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  • 1
    Publication Date: 2012-03-09
    Description: Cells are organized on length scales ranging from angstrom to micrometres. However, the mechanisms by which angstrom-scale molecular properties are translated to micrometre-scale macroscopic properties are not well understood. Here we show that interactions between diverse synthetic, multivalent macromolecules (including multi-domain proteins and RNA) produce sharp liquid-liquid-demixing phase separations, generating micrometre-sized liquid droplets in aqueous solution. This macroscopic transition corresponds to a molecular transition between small complexes and large, dynamic supramolecular polymers. The concentrations needed for phase transition are directly related to the valency of the interacting species. In the case of the actin-regulatory protein called neural Wiskott-Aldrich syndrome protein (N-WASP) interacting with its established biological partners NCK and phosphorylated nephrin, the phase transition corresponds to a sharp increase in activity towards an actin nucleation factor, the Arp2/3 complex. The transition is governed by the degree of phosphorylation of nephrin, explaining how this property of the system can be controlled to regulatory effect by kinases. The widespread occurrence of multivalent systems suggests that phase transitions may be used to spatially organize and biochemically regulate information throughout biology.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3343696/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3343696/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Pilong -- Banjade, Sudeep -- Cheng, Hui-Chun -- Kim, Soyeon -- Chen, Baoyu -- Guo, Liang -- Llaguno, Marc -- Hollingsworth, Javoris V -- King, David S -- Banani, Salman F -- Russo, Paul S -- Jiang, Qiu-Xing -- Nixon, B Tracy -- Rosen, Michael K -- P30 CA142543/CA/NCI NIH HHS/ -- P41 GM103622/GM/NIGMS NIH HHS/ -- R01 GM056322/GM/NIGMS NIH HHS/ -- R01 GM056322-13/GM/NIGMS NIH HHS/ -- R01-GM088745/GM/NIGMS NIH HHS/ -- R01-GM56322/GM/NIGMS NIH HHS/ -- RR-08630/RR/NCRR NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Mar 7;483(7389):336-40. doi: 10.1038/nature10879.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-8812, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22398450" target="_blank"〉PubMed〈/a〉
    Keywords: Actin-Related Protein 2-3 Complex/metabolism ; Adaptor Proteins, Signal Transducing/chemistry/metabolism ; Binding Sites ; Biopolymers/chemistry/metabolism ; Fluorescence Recovery After Photobleaching ; HeLa Cells ; Humans ; Ligands ; Membrane Proteins/chemistry/metabolism ; Multiprotein Complexes/*chemistry/*metabolism ; Oncogene Proteins/chemistry/metabolism ; *Phase Transition ; Phosphorylation ; Proline-Rich Protein Domains ; Protein Structure, Quaternary ; Proteins/*chemistry/*metabolism ; *Signal Transduction ; Wiskott-Aldrich Syndrome Protein, Neuronal/chemistry/metabolism ; src Homology Domains
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2012-09-21
    Description: Interferon regulatory factor 4 (IRF4) is an IRF family transcription factor with critical roles in lymphoid development and in regulating the immune response. IRF4 binds DNA weakly owing to a carboxy-terminal auto-inhibitory domain, but cooperative binding with factors such as PU.1 or SPIB in B cells increases binding affinity, allowing IRF4 to regulate genes containing ETS-IRF composite elements (EICEs; 5'-GGAAnnGAAA-3'). Here we show that in mouse CD4(+) T cells, where PU.1/SPIB expression is low, and in B cells, where PU.1 is well expressed, IRF4 unexpectedly can cooperate with activator protein-1 (AP1) complexes to bind to AP1-IRF4 composite (5'-TGAnTCA/GAAA-3') motifs that we denote as AP1-IRF composite elements (AICEs). Moreover, BATF-JUN family protein complexes cooperate with IRF4 in binding to AICEs in pre-activated CD4(+) T cells stimulated with IL-21 and in T(H)17 differentiated cells. Importantly, BATF binding was diminished in Irf4(-/-) T cells and IRF4 binding was diminished in Batf(-/-) T cells, consistent with functional cooperation between these factors. Moreover, we show that AP1 and IRF complexes cooperatively promote transcription of the Il10 gene, which is expressed in T(H)17 cells and potently regulated by IL-21. These findings reveal that IRF4 can signal via complexes containing ETS or AP1 motifs depending on the cellular context, thus indicating new approaches for modulating IRF4-dependent transcription.