National Library of Energy BETA

Sample records for bind deleted domain

  1. Cellulose binding domain proteins

    DOE Patents [OSTI]

    Shoseyov, Oded (Karmey Yosef, IL); Shpiegl, Itai (Rehovot, IL); Goldstein, Marc (Davis, CA); Doi, Roy (Davis, CA)

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  2. Cellulose binding domain proteins

    DOE Patents [OSTI]

    Shoseyov, O.; Shpiegl, I.; Goldstein, M.; Doi, R.

    1998-11-17

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

  3. Cellulose binding domain fusion proteins

    DOE Patents [OSTI]

    Shoseyov, O.; Yosef, K.; Shpiegl, I.; Goldstein, M.A.; Doi, R.H.

    1998-02-17

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

  4. Cellulose binding domain fusion proteins

    DOE Patents [OSTI]

    Shoseyov, Oded (Karmey Yosef, IL); Shpiegl, Itai (Rehovot, IL); Goldstein, Marc A. (Davis, CA); Doi, Roy H. (Davis, CA)

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  5. Nucleic acids encoding a cellulose binding domain

    DOE Patents [OSTI]

    Shoseyov, O.; Shpiegl, I.; Goldstein, M.A.; Doi, R.H.

    1996-03-05

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 15 figs.

  6. Nucleic acids encoding a cellulose binding domain

    DOE Patents [OSTI]

    Shoseyov, Oded (Karmey Yosef, IL); Shpiegl, Itai (Rehovot, IL); Goldstein, Marc A. (Davis, CA); Doi, Roy H. (Davis, CA)

    1996-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  7. Structural and Histone Binding Ability Characterizations of Human PWWP Domains

    SciTech Connect (OSTI)

    Wu, Hong; Zeng, Hong; Lam, Robert; Tempel, Wolfram; Amaya, Maria F.; Xu, Chao; Dombrovski, Ludmila; Qiu, Wei; Wang, Yanming; Min, Jinrong (Toronto); (Penn)

    2013-09-25

    The PWWP domain was first identified as a structural motif of 100-130 amino acids in the WHSC1 protein and predicted to be a protein-protein interaction domain. It belongs to the Tudor domain 'Royal Family', which consists of Tudor, chromodomain, MBT and PWWP domains. While Tudor, chromodomain and MBT domains have long been known to bind methylated histones, PWWP was shown to exhibit histone binding ability only until recently. The PWWP domain has been shown to be a DNA binding domain, but sequence analysis and previous structural studies show that the PWWP domain exhibits significant similarity to other 'Royal Family' members, implying that the PWWP domain has the potential to bind histones. In order to further explore the function of the PWWP domain, we used the protein family approach to determine the crystal structures of the PWWP domains from seven different human proteins. Our fluorescence polarization binding studies show that PWWP domains have weak histone binding ability, which is also confirmed by our NMR titration experiments. Furthermore, we determined the crystal structures of the BRPF1 PWWP domain in complex with H3K36me3, and HDGF2 PWWP domain in complex with H3K79me3 and H4K20me3. PWWP proteins constitute a new family of methyl lysine histone binders. The PWWP domain consists of three motifs: a canonical {beta}-barrel core, an insertion motif between the second and third {beta}-strands and a C-terminal {alpha}-helix bundle. Both the canonical {beta}-barrel core and the insertion motif are directly involved in histone binding. The PWWP domain has been previously shown to be a DNA binding domain. Therefore, the PWWP domain exhibits dual functions: binding both DNA and methyllysine histones.

  8. A Double-Deletion Method to Quantifying Incremental Binding Energies in Proteins from Experiment: Example of a Destabilizing Hydrogen

    E-Print Network [OSTI]

    Sancho, Javier

    A Double-Deletion Method to Quantifying Incremental Binding Energies in Proteins from Experiment: Example of a Destabilizing Hydrogen Bonding Pair Luis A. Campos,*y Santiago Cuesta-Lo´pez,*z Jon Lo of a specific hydrogen bond in apoflavodoxin to protein stability is investigated by combining theory

  9. Methods of use of cellulose binding domain proteins

    DOE Patents [OSTI]

    Shoseyov, O.; Shpiegl, I.; Goldstein, M.A.; Doi, R.H.

