jagarlapudi, Sarma ARP; Saleena, Lilly M

2012-01-01

In this study, chemical feature based pharmacophore models of MMP-1, MMP-8 and MMP-13 inhibitors have been developed with the aid of HypoGen module within Catalyst program package. In MMP-1 and MMP-13, all the compounds in the training set mapped HBA and RA, while in MMP-8, the training set mapped HBA and HY. These features revealed responsibility for the high molecular bioactivity, and this is further used as a three dimensional query to screen the knowledge based designed molecules. These pharmacophore models for collagenases picked up some potent and novel inhibitors. Subsequently, docking studies were performed for the potent molecules and novel hits were suggested for further studies based on the docking score and active site interactions in MMP-1, MMP-8 and MMP-13. PMID:22553386

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

PubMed

Lindén, Rolf O; Eronen, Ville-Pekka; Aittokallio, Tero

2011-03-24

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

Enhancing the prediction of protein pairings between interacting families using orthology information

PubMed Central

Izarzugaza, Jose MG; Juan, David; Pons, Carles; Pazos, Florencio; Valencia, Alfonso

2008-01-01

Background It has repeatedly been shown that interacting protein families tend to have similar phylogenetic trees. These similarities can be used to predicting the mapping between two families of interacting proteins (i.e. which proteins from one family interact with which members of the other). The correct mapping will be that which maximizes the similarity between the trees. The two families may eventually comprise orthologs and paralogs, if members of the two families are present in more than one organism. This fact can be exploited to restrict the possible mappings, simply by impeding links between proteins of different organisms. We present here an algorithm to predict the mapping between families of interacting proteins which is able to incorporate information regarding orthologues, or any other assignment of proteins to "classes" that may restrict possible mappings. Results For the first time in methods for predicting mappings, we have tested this new approach on a large number of interacting protein domains in order to statistically assess its performance. The method accurately predicts around 80% in the most favourable cases. We also analysed in detail the results of the method for a well defined case of interacting families, the sensor and kinase components of the Ntr-type two-component system, for which up to 98% of the pairings predicted by the method were correct. Conclusion Based on the well established relationship between tree similarity and interactions we developed a method for predicting the mapping between two interacting families using genomic information alone. The program is available through a web interface. PMID:18215279

The Evoluation Impact of the Geological Environment in Expansion of Ancient Civilization at Butrint - Foenike Region, Southern Albania.

NASA Astrophysics Data System (ADS)

Kavaja, V. S.; Durmishi, S.; Vincani, F. N.

2003-12-01

The rise, creation and decline of the ancient civilization depended on paleo-geographic development changing at the geological environmental.This region is a worldknown archaeological site protected by UNESCO. The area under investigation occupies about 80 km2 and encompassing a large expanse of land at southern and northern side of the Butrinti lake, which is with oval shape and 21.5 depth. Throughout its long history, Butrint had an interactive relationship with its hinterland and the even-changing coastline. Preliminary research suggests that in the Holocene the Lake of Butrint was a sea inlet that stretched 20 km to north of Butrint, as far as the city of Foenike, later Epirot capital. Today the Butrint Lake is just 7.5 km long, being the result of gradual silting up this inlet with soils brought down by Bistrica River in the north side and Pavllo River in the South from surrounding mountain ranges. The goal of this study is investigation of the link between the evolution of Butrinti lake and hydrologicacal systems of the lake, its silting history and how this has impacted and interacted with land and human activity. Histories of terrestrial erosion, near-shore sediment redistribution, times, subsidence and compaction, land-sea interaction are obvious now. Geophysical observation consist of vertical electric soundings (V.E.S.) and magnetic measurements inside a layout of 80 km2. The soundings data, particularly resistivity variations are the base for sedimentologic studies due to the lack of boreholes. For a gravel deposition, in addition to the usual parameter maps as resistivity and thickness maps, combined multiparametric characterization maps have been plotted. Based on the sedimentologic and structural factors studied and geophysical maps and cross-sections, plenty of geomorphic problems are resolve. The evaluations of the regional water bearing are estimated, separating salty waters area.

Resolution-Adapted All-Atomic and Coarse-Grained Model for Biomolecular Simulations.

PubMed

Shen, Lin; Hu, Hao

2014-06-10

We develop here an adaptive multiresolution method for the simulation of complex heterogeneous systems such as the protein molecules. The target molecular system is described with the atomistic structure while maintaining concurrently a mapping to the coarse-grained models. The theoretical model, or force field, used to describe the interactions between two sites is automatically adjusted in the simulation processes according to the interaction distance/strength. Therefore, all-atomic, coarse-grained, or mixed all-atomic and coarse-grained models would be used together to describe the interactions between a group of atoms and its surroundings. Because the choice of theory is made on the force field level while the sampling is always carried out in the atomic space, the new adaptive method preserves naturally the atomic structure and thermodynamic properties of the entire system throughout the simulation processes. The new method will be very useful in many biomolecular simulations where atomistic details are critically needed.

Sea-Floor Images and Data from Multibeam Surveys in San Francisco Bay, Southern California, Hawaii, the Gulf of Mexico, and Lake Tahoe, California-Nevada

USGS Publications Warehouse

Dartnell, Peter; Gardiner, James V.

1999-01-01

Accurate base maps are a prerequisite for any geologic study, regardless of the objectives. Land-based studies commonly utilize aerial photographs, USGS 7.5-minute quadrangle maps, and satellite images as base maps. Until now, studies that involve the ocean floor have been at a disadvantage due to an almost complete lack of accurate marine base maps. Many base maps of the sea floor have been constructed over the past century but with a wide range in navigational and depth accuracies. Only in the past few years has marine surveying technology advanced far enough to produce navigational accuracy of 1 meter and depth resolutions of 50 centimeters. The Pacific Seafloor Mapping Project of the U.S. Geological Survey's, Western Coastal and Marine Geology Program, Menlo Park, California, U.S.A., in cooperation with the Ocean Mapping Group, University of New Brunswick, Fredericton, Canada, is using this new technology to systematically map the ocean floor and lakes. This type of marine surveying, called multibeam surveying, collects high-resolution bathymetric and backscatter data that can be used for various base maps, GIS coverages, and scientific visualization methods. This is an interactive CD-ROM that contains images, movies, and data of all the surveys the Pacific Seafloor Mapping Project has completed up to January 1999. The images and movies on this CD-ROM, such as shaded relief of the bathymetry, backscatter, oblique views, 3-D views, and QuickTime movies help the viewer to visualize the multibeam data. This CD-ROM also contains ARC/INFO export (.e00) files and full-resolution TIFF images of all the survey sites that can be downloaded and used in many GIS packages.

Data Imputation in Epistatic MAPs by Network-Guided Matrix Completion

PubMed Central

Žitnik, Marinka; Zupan, Blaž

2015-01-01

Abstract Epistatic miniarray profile (E-MAP) is a popular large-scale genetic interaction discovery platform. E-MAPs benefit from quantitative output, which makes it possible to detect subtle interactions with greater precision. However, due to the limits of biotechnology, E-MAP studies fail to measure genetic interactions for up to 40% of gene pairs in an assay. Missing measurements can be recovered by computational techniques for data imputation, in this way completing the interaction profiles and enabling downstream analysis algorithms that could otherwise be sensitive to missing data values. We introduce a new interaction data imputation method called network-guided matrix completion (NG-MC). The core part of NG-MC is low-rank probabilistic matrix completion that incorporates prior knowledge presented as a collection of gene networks. NG-MC assumes that interactions are transitive, such that latent gene interaction profiles inferred by NG-MC depend on the profiles of their direct neighbors in gene networks. As the NG-MC inference algorithm progresses, it propagates latent interaction profiles through each of the networks and updates gene network weights toward improved prediction. In a study with four different E-MAP data assays and considered protein–protein interaction and gene ontology similarity networks, NG-MC significantly surpassed existing alternative techniques. Inclusion of information from gene networks also allowed NG-MC to predict interactions for genes that were not included in original E-MAP assays, a task that could not be considered by current imputation approaches. PMID:25658751

Combining Human and Machine Learning to Map Cropland in the 21st Century's Major Agricultural Frontier

NASA Astrophysics Data System (ADS)

Estes, L. D.; Debats, S. R.; Caylor, K. K.; Evans, T. P.; Gower, D.; McRitchie, D.; Searchinger, T.; Thompson, D. R.; Wood, E. F.; Zeng, L.

2016-12-01

In the coming decades, large areas of new cropland will be created to meet the world's rapidly growing food demands. Much of this new cropland will be in sub-Saharan Africa, where food needs will increase most and the area of remaining potential farmland is greatest. If we are to understand the impacts of global change, it is critical to accurately identify Africa's existing croplands and how they are changing. Yet the continent's smallholder-dominated agricultural systems are unusually challenging for remote sensing analyses, making accurate area estimates difficult to obtain, let alone important details related to field size and geometry. Fortunately, the rapidly growing archives of moderate to high-resolution satellite imagery hosted on open servers now offer an unprecedented opportunity to improve landcover maps. We present a system that integrates two critical components needed to capitalize on this opportunity: 1) human image interpretation and 2) machine learning (ML). Human judgment is needed to accurately delineate training sites within noisy imagery and a highly variable cover type, while ML provides the ability to scale and to interpret large feature spaces that defy human comprehension. Because large amounts of training data are needed (a major impediment for analysts), we use a crowdsourcing platform that connects amazon.com's Mechanical Turk service to satellite imagery hosted on open image servers. Workers map visible fields at pre-assigned sites, and are paid according to their mapping accuracy. Initial tests show overall high map accuracy and mapping rates >1800 km2/hour. The ML classifier uses random forests and randomized quasi-exhaustive feature selection, and is highly effective in classifying diverse agricultural types in southern Africa (AUC > 0.9). We connect the ML and crowdsourcing components to make an interactive learning framework. The ML algorithm performs an initial classification using a first batch of crowd-sourced maps, using thresholds of posterior probabilities to segregate sub-images classified with high or low confidence. Workers are then directed to collect new training data in low confidence sub-images, after which classification is repeated and re-assessed, and the entire process iterated until maximum possible accuracy is realized.

Flood-inundation maps for a 9.1-mile reach of the Coast Fork Willamette River near Creswell and Goshen, Lane County, Oregon

USGS Publications Warehouse

Hess, Glen W.; Haluska, Tana L.

2016-04-13

Digital flood-inundation maps for a 9.1-mile reach of the Coast Fork Willamette River near Creswell and Goshen, Oregon, were developed by the U.S. Geological Survey (USGS) in cooperation with the U.S. Army Corps of Engineers (USACE). The inundation maps, which can be accessed through the USGS Flood Inundation Mapping Science Web site at http://water.usgs.gov/osw/flood_inundation/, depict estimates of the areal extent and depth of flooding corresponding to selected stages at the USGS streamgage at Coast Fork Willamette River near Goshen, Oregon (14157500), at State Highway 58. Current stage at the streamgage for estimating near-real-time areas of inundation may be obtained at http://waterdata.usgs.gov/or/nwis/uv/?site_no=14157500&PARAmeter_cd=00065,00060. In addition, the National Weather Service (NWS) forecasted peak-stage information may be used in conjunction with the maps developed in this study to show predicted areas of flood inundation.In this study, areas of inundation were provided by USACE. The inundated areas were developed from flood profiles simulated by a one-dimensional unsteady step‑backwater hydraulic model. The profiles were checked by the USACE using documented high-water marks from a January 2006 flood. The model was compared and quality assured using several other methods. The hydraulic model was then used to determine eight water-surface profiles at various flood stages referenced to the streamgage datum and ranging from 11.8 to 19.8 ft, approximately 2.6 ft above the highest recorded stage at the streamgage (17.17 ft) since 1950. The intervals between stages are variable and based on annual exceedance probability discharges, some of which approximate NWS action stages.The areas of inundation and water depth grids provided to USGS by USACE were used to create interactive flood‑inundation maps. The availability of these maps with current stage from USGS streamgage and forecasted stream stages from the NWS provide emergency management personnel and residents with information that is critical for flood response activities, such as evacuations and road closures as well as for post flood recovery efforts.

Quantifying annual changes in built-up area in complex urban-rural landscapes from analyses of PALSAR and Landsat images

NASA Astrophysics Data System (ADS)

Qin, Yuanwei; Xiao, Xiangming; Dong, Jinwei; Chen, Bangqian; Liu, Fang; Zhang, Geli; Zhang, Yao; Wang, Jie; Wu, Xiaocui

2017-02-01

Built-up area supports human settlements and activities, and its spatial distribution and temporal dynamics have significant impacts on ecosystem services and global environment change. To date, most of urban remote sensing has generated the maps of impervious surfaces, and limited effort has been made to explicitly identify the area, location and density of built-up in the complex and fragmented landscapes based on the freely available datasets. In this study, we took the lower Yangtze River Delta (Landsat Path/Row: 118/038), China, where extensive urbanization and industrialization have occurred, as a case study site. We analyzed the structure and optical features of typical land cover types from (1) the HH and HV gamma-naught imagery from the Advanced Land Observation Satellite (ALOS) Phased Array type L-band Synthetic Aperture Radar (PALSAR), and (2) time series Landsat imagery. We proposed a pixel- and rule-based decision tree approach to identify and map built-up area at 30-m resolution from 2007 to 2010, using PALSAR HH gamma-naught and Landsat annual maximum Normalized Difference Vegetation Index (NDVImax). The accuracy assessment showed that the resultant annual maps of built-up had relatively high user (87-93%) and producer accuracies (91-95%) from 2007 to 2010. The built-up area was 2805 km2 in 2010, about 16% of the total land area of the study site. The annual maps of built-up in 2007-2010 show relatively small changes in the urban core regions, but large outward expansion along the peri-urban regions. The average annual increase of built-up areas was about 80 km2 per year from 2007 to 2010. Our annual maps of built-up in the lower Yangtze River Delta clearly complement the existing maps of impervious surfaces in the region. This study provides a promising new approach to identify and map built-up area, which is critical to investigate the interactions between human activities and ecosystem services in urban-rural systems.

Rumination disorder

MedlinePlus

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7 CFR 1940.309 - Responsibilities of the prospective applicant.

Code of Federal Regulations, 2014 CFR

2014-01-01

... project elements and the proposed site(s) to include location maps, topographic maps, and photographs when... agency under Public Law 103-354 of a Soil Conservation Service (SCS) environmental assessment or...

Email Updates

MedlinePlus

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A GIS-BASED MULTI-CRITERIA EVALUATION SYSTEM FOR SELECTION OF LANDFILL SITES: a case study from Abu Dhabi, United Arab Emirates

NASA Astrophysics Data System (ADS)

Issa, S. M.; Shehhi, B. Al

2012-07-01

Landfill sites receive 92% of total annual solid waste produced by municipalities in the emirate of Abu Dhabi. In this study, candidate sites for an appropriate landfill location for the Abu Dhabi municipal area are determined by integrating geographic information systems (GIS) and multi-criteria evaluation (MCE) analysis. To identify appropriate landfill sites, eight input map layers including proximity to urban areas, proximity to wells and water table depth, geology and topography, proximity to touristic and archeological sites, distance from roads network, distance from drainage networks, and land slope are used in constraint mapping. A final map was generated which identified potential areas showing suitability for the location of the landfill site. Results revealed that 30% of the study area was identified as highly suitable, 25% as suitable, and 45% as unsuitable. The selection of the final landfill site, however, requires further field research.

Direct measurement of IgM-Antigen interaction energy on individual red blood cells.

PubMed

Yeow, Natasha; Tabor, Rico F; Garnier, Gil

2017-07-01

Most blood grouping tests rely on the principle of red blood cells (RBCs) agglutination. Agglutination is triggered by the binding of specific blood grouping antibodies to the corresponding RBC surface antigen on multiple cells. The interaction energies between blood grouping antibodies and antigens have been poorly defined in immunohaematology. Here for the first time, we functionalized atomic force microscope (AFM) cantilevers with the IgM form of blood grouping antibodies to probe populations of individual RBCs of different groups under physiological conditions. The force-mapping mode of AFM allowed us to measure specific antibody - antigen interactions, and simultaneously localize and quantify antigen sites on the scanned cell surface. This study provides a new insight of the interactions between IgM antibodies and its corresponding antigen. The technique and information can be translated to develop better blood typing diagnostics and optimize target-specific drug delivery for medical applications. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

Prediction of fatty acid-binding residues on protein surfaces with three-dimensional probability distributions of interacting atoms.

PubMed

Mahalingam, Rajasekaran; Peng, Hung-Pin; Yang, An-Suei

2014-08-01

Protein-fatty acid interaction is vital for many cellular processes and understanding this interaction is important for functional annotation as well as drug discovery. In this work, we present a method for predicting the fatty acid (FA)-binding residues by using three-dimensional probability density distributions of interacting atoms of FAs on protein surfaces which are derived from the known protein-FA complex structures. A machine learning algorithm was established to learn the characteristic patterns of the probability density maps specific to the FA-binding sites. The predictor was trained with five-fold cross validation on a non-redundant training set and then evaluated with an independent test set as well as on holo-apo pair's dataset. The results showed good accuracy in predicting the FA-binding residues. Further, the predictor developed in this study is implemented as an online server which is freely accessible at the following website, http://ismblab.genomics.sinica.edu.tw/. Copyright © 2014 Elsevier B.V. All rights reserved.

PhosphOrtholog: a web-based tool for cross-species mapping of orthologous protein post-translational modifications.

PubMed

Chaudhuri, Rima; Sadrieh, Arash; Hoffman, Nolan J; Parker, Benjamin L; Humphrey, Sean J; Stöckli, Jacqueline; Hill, Adam P; James, David E; Yang, Jean Yee Hwa

2015-08-19

Most biological processes are influenced by protein post-translational modifications (PTMs). Identifying novel PTM sites in different organisms, including humans and model organisms, has expedited our understanding of key signal transduction mechanisms. However, with increasing availability of deep, quantitative datasets in diverse species, there is a growing need for tools to facilitate cross-species comparison of PTM data. This is particularly important because functionally important modification sites are more likely to be evolutionarily conserved; yet cross-species comparison of PTMs is difficult since they often lie in structurally disordered protein domains. Current tools that address this can only map known PTMs between species based on known orthologous phosphosites, and do not enable the cross-species mapping of newly identified modification sites. Here, we addressed this by developing a web-based software tool, PhosphOrtholog ( www.phosphortholog.com ) that accurately maps protein modification sites between different species. This facilitates the comparison of datasets derived from multiple species, and should be a valuable tool for the proteomics community. Here we describe PhosphOrtholog, a web-based application for mapping known and novel orthologous PTM sites from experimental data obtained from different species. PhosphOrtholog is the only generic and automated tool that enables cross-species comparison of large-scale PTM datasets without relying on existing PTM databases. This is achieved through pairwise sequence alignment of orthologous protein residues. To demonstrate its utility we apply it to two sets of human and rat muscle phosphoproteomes generated following insulin and exercise stimulation, respectively, and one publicly available mouse phosphoproteome following cellular stress revealing high mapping and coverage efficiency. Although coverage statistics are dataset dependent, PhosphOrtholog increased the number of cross-species mapped sites in all our example data sets by more than double when compared to those recovered using existing resources such as PhosphoSitePlus. PhosphOrtholog is the first tool that enables mapping of thousands of novel and known protein phosphorylation sites across species, accessible through an easy-to-use web interface. Identification of conserved PTMs across species from large-scale experimental data increases our knowledgebase of functional PTM sites. Moreover, PhosphOrtholog is generic being applicable to other PTM datasets such as acetylation, ubiquitination and methylation.

A Bayesian-Based Novel Methodology to Generate Reliable Site Response Mapping Sensitive to Data Uncertainties

NASA Astrophysics Data System (ADS)

Chakraborty, A.; Goto, H.

2017-12-01

The 2011 off the Pacific coast of Tohoku earthquake caused severe damage in many areas further inside the mainland because of site-amplification. Furukawa district in Miyagi Prefecture, Japan recorded significant spatial differences in ground motion even at sub-kilometer scales. The site responses in the damage zone far exceeded the levels in the hazard maps. A reason why the mismatch occurred is that mapping follow only the mean value at the measurement locations with no regard to the data uncertainties and thus are not always reliable. Our research objective is to develop a methodology to incorporate data uncertainties in mapping and propose a reliable map. The methodology is based on a hierarchical Bayesian modeling of normally-distributed site responses in space where the mean (μ), site-specific variance (σ2) and between-sites variance(s2) parameters are treated as unknowns with a prior distribution. The observation data is artificially created site responses with varying means and variances for 150 seismic events across 50 locations in one-dimensional space. Spatially auto-correlated random effects were added to the mean (μ) using a conditionally autoregressive (CAR) prior. The inferences on the unknown parameters are done using Markov Chain Monte Carlo methods from the posterior distribution. The goal is to find reliable estimates of μ sensitive to uncertainties. During initial trials, we observed that the tau (=1/s2) parameter of CAR prior controls the μ estimation. Using a constraint, s = 1/(k×σ), five spatial models with varying k-values were created. We define reliability to be measured by the model likelihood and propose the maximum likelihood model to be highly reliable. The model with maximum likelihood was selected using a 5-fold cross-validation technique. The results show that the maximum likelihood model (μ*) follows the site-specific mean at low uncertainties and converges to the model-mean at higher uncertainties (Fig.1). This result is highly significant as it successfully incorporates the effect of data uncertainties in mapping. This novel approach can be applied to any research field using mapping techniques. The methodology is now being applied to real records from a very dense seismic network in Furukawa district, Miyagi Prefecture, Japan to generate a reliable map of the site responses.