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3537508/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3537508/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Peng -- Spolski, Rosanne -- Liao, Wei -- Wang, Lu -- Murphy, Theresa L -- Murphy, Kenneth M -- Leonard, Warren J -- ZIA HL005402-20/Intramural NIH HHS/ -- ZIA HL005402-21/Intramural NIH HHS/ -- ZIA HL005408-05/Intramural NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Oct 25;490(7421):543-6. doi: 10.1038/nature11530. Epub 2012 Sep 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Immunology and Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892-1674, USA. lip3@nhlbi.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22992523" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Animals ; B-Lymphocytes/metabolism ; Base Sequence ; Basic-Leucine Zipper Transcription Factors/deficiency/genetics/*metabolism ; Binding Sites ; CD4-Positive T-Lymphocytes/cytology/*metabolism ; Cell Differentiation ; Female ; Interferon Regulatory Factors/deficiency/genetics/*metabolism ; Interleukin-10/genetics ; Interleukins/immunology ; Lymphocyte Activation ; Male ; Mice ; Mice, Inbred C57BL ; Molecular Sequence Data ; Nucleotide Motifs ; Proto-Oncogene Proteins/metabolism ; Proto-Oncogene Proteins c-jun/*metabolism ; Signal Transduction ; Th17 Cells/cytology/immunology ; Trans-Activators/metabolism ; Transcription Factor AP-1/metabolism ; *Transcription, Genetic ; Up-Regulation
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 1995-09-29
    Description: The baculovirus antiapoptotic protein p35 inhibited the proteolytic activity of human interleukin-1 beta converting enzyme (ICE) and three of its homologs in enzymatic assays. Coexpression of p35 prevented the autoproteolytic activation of ICE from its precursor form and blocked ICE-induced apoptosis. Inhibition of enzymatic activity correlated with the cleavage of p35 and the formation of a stable ICE-p35 complex. The ability of p35 to block apoptosis in different pathways and in distantly related organisms suggests a central and conserved role for ICE-like proteases in the induction of apoptosis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bump, N J -- Hackett, M -- Hugunin, M -- Seshagiri, S -- Brady, K -- Chen, P -- Ferenz, C -- Franklin, S -- Ghayur, T -- Li, P -- AI 38262/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1995 Sep 29;269(5232):1885-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉BASF Bioresearch Corporation, Worcester, MA 01605, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7569933" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; *Apoptosis ; Binding Sites ; Binding, Competitive ; Caspase 1 ; Cell Line ; Cysteine Endopeptidases/*metabolism ; Cysteine Proteinase Inhibitors/genetics/*metabolism/pharmacology ; Enzyme Activation/drug effects ; Humans ; Inhibitor of Apoptosis Proteins ; Molecular Sequence Data ; Recombinant Proteins/pharmacology ; Transfection ; Viral Proteins/genetics/*metabolism/pharmacology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2019-07-12
    Description: Satellite observations can play a very important role in airborne field campaigns, since they provide a comprehensive description of the environment that is essential for the experiment design, flight planning, and post-experiment scientific data analysis. In the past, it has been difficult to fully utilize data from multiple NASA satellites due to the large data volume, the complexity of accessing NASA s data in near-real-time (NRT), as well as the lack of software tools to interact with multi-sensor information. The JPL GRIP Portal is a Web portal that serves a comprehensive set of NRT observation data sets from NASA and NOAA satellites describing the atmospheric and oceanic environments related to the genesis and intensification of the tropical storms in the North Atlantic Ocean. Together with the model forecast data from four major global atmospheric models, this portal provides a useful tool for the scientists and forecasters in planning and monitoring the NASA GRIP field campaign during the 2010 Atlantic Ocean hurricane season. This portal uses the Google Earth plug-in to visualize various types of data sets, such as 2D maps, wind vectors, streamlines, 3D data sets presented at series of vertical cross-sections or pointwise vertical profiles, and hurricane best tracks and forecast tracks. Additionally, it allows users to overlap multiple data sets, change the opacity of each image layer, generate animations on the fly with selected data sets, and compare the observation data with the model forecast using two independent calendars. The portal also provides the capability to identify the geographic location of any point of interest. In addition to supporting the airborne mission planning, the NRT data and portal will serve as a very rich source of information during the post-field campaign analysis stage of the airborne experiment. By including a diverse set of satellite observations and model forecasts, it provides a good spatial and temporal context for the high-resolution, but limited in space and time, airborne observations.