    1997-09-23

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

  10. Methods of detection using a cellulose binding domain fusion product

    DOE Patents [OSTI]

    Shoseyov, Oded (Shimshon, IL); Shpiegl, Itai (North Gallilea, IL); Goldstein, Marc A. (Davis, CA); Doi, Roy H. (Davis, CA)

    1999-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  11. Methods of use of cellulose binding domain proteins

    DOE Patents [OSTI]

    Shoseyov, Oded (Karmey Yosef, IL); Shpiegl, Itai (Rehovot, IL); Goldstein, Marc A. (Davis, CA); Doi, Roy H. (Davis, CA)

    1997-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  12. Methods of detection using a cellulose binding domain fusion product

    DOE Patents [OSTI]

    Shoseyov, O.; Shpiegl, I.; Goldstein, M.A.; Doi, R.H.

    1999-01-05

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 34 figs.

  13. Calcium Binding by the N-Terminal Cellulose-Binding Domain from Cellulomonas fimi -1,4-Glucanase CenC

    E-Print Network [OSTI]

    McIntosh, Lawrence P.

    Calcium Binding by the N-Terminal Cellulose-Binding Domain from Cellulomonas fimi -1,4-Glucanase, 1998 ABSTRACT: The interaction of the N-terminal cellulose-binding domain, CBDN1, from Cellulomonas-state stability. Enzymes that degrade cellulose often contain one or more domains that mediate binding

  14. The Cellulose-binding Domains from Cellulomonas fimi bbb-1,4-Glucanase CenC Bind Nitroxide Spin-labeled

    E-Print Network [OSTI]

    McIntosh, Lawrence P.

    The Cellulose-binding Domains from Cellulomonas fimi bbb-1,4-Glucanase CenC Bind Nitroxide Spin6T 1Z3, Canada The N-terminal cellulose-binding domains CBDN1 and CBDN2 from Cellulomonas ®mi cellulase CenC each adopt a jelly-roll b-sandwich struc- ture with a cleft into which amorphous cellulose

  15. Impact of the [delta]F508 Mutation in First Nucleotide-binding Domain of Human Cystic Fibrosis Transmembrane Conductance Regulator on Domain Folding and Structure

    SciTech Connect (OSTI)

    Lewis, Hal A.; Zhao, Xun; Wang, Chi; Sauder, J. Michael; Rooney, Isabelle; Noland, Brian W.; Lorimer, Don; Kearins, Margaret C.; Conners, Kris; Condon, Brad; Maloney, Peter C.; Guggino, William B.; Hunt, John F.; Emtage, Spencer (SG); (Columbia); (JHU)

    2010-07-19

    Cystic fibrosis is caused by defects in the cystic fibrosis transmembrane conductance regulator (CFTR), commonly the deletion of residue Phe-508 (DeltaF508) in the first nucleotide-binding domain (NBD1), which results in a severe reduction in the population of functional channels at the epithelial cell surface. Previous studies employing incomplete NBD1 domains have attributed this to aberrant folding of DeltaF508 NBD1. We report structural and biophysical studies on complete human NBD1 domains, which fail to demonstrate significant changes of in vitro stability or folding kinetics in the presence or absence of the DeltaF508 mutation. Crystal structures show minimal changes in protein conformation but substantial changes in local surface topography at the site of the mutation, which is located in the region of NBD1 believed to interact with the first membrane spanning domain of CFTR. These results raise the possibility that the primary effect of DeltaF508 is a disruption of proper interdomain interactions at this site in CFTR rather than interference with the folding of NBD1. Interestingly, increases in the stability of NBD1 constructs are observed upon introduction of second-site mutations that suppress the trafficking defect caused by the DeltaF508 mutation, suggesting that these suppressors might function indirectly by improving the folding efficiency of NBD1 in the context of the full-length protein. The human NBD1 structures also solidify the understanding of CFTR regulation by showing that its two protein segments that can be phosphorylated both adopt multiple conformations that modulate access to the ATPase active site and functional interdomain interfaces.