Global Mapping of the Yeast Genetic Interaction Network

NASA Astrophysics Data System (ADS)

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

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.

7 CFR 12.31 - On-site wetland identification criteria.

Code of Federal Regulations, 2011 CFR

2011-01-01

... CONSERVATION Wetland Conservation § 12.31 On-site wetland identification criteria. (a) Hydric soils. (1) NRCS shall identify hydric soils through the use of published soil maps which reflect soil surveys completed by NRCS or through the use of on-site reviews. If a published soil map is unavailable for a given...

7 CFR 12.31 - On-site wetland identification criteria.

Code of Federal Regulations, 2014 CFR

2014-01-01

... CONSERVATION Wetland Conservation § 12.31 On-site wetland identification criteria. (a) Hydric soils. (1) NRCS shall identify hydric soils through the use of published soil maps which reflect soil surveys completed by NRCS or through the use of on-site reviews. If a published soil map is unavailable for a given...

7 CFR 12.31 - On-site wetland identification criteria.

Code of Federal Regulations, 2010 CFR

2010-01-01

... CONSERVATION Wetland Conservation § 12.31 On-site wetland identification criteria. (a) Hydric soils. (1) NRCS shall identify hydric soils through the use of published soil maps which reflect soil surveys completed by NRCS or through the use of on-site reviews. If a published soil map is unavailable for a given...

7 CFR 12.31 - On-site wetland identification criteria.

Code of Federal Regulations, 2013 CFR

2013-01-01

... CONSERVATION Wetland Conservation § 12.31 On-site wetland identification criteria. (a) Hydric soils. (1) NRCS shall identify hydric soils through the use of published soil maps which reflect soil surveys completed by NRCS or through the use of on-site reviews. If a published soil map is unavailable for a given...

7 CFR 12.31 - On-site wetland identification criteria.

Code of Federal Regulations, 2012 CFR

2012-01-01

... CONSERVATION Wetland Conservation § 12.31 On-site wetland identification criteria. (a) Hydric soils. (1) NRCS shall identify hydric soils through the use of published soil maps which reflect soil surveys completed by NRCS or through the use of on-site reviews. If a published soil map is unavailable for a given...

The LandCarbon Web Application: Advanced Geospatial Data Delivery and Visualization Tools for Communication about Ecosystem Carbon Sequestration and Greenhouse Gas Fluxes

NASA Astrophysics Data System (ADS)

Thomas, N.; Galey, B.; Zhu, Z.; Sleeter, B. M.; Lehmer, E.

2015-12-01

The LandCarbon web application (http://landcarbon.org) is a collaboration between the U.S. Geological Survey and U.C. Berkeley's Geospatial Innovation Facility (GIF). The LandCarbon project is a national assessment focused on improved understanding of carbon sequestration and greenhouse gas fluxes in and out of ecosystems related to land use, using scientific capabilities from USGS and other organizations. The national assessment is conducted at a regional scale, covers all 50 states, and incorporates data from remote sensing, land change studies, aquatic and wetland data, hydrological and biogeochemical modeling, and wildfire mapping to estimate baseline and future potential carbon storage and greenhouse gas fluxes. The LandCarbon web application is a geospatial portal that allows for a sophisticated data delivery system as well as a suite of engaging tools that showcase the LandCarbon data using interactive web based maps and charts. The web application was designed to be flexible and accessible to meet the needs of a variety of users. Casual users can explore the input data and results of the assessment for a particular area of interest in an intuitive and interactive map, without the need for specialized software. Users can view and interact with maps, charts, and statistics that summarize the baseline and future potential carbon storage and fluxes for U.S. Level 2 Ecoregions for 3 IPCC emissions scenarios. The application allows users to access the primary data sources and assessment results for viewing and download, and also to learn more about the assessment's objectives, methods, and uncertainties through published reports and documentation. The LandCarbon web application is built on free and open source libraries including Django and D3. The GIF has developed the Django-Spillway package, which facilitates interactive visualization and serialization of complex geospatial raster data. The underlying LandCarbon data is available through an open application programming interface (API), which will allow other organizations to build their own custom applications and tools. New features such as finer scale aggregation and an online carbon calculator are being added to the LandCarbon web application to continue to make the site interactive, visually compelling, and useful for a wide range of users.

Chromosome segregation drives division site selection in Streptococcus pneumoniae.

PubMed

van Raaphorst, Renske; Kjos, Morten; Veening, Jan-Willem

2017-07-18

Accurate spatial and temporal positioning of the tubulin-like protein FtsZ is key for proper bacterial cell division. Streptococcus pneumoniae (pneumococcus) is an oval-shaped, symmetrically dividing opportunistic human pathogen lacking the canonical systems for division site control (nucleoid occlusion and the Min-system). Recently, the early division protein MapZ was identified and implicated in pneumococcal division site selection. We show that MapZ is important for proper division plane selection; thus, the question remains as to what drives pneumococcal division site selection. By mapping the cell cycle in detail, we show that directly after replication both chromosomal origin regions localize to the future cell division sites, before FtsZ. Interestingly, Z-ring formation occurs coincidently with initiation of DNA replication. Perturbing the longitudinal chromosomal organization by mutating the condensin SMC, by CRISPR/Cas9-mediated chromosome cutting, or by poisoning DNA decatenation resulted in mistiming of MapZ and FtsZ positioning and subsequent cell elongation. Together, we demonstrate an intimate relationship between DNA replication, chromosome segregation, and division site selection in the pneumococcus, providing a simple way to ensure equally sized daughter cells.

Aggregation of gold nanoparticles followed by methotrexate release enables Raman imaging of drug delivery into cancer cells

NASA Astrophysics Data System (ADS)

Durgadas, C. V.; Sharma, C. P.; Paul, W.; Rekha, M. R.; Sreenivasan, K.

2012-09-01

This study refers an aqueous synthesis of methotrexate (MTX)-conjugated gold nanoparticles (GNPs), their interaction with HepG2 cells, and the use of Raman imaging to observe cellular internalization and drug delivery. GNPs of average size 3.5-5 nm were stabilized using the amine terminated bifunctional biocompatible copolymer and amended by conjugating MTX, an anticancer drug. The nanoparticles were released MTX at a faster rate in acidic pH and subsequently found to form aggregates. The Raman signals of cellular components were found to be enhanced by the aggregated particles enabling the mapping to visualize site-specific drug delivery. The methodology seems to have potential in optimizing the characteristics of nanodrug carriers for emptying the cargo precisely at specified sites.

Ten years of change: National Library of Medicine TOXMAP gets a new look.

PubMed

Hochstein, Colette; Gemoets, Darren; Goshorn, Jeanne

2014-01-01

The United States National Library of Medicine (NLM) TOXNET® databases < http://toxnet.nlm.nih.gov > provide broad coverage of environmental health information covering a wide variety of topics, including access to the U.S. Environment Protection Agency (EPA)'s Toxics Release Inventory (TRI) data. The NLM web-based geographic information system (GIS), TOXMAP® < http://toxmap.nlm.nih.gov/ >, provides interactive maps which show where TRI chemicals are released into the environment and links to TOXNET for information about these chemicals. TOXMAP also displays locations of Superfund sites on the EPA National Priority List, as well as information about the chemical contaminants at these sites. This column focuses on a new version of TOXMAP which brings it up to date with current web GIS technologies and user expectations.

Mapping of the binding sites involved in PSP94-CRISP-3 interaction by molecular dissection of the complex.

PubMed

Breed, Ananya A; Gomes, Amanda; Roy, Binita Sur; Mahale, Smita D; Pathak, Bhakti R

2013-04-01

Human Prostate Secretory Protein of 94 amino acids (PSP94) has been shown to bind human CRISP-3 (cysteine-rich secretory protein 3) with very high affinity. CRISP-3 belongs to the CRISP family of proteins having a PR-1 (pathogenesis related protein 1) domain at its N-terminal and ion channel regulatory (ICR) domain at its C-terminal connected by a hinge region. Functional significance of this complex is not yet known. In order to identify the residues and/or regions involved in PSP94-CRISP-3 interaction, site-directed mutagenesis was employed. Effect of the mutations on the interaction was studied by co-immunoprecipitation (Co-IP). For PSP94, amino acids Y(3), F(4), P(56) and the C-terminal β-strand were found to be crucial for interacting with CRISP-3. A disulfide bond between the two domains of PSP94 (C(37)A-C(73)A) was also important for this interaction. In case of CRISP-3, the N-terminal domain alone could not maintain a strong interaction with PSP94 but it required presence of the hinge region and not the C-terminal domain. Apart from CRISP-3, CRISP-2 was also found to interact with human PSP94. Based on our findings the most likely model of PSP94-CRISP-3 complex has been proposed. The terminal β-strands of PSP94 contact the first α-helix and the hinge region of CRISP-3. Involvement of the hinge region of CRISPs in interaction with PSP94 may affect the domain movement of CRISPs essential for the ion-channel regulatory activity resulting in inhibition of this activity. Copyright © 2013 Elsevier B.V. All rights reserved.

Links between geodiversity and cultural elements on three scale levels, a neglected part of geoconservation

NASA Astrophysics Data System (ADS)

van den Ancker, Hanneke; Jungerius, Pieter Dirk

2015-04-01

The best-known landscape map of The Netherlands is a simplified version of the first geological map of The Netherlands and was made between 1856 and 1867 by Winand Staring. It still is the basis of our vegetation districts. The main landscape units of this map are the sand landscape, the peat landscape, the river landscape, the marine landscape, the coastal dunes and the hills. On this scale level there is general awareness of the relationships between the geo aspects (geomorphology, geology, geohydrology and soil science) of the landscape and historical land use, e.g. in field patterns and other cultural elements (archaeology and historical geography). From three of these units, examples of interactions between geo-aspects and cultural elements are given for two different scale levels: first on a more regional scale level, then on site level. Especially the last level requires field study. The relationships between the geo and cultural aspects appear to be most intact and are most variable at the site level. Earth scientists as yet hardly involve themselves in geoconservation studies re these relationships, for which reason the geo-aspects of the cultural elements, especially those at the site level, often are not noticed and disappear during land development projects or gardening efforts. It also is a missed opportunity as these sites offer a chance to raise interest of a broader public for geomorphology and soils, which are in general more difficult to communicate. The development and management of cultural landscapes and sites, by Dutch law is the domain of land owners and landscape architects, who in the course of a project consult other experts. Our plea for future planning projects is to work with a team of experts including archaeologists, historical geographers, flora and fauna experts, geologists, geomorphologists and soil specialists. Although the costs of preparing a plan will be slightly higher, our experience is that it will improve the quality of land planning and the quality of our historical and future landscapes.

A new strategy for developing Vs30 maps

USGS Publications Warehouse

Wald, David J.; McWhirter, Leslie; Thompson, Eric; Hering, Amanda S.

2011-01-01

Despite obvious limitations as a proxy for site amplification, the use of time-averaged shear-wave velocity over the top 30m (Vs30) is useful and widely practiced, most notably through its use as an explanatory variable in ground motion prediction equations (and thus hazard maps and ShakeMaps, among other applications). Local, regional, and global Vs30 maps thus have diverse and fundamental uses in earthquake and engineering seismology. As such, we are developing an improved strategy for producing Vs30 maps given the common observational constraints available in any region for various spatial scales. We investigate a hierarchical approach to mapping Vs30, where the baseline model is derived from topographic slope because it is available globally, but geological maps and Vs30 observations contribute, where available. Using the abundant measured Vs30 values in Taiwan as an example, we analyze Vs30 versus slope per geologic unit and observe minor trends that indicate potential interaction of geologic and slope terms. We then regress Vs30 for the geologic Vs30 medians, topographic-slope, and cross-term coefficients for a hybrid model. The residuals of this hybrid model still exhibit a strong spatial correlation structure, so we use the kriging-with-a-trend method (the trend is the hybrid model) to further refine the Vs30 map so as to honor the Vs30 observations. Unlike the geology or slope models alone, this strategytakes advantage of the predictive capabilities of the two models, yet effectively defaults to ordinary kriging in the vicinity of the observed data, thereby achieving consistency with the observed data.

Assessing earthquake hazards with fault trench and LiDAR maps in the Puget Lowland, Washington, USA (Invited)

NASA Astrophysics Data System (ADS)

Nelson, A. R.; Bradley, L.; Personius, S. F.; Johnson, S. Y.

2010-12-01

Deciphering the earthquake histories of faults over the past few thousands of years in tectonically complex forearc regions relies on detailed site-specific as well as regional geologic maps. Here we present examples of site-specific USGS maps used to reconstruct earthquake histories for faults in the Puget Lowland. Near-surface faults and folds in the Puget Lowland accommodate 4-7 mm/yr of north-south shortening resulting from northward migration of forearc blocks along the Cascadia convergent margin. The shortening has produced east-trending uplifts, basins, and associated reverse faults that traverse urban areas. Near the eastern and northern flanks of the Olympic Mountains, complex interactions between north-south shortening and mountain uplift are reflected by normal, oblique-slip, and reverse surface faults. Holocene oblique-slip movement has also been mapped on Whidbey Island and on faults in the foothills of the Cascade Mountains in the northeastern lowland. The close proximity of lowland faults to urban areas may pose a greater earthquake hazard there than do much longer but more distant plate-boundary faults. LiDAR imagery of the densely forested lowland flown over the past 12 years revealed many previously unknown 0.5-m to 6-m-high scarps showing Holocene movement on upper-plate faults. This imagery uses two-way traveltimes of laser light pulses to detect as little as 0.2 m of relative relief on the forest floor. The returns of laser pulses with the longest travel times yield digital elevation models of the ground surface, which we vertically exaggerate and digitally shade from multiple directions at variable transparencies to enhance identification of scarps. Our maps include imagery at scales of 1:40,000 to 1:2500 with contour spacings of 100 m to 0.5 m. Maps of the vertical walls of fault-scarp trenches show complex stratigraphies and structural relations used to decipher the histories of large surface-rupturing earthquakes. These logs (field mapping at 1:8 to 1:20 scales) of 25 trenches are included in five published (and one in preparation) maps along with lithologic descriptions of stratigraphic units and tables of 14C, structural, and stratigraphic data. Maps include soil profile data, topographic profiles across scarps, structural orientation data, or photographs of trench sites or trench walls. Stratigraphy and 14C ages suggest that earthquake recurrence varies from less than a century to many thousands of years. Interpretation and synthesis of such data are reserved for journal papers, which commonly cannot accommodate the detailed, large-format information shown on the maps. Many thanks to Brian Sherrod, Harvey Kelsey, Jason Buck, Ray Wells, Liz Schermer, Rob Witter, Rich Koehler, Rich Briggs, Robert Bogar, Gary Henley, Dave Harding, Koji Okumura, Silvio Pezzopane, Bob Bucknam, Zeb Maharrey, Bill Laprade, Ralph Haugerud, Lee Liberty, Michael Polenz, Eliza Nemser, Trenton Cladouhos, and many others for days to many weeks of effort in our trenches over the past 12 years.

3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling

PubMed Central

Segura, Joan; Sanchez-Garcia, Ruben; Tabas-Madrid, Daniel; Cuenca-Alba, Jesus; Sorzano, Carlos Oscar S.; Carazo, Jose Maria

2016-01-01

Electron microscopy (EM) is experiencing a revolution with the advent of a new generation of Direct Electron Detectors, enabling a broad range of large and flexible structures to be resolved well below 1 nm resolution. Although EM techniques are evolving to the point of directly obtaining structural data at near-atomic resolution, for many molecules the attainable resolution might not be enough to propose high-resolution structural models. However, accessing information on atomic coordinates is a necessary step toward a deeper understanding of the molecular mechanisms that allow proteins to perform specific tasks. For that reason, methods for the integration of EM three-dimensional maps with x-ray and NMR structural data are being developed, a modeling task that is normally referred to as fitting, resulting in the so called hybrid models. In this work, we present a novel application—3DIANA—specially targeted to those cases in which the EM map resolution is medium or low and additional experimental structural information is scarce or even lacking. In this way, 3DIANA statistically evaluates proposed/potential contacts between protein domains, presents a complete catalog of both structurally resolved and predicted interacting regions involving these domains and, finally, suggests structural templates to model the interaction between them. The evaluation of the proposed interactions is computed with DIMERO, a new method that scores physical binding sites based on the topology of protein interaction networks, which has recently shown the capability to increase by 200% the number of domain-domain interactions predicted in interactomes as compared to previous approaches. The new application displays the information at a sequence and structural level and is accessible through a web browser or as a Chimera plugin at http://3diana.cnb.csic.es. PMID:26772592

The potential of seismic methods for detecting cavities and buried objects: experimentation at a test site

NASA Astrophysics Data System (ADS)

Grandjean, Gilles; Leparoux, Donatienne

2004-06-01

One of the recurring problems in civil engineering and landscape management is the detection of natural and man-made cavities in order to mitigate the problems of collapse and subsurface subsidence. In general, the position of the cavities is not known, either because they are not recorded in a database or because location maps are not available. In such cases, geophysical methods can provide an effective alternative for cavity detection, particularly ground-penetrating radar (GPR) and seismic methods, for which pertinent results have been recently obtained. Many studies carried out under real conditions have revealed that the signatures derived from interaction between seismic signals and voids are affected by complex geology, thus making them difficult to interpret. We decided to analyze this interaction under physical conditions as simple as possible, i.e., at a test site built specifically for that purpose. The test site was constructed of a homogeneous material and a void-equivalent body so that the ratio between wavelength and heterogeneity size was compatible with that encountered in reality. Numerical modeling was initially used to understand wave interaction with the body, prior to the design of various data-processing protocols. P-wave imagery and surface-wave sections were then acquired and processed. The work involved in this experiment and the associated results are presented, followed by a discussion concerning the reliability of such a study, and its consequences for future seismic projects.

Coastline Mapping and Cultural Review to Predict Sea Level Rise Impact on Hawaiian Archeological Sites

NASA Astrophysics Data System (ADS)

Clinton, J.

2017-12-01

Much of Hawaii's history is recorded in archeological sites. Researchers and cultural practitioners have been studying and reconstructing significant archeological sites for generations. Climate change, and more specifically, sea level rise may threaten these sites. Our research records current sea levels and then projects possible consequences to these cultural monuments due to sea level rise. In this mixed methods study, research scientists, cultural practitioners, and secondary students use plane-table mapping techniques to create maps of coastlines and historic sites. Students compare historical records to these maps, analyze current sea level rise trends, and calculate future sea levels. They also gather data through interviews with community experts and kupuna (elders). If climate change continues at projected rates, some historic sites will be in danger of negative impact due to sea level rise. Knowing projected sea levels at specific sites allows for preventative action and contributes to raised awareness of the impacts of climate change to the Hawaiian Islands. Students will share results with the community and governmental agencies in hopes of inspiring action to minimize climate change. It will take collaboration between scientists and cultural communities to inspire future action on climate change.

PolyaPeak: Detecting Transcription Factor Binding Sites from ChIP-seq Using Peak Shape Information

PubMed Central

Wu, Hao; Ji, Hongkai

2014-01-01

ChIP-seq is a powerful technology for detecting genomic regions where a protein of interest interacts with DNA. ChIP-seq data for mapping transcription factor binding sites (TFBSs) have a characteristic pattern: around each binding site, sequence reads aligned to the forward and reverse strands of the reference genome form two separate peaks shifted away from each other, and the true binding site is located in between these two peaks. While it has been shown previously that the accuracy and resolution of binding site detection can be improved by modeling the pattern, efficient methods are unavailable to fully utilize that information in TFBS detection procedure. We present PolyaPeak, a new method to improve TFBS detection by incorporating the peak shape information. PolyaPeak describes peak shapes using a flexible Pólya model. The shapes are automatically learnt from the data using Minorization-Maximization (MM) algorithm, then integrated with the read count information via a hierarchical model to distinguish true binding sites from background noises. Extensive real data analyses show that PolyaPeak is capable of robustly improving TFBS detection compared with existing methods. An R package is freely available. PMID:24608116

Geophysical identification of subsurface cavities and fractures near a Superfund site south of Rockford, Illinois

NASA Astrophysics Data System (ADS)

Adams, Ryan Frye

The ACME Superfund site is one of many Superfund sites in Northern Illinois. This 20 acre (8.1 ha) site was contaminated by various volatile organic compounds (VOC's) and heavy metals during the 1960-1980s. To more fully understand the potential extent of the karst system and its interaction with contaminants, both surface and borehole geophysics including seismic refraction tomography, frequency domain electromagnetics, electrical resistivity, ground penetrating radar, as well as natural gamma and electromagnetic well logs, were undertaken over an approximately 3,000 square meter grid in a field immediately south of the ACME site. Seismic refraction tomography provided information on lithology and fluctuations in the bedrock surface in the depth range 6 to 8 m. Refraction, combined with electromagnetic conductivity, also allowed mapping of potential soil pipes and/or filled sinkholes in the overlying soils. These could channel surface waters into the karst conduit system. Frequency domain electromagnetics proved to be the most successful tool for the identifying possible karst conduits below the bedrock surface. Zones of reduced conductivity suggest a series of interconnected solutionally enlarged fractures in an orthogonal pattern at a depth of approximately 8 m immediately south of the ACME site.