    Keywords: Man/System Technology and Life Support
    Type: NPO-47787 , NASA Tech Briefs, June 2012; 16
    Format: application/pdf
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  • 5
    Publication Date: 2019-07-12
    Description: Multi Surface Light Table (MSLT) is an interactive software tool that was developed in support of the QuakeSim project, which has created an earthquake- fault database and a set of earthquake- simulation software tools. MSLT visualizes the three-dimensional geometries of faults embedded below the terrain and animates time-varying simulations of stress and slip. The fault segments, represented as rectangular surfaces at dip angles, are organized into collections, that is, faults. An interface built into MSLT queries and retrieves fault definitions from the QuakeSim fault database. MSLT also reads time-varying output from one of the QuakeSim simulation tools, called "Virtual California." Stress intensity is represented by variations in color. Slips are represented by directional indicators on the fault segments. The magnitudes of the slips are represented by the duration of the directional indicators in time. The interactive controls in MSLT provide a virtual track-ball, pan and zoom, translucency adjustment, simulation playback, and simulation movie capture. In addition, geographical information on the fault segments and faults is displayed on text windows. Because of the extensive viewing controls, faults can be seen in relation to one another, and to the terrain. These relations can be realized in simulations. Correlated slips in parallel faults are visible in the playback of Virtual California simulations.
    Keywords: Man/System Technology and Life Support
    Type: NPO-40781 , NASA Tech Briefs, December 2005; 14
    Format: application/pdf
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  • 6
    Publication Date: 2019-07-12
    Description: SOM_VIS is a computer program for analysis and display of multidimensional sets of Earth-image data typified by the data acquired by the Multi-angle Imaging Spectro-Radiometer [MISR (a spaceborne instrument)]. In SOM_VIS, an enhanced self-organizing-map (SOM) algorithm is first used to project a multidimensional set of data into a nonuniform three-dimensional lattice structure. The lattice structure is mapped to a color space to obtain a color map for an image. The Voronoi cell-refinement algorithm is used to map the SOM lattice structure to various levels of color resolution. The final result is a false-color image in which similar colors represent similar characteristics across all its data dimensions. SOM_VIS provides a control panel for selection of a subset of suitably preprocessed MISR radiance data, and a control panel for choosing parameters to run SOM training. SOM_VIS also includes a component for displaying the false-color SOM image, a color map for the trained SOM lattice, a plot showing an original input vector in 36 dimensions of a selected pixel from the SOM image, the SOM vector that represents the input vector, and the Euclidean distance between the two vectors.
    Keywords: Man/System Technology and Life Support
    Type: NPO-40666 , NASA Tech Briefs, December 2005; 15
    Format: application/pdf
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  • 7
    Publication Date: 2019-07-12
    Description: GeoFEST(P) is a computer program written for use in the QuakeSim project, which is devoted to development and improvement of means of computational simulation of earthquakes. GeoFEST(P) models interacting earthquake fault systems from the fault-nucleation to the tectonic scale. The development of GeoFEST( P) has involved coupling of two programs: GeoFEST and the Pyramid Adaptive Mesh Refinement Library. GeoFEST is a message-passing-interface-parallel code that utilizes a finite-element technique to simulate evolution of stress, fault slip, and plastic/elastic deformation in realistic materials like those of faulted regions of the crust of the Earth. The products of such simulations are synthetic observable time-dependent surface deformations on time scales from days to decades. Pyramid Adaptive Mesh Refinement Library is a software library that facilitates the generation of computational meshes for solving physical problems. In an application of GeoFEST(P), a computational grid can be dynamically adapted as stress grows on a fault. Simulations on workstations using a few tens of thousands of stress and displacement finite elements can now be expanded to multiple millions of elements with greater than 98-percent scaled efficiency on over many hundreds of parallel processors (see figure).
    Keywords: Man/System Technology and Life Support
    Type: NPO-41079 , NASA Tech Briefs, September 2006; 43
    Format: application/pdf
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  • 8
    Publication Date: 2019-07-12
    Description: This Web-based tsunami simulation system allows users to remotely run a model on JPL s supercomputers for a given undersea earthquake. At the time of this reporting, predicting tsunamis on the Internet has never happened before. This new code directly couples the earthquake model and the ocean model on parallel computers and improves simulation speed. Seismometers can only detect information from earthquakes; they cannot detect whether or not a tsunami may occur as a result of the earthquake. When earthquake-tsunami models are coupled with the improved computational speed of modern, high-performance computers and constrained by remotely sensed data, they are able to provide early warnings for those coastal regions at risk. The software is capable of testing NASA s satellite observations of tsunamis. It has been successfully tested for several historical tsunamis, has passed all alpha and beta testing, and is well documented for users.
    Keywords: Man/System Technology and Life Support
    Type: NPO-44443 , NASA Tech Briefs, September 2007; 52
    Format: application/pdf
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