  16. A Ternary Metal Binding Site in the C2 Domain of Phosphoinositide-Specific Phospholipase C-1,

    E-Print Network [OSTI]

    Williams, Roger L.

    A Ternary Metal Binding Site in the C2 Domain of Phosphoinositide-Specific Phospholipase C-1, Lars. Binding of these metal ions is observed in the active site of the catalytic TIM barrel and in the calcium adjacent binding sites in the C2 domain were observed for calcium and the other metal/enzyme complexes

  17. Mapping small molecule binding data to structural domains

    E-Print Network [OSTI]

    Kruger, Felix A.; Rostom, Raghd; Overington, John P.

    2012-12-07

    R_lig-bind 25 128 P40238 fn3 391 475 P48443 Nuc_recep-AF1 24 134 P48443 Hormone_recep 248 443 P48443 zf-C4 137 206 P54219 MFS_1 77 433 P54219 MFS_1 422 493 Q92813 T4_deiodinase 4 262 P08506 PBP5_C 285 376 P08506 Peptidase_S11 28 266 P10826 Hormone_recep 222 406... P10826 zf-C4 86 155 P10828 Hormone_recep 257 445 P10828 zf-C4 105 176 P11926 Orn_Arg_deC_N 44 282 P11926 Orn_DAP_Arg_deC 285 408 P19793 Nuc_recep-AF1 16 127 P19793 Hormone_recep 251 442 P19793 zf-C4 133 202 P27815 PDEase_I 432 676 P28702 Hormone...

  18. A new protein folding screen: Application to the ligand binding domains of a glutamate and kainate

    E-Print Network [OSTI]

    Lebendiker, Mario

    A new protein folding screen: Application to the ligand binding domains of a glutamate and kainate of determining and evaluating protein folding conditions, we have designed a new fractional factorial protein folding screen. The screen includes 12 factors shown by previous experiments to enhance protein folding

  19. Kits and methods of detection using cellulose binding domain fusion proteins

    DOE Patents [OSTI]

    Shoseyov, Oded (Karmey Yosef, IL)

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  20. Kits and methods of detection using cellulose binding domain fusion proteins

    DOE Patents [OSTI]

    Shoseyov, O.; Yosef, K.

    1998-04-14

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

  1. Structural and Energetic Analysis of Activiation by a Cyclic Nucleotide Binding Domain

    SciTech Connect (OSTI)

    Altieri,S.; Clayton, G.; Silverman, W.; Olivares, A.; De La Cruz, E.; Thomas, L.; Morais-Cabral, J.

    2008-01-01

    MlotiK1 is a prokaryotic homolog of cyclic-nucleotide-dependent ion channels that contains an intracellular C-terminal cyclic nucleotide binding (CNB) domain. X-ray structures of the CNB domain have been solved in the absence of ligand and bound to cAMP. Both the full-length channel and CNB domain fragment are easily expressed and purified, making MlotiK1 a useful model system for dissecting activation by ligand binding. We have used X-ray crystallography to determine three new MlotiK1 CNB domain structures: a second apo configuration, a cGMP-bound structure, and a second cAMP-bound structure. In combination, the five MlotiK1 CNB domain structures provide a unique opportunity for analyzing, within a single protein, the structural differences between the apo state and the bound state, and the structural variability within each state. With this analysis as a guide, we have probed the nucleotide selectivity and importance of specific residue side chains in ligand binding and channel activation. These data help to identify ligand-protein interactions that are important for ligand dependence in MlotiK1 and, more globally, in the class of nucleotide-dependent proteins.

  2. LINC Complexes Form by Binding of Three KASH Peptides to Domain Interfaces of Trimeric SUN Proteins

    SciTech Connect (OSTI)

    Sosa, Brian A.; Rothballer, Andrea; Kutay, Ulrike; Schwartz, Thomas U.