The MUSE view of the host galaxy of GRB 100316D

NASA Astrophysics Data System (ADS)

Izzo, L.; Thöne, C. C.; Schulze, S.; Mehner, A.; Flores, H.; Cano, Z.; de Ugarte Postigo, A.; Kann, D. A.; Amorín, R.; Anderson, J. P.; Bauer, F. E.; Bensch, K.; Christensen, L.; Covino, S.; Della Valle, M.; Fynbo, J. P. U.; Jakobsson, P.; Klose, S.; Kuncarayakti, H.; Leloudas, G.; Milvang-Jensen, B.; Møller, P.; Puech, M.; Rossi, A.; Sánchez-Ramírez, R.; Vergani, S. D.

2017-12-01

The low distance, z = 0.0591, of GRB 100316D and its association with SN 2010bh represent two important motivations for studying this host galaxy and the GRB's immediate environment with the integral field spectrographs like Very Large Telescope/Multi-Unit Spectroscopic Explorer. Its large field of view allows us to create 2D maps of gas metallicity, ionization level and the star formation rate (SFR) distribution maps, as well as to investigate the presence of possible host companions. The host is a late-type dwarf irregular galaxy with multiple star-forming regions and an extended central region with signatures of on-going shock interactions. The gamma-ray burst (GRB) site is characterized by the lowest metallicity, the highest SFR and the youngest (∼20-30 Myr) stellar population in the galaxy, which suggest a GRB progenitor stellar population with masses up to 20-40 M⊙. We note that the GRB site has an offset of ∼660 pc from the most luminous SF region in the host. The observed SF activity in this galaxy may have been triggered by a relatively recent gravitational encounter between the host and a small undetected (LH α ≤ 1036 erg s-1) companion.

3D Structure and Interaction of p24β and p24δ Golgi Dynamics Domains: Implication for p24 Complex Formation and Cargo Transport.

PubMed

Nagae, Masamichi; Hirata, Tetsuya; Morita-Matsumoto, Kana; Theiler, Romina; Fujita, Morihisa; Kinoshita, Taroh; Yamaguchi, Yoshiki

2016-10-09

The p24 family consists of four subfamilies (p24α, p24β, p24γ, and p24δ), and the proteins are thought to form hetero-oligomeric complexes for efficient transport of cargo proteins from the endoplasmic reticulum to the Golgi apparatus. The proteins possess a conserved luminal Golgi dynamics (GOLD) domain, whose functions are largely unknown. Here, we present structural and biochemical studies of p24β1 and p24δ1 GOLD domains. Use of GOLD domain-deleted mutants revealed that the GOLD domain of p24δ1 is required for proper p24 hetero-oligomeric complex formation and efficient transport of GPI-anchored proteins. The p24β1 and p24δ1 GOLD domains share a common β-sandwich fold with a characteristic intrasheet disulfide bond. The GOLD domain of p24δ1 crystallized as dimers, allowing the analysis of a homophilic interaction site. Surface plasmon resonance and solution NMR analyses revealed that p24β1 and p24δ1 GOLD domains interact weakly (K d = ~10 -4 M). Bi-protein titration provided interaction site maps. We propose that the heterophilic interaction of p24 GOLD domains contributes to the formation of the p24 hetero-oligomeric complex and to efficient cargo transport. Copyright © 2016 Elsevier Ltd. All rights reserved.

Interaction of the BKCa channel gating ring with dendrotoxins

PubMed Central

Takacs, Zoltan; Imredy, John P; Bingham, Jon-Paul; Zhorov, Boris S; Moczydlowski, Edward G

2014-01-01

Two classes of small homologous basic proteins, mamba snake dendrotoxins (DTX) and bovine pancreatic trypsin inhibitor (BPTI), block the large conductance Ca2+-activated K+ channel (BKCa, KCa1.1) by production of discrete subconductance events when added to the intracellular side of the membrane. This toxin-channel interaction is unlikely to be pharmacologically relevant to the action of mamba venom, but as a fortuitous ligand-protein interaction, it has certain biophysical implications for the mechanism of BKCa channel gating. In this work we examined the subconductance behavior of 9 natural dendrotoxin homologs and 6 charge neutralization mutants of δ-dendrotoxin in the context of current structural information on the intracellular gating ring domain of the BKCa channel. Calculation of an electrostatic surface map of the BKCa gating ring based on the Poisson-Boltzmann equation reveals a predominantly electronegative surface due to an abundance of solvent-accessible side chains of negatively charged amino acids. Available structure-activity information suggests that cationic DTX/BPTI molecules bind by electrostatic attraction to site(s) on the gating ring located in or near the cytoplasmic side portals where the inactivation ball peptide of the β2 subunit enters to block the channel. Such an interaction may decrease the apparent unitary conductance by altering the dynamic balance of open versus closed states of BKCa channel activation gating. PMID:25483585

From Open Geographical Data to Tangible Maps: Improving the Accessibility of Maps for Visually Impaired People

NASA Astrophysics Data System (ADS)

Ducasse, J.; Macé, M.; Jouffrais, C.

2015-08-01

Visual maps must be transcribed into (interactive) raised-line maps to be accessible for visually impaired people. However, these tactile maps suffer from several shortcomings: they are long and expensive to produce, they cannot display a large amount of information, and they are not dynamically modifiable. A number of methods have been developed to automate the production of raised-line maps, but there is not yet any tactile map editor on the market. Tangible interactions proved to be an efficient way to help a visually impaired user manipulate spatial representations. Contrary to raised-line maps, tangible maps can be autonomously constructed and edited. In this paper, we present the scenarios and the main expected contributions of the AccessiMap project, which is based on the availability of many sources of open spatial data: 1/ facilitating the production of interactive tactile maps with the development of an open-source web-based editor; 2/ investigating the use of tangible interfaces for the autonomous construction and exploration of a map by a visually impaired user.

Blocking the association of HDAC4 with MAP1S accelerates autophagy clearance of mutant Huntingtin

PubMed Central

Yue, Fei; Li, Wenjiao; Zou, Jing; Chen, Qi; Xu, Guibin; Huang, Hai; Xu, Zhen; Zhang, Sheng; Gallinari, Paola; Wang, Fen; McKeehan, Wallace L.; Liu, Leyuan

2015-01-01

Autophagy controls and executes the turnover of abnormally aggregated proteins. MAP1S interacts with the autophagy marker LC3 and positively regulates autophagy flux. HDAC4 associates with the aggregation-prone mutant huntingtin protein (mHTT) that causes Huntington's disease, and colocalizes with it in cytosolic inclusions. It was suggested HDAC4 interacts with MAP1S in a yeast two-hybrid screening. Here, we found that MAP1S interacts with HDAC4 via a HDAC4-binding domain (HBD). HDAC4 destabilizes MAP1S, suppresses autophagy flux and promotes the accumulation of mHTT aggregates. This occurs by an increase in the deacetylation of the acetylated MAP1S. Either suppression of HDAC4 with siRNA or overexpression of the MAP1S HBD leads to stabilization of MAP1S, activation of autophagy flux and clearance of mHTT aggregates. Therefore, specific interruption of the HDAC4-MAP1S interaction with short peptides or small molecules to enhance autophagy flux may relieve the toxicity of mHTT associated with Huntington's disease and improve symptoms of HD patients. PMID:26540094

TSEMA: interactive prediction of protein pairings between interacting families

PubMed Central

Izarzugaza, José M. G.; Juan, David; Pons, Carles; Ranea, Juan A. G.; Valencia, Alfonso; Pazos, Florencio

2006-01-01

An entire family of methodologies for predicting protein interactions is based on the observed fact that families of interacting proteins tend to have similar phylogenetic trees due to co-evolution. One application of this concept is the prediction of the mapping between the members of two interacting protein families (which protein within one family interacts with which protein within the other). The idea is that the real mapping would be the one maximizing the similarity between the trees. Since the exhaustive exploration of all possible mappings is not feasible for large families, current approaches use heuristic techniques which do not ensure the best solution to be found. This is why it is important to check the results proposed by heuristic techniques and to manually explore other solutions. Here we present TSEMA, the server for efficient mapping assessment. This system calculates an initial mapping between two families of proteins based on a Monte Carlo approach and allows the user to interactively modify it based on performance figures and/or specific biological knowledge. All the explored mappings are graphically shown over a representation of the phylogenetic trees. The system is freely available at . Standalone versions of the software behind the interface are available upon request from the authors. PMID:16845017

Development of a site analysis tool for distributed wind projects

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shaw, Shawn

The Cadmus Group, Inc., in collaboration with the National Renewable Energy Laboratory (NREL) and Encraft, was awarded a grant from the Department of Energy (DOE) to develop a site analysis tool for distributed wind technologies. As the principal investigator for this project, Mr. Shawn Shaw was responsible for overall project management, direction, and technical approach. The product resulting from this project is the Distributed Wind Site Analysis Tool (DSAT), a software tool for analyzing proposed sites for distributed wind technology (DWT) systems. This user-friendly tool supports the long-term growth and stability of the DWT market by providing reliable, realistic estimatesmore » of site and system energy output and feasibility. DSAT-which is accessible online and requires no purchase or download of software-is available in two account types; Standard: This free account allows the user to analyze a limited number of sites and to produce a system performance report for each; and Professional: For a small annual fee users can analyze an unlimited number of sites, produce system performance reports, and generate other customizable reports containing key information such as visual influence and wind resources. The tool’s interactive maps allow users to create site models that incorporate the obstructions and terrain types present. Users can generate site reports immediately after entering the requisite site information. Ideally, this tool also educates users regarding good site selection and effective evaluation practices.« less

Histocompatibility antigen test

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Stress and your heart

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Premenstrual dysphoric disorder

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Learn to manage stress

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Site plan, map, and statement of significance Promontory Route ...

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

Site plan, map, and statement of significance - Promontory Route Railroad Trestles, S.P. Trestle 779.91, One mile southwest of junction of State Highway 83 and Blue Creek, Corinne, Box Elder County, UT

Constraining the interaction between dark sectors with future HI intensity mapping observations

NASA Astrophysics Data System (ADS)

Xu, Xiaodong; Ma, Yin-Zhe; Weltman, Amanda

2018-04-01

We study a model of interacting dark matter and dark energy, in which the two components are coupled. We calculate the predictions for the 21-cm intensity mapping power spectra, and forecast the detectability with future single-dish intensity mapping surveys (BINGO, FAST and SKA-I). Since dark energy is turned on at z ˜1 , which falls into the sensitivity range of these radio surveys, the HI intensity mapping technique is an efficient tool to constrain the interaction. By comparing with current constraints on dark sector interactions, we find that future radio surveys will produce tight and reliable constraints on the coupling parameters.

Investigating the Interaction between the Neonatal Fc Receptor and Monoclonal Antibody Variants by Hydrogen/Deuterium Exchange Mass Spectrometry*

PubMed Central

Jensen, Pernille Foged; Larraillet, Vincent; Schlothauer, Tilman; Kettenberger, Hubert; Hilger, Maximiliane; Rand, Kasper D.

2015-01-01

The recycling of immunoglobulins by the neonatal Fc receptor (FcRn) is of crucial importance in the maintenance of antibody levels in plasma and is responsible for the long half-lives of endogenous and recombinant monoclonal antibodies. From a therapeutic point of view there is great interest in understanding and modulating the IgG–FcRn interaction to optimize antibody pharmacokinetics and ultimately improve efficacy and safety. Here we studied the interaction between a full-length human IgG1 and human FcRn via hydrogen/deuterium exchange mass spectrometry and targeted electron transfer dissociation to map sites perturbed by binding on both partners of the IgG–FcRn complex. Several regions in the antibody Fc region and the FcRn were protected from exchange upon complex formation, in good agreement with previous crystallographic studies of FcRn in complex with the Fc fragment. Interestingly, we found that several regions in the IgG Fab region also showed reduced deuterium uptake. Our findings indicate the presence of hitherto unknown FcRn interaction sites in the Fab region or a possible conformational link between the IgG Fc and Fab regions upon FcRn binding. Further, we investigated the role of IgG glycosylation in the conformational response of the IgG–FcRn interaction. Removal of antibody glycans increased the flexibility of the FcRn binding site in the Fc region. Consequently, FcRn binding did not induce a similar conformational stabilization of deglycosylated IgG as observed for the wild-type glycosylated IgG. Our results provide new molecular insight into the IgG–FcRn interaction and illustrate the capability of hydrogen/deuterium exchange mass spectrometry to advance structural proteomics by providing detailed information on the conformation and dynamics of large protein complexes in solution. PMID:25378534

Multiscale site-response mapping: A case study of Parkfield, California

USGS Publications Warehouse

Thompson, E.M.; Baise, L.G.; Kayen, R.E.; Morgan, E.C.; Kaklamanos, J.

2011-01-01

The scale of previously proposed methods for mapping site-response ranges from global coverage down to individual urban regions. Typically, spatial coverage and accuracy are inversely related.We use the densely spaced strong-motion stations in Parkfield, California, to estimate the accuracy of different site-response mapping methods and demonstrate a method for integrating multiple site-response estimates from the site to the global scale. This method is simply a weighted mean of a suite of different estimates, where the weights are the inverse of the variance of the individual estimates. Thus, the dominant site-response model varies in space as a function of the accuracy of the different models. For mapping applications, site-response models should be judged in terms of both spatial coverage and the degree of correlation with observed amplifications. Performance varies with period, but in general the Parkfield data show that: (1) where a velocity profile is available, the square-rootof- impedance (SRI) method outperforms the measured VS30 (30 m divided by the S-wave travel time to 30 m depth) and (2) where velocity profiles are unavailable, the topographic slope method outperforms surficial geology for short periods, but geology outperforms slope at longer periods. We develop new equations to estimate site response from topographic slope, derived from the Next Generation Attenuation (NGA) database.

Astronaut Kevin Chilton displays map of Scandinavia on flight deck

NASA Technical Reports Server (NTRS)

1994-01-01

Astronaut Kevin P. Chilton, pilot, displays a map of Scandinavia on the Space Shuttle Endeavour's flight deck. Large scale maps such as this were used by the crew to locate specific sites of interest to the Space Radar Laboratory scientists. The crew then photographed the sites at the same time as the radar in the payload bay imaged them.

Reproducing Crystal Binding Modes of Ligand Functional Groups using Site-Identification by Ligand Competitive Saturation (SILCS) Simulations

PubMed Central

Raman, E. Prabhu; Yu, Wenbo; Guvench, Olgun; MacKerell, Alexander D.

2011-01-01

The applicability of a computational method, Site Identification by Ligand Competitive Saturation (SILCS), to identify regions on a protein surface with which different types of functional groups on low-molecular weight inhibitors interact is demonstrated. The method involves molecular dynamics (MD) simulations of a protein in an aqueous solution of chemically diverse small molecules from which probability distributions of fragments types, termed FragMaps, are obtained. In the present application, SILCS simulations are performed with an aqueous solution of 1 M benzene and propane to map the affinity pattern of the protein for aromatic and aliphatic functional groups. In addition, water hydrogen and oxygen atoms serve as probes for hydrogen bond donor and acceptor affinity, respectively. The method is tested using a set of 7 proteins for which crystal structures of complexes with several high affinity inhibitors are known. Good agreement is obtained between FragMaps and the positions of chemically similar functional groups in inhibitors as observed in the X-ray crystallographic structures. Quantitative capabilities of the SILCS approach are demonstrated by converting FragMaps to free energies, termed Grid Free Energies (GFE), and showing correlation between the GFE values and experimental binding affinities. For proteins for which ligand decoy sets are available, GFE values are shown to typically score the crystal conformation and conformations similar to it more favorable than decoys. Additionally, SILCS is tested for its ability to capture the subtle differences in ligand affinity across homologous proteins, information which may be of utility towards specificity-guided drug design. Taken together, our results show that SILCS can recapitulate the known location of functional groups of bound inhibitors for a number of proteins, suggesting that the method may be of utility for rational drug design. PMID:21456594

How integrated are neurology and palliative care services? Results of a multicentre mapping exercise.

PubMed

van Vliet, Liesbeth M; Gao, Wei; DiFrancesco, Daniel; Crosby, Vincent; Wilcock, Andrew; Byrne, Anthony; Al-Chalabi, Ammar; Chaudhuri, K Ray; Evans, Catherine; Silber, Eli; Young, Carolyn; Malik, Farida; Quibell, Rachel; Higginson, Irene J

2016-05-10

Patients affected by progressive long-term neurological conditions might benefit from specialist palliative care involvement. However, little is known on how neurology and specialist palliative care services interact. This study aimed to map the current level of connections and integration between these services. The mapping exercise was conducted in eight centres with neurology and palliative care services in the United Kingdom. The data were provided by the respective neurology and specialist palliative care teams. Questions focused on: i) catchment and population served; ii) service provision and staffing; iii) integration and relationships. Centres varied in size of catchment areas (39-5,840 square miles) and population served (142,000-3,500,000). Neurology and specialist palliative care were often not co-terminus. Service provisions for neurology and specialist palliative care were also varied. For example, neurology services varied in the number and type of provided clinics and palliative care services in the settings they work in. Integration was most developed in Motor Neuron Disease (MND), e.g., joint meetings were often held, followed by Parkinsonism (made up of Parkinson's Disease (PD), Multiple-System Atrophy (MSA) and Progressive Supranuclear Palsy (PSP), with integration being more developed for MSA and PSP) and least in Multiple Sclerosis (MS), e.g., most sites had no formal links. The number of neurology patients per annum receiving specialist palliative care reflected these differences in integration (range: 9-88 MND, 3-25 Parkinsonism, and 0-5 MS). This mapping exercise showed heterogeneity in service provision and integration between neurology and specialist palliative care services, which varied not only between sites but also between diseases. This highlights the need and opportunities for improved models of integration, which should be rigorously tested for effectiveness.

The active enhancer network operated by liganded RXR supports angiogenic activity in macrophages

PubMed Central

Daniel, Bence; Hah, Nasun; Horvath, Attila; Czimmerer, Zsolt; Poliska, Szilard; Gyuris, Tibor; Keirsse, Jiri; Gysemans, Conny; Van Ginderachter, Jo A.; Balint, Balint L.; Evans, Ronald M.; Barta, Endre; Nagy, Laszlo

2014-01-01

RXR signaling is predicted to have a major impact in macrophages, but neither the biological consequence nor the genomic basis of its ligand activation is known. Comprehensive genome-wide studies were carried out to map liganded RXR-mediated transcriptional changes, active binding sites, and cistromic interactions in the context of the macrophage genome architecture. The macrophage RXR cistrome has 5200 genomic binding sites, which are not impacted by ligand. Active enhancers are characterized by PU.1 binding, an increase of enhancer RNA, and P300 recruitment. Using these features, 387 liganded RXR-bound enhancers were linked to 226 genes, which predominantly reside in CTCF/cohesin-limited functional domains. These findings were molecularly validated using chromosome conformation capture (3C) and 3C combined with sequencing (3C-seq), and we show that selected long-range enhancers communicate with promoters via stable or RXR-induced loops and that some of the enhancers interact with each other, forming an interchromosomal network. A set of angiogenic genes, including Vegfa, has liganded RXR-controlled enhancers and provides the macrophage with a novel inducible program. PMID:25030696

The Barium Site in a Potassium Channel by X-Ray Crystallography

PubMed Central

Jiang, Youxing; MacKinnon, Roderick

2000-01-01

X-ray diffraction data were collected from frozen crystals (100°K) of the KcsA K+ channel equilibrated with solutions containing barium chloride. Difference electron density maps (Fbarium − Fnative, 5.0 Å resolution) show that Ba2+ resides at a single location within the selectivity filter. The Ba2+ blocking site corresponds to the internal aspect (adjacent to the central cavity) of the “inner ion” position where an alkali metal cation is found in the absence of the blocking Ba2+ ion. The location of Ba2+ with respect to Rb+ ions in the pore is in good agreement with the findings on the functional interaction of Ba2+ with K+ (and Rb+) in Ca2+-activated K+ channels (Neyton, J., and C. Miller. 1988. J. Gen. Physiol. 92:549–567). Taken together, these structural and functional data imply that at physiological ion concentrations a third ion may interact with two ions in the selectivity filter, perhaps by entering from one side and displacing an ion on the opposite side. PMID:10694255

Structural and Functional Analyses of the Severe Acute Respiratory Syndrome Coronavirus Endoribonuclease Nsp15

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhardwaj, Kanchan; Palaninathan, Satheesh; Alcantara, Joanna Maria Ortiz

2008-03-31

The severe acute respiratory syndrome (SARS) coronavirus encodes several RNA-processing enzymes that are unusual for RNA viruses, including Nsp15 (nonstructural protein 15), a hexameric endoribonuclease that preferentially cleaves 3' of uridines. We solved the structure of a catalytically inactive mutant version of Nsp15, which was crystallized as a hexamer. The structure contains unreported flexibility in the active site of each subunit. Substitutions in the active site residues serine 293 and proline 343 allowed Nsp15 to cleave at cytidylate, whereas mutation of leucine 345 rendered Nsp15 able to cleave at purines as well as pyrimidines. Mutations that targeted the residues involvedmore » in subunit interactions generally resulted in the formation of catalytically inactive monomers. The RNA-binding residues were mapped by a method linking reversible cross-linking, RNA affinity purification, and peptide fingerprinting. Alanine substitution of several residues in the RNA-contacting portion of Nsp15 did not affect hexamer formation but decreased the affinity of RNA binding and reduced endonuclease activity. This suggests a model for Nsp15 hexamer interaction with RNA.« less

Domain repertoires as a tool to derive protein recognition rules.