    2012-08-31

    Linker of nucleoskeleton and cytoskeleton (LINC) complexes span the nuclear envelope and are composed of KASH and SUN proteins residing in the outer and inner nuclear membrane, respectively. LINC formation relies on direct binding of KASH and SUN in the perinuclear space. Thereby, molecular tethers are formed that can transmit forces for chromosome movements, nuclear migration, and anchorage. We present crystal structures of the human SUN2-KASH1/2 complex, the core of the LINC complex. The SUN2 domain is rigidly attached to a trimeric coiled coil that prepositions it to bind three KASH peptides. The peptides bind in three deep and expansive grooves formed between adjacent SUN domains, effectively acting as molecular glue. In addition, a disulfide between conserved cysteines on SUN and KASH covalently links both proteins. The structure provides the basis of LINC complex formation and suggests a model for how LINC complexes might arrange into higher-order clusters to enhance force-coupling.

  3. Adhesion of membranes via receptor-ligand complexes: Domain formation, binding cooperativity, and active processes

    E-Print Network [OSTI]

    Thomas R. Weikl; Mesfin Asfaw; Heinrich Krobath; Bartosz Rozycki; Reinhard Lipowsky

    2009-06-09

    Cell membranes interact via anchored receptor and ligand molecules. Central questions on cell adhesion concern the binding affinity of these membrane-anchored molecules, the mechanisms leading to the receptor-ligand domains observed during adhesion, and the role of cytoskeletal and other active processes. In this review, these questions are addressed from a theoretical perspective. We focus on models in which the membranes are described as elastic sheets, and the receptors and ligands as anchored molecules. In these models, the thermal membrane roughness on the nanometer scale leads to a cooperative binding of anchored receptor and ligand molecules, since the receptor-ligand binding smoothens out the membranes and facilitates the formation of additional bonds. Patterns of receptor domains observed in Monte Carlo simulations point towards a joint role of spontaneous and active processes in cell adhesion. The interactions mediated by the receptors and ligand molecules can be characterized by effective membrane adhesion potentials that depend on the concentrations and binding energies of the molecules.

  4. Insights into the binding of PARP inhibitors to the catalytic domain of human tankyrase-2

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Qiu, Wei; Lam, Robert; Voytyuk, Oleksandr; Romanov, Vladimir; Gordon, Roni; Gebremeskel, Simon; Vodsedalek, Jakub; Thompson, Christine; Beletskaya, Irina; Battaile, Kevin P.; et al

    2014-07-31

    The poly(ADP-ribose) polymerase (PARP) family represents a new class of therapeutic targets with diverse potential disease indications. PARP1 and PARP2 inhibitors have been developed for breast and ovarian tumors manifesting double-stranded DNA-repair defects, whereas tankyrase 1 and 2 (TNKS1 and TNKS2, also known as PARP5a and PARP5b, respectively) inhibitors have been developed for tumors with elevated ?-catenin activity. As the clinical relevance of PARP inhibitors continues to be actively explored, there is heightened interest in the design of selective inhibitors based on the detailed structural features of how small-molecule inhibitors bind to each of the PARP family members. Here, themore »high-resolution crystal structures of the human TNKS2 PARP domain in complex with 16 various PARP inhibitors are reported, including the compounds BSI-201, AZD-2281 and ABT-888, which are currently in Phase 2 or 3 clinical trials. These structures provide insight into the inhibitor-binding modes for the tankyrase PARP domain and valuable information to guide the rational design of future tankyrase-specific inhibitors.« less

  5. Insights into the binding of PARP inhibitors to the catalytic domain of human tankyrase-2

    SciTech Connect (OSTI)

    Qiu, Wei; Lam, Robert; Voytyuk, Oleksandr; Romanov, Vladimir; Gordon, Roni; Gebremeskel, Simon; Vodsedalek, Jakub; Thompson, Christine; Beletskaya, Irina; Battaile, Kevin P.; Pai, Emil F.; Rottapel, Robert; Chirgadze, Nickolay Y.

    2014-07-31

    The poly(ADP-ribose) polymerase (PARP) family represents a new class of therapeutic targets with diverse potential disease indications. PARP1 and PARP2 inhibitors have been developed for breast and ovarian tumors manifesting double-stranded DNA-repair defects, whereas tankyrase 1 and 2 (TNKS1 and TNKS2, also known as PARP5a and PARP5b, respectively) inhibitors have been developed for tumors with elevated ?-catenin activity. As the clinical relevance of PARP inhibitors continues to be actively explored, there is heightened interest in the design of selective inhibitors based on the detailed structural features of how small-molecule inhibitors bind to each of the PARP family members. Here, the high-resolution crystal structures of the human TNKS2 PARP domain in complex with 16 various PARP inhibitors are reported, including the compounds BSI-201, AZD-2281 and ABT-888, which are currently in Phase 2 or 3 clinical trials. These structures provide insight into the inhibitor-binding modes for the tankyrase PARP domain and valuable information to guide the rational design of future tankyrase-specific inhibitors.

  6. Mutational analysis of the RNA-binding domain of the Prunus necrotic ringspot virus (PNRSV) movement protein reveals its requirement for cell-to-cell movement

    SciTech Connect (OSTI)

    Carmen Herranz, Ma [Instituto de Biologia Molecular y Celular de Plantas (IBMCP), UPV-CSIC, Avda. de los Naranjos, s/n, 46022, Valencia (Spain); Sanchez-Navarro, Jesus-Angel [Instituto de Biologia Molecular y Celular de Plantas (IBMCP), UPV-CSIC, Avda. de los Naranjos, s/n, 46022, Valencia (Spain); Sauri, Ana [Departament de Bioquimica i Biologia Molecular, Universitat de Valencia, E-46100 Burjassot (Spain); Mingarro, Ismael [Departament de Bioquimica i Biologia Molecular, Universitat de Valencia, E-46100 Burjassot (Spain); Pallas, Vicente [Instituto de Biologia Molecular y Celular de Plantas (IBMCP), UPV-CSIC, Avda. de los Naranjos, s/n, 46022, Valencia (Spain)]. E-mail: vpallas@ibmcp.upv.es

    2005-08-15

    The movement protein (MP) of Prunus necrotic ringspot virus (PNRSV) is required for cell-to-cell movement. MP subcellular localization studies using a GFP fusion protein revealed highly punctate structures between neighboring cells, believed to represent plasmodesmata. Deletion of the RNA-binding domain (RBD) of PNRSV MP abolishes the cell-to-cell movement. A mutational analysis on this RBD was performed in order to identify in vivo the features that govern viral transport. Loss of positive charges prevented the cell-to-cell movement even though all mutants showed a similar accumulation level in protoplasts to those observed with the wild-type (wt) MP. Synthetic peptides representing the mutants and wild-type RBDs were used to study RNA-binding affinities by EMSA assays being approximately 20-fold lower in the mutants. Circular dichroism analyses revealed that the secondary structure of the peptides was not significantly affected by mutations. The involvement of the affinity changes between the viral RNA and the MP in the viral cell-to-cell movement is discussed.

  7. The structures of non-CG-repeat Z-DNAs co-crystallized with the Z-DNA-binding domain, hZ?ADAR1

    E-Print Network [OSTI]

    Ha, Sung Chul

    The Z-DNA conformation preferentially occurs at alternating purine-pyrimidine repeats, and is specifically recognized by Z? domains identified in several Z-DNA-binding proteins. The binding of Z? to foreign or chromosomal ...

  8. NMR Structures of Salt-Refolded Forms of the 434-Repressor DNA-Binding Domain in 6 M Urea

    E-Print Network [OSTI]

    Wider, Gerhard

    NMR Structures of Salt-Refolded Forms of the 434-Repressor DNA-Binding Domain in 6 M Urea- 8). Examples are salt-induced refolding of proteins at acidic pH (9), leading to the formation), and lysozyme (14) allowed detailed structural and dynamic characterization of salt-stabilized A-states, which

  9. The tip of the iceberg: RNA-binding proteins with prion-like domains in neurodegenerative disease

    E-Print Network [OSTI]

    Shorter, James

    ) and a putative prion do- main. Indeed, of 210 human RRM-bearing proteins, 29 have a putative prion domain, and 12 1st and 10th among RRM-bearing prion candidates, form cytoplasmic inclusions in the degenerating RNA-binding proteostasis of TAF15, which is the 2nd ranked RRM-bearing prion candidate, has been con