PubMed

Zucconi, A; Panni, S; Paoluzi, S; Castagnoli, L; Dente, L; Cesareni, G

2000-08-25

Several approaches, some of which are described in this issue, have been proposed to assemble a complete protein interaction map. These are often based on high throughput methods that explore the ability of each gene product to bind any other element of the proteome of the organism. Here we propose that a large number of interactions can be inferred by revealing the rules underlying recognition specificity of a small number (a few hundreds) of families of protein recognition modules. This can be achieved through the construction and characterization of domain repertoires. A domain repertoire is assembled in a combinatorial fashion by allowing each amino acid position in the binding site of a given protein recognition domain to vary to include all the residues allowed at that position in the domain family. The repertoire is then searched by phage display techniques with any target of interest and from the primary structure of the binding site of the selected domains one derives rules that are used to infer the formation of complexes between natural proteins in the cell.

On the molecular interaction between lactoferrin and the dye Red HE-3B. A novel approach for docking a charged and highly flexible molecule to protein surfaces

NASA Astrophysics Data System (ADS)

Grasselli, Mariano; Cascone, Osvaldo; Anspach, F. Birger; Delfino, Jose M.

2002-12-01

Lactoferrin (Lf) is a non-heme, iron binding protein present in many physiological fluids of vertebrates where its main role is the microbicidal activity. It has been isolated by different methods, including dye-affinity chromatography. Red HE-3B is one of the most common triazinic dyes applied in protein purification, but scant knowledge is available on structural details and on the energetics of its interaction with proteins. In this work we present a computational approach useful for identifying possible binding sites for Red HE-3B in apo and holo forms of Lfs from human and bovine source. A new geometrical description of Red HE-3B is introduced which greatly simplifies the conformational analysis. This approach proved to be of particular advantage for addressing conformational ensembles of highly flexible molecules. Predictions from this analysis were correlated with experimentally observed dye-binding sites, as mapped by protection from proteolysis in Red HE-3B/Lf complexes. This method could bear relevance for the screening of possible dye-binding sites in proteins whose structure is known and as a potential tool for the design of engineered protein variants which could be purified by dye-affinity chromatography.

On the molecular interaction between lactoferrin and the dye Red HE-3b. A novel approach for docking a charged and highly flexible molecule to protein surfaces.

PubMed

Grasselli, Mariano; Cascone, Osvaldo; Birger Anspach, F; Delfino, Jose M

2002-12-01

Lactoferrin (Lf) is a non-heme, iron binding protein present in many physiological fluids of vertebrates where its main role is the microbicidal activity. It has been isolated by different methods, including dye-affinity chromatography. Red HE-3B is one of the most common triazinic dyes applied in protein purification, but scant knowledge is available on structural details and on the energetics of its interaction with proteins. In this work we present a computational approach useful for identifying possible binding sites for Red HE-3B in apo and holo forms of Lfs from human and bovine source. A new geometrical description of Red HE-3B is introduced which greatly simplifies the conformational analysis. This approach proved to be of particular advantage for addressing conformational ensembles of highly flexible molecules. Predictions from this analysis were correlated with experimentally observed dye-binding sites, as mapped by protection from proteolysis in Red HE-3B/Lf complexes. This method could bear relevance for the screening of possible dye-binding sites in proteins whose structure is known and as a potential tool for the design of engineered protein variants which could be purified by dye-affinity chromatography.

Imaging of drug loading distributions in individual microspheres of calcium silicate hydrate - an X-ray spectromicroscopy study

NASA Astrophysics Data System (ADS)

Guo, Xiaoxuan; Wang, Zhiqiang; Wu, Jin; Wang, Jian; Zhu, Ying-Jie; Sham, Tsun-Kong

2015-04-01

Imaging is one of the most direct and ideal ways to track drug loading distributions in drug carriers on the molecular level, which will facilitate the optimization of drug carriers and drug loading capacities. Herein, we report the mapping of an individual mesoporous calcium silicate hydrate (CSH) microsphere before and after the loading of ibuprofen (IBU) and the interactions between drug carriers and drug molecules simultaneously by scanning transmission X-ray microscopy (STXM). Nanoscaled X-ray absorption near edge structure (XANES) spectroscopy clearly indicates that IBU is bonded to calcium and silicate sites via carboxylic acid groups. More importantly, STXM has been successfully used to determine the absolute thickness of IBU, revealing its distribution in the CSH microsphere.Imaging is one of the most direct and ideal ways to track drug loading distributions in drug carriers on the molecular level, which will facilitate the optimization of drug carriers and drug loading capacities. Herein, we report the mapping of an individual mesoporous calcium silicate hydrate (CSH) microsphere before and after the loading of ibuprofen (IBU) and the interactions between drug carriers and drug molecules simultaneously by scanning transmission X-ray microscopy (STXM). Nanoscaled X-ray absorption near edge structure (XANES) spectroscopy clearly indicates that IBU is bonded to calcium and silicate sites via carboxylic acid groups. More importantly, STXM has been successfully used to determine the absolute thickness of IBU, revealing its distribution in the CSH microsphere. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr07471h

Healthy habits for weight loss

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Regional Topographic Views of Mars from MOLA

NASA Technical Reports Server (NTRS)

2000-01-01

With one year of global mapping of the Mars Global Surveyor mission completed, the MOLA dataset has achieved excellent spatial and vertical resolution. The maps below (and above) have been produced from the altimetric observations collected during MOLA's first year of global mapping and provide a variety of regional topographic views of the Martian surface. The maps were compiled from a data base of 266.7 million laser altimetric measurements collected between March 1, 1999 and February 29, 2000. In each map the spatial resolution is approximately 1/16o by 1/32o (where 1o on Mars is about 59 km) and the vertical accuracy is approximately 1 meter. Note that the sizes of the regions vary. Click on image for to see full resolution (Warning! these are large files) [figure removed for brevity, see original site] Nirgal Vallis region: 23o to 33o S; 313 to 323o E.

[figure removed for brevity, see original site] Locras Valles region: 5o to 15o N; 45 to 55o E.

[figure removed for brevity, see original site] Syrtis Major: 5o to 15o S; 62 to 72o E.

[figure removed for brevity, see original site] Viking 1 landing site: 20o to 25o N; 310 to 315o E. The landing site is marked by the plus sign.

[figure removed for brevity, see original site] Nicholson crater: 5o S to 5o N; 190 to 200o E. [figure removed for brevity, see original site] Schiaparelli crater: 8o S to 2o N; 12 to 22o E.

Interstitial telomeric sequences in human chromosomes cluster with common fragile sites, mutagen sensitive sites, viral integration sites, cancer breakpoints, proto-oncogenes and breakpoints involved in primate evolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adekunle, S.S.A.; Wyandt, H.; Mark, H.F.L.

1994-09-01

Recently we mapped the telomeric repeat sequences to 111 interstitial sites in the human genome and to sites of gaps and breaks induced by aphidicolin and sister chromatid exchange sites detected by BrdU. Many of these sites correspond to conserved fragile sites in man, gorilla and chimpazee, to sites of conserved sister chromatid exchange in the mammalian X chromosome, to mutagenic sensitive sites, mapped locations of proto-oncogenes, breakpoints implicated in primate evolution and to breakpoints indicated as the sole anomaly in neoplasia. This observation prompted us to investigate if the interstitial telomeric sites cluster with these sites. An extensive literaturemore » search was carried out to find all the available published sites mentioned above. For comparison, we also carried out a statistical analysis of the clustering of the sites of the telomeric repeats with the gene locations where only nucleotide mutations have been observed as the only chromosomal abnormality. Our results indicate that the telomeric repeats cluster most with fragile sites, mutagenic sensitive sites and breakpoints implicated in primate evolution and least with cancer breakpoints, mapped locations of proto-oncogenes and other genes with nucleotide mutations.« less

Quantification of map similarity to magnetic pre-screening for heavy metal pollution assessment in top soil

NASA Astrophysics Data System (ADS)

Cao, L.; Appel, E.; Roesler, W.; Ojha, G.

2013-12-01

From numerous published results, the link between magnetic concentration and heavy metal (HM) concentrations is well established. However, bivariate correlation analysis does not imply causality, and if there are extreme values, which often appear in magnetic data, they can lead to seemingly excellent correlation. It seems clear that site selection for chemical sampling based on magnetic pre-screening can deliver a superior result for outlining HM pollution, but this conclusion has only been drawn from qualitative evaluation so far. In this study, we use map similarity comparison techniques to demonstrate the usefulness of a combined magnetic-chemical approach quantitatively. We chose available data around the 'Schwarze Pumpe', a large coal burning power plant complex located in eastern Germany. The site of 'Schwarze Pumpe' is suitable for a demonstration study as soil in its surrounding is heavy fly-ash polluted, the magnetic natural background is very low, and magnetic investigations can be done in undisturbed forest soil. Magnetic susceptibility (MS) of top soil was measured by a Bartington MS2D surface sensor at 180 locations and by a SM400 downhole device in ~0.5m deep vertical sections at 90 locations. Cores from the 90 downhole sites were also studied for HM analysis. From these results 85 sites could be used to determine a spatial distribution map of HM contents reflecting the 'True' situation of pollution. Different sets comprising 30 sites were chosen by arbitrarily selection from the above 85 sample sites (we refer to four such maps here: S1-4). Additionally, we determined a 'Targeted' map from 30 sites selected on the basis of the pre-screening MS results. The map comparison process is as follows: (1) categorization of all absolute values into five classes by the Natural Breaks classification method; (2) use Delaunay triangulation for connecting the sample locations in the x-y plane; (3) determination of a distribution map of triangular planes with classified values as the Z coordinate; (4) calculation of normal vectors for each individual triangular plane; (5)transformation to the TINs into raster data assigning the same normal vectors to all grid-points which are inside the same TIN; (6) calculation of the root-mean-square of angles between normal vectors of two maps at the same grid points. Additionally, we applied the kappa statistics method to assess map similarities, and moreover developed a Fuzzy set approach. Combining both methods using indices of Khisto, Klocation, Kappa, Kfuzzy obtains a broad comparison system, which allows determining the degree of similarity and also the spatial distribution of similarity between two maps. The results indicate that the similarity between the 'Targeted' and 'True' distribution map is higher than that between 'S1-4' and the 'True' map. It manifests that magnetic pre-screening can provide a reliable basis for targeted selection of chemical sampling sites demonstrating the superior efficiency of a combined magnetic-chemical site assessment in comparison to a traditional chemical-only approach.

Coevolution study of mitochondria respiratory chain proteins: toward the understanding of protein--protein interaction.

PubMed

Yang, Ming; Ge, Yan; Wu, Jiayan; Xiao, Jingfa; Yu, Jun

2011-05-20

Coevolution can be seen as the interdependency between evolutionary histories. In the context of protein evolution, functional correlation proteins are ever-present coordinated evolutionary characters without disruption of organismal integrity. As to complex system, there are two forms of protein--protein interactions in vivo, which refer to inter-complex interaction and intra-complex interaction. In this paper, we studied the difference of coevolution characters between inter-complex interaction and intra-complex interaction using "Mirror tree" method on the respiratory chain (RC) proteins. We divided the correlation coefficients of every pairwise RC proteins into two groups corresponding to the binary protein--protein interaction in intra-complex and the binary protein--protein interaction in inter-complex, respectively. A dramatical discrepancy is detected between the coevolution characters of the two sets of protein interactions (Wilcoxon test, p-value = 4.4 × 10(-6)). Our finding reveals some critical information on coevolutionary study and assists the mechanical investigation of protein--protein interaction. Furthermore, the results also provide some unique clue for supramolecular organization of protein complexes in the mitochondrial inner membrane. More detailed binding sites map and genome information of nuclear encoded RC proteins will be extraordinary valuable for the further mitochondria dynamics study. Copyright © 2011. Published by Elsevier Ltd.

SLX4 Assembles a Telomere Maintenance Toolkit by Bridging Multiple Endonucleases with Telomeres

PubMed Central

Wan, Bingbing; Yin, Jinhu; Horvath, Kent; Sarkar, Jaya; Chen, Yong; Wu, Jian; Wan, Ke; Lu, Jian; Gu, Peili; Yu, Eun Young; Lue, Neal F.; Chang, Sandy

2014-01-01

Summary SLX4 interacts with several endonucleases to resolve structural barriers in DNA metabolism. SLX4 also interacts with telomeric protein TRF2 in human cells. The molecular mechanism of these interactions at telomeres remains unknown. Here, we report the crystal structure of the TRF2-binding motif of SLX4 (SLX4TBM) in complex with the TRFH domain of TRF2 (TRF2TRFH) and map the interactions of SLX4 with endonucleases SLX1, XPF, and MUS81. TRF2 recognizes a unique HxLxP motif on SLX4 via the peptide-binding site in its TRFH domain. Telomeric localization of SLX4 and associated nucleases depend on the SLX4-endonuclease and SLX4-TRF2 interactions and the protein levels of SLX4 and TRF2. SLX4 assembles an endonuclease toolkit that negatively regulates telomere length via SLX1-catalyzed nucleolytic resolution of telomere DNA structures. We propose that the SLX4-TRF2 complex serves as a double-layer scaffold bridging multiple endonucleases with telomeres for recombination-based telomere maintenance. PMID:24012755

Exact ground states and topological order in interacting Kitaev/Majorana chains

NASA Astrophysics Data System (ADS)

Katsura, Hosho; Schuricht, Dirk; Takahashi, Masahiro

2015-09-01

We study a system of interacting spinless fermions in one dimension that, in the absence of interactions, reduces to the Kitaev chain [Kitaev, Phys. Usp. 44, 131 (2001), 10.1070/1063-7869/44/10S/S29]. In the noninteracting case, a signal of topological order appears as zero-energy modes localized near the edges. We show that the exact ground states can be obtained analytically even in the presence of nearest-neighbor repulsive interactions when the on-site (chemical) potential is tuned to a particular function of the other parameters. As with the noninteracting case, the obtained ground states are twofold degenerate and differ in fermionic parity. We prove the uniqueness of the obtained ground states and show that they can be continuously deformed to the ground states of the noninteracting Kitaev chain without gap closing. We also demonstrate explicitly that there exists a set of operators each of which maps one of the ground states to the other with opposite fermionic parity. These operators can be thought of as an interacting generalization of Majorana edge zero modes.

Evaluation of Structural Isomers, Molecular Interactions, Reactivity Descriptors, and Vibrational Analysis of Tretinoin.

PubMed

Karthick, T; Tandon, Poonam; Singh, Swapnil

2017-01-01

Tretinoin is known to be a pharmaceutical drug for treating acne vulgaris, keratosis pilaris, and acute promyelocytic leukemia. In order to reveal the possible conformers of tretinoin, the energies of all the conformers through rotational bonds have been evaluated by systematic rotor search analysis. The intramolecular interactions ranging from strong hydrogen bonds to weak van der Waals forces present in tretinoin have been distinguished with the help of electron density mapping and wavefunction analysis. The global reactivity descriptors and Fukui functions of tretinoin have been calculated and discussed. The sites suitable for electrophilic attack and nucleophilic attack have been identified with the help of Hirshfeld partitioning. The vibrational spectroscopic signature of tretinoin and mixed mode band assignments have been elucidated with the help of experimental and simulated spectra.

Multivariate spatiotemporal visualizations for mobile devices in Flyover Country

NASA Astrophysics Data System (ADS)

Loeffler, S.; Thorn, R.; Myrbo, A.; Roth, R.; Goring, S. J.; Williams, J.

2017-12-01

Visualizing and interacting with complex multivariate and spatiotemporal datasets on mobile devices is challenging due to their smaller screens, reduced processing power, and limited data connectivity. Pollen data require visualizing pollen assemblages spatially, temporally, and across multiple taxa to understand plant community dynamics through time. Drawing from cartography, information visualization, and paleoecology, we have created new mobile-first visualization techniques that represent multiple taxa across many sites and enable user interaction. Using pollen datasets from the Neotoma Paleoecology Database as a case study, the visualization techniques allow ecological patterns and trends to be quickly understood on a mobile device compared to traditional pollen diagrams and maps. This flexible visualization system can be used for datasets beyond pollen, with the only requirements being point-based localities and multiple variables changing through time or depth.

Spin-imbalance in a 2D Fermi-Hubbard system

NASA Astrophysics Data System (ADS)

Brown, Peter T.; Mitra, Debayan; Guardado-Sanchez, Elmer; Schauß, Peter; Kondov, Stanimir S.; Khatami, Ehsan; Paiva, Thereza; Trivedi, Nandini; Huse, David A.; Bakr, Waseem S.

2017-09-01

The interplay of strong interactions and magnetic fields gives rise to unusual forms of superconductivity and magnetism in quantum many-body systems. Here, we present an experimental study of the two-dimensional Fermi-Hubbard model—a paradigm for strongly correlated fermions on a lattice—in the presence of a Zeeman field and varying doping. Using site-resolved measurements, we revealed anisotropic antiferromagnetic correlations, a precursor to long-range canted order. We observed nonmonotonic behavior of the local polarization with doping for strong interactions, which we attribute to the evolution from an antiferromagnetic insulator to a metallic phase. Our results pave the way to experimentally mapping the low-temperature phase diagram of the Fermi-Hubbard model as a function of both doping and spin polarization, for which many open questions remain.

Regulation of Stress-Inducible Phosphoprotein 1 Nuclear Retention by Protein Inhibitor of Activated STAT PIAS1

PubMed Central

Soares, Iaci N.; Caetano, Fabiana A.; Pinder, Jordan; Rodrigues, Bruna Roz; Beraldo, Flavio H.; Ostapchenko, Valeriy G.; Durette, Chantal; Pereira, Grace Schenatto; Lopes, Marilene H.; Queiroz-Hazarbassanov, Nicolle; Cunha, Isabela W.; Sanematsu, Paulo I.; Suzuki, Sergio; Bleggi-Torres, Luiz F.; Schild-Poulter, Caroline; Thibault, Pierre; Dellaire, Graham; Martins, Vilma R.; Prado, Vania F.; Prado, Marco A. M.

2013-01-01

Stress-inducible phosphoprotein 1 (STI1), a cochaperone for Hsp90, has been shown to regulate multiple pathways in astrocytes, but its contributions to cellular stress responses are not fully understood. We show that in response to irradiation-mediated DNA damage stress STI1 accumulates in the nucleus of astrocytes. Also, STI1 haploinsufficiency decreases astrocyte survival after irradiation. Using yeast two-hybrid screenings we identified several nuclear proteins as STI1 interactors. Overexpression of one of these interactors, PIAS1, seems to be specifically involved in STI1 nuclear retention and in directing STI1 and Hsp90 to specific sub-nuclear regions. PIAS1 and STI1 co-immunoprecipitate and PIAS1 can function as an E3 SUMO ligase for STI. Using mass spectrometry we identified five SUMOylation sites in STI1. A STI1 mutant lacking these five sites is not SUMOylated, but still accumulates in the nucleus in response to increased expression of PIAS1, suggesting the possibility that a direct interaction with PIAS1 could be responsible for STI1 nuclear retention. To test this possibility, we mapped the interaction sites between PIAS1 and STI1 using yeast-two hybrid assays and surface plasmon resonance and found that a large domain in the N-terminal region of STI1 interacts with high affinity with amino acids 450–480 of PIAS1. Knockdown of PIAS1 in astrocytes impairs the accumulation of nuclear STI1 in response to irradiation. Moreover, a PIAS1 mutant lacking the STI1 binding site is unable to increase STI1 nuclear retention. Interestingly, in human glioblastoma multiforme PIAS1 expression is increased and we found a significant correlation between increased PIAS1 expression and STI1 nuclear localization. These experiments provide evidence that direct interaction between STI1 and PIAS1 is involved in the accumulation of nuclear STI1. This retention mechanism could facilitate nuclear chaperone activity. PMID:23938469

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

PubMed Central

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

2012-01-01

Activation of voltage-gated sodium (Nav) channels initiates and propagates action potentials in electrically excitable cells. β-Scorpion toxins, including toxin IV from Centruroides suffusus suffusus (CssIV), enhance activation of NaV channels. CssIV stabilizes the voltage sensor in domain II in its activated state via a voltage-sensor trapping mechanism. Amino acid residues required for the action of CssIV have been identified in the S1-S2 and S3-S4 extracellular loops of domain II. The extracellular loops of domain III are also involved in toxin action, but individual amino acid residues have not been identified. We used site-directed mutagenesis and voltage clamp recording to investigate amino acid residues of domain III that are involved in CssIV action. In the IIISS2-S6 loop, five substitutions at four positions altered voltage-sensor trapping by CssIVE15A. Three substitutions (E1438A, D1445A, and D1445Y) markedly decreased voltage-sensor trapping, whereas the other two substitutions (N1436G and L1439A) increased voltage-sensor trapping. These bidirectional effects suggest that residues in IIISS2-S6 make both positive and negative interactions with CssIV. N1436G enhanced voltage-sensor trapping via increased binding affinity to the resting state, whereas L1439A increased voltage-sensor trapping efficacy. Based on these results, a three-dimensional model of the toxin-channel interaction was developed using the Rosetta modeling method. These data provide additional molecular insight into the voltage-sensor trapping mechanism of toxin action and define a three-point interaction site for β-scorpion toxins on NaV channels. Binding of α- and β-scorpion toxins to two distinct, pseudo-symmetrically organized receptor sites on NaV channels acts synergistically to modify channel gating and paralyze prey. PMID:22761417

A surface plasmon resonance assay for characterisation and epitope mapping of anti-GLP-1 antibodies.

PubMed

Thomsen, Lasse; Gurevich, Leonid

2018-04-19

The incretin hormone glucagon-like peptide-1 (GLP-1) has been subject to substantial pharmaceutical research regarding the treatment of type 2 diabetes mellitus. However, quantification of GLP-1 levels remains complicated due to the low circulation concentration and concurrent existence of numerous metabolites, homologous peptides, and potentially introduced GLP-1 receptor agonists. Surface plasmon resonance (SPR) facilitates real-time monitoring allowing a more detailed characterisation of the interaction compared with conventional enzyme-linked immunosorbent assays (ELISA). In this paper, we describe the development of the first SPR assays for characterisation of anti-GLP-1 antibodies for ELISA purposes. Binding responses were obtained on covalently immobilised anti-GLP-1 antibodies at 12°C, 25°C, and 40°C and fitted to a biomolecular (1:1) interaction model showing association rates of 1.01 × 10 3 to 4.54 × 10 3  M -1  s -1 and dissociation rates of 3.56 × 10 -5 to 1.56 × 10 -3  s -1 leading to affinities of 35.2 to 344 nM, depending on the temperature. Determination of thermodynamic properties revealed an enthalpy driven interaction (ΔH < ΔS < 0) with higher affinities at lower temperatures due to the formation and stabilisation of hydrogen bonds within the binding site primarily composed of polar amino acids (ΔC p  < 0). Pair-wise epitope mapping was performed on captured anti-GLP-1 antibodies followed by subsequent interaction with GLP-1 (7-36) and other anti-GLP-1 antibodies. A global evaluation of every binding response led to an epitope map elucidating the potential of various anti-GLP-1 antibody pairs for sandwich ELISA and hence pinpointing the optimal antibody combinations. The SPR assays proved capable of providing vital information for ELISA development endorsing it as a useful optimisation tool. Copyright © 2018 John Wiley & Sons, Ltd.

Oncoprotein AEG-1 is an endoplasmic reticulum RNA-binding protein whose interactome is enriched in organelle resident protein-encoding mRNAs.

PubMed

Hsu, Jack C-C; Reid, David W; Hoffman, Alyson M; Sarkar, Devanand; Nicchitta, Christopher V

2018-05-01

Astrocyte elevated gene-1 (AEG-1), an oncogene whose overexpression promotes tumor cell proliferation, angiogenesis, invasion, and enhanced chemoresistance, is thought to function primarily as a scaffolding protein, regulating PI3K/Akt and Wnt/β-catenin signaling pathways. Here we report that AEG-1 is an endoplasmic reticulum (ER) resident integral membrane RNA-binding protein (RBP). Examination of the AEG-1 RNA interactome by HITS-CLIP and PAR-CLIP methodologies revealed a high enrichment for endomembrane organelle-encoding transcripts, most prominently those encoding ER resident proteins, and within this cohort, for integral membrane protein-encoding RNAs. Cluster mapping of the AEG-1/RNA interaction sites demonstrated a normalized rank order interaction of coding sequence >5' untranslated region, with 3' untranslated region interactions only weakly represented. Intriguingly, AEG-1/membrane protein mRNA interaction sites clustered downstream from encoded transmembrane domains, suggestive of a role in membrane protein biogenesis. Secretory and cytosolic protein-encoding mRNAs were also represented in the AEG-1 RNA interactome, with the latter category notably enriched in genes functioning in mRNA localization, translational regulation, and RNA quality control. Bioinformatic analyses of RNA-binding motifs and predicted secondary structure characteristics indicate that AEG-1 lacks established RNA-binding sites though shares the property of high intrinsic disorder commonly seen in RBPs. These data implicate AEG-1 in the localization and regulation of secretory and membrane protein-encoding mRNAs and provide a framework for understanding AEG-1 function in health and disease. © 2018 Hsu et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Structure-function analysis of the extracellular domain of the pneumococcal cell division site positioning protein MapZ

NASA Astrophysics Data System (ADS)

Manuse, Sylvie; Jean, Nicolas L.; Guinot, Mégane; Lavergne, Jean-Pierre; Laguri, Cédric; Bougault, Catherine M.; Vannieuwenhze, Michael S.; Grangeasse, Christophe; Simorre, Jean-Pierre

2016-06-01

Accurate placement of the bacterial division site is a prerequisite for the generation of two viable and identical daughter cells. In Streptococcus pneumoniae, the positive regulatory mechanism involving the membrane protein MapZ positions precisely the conserved cell division protein FtsZ at the cell centre. Here we characterize the structure of the extracellular domain of MapZ and show that it displays a bi-modular structure composed of two subdomains separated by a flexible serine-rich linker. We further demonstrate in vivo that the N-terminal subdomain serves as a pedestal for the C-terminal subdomain, which determines the ability of MapZ to mark the division site. The C-terminal subdomain displays a patch of conserved amino acids and we show that this patch defines a structural motif crucial for MapZ function. Altogether, this structure-function analysis of MapZ provides the first molecular characterization of a positive regulatory process of bacterial cell division.

Structure of the Nucleoprotein Binding Domain of Mokola Virus Phosphoprotein▿

PubMed Central

Assenberg, René; Delmas, Olivier; Ren, Jingshan; Vidalain, Pierre-Olivier; Verma, Anil; Larrous, Florence; Graham, Stephen C.; Tangy, Frédéric; Grimes, Jonathan M.; Bourhy, Hervé

2010-01-01

Mokola virus (MOKV) is a nonsegmented, negative-sense RNA virus that belongs to the Lyssavirus genus and Rhabdoviridae family. MOKV phosphoprotein P is an essential component of the replication and transcription complex and acts as a cofactor for the viral RNA-dependent RNA polymerase. P recruits the viral polymerase to the nucleoprotein-bound viral RNA (N-RNA) via an interaction between its C-terminal domain and the N-RNA complex. Here we present a structure for this domain of MOKV P, obtained by expression of full-length P in Escherichia coli, which was subsequently truncated during crystallization. The structure has a high degree of homology with P of rabies virus, another member of Lyssavirus genus, and to a lesser degree with P of vesicular stomatitis virus (VSV), a member of the related Vesiculovirus genus. In addition, analysis of the crystal packing of this domain reveals a potential binding site for the nucleoprotein N. Using both site-directed mutagenesis and yeast two-hybrid experiments to measure P-N interaction, we have determined the relative roles of key amino acids involved in this interaction to map the region of P that binds N. This analysis also reveals a structural relationship between the N-RNA binding domain of the P proteins of the Rhabdoviridae and the Paramyxoviridae. PMID:19906936

Engaging Undergraduate Math Majors in Geoscience Research using Interactive Simulations and Computer Art

NASA Astrophysics Data System (ADS)

Matott, L. S.; Hymiak, B.; Reslink, C. F.; Baxter, C.; Aziz, S.

2012-12-01

As part of the NSF-sponsored 'URGE (Undergraduate Research Group Experiences) to Compute' program, Dr. Matott has been collaborating with talented Math majors to explore the design of cost-effective systems to safeguard groundwater supplies from contaminated sites. Such activity is aided by a combination of groundwater modeling, simulation-based optimization, and high-performance computing - disciplines largely unfamiliar to the students at the outset of the program. To help train and engage the students, a number of interactive and graphical software packages were utilized. Examples include: (1) a tutorial for exploring the behavior of evolutionary algorithms and other heuristic optimizers commonly used in simulation-based optimization; (2) an interactive groundwater modeling package for exploring alternative pump-and-treat containment scenarios at a contaminated site in Billings, Montana; (3) the R software package for visualizing various concepts related to subsurface hydrology; and (4) a job visualization tool for exploring the behavior of numerical experiments run on a large distributed computing cluster. Further engagement and excitement in the program was fostered by entering (and winning) a computer art competition run by the Coalition for Academic Scientific Computation (CASC). The winning submission visualizes an exhaustively mapped optimization cost surface and dramatically illustrates the phenomena of artificial minima - valley locations that correspond to designs whose costs are only partially optimal.

Physical and Functional Interaction between the Eukaryotic Orthologs of Prokaryotic Translation Initiation Factors IF1 and IF2

PubMed Central

Choi, Sang Ki; Olsen, DeAnne S.; Roll-Mecak, Antonina; Martung, Agnes; Remo, Keith L.; Burley, Stephen K.; Hinnebusch, Alan G.; Dever, Thomas E.

2000-01-01

To initiate protein synthesis, a ribosome with bound initiator methionyl-tRNA must be assembled at the start codon of an mRNA. This process requires the coordinated activities of three translation initiation factors (IF) in prokaryotes and at least 12 translation initiation factors in eukaryotes (eIF). The factors eIF1A and eIF5B from eukaryotes show extensive amino acid sequence similarity to the factors IF1 and IF2 from prokaryotes. By a combination of two-hybrid, coimmunoprecipitation, and in vitro binding assays eIF1A and eIF5B were found to interact directly, and the eIF1A binding site was mapped to the C-terminal region of eIF5B. This portion of eIF5B was found to be critical for growth in vivo and for translation in vitro. Overexpression of eIF1A exacerbated the slow-growth phenotype of yeast strains expressing C-terminally truncated eIF5B. These findings indicate that the physical interaction between the evolutionarily conserved factors eIF1A and eIF5B plays an important role in translation initiation, perhaps to direct or stabilize the binding of methionyl-tRNA to the ribosomal P site. PMID:10982835

Calculating Water Thermodynamics in the Binding Site of Proteins - Applications of WaterMap to Drug Discovery.

PubMed

Cappel, Daniel; Sherman, Woody; Beuming, Thijs

2017-01-01

The ability to accurately characterize the solvation properties (water locations and thermodynamics) of biomolecules is of great importance to drug discovery. While crystallography, NMR, and other experimental techniques can assist in determining the structure of water networks in proteins and protein-ligand complexes, most water molecules are not fully resolved and accurately placed. Furthermore, understanding the energetic effects of solvation and desolvation on binding requires an analysis of the thermodynamic properties of solvent involved in the interaction between ligands and proteins. WaterMap is a molecular dynamics-based computational method that uses statistical mechanics to describe the thermodynamic properties (entropy, enthalpy, and free energy) of water molecules at the surface of proteins. This method can be used to assess the solvent contributions to ligand binding affinity and to guide lead optimization. In this review, we provide a comprehensive summary of published uses of WaterMap, including applications to lead optimization, virtual screening, selectivity analysis, ligand pose prediction, and druggability assessment. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Land use and environmental assessment in the central Atlantic region

NASA Technical Reports Server (NTRS)

Alexander, R. H.; Fitzpatrick, K.; Lins, H. F., Jr.; Mcginty, H. K., III

1975-01-01

Data from high altitude aircraft, LANDSAT and Skylab were used in a comprehensive regional survey of land use and its associated environmental impact in the Central Atlantic Regional Ecological Test Site (CARETS). Each sensor system has advantages that were demonstrated by producing experimental land use maps and other data products, applying them to typical problems encountered in regional planning and environmental impact assessment, and presenting the results to prospective users for evaluation. An archival collection of imagery, maps, data summaries, and technical reports was assembled, constituting an environmental profile of the central Atlantic region. The investigation was organized into four closely-related modules, a land use information module, an environmental impact module, a user interaction and evaluation module, and a geographic information systems module. Results revealed a heterogeneous user community with diverse information needs, tending, however, definitely toward the higher-resolution sensor data and the larger-scale land use maps and related information products. Among project recommendations are greater efforts toward improving compatibility of federal, state, and local land use information programs, and greater efforts toward a broader exchange of imagery, computer tapes, and land use information derived therefrom.

Chapter 4: The GIS Project for the Geologic Assessment of Undiscovered Oil and Gas in the Upper Cretaceous Navarro and Taylor Groups, Western Gulf Province, Texas

USGS Publications Warehouse

Biewick, Laura

2006-01-01

A geographic information system (GIS) focusing on the Upper Cretaceous Navarro and Taylor Groups in the Gulf Coast region was developed as a visual-analysis tool for the U.S. Geological Survey's 2003 assessment of undiscovered, technically recoverable oil and natural gas resources in the Western Gulf Province. The Central Energy Resources Team of the U.S. Geological Survey has also developed an Internet Map Service to deliver the GIS data to the general public. This mapping tool utilizes information from a database about the oil and natural gas endowment of the United States - including physical locations of geologic and geographic data - and converts the data into visual layers. Portrayal and analysis of geologic features on an interactive map provide an excellent tool for understanding domestic oil and gas resources for strategic planning, formulating economic and energy policies, evaluating lands under the purview of the Federal Government, and developing sound environmental policies. Assessment results can be viewed and analyzed or downloaded from the internet web site.

Protostellar Outflows Mapped with ALMA and Techniques to Include Short Spacings

NASA Astrophysics Data System (ADS)

Plunkett, Adele

2018-01-01

Protostellar outflows are early signs of star formation, yet in cluster environments - common sites of star formation - their role and interaction with surrounding gas are complicated. Protostellar outflows are interesting and complex because they connect protostars (scales 10s au) to the surrounding gas environment (few pc), and their morphology constrains launching and/or accretion modes. A complete outflow study must use observing methods that recover several orders of magnitude of spatial scales, ideally with sub-arcsecond resolution and mapping over a few parsecs. ALMA provides high-resolution observations of outflows, and in some cases outflows have been mapped in clusters. Combining with observations using the Total Power array is possible, but challenging, and a large single dish telescope providing more overlap in uv space is advantageous. In this presentation I show protostellar outflows observed with ALMA using 12m, 7m, and To tal Power arrays. With a new CASA tool TP2VIS we create total power ``visibility'' data and perform joint imaging and deconvolution of interferometry and single dish data. TP2VIS will ultimately provide synergy between ALMA and AtLAST data.

A Three-Dimensional Model of the Yeast Genome

NASA Astrophysics Data System (ADS)

Noble, William; Duan, Zhi-Jun; Andronescu, Mirela; Schutz, Kevin; McIlwain, Sean; Kim, Yoo Jung; Lee, Choli; Shendure, Jay; Fields, Stanley; Blau, C. Anthony

Layered on top of information conveyed by DNA sequence and chromatin are higher order structures that encompass portions of chromosomes, entire chromosomes, and even whole genomes. Interphase chromosomes are not positioned randomly within the nucleus, but instead adopt preferred conformations. Disparate DNA elements co-localize into functionally defined aggregates or factories for transcription and DNA replication. In budding yeast, Drosophila and many other eukaryotes, chromosomes adopt a Rabl configuration, with arms extending from centromeres adjacent to the spindle pole body to telomeres that abut the nuclear envelope. Nonetheless, the topologies and spatial relationships of chromosomes remain poorly understood. Here we developed a method to globally capture intra- and inter-chromosomal interactions, and applied it to generate a map at kilobase resolution of the haploid genome of Saccharomyces cerevisiae. The map recapitulates known features of genome organization, thereby validating the method, and identifies new features. Extensive regional and higher order folding of individual chromosomes is observed. Chromosome XII exhibits a striking conformation that implicates the nucleolus as a formidable barrier to interaction between DNA sequences at either end. Inter-chromosomal contacts are anchored by centromeres and include interactions among transfer RNA genes, among origins of early DNA replication and among sites where chromosomal breakpoints occur. Finally, we constructed a three-dimensional model of the yeast genome. Our findings provide a glimpse of the interface between the form and function of a eukaryotic genome.

Image Analysis for Facility Siting: a Comparison of Lowand High-altitude Image Interpretability for Land Use/land Cover Mapping

NASA Technical Reports Server (NTRS)

Borella, H. M.; Estes, J. E.; Ezra, C. E.; Scepan, J.; Tinney, L. R.

1982-01-01

For two test sites in Pennsylvania the interpretability of commercially acquired low-altitude and existing high-altitude aerial photography are documented in terms of time, costs, and accuracy for Anderson Level II land use/land cover mapping. Information extracted from the imagery is to be used in the evaluation process for siting energy facilities. Land use/land cover maps were drawn at 1:24,000 scale using commercially flown color infrared photography obtained from the United States Geological Surveys' EROS Data Center. Detailed accuracy assessment of the maps generated by manual image analysis was accomplished employing a stratified unaligned adequate class representation. Both 'area-weighted' and 'by-class' accuracies were documented and field-verified. A discrepancy map was also drawn to illustrate differences in classifications between the two map scales. Results show that the 1:24,000 scale map set was more accurate (99% to 94% area-weighted) than the 1:62,500 scale set, especially when sampled by class (96% to 66%). The 1:24,000 scale maps were also more time-consuming and costly to produce, due mainly to higher image acquisition costs.

National Park Service Vegetation Mapping Inventory Program: Appalachian National Scenic Trail vegetation mapping project

USGS Publications Warehouse

Hop, Kevin D.; Strassman, Andrew C.; Hall, Mark; Menard, Shannon; Largay, Ery; Sattler, Stephanie; Hoy, Erin E.; Ruhser, Janis; Hlavacek, Enrika; Dieck, Jennifer

2017-01-01

The National Park Service (NPS) Vegetation Mapping Inventory (VMI) Program classifies, describes, and maps existing vegetation of national park units for the NPS Natural Resource Inventory and Monitoring (I&M) Program. The NPS VMI Program is managed by the NPS I&M Division and provides baseline vegetation information to the NPS Natural Resource I&M Program. The U.S. Geological Survey Upper Midwest Environmental Sciences Center, NatureServe, NPS Northeast Temperate Network, and NPS Appalachian National Scenic Trail (APPA) have completed vegetation classification and mapping of APPA for the NPS VMI Program.Mappers, ecologists, and botanists collaborated to affirm vegetation types within the U.S. National Vegetation Classification (USNVC) of APPA and to determine how best to map the vegetation types by using aerial imagery. Analyses of data from 1,618 vegetation plots were used to describe USNVC associations of APPA. Data from 289 verification sites were collected to test the field key to vegetation associations and the application of vegetation associations to a sample set of map polygons. Data from 269 validation sites were collected to assess vegetation mapping prior to submitting the vegetation map for accuracy assessment (AA). Data from 3,265 AA sites were collected, of which 3,204 were used to test accuracy of the vegetation map layer. The collective of these datasets affirmed 280 USNVC associations for the APPA vegetation mapping project.To map the vegetation and land cover of APPA, 169 map classes were developed. The 169 map classes consist of 150 that represent natural (including ruderal) vegetation types in the USNVC, 11 that represent cultural (agricultural and developed) vegetation types in the USNVC, 5 that represent natural landscapes with catastrophic disturbance or some other modification to natural vegetation preventing accurate classification in the USNVC, and 3 that represent nonvegetated water (non-USNVC). Features were interpreted from viewing 4-band digital aerial imagery using digital onscreen three-dimensional stereoscopic workflow systems in geographic information systems (GIS). (Digital aerial imagery was collected each fall during 2009–11 to capture leaf-phenology change of hardwood trees across the latitudinal range of APPA.) The interpreted data were digitally and spatially referenced, thus making the spatial-database layers usable in GIS. Polygon units were mapped to either a 0.5-hectare (ha) or 0.25-ha minimum mapping unit, depending on vegetation type or scenario; however, polygon units were mapped to 0.1 ha for alpine vegetation.A geodatabase containing various feature-class layers and tables provide locations and support data to USNVC vegetation types (vegetation map layer), vegetation plots, verification sites, validation sites, AA sites, project boundary extent and zones, and aerial image centers and flight lines. The feature-class layer and related tables of the vegetation map layer provide 30,395 polygons of detailed attribute data covering 110,919.7 ha, with an average polygon size of 3.6 ha; the vegetation map coincides closely with the administrative boundary for APPA.Summary reports generated from the vegetation map layer of the map classes representing USNVC natural (including ruderal) vegetation types apply to 28,242 polygons (92.9% of polygons) and cover 106,413.0 ha (95.9%) of the map extent for APPA. The map layer indicates APPA to be 92.4% forest and woodland (102,480.8 ha), 1.7% shrubland (1866.3 ha), and 1.8% herbaceous cover (2,065.9 ha). Map classes representing park-special vegetation (undefined in the USNVC) apply to 58 polygons (0.2% of polygons) and cover 404.3 ha (0.4%) of the map extent. Map classes representing USNVC cultural types apply to 1,777 polygons (5.8% of polygons) and cover 2,516.3 ha (2.3%) of the map extent. Map classes representing nonvegetated water (non-USNVC) apply to 332 polygons (1.1% of polygons) and cover 1,586.2 ha (1.4%) of the map extent.

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

USGS Publications Warehouse

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

2001-01-01

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

Independent mapping methods reveal rotational activation near pulmonary veins where atrial fibrillation terminates before pulmonary vein isolation.

PubMed

Navara, Rachita; Leef, George; Shenasa, Fatemah; Kowalewski, Christopher; Rogers, Albert J; Meckler, Gabriela; Zaman, Junaid A B; Baykaner, Tina; Park, Shirley; Turakhia, Mintu P; Zei, Paul; Viswanathan, Mohan; Wang, Paul J; Narayan, Sanjiv M

2018-01-29

To investigate mechanisms by which atrial fibrillation (AF) may terminate during ablation near the pulmonary veins before the veins are isolated (PVI). It remains unstudied how AF may terminate during ablation before PVs are isolated, or how patients with PV reconnection can be arrhythmia-free. We studied patients in whom PV antral ablation terminated AF before PVI, using two independent mapping methods. We studied patients with AF referred for ablation, in whom biatrial contact basket electrograms were studied by both an activation/phase mapping method and by a second validated mapping method reported not to create false rotational activity. In 22 patients (age 60.1 ± 10.4, 36% persistent AF), ablation at sites near the PVs terminated AF (77% to sinus rhythm) prior to PVI. AF propagation revealed rotational (n  =  20) and focal (n  =  2) patterns at sites of termination by mapping method 1 and method 2. Both methods showed organized sites that were spatially concordant (P < 0.001) with similar stability (P < 0.001). Vagal slowing was not observed at sites of AF termination. PV antral regions where ablation terminated AF before PVI exhibited rotational and focal activation by two independent mapping methods. These data provide an alternative mechanism for the success of PVI, and may explain AF termination before PVI or lack of arrhythmias despite PV reconnection. Mapping such sites may enable targeted PV lesion sets and improved freedom from AF. © 2018 Wiley Periodicals, Inc.

Cancer--Living with Cancer: MedlinePlus Health Topic

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Selecting PPE for the Workplace (Personal Protective Equipment for the Eyes and Face)

MedlinePlus

... Additional References Site Map Credits Selecting Personal Protective Equipment (PPE) for the Workplace Impact Heat Chemicals Dust Optical Radiation OSHA Requirements Home | Selecting Personal Protective Equipment (PPE) for the Workplace | OSHA Requirements Site Map | ...

Functional Interaction Map of Lyssavirus Phosphoprotein: Identification of the Minimal Transcription Domains

PubMed Central

Jacob, Yves; Real, Eléonore; Tordo, Noël

2001-01-01

Lyssaviruses, the causative agents of rabies encephalitis, are distributed in seven genotypes. The phylogenetically distant rabies virus (PV strain, genotype 1) and Mokola virus (genotype 3) were used to develop a strategy to identify functional homologous interactive domains from two proteins (P and N) which participate in the viral ribonucleoprotein (RNP) transcription-replication complex. This strategy combined two-hybrid and green fluorescent protein–reverse two-hybrid assays in Saccharomyces cerevisiae to analyze protein-protein interactions and a reverse genetic assay in mammalian cells to study the transcriptional activity of the reconstituted RNP complex. Lyssavirus P proteins contain two N-binding domains (N-BDs), a strong one encompassing amino acid (aa) 176 to the C terminus and a weak one in the 189 N-terminal aa. The N-terminal portion of P (aa 52 to 189) also contains a homomultimerization site. Here we demonstrate that N-P interactions, although weaker, are maintained between proteins of the different genotypes. A minimal transcriptional module of the P protein was obtained by fusing the first 60 N-terminal aa containing the L protein binding site to the C-terminal strong N-BD. Random mutation of the strong N-BD on P protein identified three highly conserved K residues crucial for N-P interaction. Their mutagenesis in full-length P induced a transcriptionally defective RNP. The analysis of homologous interactive domains presented here and previously reported dissections of the P protein allowed us to propose a model of the functional interaction network of the lyssavirus P protein. This model underscores the central role of P at the interface between L protein and N-RNA template. PMID:11559793

Epicardial-endocardial breakthrough during stable atrial macroreentry: Evidence from ultra-high-resolution 3-dimensional mapping.

PubMed

Pathik, Bhupesh; Lee, Geoffrey; Sacher, Frédéric; Haïssaguerre, Michel; Jaïs, Pierre; Massoullié, Grégoire; Derval, Nicolas; Sanders, Prashanthan; Kistler, Peter; Kalman, Jonathan M

2017-08-01

Evidence for epicardial-endocardial breakthrough (EEB) is derived from mapping inferences in patients with atrial fibrillation who may also have focal activations. The purpose of this study was to investigate whether EEB could be discerned during stable right atrial (RA) macroreentry using high-density high-spatial resolution 3-dimensional mapping. Macroreentry was diagnosed using 3-dimensional mapping and entrainment. Bipolar maps were reviewed for EEB defined as (1) presence of focal endocardial activation with radial spread unaccounted for by an endocardial wavefront and (2) present with the same timing on every tachycardia cycle. The EEB site was always in proximity to a line of endocardial conduction slowing or block. Distance and conduction velocity from the line of block to the EEB site was calculated. Electrograms at EEB sites were individually analyzed for morphology and to confirm direction of activation. Entrainment was performed at EEB sites. Twenty-six patients were studied. Fourteen examples of EEB were seen: 11 at the posterior RA (4 at the superior portion of the posterior wall and 7 at the inferior section) and 1 each at the cavotricuspid isthmus postablation, RA septum, and inferolateral RA. The mean area of the EEB site was 0.6 ± 0.2 cm 2 . A mean of 79.5% ± 18.6% of unipolar electrograms at the EEB site demonstrated an rS morphology. The mean distance and conduction velocity from the line of endocardial block to the EEB site at the posterior RA was 13.6 ± 2.3 mm and 59.3 ± 12.3 cm/s, respectively. In 4 patients, entrainment demonstrated that EEB sites were within the circuit and in 1 of these patients critical to arrhythmia maintenance. Activation maps during tachycardia and coronary sinus pacing demonstrated EEB at the same anatomic site. EEB sites were demonstrated in stable atrial macroreentry supported by systematic entrainment confirmation and demonstration of the same phenomenon during pacing. Copyright © 2017 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.

Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains

PubMed Central

Brackley, Chris A.; Johnson, James; Kelly, Steven; Cook, Peter R.; Marenduzzo, Davide

2016-01-01

Biophysicists are modeling conformations of interphase chromosomes, often basing the strengths of interactions between segments distant on the genetic map on contact frequencies determined experimentally. Here, instead, we develop a fitting-free, minimal model: bivalent or multivalent red and green ‘transcription factors’ bind to cognate sites in strings of beads (‘chromatin’) to form molecular bridges stabilizing loops. In the absence of additional explicit forces, molecular dynamic simulations reveal that bound factors spontaneously cluster—red with red, green with green, but rarely red with green—to give structures reminiscent of transcription factories. Binding of just two transcription factors (or proteins) to active and inactive regions of human chromosomes yields rosettes, topological domains and contact maps much like those seen experimentally. This emergent ‘bridging-induced attraction’ proves to be a robust, simple and generic force able to organize interphase chromosomes at all scales. PMID:27060145

High resolution fate map of the zebrafish diencephalon.

PubMed

Russek-Blum, Niva; Nabel-Rosen, Helit; Levkowitz, Gil

2009-07-01

The diencephalon acts as an interactive site between the sensory, central, and endocrine systems and is one of the most elaborate structures in the vertebrate brain. To better understand the embryonic development and morphogenesis of the diencephalon, we developed an improved photoactivation (uncaging)-based lineage tracing strategy. To determine the exact position of a given diencephalic progenitor domain, we used a transgenic line driving green fluorescent protein (GFP) in cells expressing the proneural protein, Neurogenin1 (Neurog1), which was used as a visible neural plate landmark. This approach facilitated precise labeling of defined groups of cells in the prospective diencephalon of the zebrafish neural plate. In this manner, we labeled multiple overlapping areas of the diencephalon, thereby ensuring both accuracy and reproducibility of our lineage tracing regardless of the dynamic changes of the developing neural plate. We present a fate map of the zebrafish diencephalon at a higher spatial resolution than previously described. (c) 2009 Wiley-Liss, Inc.

PDBe: towards reusable data delivery infrastructure at protein data bank in Europe

PubMed Central

Alhroub, Younes; Anyango, Stephen; Armstrong, David R; Berrisford, John M; Clark, Alice R; Conroy, Matthew J; Dana, Jose M; Gupta, Deepti; Gutmanas, Aleksandras; Haslam, Pauline; Mak, Lora; Mukhopadhyay, Abhik; Nadzirin, Nurul; Paysan-Lafosse, Typhaine; Sehnal, David; Sen, Sanchayita; Smart, Oliver S; Varadi, Mihaly; Kleywegt, Gerard J

2018-01-01

Abstract The Protein Data Bank in Europe (PDBe, pdbe.org) is actively engaged in the deposition, annotation, remediation, enrichment and dissemination of macromolecular structure data. This paper describes new developments and improvements at PDBe addressing three challenging areas: data enrichment, data dissemination and functional reusability. New features of the PDBe Web site are discussed, including a context dependent menu providing links to raw experimental data and improved presentation of structures solved by hybrid methods. The paper also summarizes the features of the LiteMol suite, which is a set of services enabling fast and interactive 3D visualization of structures, with associated experimental maps, annotations and quality assessment information. We introduce a library of Web components which can be easily reused to port data and functionality available at PDBe to other services. We also introduce updates to the SIFTS resource which maps PDB data to other bioinformatics resources, and the PDBe REST API. PMID:29126160

Disentangling the many layers of eukaryotic transcriptional regulation.

PubMed

Lelli, Katherine M; Slattery, Matthew; Mann, Richard S

2012-01-01

Regulation of gene expression in eukaryotes is an extremely complex process. In this review, we break down several critical steps, emphasizing new data and techniques that have expanded current gene regulatory models. We begin at the level of DNA sequence where cis-regulatory modules (CRMs) provide important regulatory information in the form of transcription factor (TF) binding sites. In this respect, CRMs function as instructional platforms for the assembly of gene regulatory complexes. We discuss multiple mechanisms controlling complex assembly, including cooperative DNA binding, combinatorial codes, and CRM architecture. The second section of this review places CRM assembly in the context of nucleosomes and condensed chromatin. We discuss how DNA accessibility and histone modifications contribute to TF function. Lastly, new advances in chromosomal mapping techniques have provided increased understanding of intra- and interchromosomal interactions. We discuss how these topological maps influence gene regulatory models.

Polaris Undergraduates Connecting With K-12 Students Though Story Telling-Learning About Climate Change Using Web-Mapping Based Investigations

NASA Astrophysics Data System (ADS)

Wood, J. H.; Natali, S.; Schade, J. D.; Fiske, G. J.; Linder, C.; Ramos, E.; Weber, L. R.; Kuhn, M. A.

2014-12-01

The Polaris Project is a unique undergraduate education, research, and outreach initiative that examines global climate change in the Siberian Arctic. The program focuses on permafrost and carbon processes in the boreal and tundra ecosystems of the Kolyma Watershed, the largest watershed underlain by continuous permafrost. Each summer, a diverse group of undergraduate students and faculty mentors spends one month living on the Kolyma River, developing independent projects that engage the students directly in the biogeosciences through authentic scientific research experiences in remote field sites. In all cases the student projects contribute to the overall goal of the Polaris Project to investigate the transport and transformations of carbon and nutrients as they move among terrestrial and aquatic ecosystems and the atmosphere. Through the use of online interactive ArcGIS maps the students share their experiences and learning, while posing questions in a format that can be used to engage K-12 learners in the classroom. By embedding information; including databases, photographs and video, informational text, and geospatial data; into user-friendly maps the Polaris Project students will "tell the story" of studying climate change in the Siberian tundra in a way that allows the users to explore climate science through inquiry and web-map based investigation. Through performance expectation topics including Weather and Climate, Interactions, Earth's Systems, and Human impacts, this investigation uses consideration of the vast amounts of ancient organic matter locked up in permafrost in the region, and concerns about the fate of this ancient organic carbon as temperatures warm and permafrost thaws, to make K-12 climate change connections with the Next Generation Science Standards (NGSS).

Quantifying the uncertainty in site amplification modeling and its effects on site-specific seismic-hazard estimation in the upper Mississippi embayment and adjacent areas

USGS Publications Warehouse

Cramer, C.H.

2006-01-01

The Mississippi embayment, located in the central United States, and its thick deposits of sediments (over 1 km in places) have a large effect on earthquake ground motions. Several previous studies have addressed how these thick sediments might modify probabilistic seismic-hazard maps. The high seismic hazard associated with the New Madrid seismic zone makes it particularly important to quantify the uncertainty in modeling site amplification to better represent earthquake hazard in seismic-hazard maps. The methodology of the Memphis urban seismic-hazard-mapping project (Cramer et al., 2004) is combined with the reference profile approach of Toro and Silva (2001) to better estimate seismic hazard in the Mississippi embayment. Improvements over previous approaches include using the 2002 national seismic-hazard model, fully probabilistic hazard calculations, calibration of site amplification with improved nonlinear soil-response estimates, and estimates of uncertainty. Comparisons are made with the results of several previous studies, and estimates of uncertainty inherent in site-amplification modeling for the upper Mississippi embayment are developed. I present new seismic-hazard maps for the upper Mississippi embayment with the effects of site geology incorporating these uncertainties.

Study of Citizen Scientist Motivations and Effectiveness of Social Media Campaigns

NASA Astrophysics Data System (ADS)

Gugliucci, Nicole E.; Gay, P. L.; Bracey, G.; Lehan, C.; Lewis, S.; Moore, J.; Rhea, J.

2013-01-01

CosmoQuest is an online citizen science and astronomy education portal that invites users to explore the universe. Since its launch in January 2012, several thousand citizen scientists have participated in mapping and discovery projects involving the Moon, the Kuiper Belt, and asteroid Vesta. Since our goal is to support community building as well as involving users with citizen science tasks, we are interested in what motivates users to join the site, participate in the science, participate in the forums, and come back to the site over a period of time. We would also like to efficiently target our social media interactions towards activities that are more likely to bring new and existing users to the site. With those goals in mind, we analyze site usage statistics and correlate them with specific, targeted social media campaigns to highlight events or projects that CosmoQuest has hosted in its first year. We also survey our users to get a more detailed look at citizen scientist motivations and the efficacy of our community building activities.

Detection of Splice Sites Using Support Vector Machine

NASA Astrophysics Data System (ADS)

Varadwaj, Pritish; Purohit, Neetesh; Arora, Bhumika

Automatic identification and annotation of exon and intron region of gene, from DNA sequences has been an important research area in field of computational biology. Several approaches viz. Hidden Markov Model (HMM), Artificial Intelligence (AI) based machine learning and Digital Signal Processing (DSP) techniques have extensively and independently been used by various researchers to cater this challenging task. In this work, we propose a Support Vector Machine based kernel learning approach for detection of splice sites (the exon-intron boundary) in a gene. Electron-Ion Interaction Potential (EIIP) values of nucleotides have been used for mapping character sequences to corresponding numeric sequences. Radial Basis Function (RBF) SVM kernel is trained using EIIP numeric sequences. Furthermore this was tested on test gene dataset for detection of splice site by window (of 12 residues) shifting. Optimum values of window size, various important parameters of SVM kernel have been optimized for a better accuracy. Receiver Operating Characteristic (ROC) curves have been utilized for displaying the sensitivity rate of the classifier and results showed 94.82% accuracy for splice site detection on test dataset.

MedlinePlus - Health Information from the National Library of Medicine

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Map of assessed shale gas in the United States, 2012

USGS Publications Warehouse

,; Biewick, Laura R. H.

2013-01-01

The U.S. Geological Survey has compiled a map of shale-gas assessments in the United States that were completed by 2012 as part of the National Assessment of Oil and Gas Project. Using a geology-based assessment methodology, the U.S. Geological Survey quantitatively estimated potential volumes of undiscovered gas within shale-gas assessment units. These shale-gas assessment units are mapped, and square-mile cells are shown to represent proprietary shale-gas wells. The square-mile cells include gas-producing wells from shale intervals. In some cases, shale-gas formations contain gas in deeper parts of a basin and oil at shallower depths (for example, the Woodford Shale and the Eagle Ford Shale). Because a discussion of shale oil is beyond the scope of this report, only shale-gas assessment units and cells are shown. The map can be printed as a hardcopy map or downloaded for interactive analysis in a Geographic Information System data package using the ArcGIS map document (file extension MXD) and published map file (file extension PMF). Also available is a publications access table with hyperlinks to current U.S. Geological Survey shale gas assessment publications and web pages. Assessment results and geologic reports are available as completed at the U.S. Geological Survey Energy Resources Program Web Site, http://energy.usgs.gov/OilGas/AssessmentsData/NationalOilGasAssessment.aspx. A historical perspective of shale gas activity in the United States is documented and presented in a video clip included as a PowerPoint slideshow.

The Structural Interface between HIV-1 Vif and Human APOBEC3H.

PubMed

Ooms, Marcel; Letko, Michael; Simon, Viviana

2017-03-01

Human APOBEC3H (A3H) is a cytidine deaminase that inhibits HIV-1 replication. To evade this restriction, the HIV-1 Vif protein binds A3H and mediates its proteasomal degradation. To date, little information on the Vif-A3H interface has been available. To decipher how both proteins interact, we first mapped the Vif-binding site on A3H by functionally testing a large set of A3H mutants in single-cycle infectivity and replication assays. Our data show that the two A3H α-helixes α3 and α4 represent the Vif-binding site of A3H. We next used viral adaptation and a set of Vif mutants to identify novel, reciprocal Vif variants that rescued viral infectivity in the presence of two Vif-resistant A3H mutants. These A3H-Vif interaction points were used to generate the first A3H-Vif structure model, which revealed that the A3H helixes α3 and α4 interact with the Vif β-sheet (β2-β5). This model is in good agreement with previously reported Vif and A3H amino acids important for interaction. Based on the predicted A3H-Vif interface, we tested additional points of contact, which validated our model. Moreover, these experiments showed that the A3H and A3G binding sites on HIV-1 Vif are largely distinct, with both host proteins interacting with Vif β-strand 2. Taken together, this virus-host interface model explains previously reported data and will help to identify novel drug targets to combat HIV-1 infection. IMPORTANCE HIV-1 needs to overcome several intracellular restriction factors in order to replicate efficiently. The human APOBEC3 locus encodes seven proteins, of which A3D, A3F, A3G, and A3H restrict HIV-1. HIV encodes the Vif protein, which binds to the APOBEC3 proteins and leads to their proteasomal degradation. No HIV-1 Vif-APOBEC3 costructure exists to date despite extensive research. We and others previously generated HIV-1 Vif costructure models with A3G and A3F by mapping specific contact points between both proteins. Here, we applied a similar approach to HIV-1 Vif and A3H and successfully generated a Vif-A3H interaction model. Importantly, we find that the HIV-1 Vif-A3H interface is distinct from the Vif-A3G and Vif-A3F interfaces, with a small Vif region being important for recognition of both A3G and A3H. Our Vif-A3H structure model informs on how both proteins interact and could guide toward approaches to block the Vif-A3H interface to target HIV replication. Copyright © 2017 American Society for Microbiology.

Standard map in magnetized relativistic systems: fixed points and regular acceleration.

PubMed

de Sousa, M C; Steffens, F M; Pakter, R; Rizzato, F B

2010-08-01

We investigate the concept of a standard map for the interaction of relativistic particles and electrostatic waves of arbitrary amplitudes, under the action of external magnetic fields. The map is adequate for physical settings where waves and particles interact impulsively, and allows for a series of analytical result to be exactly obtained. Unlike the traditional form of the standard map, the present map is nonlinear in the wave amplitude and displays a series of peculiar properties. Among these properties we discuss the relation involving fixed points of the maps and accelerator regimes.

Maps | Geospatial Data Science | NREL

Science.gov Websites

Maps Maps NREL develops an array of maps to support renewable energy development and generation resource in the United States by county Geothermal Maps of geothermal power plants, resources for enhanced geothermal systems, and hydrothermal sites in the United States Hydrogen Maps of hydrogen production

Roles of nitric oxide synthase isoforms in cutaneous vasodilation induced by local warming of the skin and whole body heat stress in humans

PubMed Central

Zhao, Joan L.; Wu, Yubo

2009-01-01

Nitric oxide (NO) participates in the cutaneous vasodilation caused by increased local skin temperature (Tloc) and whole body heat stress in humans. In forearm skin, endothelial NO synthase (eNOS) participates in vasodilation due to elevated Tloc and neuronal NO synthase (nNOS) participates in vasodilation due to heat stress. To explore the relative roles and interactions of these isoforms, we examined the effects of a relatively specific eNOS inhibitor, Nω-amino-l-arginine (LNAA), and a specific nNOS inhibitor, Nω-propyl-l-arginine (NPLA), both separately and in combination, on skin blood flow (SkBF) responses to increased Tloc and heat stress in two protocols. In each protocol, SkBF was monitored by laser-Doppler flowmetry (LDF) and mean arterial pressure (MAP) by Finapres. Cutaneous vascular conductance (CVC) was calculated (CVC = LDF/MAP). Intradermal microdialysis was used to treat one site with 5 mM LNAA, another with 5 mM NPLA, a third with combined 5 mM LNAA and 5 mM NPLA (Mix), and a fourth site with Ringer only. In protocol 1, Tloc was controlled with combined LDF/local heating units. Tloc was increased from 34°C to 41.5°C to cause local vasodilation. In protocol 2, after a period of normothermia, whole body heat stress was induced (water-perfused suits). At the end of each protocol, all sites were perfused with 58 mM nitroprusside to effect maximal vasodilation for data normalization. In protocol 1, at Tloc = 34°C, CVC did not differ between sites (P > 0.05). LNAA and Mix attenuated CVC increases at Tloc = 41.5°C to similar extents (P < 0.05, LNAA or Mix vs. untreated or NPLA). In protocol 2, in normothermia, CVC did not differ between sites (P > 0.05). During heat stress, NPLA and Mix attenuated CVC increases to similar extents, but no significant attenuation occurred with LNAA (P < 0.05, NPLA or Mix vs. untreated or LNAA). In forearm skin, eNOS mediates the vasodilator response to increased Tloc and nNOS mediates the vasodilator response to heat stress. The two isoforms do not appear to interact during either response. PMID:19745188

Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomes.

PubMed

Minkah, Nana; Hwang, Young; Perry, Kay; Van Duyne, Gregory D; Hendrickson, Robert; Lefkowitz, Elliot J; Hannenhalli, Sridhar; Bushman, Frederic D

2007-08-15

Topoisomerase enzymes regulate superhelical tension in DNA resulting from transcription, replication, repair, and other molecular transactions. Poxviruses encode an unusual type IB topoisomerase that acts only at conserved DNA sequences containing the core pentanucleotide 5'-(T/C)CCTT-3'. In X-ray structures of the variola virus topoisomerase bound to DNA, protein-DNA contacts were found to extend beyond the core pentanucleotide, indicating that the full recognition site has not yet been fully defined in functional studies. Here we report quantitation of DNA cleavage rates for an optimized 13 bp site and for all possible single base substitutions (40 total sites), with the goals of understanding the molecular mechanism of recognition and mapping topoisomerase sites in poxvirus genome sequences. The data allow a precise definition of enzyme-DNA interactions and the energetic contributions of each. We then used the resulting "action matrix" to show that favorable topoisomerase sites are distributed all along the length of poxvirus DNA sequences, consistent with a requirement for local release of superhelical tension in constrained topological domains. In orthopox genomes, an additional central cluster of sites was also evident. A negative correlation of predicted topoisomerase sites was seen relative to early terminators, but no correlation was seen with early or late promoters. These data define the full variola virus topoisomerase recognition site and provide a new window on topoisomerase function in vivo.

Gamma-sky.net: Portal to the gamma-ray sky

NASA Astrophysics Data System (ADS)

Voruganti, Arjun; Deil, Christoph; Donath, Axel; King, Johannes

2017-01-01

http://gamma-sky.net is a novel interactive website designed for exploring the gamma-ray sky. The Map View portion of the site is powered by the Aladin Lite sky atlas, providing a scalable survey image tesselated onto a three-dimensional sphere. The map allows for interactive pan and zoom navigation as well as search queries by sky position or object name. The default image overlay shows the gamma-ray sky observed by the Fermi-LAT gamma-ray space telescope. Other survey images (e.g. Planck microwave images in low/high frequency bands, ROSAT X-ray image) are available for comparison with the gamma-ray data. Sources from major gamma-ray source catalogs of interest (Fermi-LAT 2FHL, 3FGL and a TeV source catalog) are overlaid over the sky map as markers. Clicking on a given source shows basic information in a popup, and detailed pages for every source are available via the Catalog View component of the website, including information such as source classification, spectrum and light-curve plots, and literature references. We intend for gamma-sky.net to be applicable for both professional astronomers as well as the general public. The website started in early June 2016 and is being developed as an open-source, open data project on GitHub (https://github.com/gammapy/gamma-sky). We plan to extend it to display more gamma-ray and multi-wavelength data. Feedback and contributions are very welcome!

Geomorphic Mapping and Paleoterrain Generation for use in Modeling Holocene (8,000 1,500 yr) Agropastoral Landuse and Landscape Interactions in Southeast Spain

NASA Astrophysics Data System (ADS)

Arrowsmith, J. R.; Dimaggio, E. N.; Barton, C. M.; Sarjoughian, H. S.; Fall, P.; Falconer, S. E.; Ullah, I. I.

2006-12-01

Dramatic changes in land use were associated with the rise of agriculture in the mid Holocene. Both the surface properties and the drainage networks were changed. Along with the direct modifications to surface properties (vegetation change, sediment liberation, and compaction) and drainage network alteration (terracing, canals), up and downstream responses in the watersheds communicated these changes throughout the landscape. The magnitude, rate, and feedbacks with the growing human populations are critical questions in our effort to assess human-landscape interactions. Our interdisciplinary team has focused on two field sites around the Mediterranean for model development and testing. We are combining high resolution process- based models of landscape change implemented within the GRASS GIS with agent based models of agropastoral behavior and driven by high resolution climate and vegetation models. In the Spanish field area (Penaguila Valley, 38.41 N 0.23 W), we have produced detailed (1:10,000) geomorphic maps which we combine with high resolution Digital Elevation Models (DEMs) on which we can run the surface process models to assess the portions of the landscape that are most sensitive to the postulated agropastoral landuse changes. To support this modeling we have produced the 1 m DEMs from softcopy photogrammetry. This DEM has greatly improved our overall spatial resolution to permit more accurate terrace correlations and improved quantitative assessment of morphologic processes (e.g. channel erosion, slope stability). In stereo, we have mapped overall landscape morphology that emphasizes areas of active erosion and alluvial terrace surfaces. Alluvial terraces are crucial to this research because they record periods of past stable topography and those of mid Holocene age were settled and farmed. We have correlated mapped terraces across the landscape using elevation and morphological distinctions. Using ArcGIS, we interpolated surfaces across equivalent terraces using triangulated irregular networks (TINs) allowing reconstruction of multiple regional landscapes to establish a chronosequence of absolute landscape change. This mapping and reconstruction will be field checked and numerical age constraints applied. Interestingly, our tentative age assessment of the lowest broad surface indicates that it was occupied about 5 ka, and now has been incised by 20 m. Archeological sites have been cut by the incision. This change from a broad low relief alluvial surface to one cut by narrow channels may have been an important change for the local populations and caused them to change their behaviors, even though it may have been initially triggered by distributed landscape change in the watershed, due to agropastoral activities.

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

USGS Publications Warehouse

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

1997-01-01

Forty years of geologic investigations at the Nevada Test Site (NTS) have been digitized. These data include all geologic information that: (1) has been collected, and (2) can be represented on a map within the map borders at the map scale is included in the map digital coverages. The following coverages are included with this dataset: Coverage Type Description geolpoly Polygon Geologic outcrops geolflts line Fault traces geolatts Point Bedding attitudes, etc. geolcald line Caldera boundaries geollins line Interpreted lineaments geolmeta line Metamorphic gradients The above coverages are attributed with numeric values and interpreted information. The entity files documented below show the data associated with each coverage.

Application of remote sensor data to geologic analysis of the Bonanza Test Site Colorado

NASA Technical Reports Server (NTRS)

Lee, K. (Compiler)

1973-01-01

A geologic map of the Bonanza Test Site is nearing completion. Using published large scale geologic maps from various sources, the geology of the area is being compiled on a base scaled at 1:250,000. Sources of previously published geologic mapping include: (1) USGS Bulletins; (2) professional papers and geologic quadrangle maps; (3) Bureau of Mines reports; (4) Colorado School of Mines quarterlies; and (5) Rocky Mountain Association of Geologist Guidebooks. This compilation will be used to evaluate ERTS, Skylab, and remote sensing underflight data.

Evaluation of Story Maps to Enhance Public Engagement and Communication at Legacy Management Sites – 17334

DOE Office of Scientific and Technical Information (OSTI.GOV)

Castillo, Darina; Carpenter, Cliff; Linard, Joshua

Story Maps are being used in both public and private sectors to convey information to stakeholders, create enterprise platforms, and assist in decision making. Story Maps are web applications that combine maps, narrative text, images, and multimedia content to provide information. These applications provide a user-friendly platform to share the remarkable history of our sites, the complexity of their contamination and remediation, successes we achieve in our LTS&M activities, and even the challenges we face as we aim to fulfill our mission.

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

NASA Technical Reports Server (NTRS)

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

1978-01-01

The areas of the United States that were not available as potential sites for receiving antennas that are an integral part of the Satellite Power System concept are presented. Thirty-six variables with the potential to exclude the rectenna were mapped and coded in a computer. Some of these variables exclude a rectenna from locating within the area of its spatial influence, and other variables potentially exclude the rectenna. These maps of variables were assembled from existing data and were mapped on a grid system.

Application of molecular docking and ONIOM methods for the description of interactions between anti-quorum sensing active (AHL) analogues and the Pseudomonas aeruginosa LasR binding site.

PubMed

Ahumedo, Maicol; Drosos, Juan Carlos; Vivas-Reyes, Ricardo

2014-05-01

Molecular docking methods were applied to simulate the coupling of a set of nineteen acyl homoserine lactone analogs into the binding site of the transcriptional receptor LasR. The best pose of each ligand was explored and a qualitative analysis of the possible interactions present in the complex was performed. From the results of the protein-ligand complex analysis, it was found that residues Tyr-64 and Tyr-47 are involved in important interactions, which mainly determine the antagonistic activity of the AHL analogues considered for this study. The effect of different substituents on the aromatic ring, the common structure to all ligands, was also evaluated focusing on how the interaction with the two previously mentioned tyrosine residues was affected. Electrostatic potential map calculations based on the electron density and the van der Waals radii were performed on all ligands to graphically aid in the explanation of the variation of charge density on their structures when the substituent on the aromatic ring is changed through the elements of the halogen group series. A quantitative approach was also considered and for that purpose the ONIOM method was performed to estimate the energy change in the different ligand-receptor complex regions. Those energy values were tested for their relationship with the corresponding IC50 in order to establish if there is any correlation between energy changes in the selected regions and the biological activity. The results obtained using the two approaches may contribute to the field of quorum sensing active molecules; the docking analysis revealed the role of some binding site residues involved in the formation of a halogen bridge with ligands. These interactions have been demonstrated to be responsible for the interruption of the signal propagation needed for the quorum sensing circuit. Using the other approach, the structure-activity relationship (SAR) analysis, it was possible to establish which structural characteristics and chemical requirements are necessary to classify a compound as a possible agonist or antagonist against the LasR binding site.

15q11.2–13.3 chromatin analysis reveals epigenetic regulation of CHRNA7 with deficiencies in Rett and autism brain

PubMed Central

Yasui, Dag H.; Scoles, Haley A.; Horike, Shin-ichi; Meguro-Horike, Makiko; Dunaway, Keith W.; Schroeder, Diane I.; LaSalle, Janine M.

2011-01-01

Copy number variations (CNVs) within human 15q11.2–13.3 show reduced penetrance and variable expressivity in a range of neurologic disorders. Therefore, characterizing 15q11.2–13.3 chromatin structure is important for understanding the regulation of this locus during normal neuronal development. Deletion of the Prader–Willi imprinting center (PWS-IC) within 15q11.2–13.3 disrupts long-range imprinted gene expression resulting in Prader–Willi syndrome. Previous results establish that MeCP2 binds to the PWS-IC and is required for optimal expression of distal GABRB3 and UBE3A. To examine the hypothesis that MeCP2 facilitates 15q11.2–13.3 transcription by linking the PWS-IC with distant elements, chromosome capture conformation on chip (4C) analysis was performed in human SH-SY5Y neuroblastoma cells. SH-SY5Y neurons had 2.84-fold fewer 15q11.2–13.3 PWS-IC chromatin interactions than undifferentiated SH-SY5Y neuroblasts, revealing developmental chromatin de-condensation of the locus. Out of 68 PWS-IC interactions with15q11.2–13.3 identified by 4C analysis and 62 15q11.2–13.3 MeCP2-binding sites identified by previous ChIP-chip studies, only five sites showed overlap. Remarkably, two of these overlapping PWS-IC- and MeCP2-bound sites mapped to sites flanking CHRNA7 (cholinergic receptor nicotinic alpha 7) encoding the cholinergic receptor, nicotinic, alpha 7. PWS-IC interaction with CHRNA7 in neurons was independently confirmed by fluorescent in situ hybridization analysis. Subsequent quantitative transcriptional analyses of frontal cortex from Rett syndrome and autism patients revealed significantly reduced CHRNA7 expression compared with controls. Together, these results suggest that transcription of CHRNA7 is modulated by chromatin interactions with the PWS-IC. Thus, loss of long-range chromatin interactions within 15q11.2–13.3 may contribute to multiple human neurodevelopmental disorders. PMID:21840925

15q11.2-13.3 chromatin analysis reveals epigenetic regulation of CHRNA7 with deficiencies in Rett and autism brain.

PubMed

Yasui, Dag H; Scoles, Haley A; Horike, Shin-Ichi; Meguro-Horike, Makiko; Dunaway, Keith W; Schroeder, Diane I; Lasalle, Janine M

2011-11-15

Copy number variations (CNVs) within human 15q11.2-13.3 show reduced penetrance and variable expressivity in a range of neurologic disorders. Therefore, characterizing 15q11.2-13.3 chromatin structure is important for understanding the regulation of this locus during normal neuronal development. Deletion of the Prader-Willi imprinting center (PWS-IC) within 15q11.2-13.3 disrupts long-range imprinted gene expression resulting in Prader-Willi syndrome. Previous results establish that MeCP2 binds to the PWS-IC and is required for optimal expression of distal GABRB3 and UBE3A. To examine the hypothesis that MeCP2 facilitates 15q11.2-13.3 transcription by linking the PWS-IC with distant elements, chromosome capture conformation on chip (4C) analysis was performed in human SH-SY5Y neuroblastoma cells. SH-SY5Y neurons had 2.84-fold fewer 15q11.2-13.3 PWS-IC chromatin interactions than undifferentiated SH-SY5Y neuroblasts, revealing developmental chromatin de-condensation of the locus. Out of 68 PWS-IC interactions with15q11.2-13.3 identified by 4C analysis and 62 15q11.2-13.3 MeCP2-binding sites identified by previous ChIP-chip studies, only five sites showed overlap. Remarkably, two of these overlapping PWS-IC- and MeCP2-bound sites mapped to sites flanking CHRNA7 (cholinergic receptor nicotinic alpha 7) encoding the cholinergic receptor, nicotinic, alpha 7. PWS-IC interaction with CHRNA7 in neurons was independently confirmed by fluorescent in situ hybridization analysis. Subsequent quantitative transcriptional analyses of frontal cortex from Rett syndrome and autism patients revealed significantly reduced CHRNA7 expression compared with controls. Together, these results suggest that transcription of CHRNA7 is modulated by chromatin interactions with the PWS-IC. Thus, loss of long-range chromatin interactions within 15q11.2-13.3 may contribute to multiple human neurodevelopmental disorders.

Retrotransposon Tf1 is targeted to pol II promoters by transcription activators

PubMed Central

Leem, Young-Eun; Ripmaster, Tracy; Kelly, Felice; Ebina, Hirotaka; Heincelman, Marc; Zhang, Ke; Grewal, Shiv I. S.; Hoffman, Charles S.; Levin, Henry L.

2008-01-01

SUMMARY The LTR-retrotransposon Tf1 preserves the coding capacity of its host Schizosaccharomyces pombe by integrating upstream of open reading frames (ORFs). To determine which features of the target sites were recognized by the transposon, we introduced plasmids containing candidate insertion sites into S. pombe and mapped the positions of integration. We found that Tf1 was targeted specifically to the promoters of pol II transcribed genes. A detailed analysis of integration in plasmids that contained either ade6 or fbp1 revealed insertions occurred in the promoters at positions where transcription factors bound. Further experiments revealed that the activator Atf1p and its binding site were required for directing integration to the promoter of fbp1. An interaction between Tf1 integrase and Atf1p was observed indicating that integration at fbp1 was mediated by the activator bound to its promoter. Surprisingly we found Tf1 contained sequences that activated transcription and these substituted for elements of the ade6 promoter disrupted by integration. PMID:18406330

Retrotransposon Tf1 is targeted to Pol II promoters by transcription activators.

PubMed

Leem, Young-Eun; Ripmaster, Tracy L; Kelly, Felice D; Ebina, Hirotaka; Heincelman, Marc E; Zhang, Ke; Grewal, Shiv I S; Hoffman, Charles S; Levin, Henry L

2008-04-11

The LTR-retrotransposon Tf1 preserves the coding capacity of its host Schizosaccharomyces pombe by integrating upstream of open reading frames (ORFs). To determine which features of the target sites were recognized by the transposon, we introduced plasmids containing candidate insertion sites into S. pombe and mapped the positions of integration. We found that Tf1 was targeted specifically to the promoters of Pol II-transcribed genes. A detailed analysis of integration in plasmids that contained either ade6 or fbp1 revealed insertions occurred in the promoters at positions where transcription factors bound. Further experiments revealed that the activator Atf1p and its binding site were required for directing integration to the promoter of fbp1. An interaction between Tf1 integrase and Atf1p was observed, indicating that integration at fbp1 was mediated by the activator bound to its promoter. Surprisingly, we found Tf1 contained sequences that activated transcription, and these substituted for elements of the ade6 promoter disrupted by integration.

The Interaction of Integrin αIIbβ3 with Fibrin Occurs through Multiple Binding Sites in the αIIb β-Propeller Domain*

PubMed Central

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

2014-01-01

The currently available antithrombotic agents target the interaction of platelet integrin αIIbβ3 (GPIIb-IIIa) with fibrinogen during platelet aggregation. Platelets also bind fibrin formed early during thrombus growth. It was proposed that inhibition of platelet-fibrin interactions may be a necessary and important property of αIIbβ3 antagonists; however, the mechanisms by which αIIbβ3 binds fibrin are uncertain. We have previously identified the γ370–381 sequence (P3) in the γC domain of fibrinogen as the fibrin-specific binding site for αIIbβ3 involved in platelet adhesion and platelet-mediated fibrin clot retraction. In the present study, we have demonstrated that P3 can bind to several discontinuous segments within the αIIb β-propeller domain of αIIbβ3 enriched with negatively charged and aromatic residues. By screening peptide libraries spanning the sequence of the αIIb β-propeller, several sequences were identified as candidate contact sites for P3. Synthetic peptides duplicating these segments inhibited platelet adhesion and clot retraction but not platelet aggregation, supporting the role of these regions in fibrin recognition. Mutant αIIbβ3 receptors in which residues identified as critical for P3 binding were substituted for homologous residues in the I-less integrin αMβ2 exhibited reduced cell adhesion and clot retraction. These residues are different from those that are involved in the coordination of the fibrinogen γ404–411 sequence and from auxiliary sites implicated in binding of soluble fibrinogen. These results map the binding of fibrin to multiple sites in the αIIb β-propeller and further indicate that recognition specificity of αIIbβ3 for fibrin differs from that for soluble fibrinogen. PMID:24338009

The Origin of Cosmic Rays: What can GLAST Say?

NASA Technical Reports Server (NTRS)

Ormes, Jonathan F.; Digel, Seith; Moskalenko, Igor V.; Moiseev, Alexander; Williamson, Roger

2000-01-01

Gamma rays in the band from 30 MeV to 300 GeV, used in combination with direct measurements and with data from radio and X-ray bands, provide a powerful tool for studying the origin of Galactic cosmic rays. Gamma-ray Large Area Space Telescope (GLAST) with its fine 10-20 arcmin angular resolution will be able to map the sites of acceleration of cosmic rays and their interactions with interstellar matter, It will provide information that is necessary to study the acceleration of energetic particles in supernova shocks, their transport in the interstellar medium and penetration into molecular clouds.

D Modelling and Mapping for Virtual Exploration of Underwater Archaeology Assets

NASA Astrophysics Data System (ADS)

Liarokapis, F.; Kouřil, P.; Agrafiotis, P.; Demesticha, S.; Chmelík, J.; Skarlatos, D.

2017-02-01

This paper investigates immersive technologies to increase exploration time in an underwater archaeological site, both for the public, as well as, for researchers and scholars. Focus is on the Mazotos shipwreck site in Cyprus, which is located 44 meters underwater. The aim of this work is two-fold: (a) realistic modelling and mapping of the site and (b) an immersive virtual reality visit. For 3D modelling and mapping optical data were used. The underwater exploration is composed of a variety of sea elements including: plants, fish, stones, and artefacts, which are randomly positioned. Users can experience an immersive virtual underwater visit in Mazotos shipwreck site and get some information about the shipwreck and its contents for raising their archaeological knowledge and cultural awareness.

kmos: A lattice kinetic Monte Carlo framework

NASA Astrophysics Data System (ADS)

Hoffmann, Max J.; Matera, Sebastian; Reuter, Karsten

2014-07-01

Kinetic Monte Carlo (kMC) simulations have emerged as a key tool for microkinetic modeling in heterogeneous catalysis and other materials applications. Systems, where site-specificity of all elementary reactions allows a mapping onto a lattice of discrete active sites, can be addressed within the particularly efficient lattice kMC approach. To this end we describe the versatile kmos software package, which offers a most user-friendly implementation, execution, and evaluation of lattice kMC models of arbitrary complexity in one- to three-dimensional lattice systems, involving multiple active sites in periodic or aperiodic arrangements, as well as site-resolved pairwise and higher-order lateral interactions. Conceptually, kmos achieves a maximum runtime performance which is essentially independent of lattice size by generating code for the efficiency-determining local update of available events that is optimized for a defined kMC model. For this model definition and the control of all runtime and evaluation aspects kmos offers a high-level application programming interface. Usage proceeds interactively, via scripts, or a graphical user interface, which visualizes the model geometry, the lattice occupations and rates of selected elementary reactions, while allowing on-the-fly changes of simulation parameters. We demonstrate the performance and scaling of kmos with the application to kMC models for surface catalytic processes, where for given operation conditions (temperature and partial pressures of all reactants) central simulation outcomes are catalytic activity and selectivities, surface composition, and mechanistic insight into the occurrence of individual elementary processes in the reaction network.

The common C-terminal sequences of substance P and neurokinin A contact the same region of the NK-1 receptor.

PubMed

Bremer, A A; Leeman, S E; Boyd, N D

2000-12-01

Although neurokinin A (NKA), a tachykinin peptide with sequence homology to substance P (SP), is a weak competitor of radiolabeled SP binding to the NK-1 receptor (NK-1R), more recent direct binding studies using radiolabeled NKA have demonstrated an unexpected high-affinity interaction with this receptor. To document the site of interaction between NKA and the NK-1R, we have used a photoreactive analogue of NKA containing p-benzoyl-L-phenylalanine (Bpa) substituted in position 7 of the peptide. Peptide mapping studies of the receptor photolabeled by (125)I-iodohistidyl(1)-Bpa(7)NKA have established that the site of photoinsertion is located within a segment of the receptor extending from residues 178 to 190 (VVCMIEWPEHPNR). We have previously shown that (125)I-BH-Bpa(8)SP, a photoreactive analogue of SP, covalently attaches to M(181) within this same receptor sequence. Importantly, both of these peptides ((125)I-iodohistidyl(1)-Bpa(7)NKA and (125)I-BH-Bpa(8)SP) have the photoreactive amino acid in an equivalent position within the conserved tachykinin carboxyl-terminal tail. In this report, we also show that site-directed mutagenesis of M(181) to A(181) in the NK-1R results in a complete loss of photolabeling of both peptides to this receptor site, indicating that the equivalent position of SP and NKA, when bound to the NK-1R, contact the same residue.

Shear-wave velocity characterization of the USGS Hawaiian strong-motion network on the Island of Hawaii and development of an NEHRP site-class map

USGS Publications Warehouse

Wong, Ivan G.; Stokoe, Kenneth; Cox, Brady R.; Yuan, Jiabei; Knudsen, Keith L.; Terra, Fabia; Okubo, Paul G.; Lin, Yin-Cheng

2011-01-01

To assess the level and nature of ground shaking in Hawaii for the purposes of earthquake hazard mitigation and seismic design, empirical ground-motion prediction models are desired. To develop such empirical relationships, knowledge of the subsurface site conditions beneath strong-motion stations is critical. Thus, as a first step to develop ground-motion prediction models for Hawaii, spectral-analysis-of-surface-waves (SASW) profiling was performed at the 22 free-field U.S. Geological Survey (USGS) strong-motion sites on the Big Island to obtain shear-wave velocity (VS) data. Nineteen of these stations recorded the 2006 Kiholo Bay moment magnitude (M) 6.7 earthquake, and 17 stations recorded the triggered M 6.0 Mahukona earthquake. VS profiling was performed to reach depths of more than 100 ft. Most of the USGS stations are situated on sites underlain by basalt, based on surficial geologic maps. However, the sites have varying degrees of weathering and soil development. The remaining strong-motion stations are located on alluvium or volcanic ash. VS30 (average VS in the top 30 m) values for the stations on basalt ranged from 906 to 1908 ft/s [National Earthquake Hazards Reduction Program (NEHRP) site classes C and D], because most sites were covered with soil of variable thickness. Based on these data, an NEHRP site-class map was developed for the Big Island. These new VS data will be a significant input into an update of the USGS statewide hazard maps and to the operation of ShakeMap on the island of Hawaii.

Two decision-support tools for assessing the potential effects of energy development on hydrologic resources as part of the Energy and Environment in the Rocky Mountain Area interactive energy atlas

USGS Publications Warehouse

Linard, Joshua I.; Matherne, Anne Marie; Leib, Kenneth J.; Carr, Natasha B.; Diffendorfer, James E.; Hawkins, Sarah J.; Latysh, Natalie; Ignizio, Drew A.; Babel, Nils C.

2014-01-01

The U.S. Geological Survey project—Energy and Environment in the Rocky Mountain Area (EERMA)—has developed a set of virtual tools in the form of an online interactive energy atlas for Colorado and New Mexico to facilitate access to geospatial data related to energy resources, energy infrastructure, and natural resources that may be affected by energy development. The interactive energy atlas currently (2014) consists of three components: (1) a series of interactive maps; (2) downloadable geospatial datasets; and (3) decison-support tools, including two maps related to hydrologic resources discussed in this report. The hydrologic-resource maps can be used to examine the potential effects of energy development on hydrologic resources with respect to (1) groundwater vulnerability, by using the depth to water, recharge, aquifer media, soil media, topography, impact of the vadose zone, and hydraulic conductivity of the aquifer (DRASTIC) model, and (2) landscape erosion potential, by using the revised universal soil loss equation (RUSLE). The DRASTIC aquifer vulnerability index value for the two-State area ranges from 48 to 199. Higher values, indicating greater relative aquifer vulnerability, are centered in south-central Colorado, areas in southeastern New Mexico, and along riparian corridors in both States—all areas where the water table is relatively close to the land surface and the aquifer is more susceptible to surface influences. As calculated by the RUSLE model, potential mean annual erosion, as soil loss in units of tons per acre per year, ranges from 0 to 12,576 over the two-State area. The RUSLE model calculated low erosion potential over most of Colorado and New Mexico, with predictions of highest erosion potential largely confined to areas of mountains or escarpments. An example is presented of how a fully interactive RUSLE model could be further used as a decision-support tool to evaluate the potential hydrologic effects of energy development on a site-specific basis and to explore the effectiveness of various mitigation practices.

Interactive Videodisc Learning Systems.

ERIC Educational Resources Information Center

Currier, Richard L.

1983-01-01

Discussion of capabilities of interactive videodisc, which combines video images recorded on disc and random-access, highlights interactivity; teaching techniques with videodiscs (including masking, disassembly, movie maps, tactical maps, action code, and simulation); costs; and games. Illustrative material is provided. (High Technology, P. O. Box…

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

PubMed Central

Boulos, Maged N Kamel

2005-01-01

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

Patterns of vegetation in the Owens Valley, California

NASA Technical Reports Server (NTRS)

Ustin, S. L.; Rock, B. N.; Woodward, R. A.

1986-01-01

Spectral characteristics of semi-arid shrub communities were examined using Airborne Imaging Spectrometer (AIS) data collected in the tree mode on 23 May 1985. Mesic sites with relatively high vegetation density and distinct zonation patterns exhibited greater spectral signature variations than sites with more xeric shrub communities. Spectral signature patterns were not directly related to vegetation density or physiognomy, although spatial maps derived from an 8-channel maximum likelihood classification were supported by photo-interpreted surface features. In AIS data, the principal detected effect of shrub vegetation on the alluvial fans is to lower reflectance across the spectrum. These results are similar to those reported during a period of minimal physiological activity in autumn, indicating that shadows cast by vegetation canopies are an important element of soil-vegetation interaction under conditions of relatively low canopy cover.

N-(6-Methylpyridin-2-yl)mesitylenesulfonamide and acetic acid--a salt, a cocrystal or both?

PubMed

Pan, Fangfang; Kalf, Irmgard; Englert, Ulli

2015-08-01

In the solid obtained from N-(6-methylpyridin-2-yl)mesitylenesulfonamide and acetic acid, the constituents interact via two N-H···O hydrogen bonds. The H atom situated in one of these short contacts is disordered over two positions: one of these positions is formally associated with an adduct of the neutral sulfonamide molecule and the neutral acetic acid molecule, and corresponds to a cocrystal, while the alternative site is associated with salt formation between a protonated sulfonamide molecule and deprotonated acetic acid molecule. Site-occupancy refinements and electron densities from difference Fourier maps suggest a trend with temperature, albeit of limited significance; the cocrystal is more relevant at 100 K, whereas the intensity data collected at room temperature match the description as cocrystal and salt equally well.

National Geothermal Data System: Open Access to Geoscience Data, Maps, and Documents

NASA Astrophysics Data System (ADS)

Caudill, C. M.; Richard, S. M.; Musil, L.; Sonnenschein, A.; Good, J.

2014-12-01

The U.S. National Geothermal Data System (NGDS) provides free open access to millions of geoscience data records, publications, maps, and reports via distributed web services to propel geothermal research, development, and production. NGDS is built on the US Geoscience Information Network (USGIN) data integration framework, which is a joint undertaking of the USGS and the Association of American State Geologists (AASG), and is compliant with international standards and protocols. NGDS currently serves geoscience information from 60+ data providers in all 50 states. Free and open source software is used in this federated system where data owners maintain control of their data. This interactive online system makes geoscience data easily discoverable, accessible, and interoperable at no cost to users. The dynamic project site http://geothermaldata.org serves as the information source and gateway to the system, allowing data and applications discovery and availability of the system's data feed. It also provides access to NGDS specifications and the free and open source code base (on GitHub), a map-centric and library style search interface, other software applications utilizing NGDS services, NGDS tutorials (via YouTube and USGIN site), and user-created tools and scripts. The user-friendly map-centric web-based application has been created to support finding, visualizing, mapping, and acquisition of data based on topic, location, time, provider, or key words. Geographic datasets visualized through the map interface also allow users to inspect the details of individual GIS data points (e.g. wells, geologic units, etc.). In addition, the interface provides the information necessary for users to access the GIS data from third party software applications such as GoogleEarth, UDig, and ArcGIS. A redistributable, free and open source software package called GINstack (USGIN software stack) was also created to give data providers a simple way to release data using interoperable and shareable standards, upload data and documents, and expose those data as a node in the NGDS or any larger data system through a CSW endpoint. The easy-to-use interface is supported by back-end software including Postgres, GeoServer, and custom CKAN extensions among others.

Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease.

PubMed

Torres, Matthew P; Dewhurst, Henry; Sundararaman, Niveda

2016-11-01

Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function - a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) - a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al., 2015). Here, we apply SAPH-ire to the set of eukaryotic protein families containing experimental PTM and 3D structure data - capturing 1,325 protein families with 50,839 unique PTM sites organized into 31,747 modified alignment positions (MAPs), of which 2010 (∼6%) possess known biological function. Here, we show that using an artificial neural network model (SAPH-ire NN) trained to identify MAP hotspots with biological function results in prediction outcomes that far surpass the use of single hotspot features, including nearest neighbor PTM clustering methods. We find the greatest enhancement in prediction for positions with PTM counts of five or less, which represent 98% of all MAPs in the eukaryotic proteome and 90% of all MAPs found to have biological function. Analysis of the top 1092 MAP hotspots revealed 267 of truly unknown function (containing 5443 distinct PTMs). Of these, 165 hotspots could be mapped to human KEGG pathways for normal and/or disease physiology. Many high-ranking hotspots were also found to be disease-associated pathogenic sites of amino acid substitution despite the lack of observable PTM in the human protein family member. Taken together, these experiments demonstrate that the functional relevance of a PTM can be predicted very effectively by neural network models, revealing a large but testable body of potential regulatory elements that impact hundreds of different biological processes important in eukaryotic biology and human health. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease*

PubMed Central

Dewhurst, Henry; Sundararaman, Niveda

2016-01-01

Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function - a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) - a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al., 2015). Here, we apply SAPH-ire to the set of eukaryotic protein families containing experimental PTM and 3D structure data - capturing 1,325 protein families with 50,839 unique PTM sites organized into 31,747 modified alignment positions (MAPs), of which 2010 (∼6%) possess known biological function. Here, we show that using an artificial neural network model (SAPH-ire NN) trained to identify MAP hotspots with biological function results in prediction outcomes that far surpass the use of single hotspot features, including nearest neighbor PTM clustering methods. We find the greatest enhancement in prediction for positions with PTM counts of five or less, which represent 98% of all MAPs in the eukaryotic proteome and 90% of all MAPs found to have biological function. Analysis of the top 1092 MAP hotspots revealed 267 of truly unknown function (containing 5443 distinct PTMs). Of these, 165 hotspots could be mapped to human KEGG pathways for normal and/or disease physiology. Many high-ranking hotspots were also found to be disease-associated pathogenic sites of amino acid substitution despite the lack of observable PTM in the human protein family member. Taken together, these experiments demonstrate that the functional relevance of a PTM can be predicted very effectively by neural network models, revealing a large but testable body of potential regulatory elements that impact hundreds of different biological processes important in eukaryotic biology and human health. PMID:27697855

SITE-SPECIFIC MEASUREMENTS OF RESIDENTIAL RADON PROTECTION CATEGORY

EPA Science Inventory

The report describes a series of benchmark measurements of soil radon potential at seven Florida sites and compares the measurements with regional estimates of radon potential from the Florida radon protection map. The measurements and map were developed under the Florida Radon R...

CIDR

Science.gov Websites

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Semi-automatic mapping of geological Structures using UAV-based photogrammetric data: An image analysis approach

NASA Astrophysics Data System (ADS)

Vasuki, Yathunanthan; Holden, Eun-Jung; Kovesi, Peter; Micklethwaite, Steven

2014-08-01

Recent advances in data acquisition technologies, such as Unmanned Aerial Vehicles (UAVs), have led to a growing interest in capturing high-resolution rock surface images. However, due to the large volumes of data that can be captured in a short flight, efficient analysis of this data brings new challenges, especially the time it takes to digitise maps and extract orientation data. We outline a semi-automated method that allows efficient mapping of geological faults using photogrammetric data of rock surfaces, which was generated from aerial photographs collected by a UAV. Our method harnesses advanced automated image analysis techniques and human data interaction to rapidly map structures and then calculate their dip and dip directions. Geological structures (faults, joints and fractures) are first detected from the primary photographic dataset and the equivalent three dimensional (3D) structures are then identified within a 3D surface model generated by structure from motion (SfM). From this information the location, dip and dip direction of the geological structures are calculated. A structure map generated by our semi-automated method obtained a recall rate of 79.8% when compared against a fault map produced using expert manual digitising and interpretation methods. The semi-automated structure map was produced in 10 min whereas the manual method took approximately 7 h. In addition, the dip and dip direction calculation, using our automated method, shows a mean±standard error of 1.9°±2.2° and 4.4°±2.6° respectively with field measurements. This shows the potential of using our semi-automated method for accurate and efficient mapping of geological structures, particularly from remote, inaccessible or hazardous sites.

A hyper-temporal remote sensing protocol for high-resolution mapping of ecological sites

PubMed Central

Karl, Jason W.

2017-01-01

Ecological site classification has emerged as a highly effective land management framework, but its utility at a regional scale has been limited due to the spatial ambiguity of ecological site locations in the U.S. or the absence of ecological site maps in other regions of the world. In response to these shortcomings, this study evaluated the use of hyper-temporal remote sensing (i.e., hundreds of images) for high spatial resolution mapping of ecological sites. We posit that hyper-temporal remote sensing can provide novel insights into the spatial variability of ecological sites by quantifying the temporal response of land surface spectral properties. This temporal response provides a spectral ‘fingerprint’ of the soil-vegetation-climate relationship which is central to the concept of ecological sites. Consequently, the main objective of this study was to predict the spatial distribution of ecological sites in a semi-arid rangeland using a 28-year time series of normalized difference vegetation index from Landsat TM 5 data and modeled using support vector machine classification. Results from this study show that support vector machine classification using hyper-temporal remote sensing imagery was effective in modeling ecological site classes, with a 62% correct classification. These results were compared to Gridded Soil Survey Geographic database and expert delineated maps of ecological sites which had a 51 and 89% correct classification, respectively. An analysis of the effects of ecological state on ecological site misclassifications revealed that sites in degraded states (e.g., shrub-dominated/shrubland and bare/annuals) had a higher rate of misclassification due to their close spectral similarity with other ecological sites. This study identified three important factors that need to be addressed to improve future model predictions: 1) sampling designs need to fully represent the range of both within class (i.e., states) and between class (i.e., ecological sites) spectral variability through time, 2) field sampling protocols that accurately characterize key soil properties (e.g., texture, depth) need to be adopted, and 3) additional environmental covariates (e.g. terrain attributes) need to be evaluated that may help further differentiate sites with similar spectral signals. Finally, the proposed hyper-temporal remote sensing framework may provide a standardized approach to evaluate and test our ecological site concepts through examining differences in vegetation dynamics in response to climatic variability and other drivers of land-use change. Results from this study demonstrate the efficacy of the hyper-temporal remote sensing approach for high resolution mapping of ecological sites, and highlights its utility in terms of reduced cost and time investment relative to traditional manual mapping approaches. PMID:28414731

A hyper-temporal remote sensing protocol for high-resolution mapping of ecological sites.

PubMed

Maynard, Jonathan J; Karl, Jason W

2017-01-01

Ecological site classification has emerged as a highly effective land management framework, but its utility at a regional scale has been limited due to the spatial ambiguity of ecological site locations in the U.S. or the absence of ecological site maps in other regions of the world. In response to these shortcomings, this study evaluated the use of hyper-temporal remote sensing (i.e., hundreds of images) for high spatial resolution mapping of ecological sites. We posit that hyper-temporal remote sensing can provide novel insights into the spatial variability of ecological sites by quantifying the temporal response of land surface spectral properties. This temporal response provides a spectral 'fingerprint' of the soil-vegetation-climate relationship which is central to the concept of ecological sites. Consequently, the main objective of this study was to predict the spatial distribution of ecological sites in a semi-arid rangeland using a 28-year time series of normalized difference vegetation index from Landsat TM 5 data and modeled using support vector machine classification. Results from this study show that support vector machine classification using hyper-temporal remote sensing imagery was effective in modeling ecological site classes, with a 62% correct classification. These results were compared to Gridded Soil Survey Geographic database and expert delineated maps of ecological sites which had a 51 and 89% correct classification, respectively. An analysis of the effects of ecological state on ecological site misclassifications revealed that sites in degraded states (e.g., shrub-dominated/shrubland and bare/annuals) had a higher rate of misclassification due to their close spectral similarity with other ecological sites. This study identified three important factors that need to be addressed to improve future model predictions: 1) sampling designs need to fully represent the range of both within class (i.e., states) and between class (i.e., ecological sites) spectral variability through time, 2) field sampling protocols that accurately characterize key soil properties (e.g., texture, depth) need to be adopted, and 3) additional environmental covariates (e.g. terrain attributes) need to be evaluated that may help further differentiate sites with similar spectral signals. Finally, the proposed hyper-temporal remote sensing framework may provide a standardized approach to evaluate and test our ecological site concepts through examining differences in vegetation dynamics in response to climatic variability and other drivers of land-use change. Results from this study demonstrate the efficacy of the hyper-temporal remote sensing approach for high resolution mapping of ecological sites, and highlights its utility in terms of reduced cost and time investment relative to traditional manual mapping approaches.