  10. Membrane binding mode of intrinsically disordered cytoplasmic domains of T cell receptor signaling subunits depends on lipid composition

    SciTech Connect (OSTI)

    Sigalov, Alexander B., E-mail: Alexander.sigalov@umassmed.edu [University of Massachusetts Medical School, Worcester, MA 01655 (United States); Hendricks, Gregory M. [University of Massachusetts Medical School, Worcester, MA 01655 (United States)] [University of Massachusetts Medical School, Worcester, MA 01655 (United States)

    2009-11-13

    Intrinsically disordered cytoplasmic domains of T cell receptor (TCR) signaling subunits including {zeta}{sub cyt} and CD3{epsilon}{sub cyt} all contain one or more copies of an immunoreceptor tyrosine-based activation motif (ITAM), tyrosine residues of which are phosphorylated upon receptor triggering. Membrane binding-induced helical folding of {zeta}{sub cyt} and CD3{epsilon}{sub cyt} ITAMs is thought to control TCR activation. However, the question whether or not lipid binding of {zeta}{sub cyt} and CD3{epsilon}{sub cyt} is necessarily accompanied by a folding transition of ITAMs remains open. In this study, we investigate whether the membrane binding mechanisms of {zeta}{sub cyt} and CD3{epsilon}{sub cyt} depend on the membrane model used. Circular dichroic and fluorescence data indicate that binding of {zeta}{sub cyt} and CD3{epsilon}{sub cyt} to detergent micelles and unstable vesicles is accompanied by a disorder-to-order transition, whereas upon binding to stable vesicles these proteins remain unfolded. Using electron microscopy and dynamic light scattering, we show that upon protein binding, unstable vesicles fuse and rupture. In contrast, stable vesicles remain intact under these conditions. This suggests different membrane binding modes for {zeta}{sub cyt} and CD3{epsilon}{sub cyt} depending on the bilayer stability: (1) coupled binding and folding, and (2) binding without folding. These findings explain the long-standing puzzle in the literature and highlight the importance of the choice of an appropriate membrane model for protein-lipid interactions studies.

  11. Domain

    E-Print Network [OSTI]

    charlotb

    2010-08-31

    Fish. Dog. Chicken. Shark. Man. Tiger. Dog. Domain. Correspondence. Range. 3. Members of a an instrument the a set of. Rock Band member can play.

  12. Structural Insights into the Functional Role of the Hcn Sub-domain of the Receptor-Binding Domain of the Botulinum Neurotoxin Mosaic Serotype C/D

    SciTech Connect (OSTI)

    Zhang, Yanfeng; Gardberg, Anna; Edwards, Tom E.; Sankaran, Banumathi; Robinson, Howard; Varnum, Susan M.; Buchko, Garry W.

    2013-07-01

    Botulinum neurotoxin (BoNT), the causative agent of the deadly neuroparalytic disease botulism, is the most poisonous protein known for humans. Produced by different strains of the anaerobic bacterium Clostridium botulinum, BoNT effects cellular intoxication via a multistep mechanism executed by the three modules of the activated protein. Endocytosis, the first step of cellular intoxication, is triggered by the ~50 kDa, heavy-chain receptor-binding module (HCR) that is specific for a ganglioside and a protein receptor on neuronal cell surfaces. This dual receptor recognition mechanism between BoNT and the host cell’s membrane is well documented and occurs via specific intermolecular interactions with the C-terminal sub-domain, Hcc, of BoNT-HCR. The N-terminal sub-domain of BoNT-HCR, Hcn, comprises ~50% of BoNT-HCR and adopts a B-sheet jelly roll fold. While suspected in assisting cell surface recognition, no unambiguous function for the Hcn sub-domain in BoNT has been indentified. To obtain insights into the potential function of the Hcn sub-domain in BoNT, the first crystal structure of a BoNT with an organic ligand bound to the Hcn sub-domain has been obtained. Here, we describe the crystal structure of BoNT/CD-HCR determined at 1.70 Å resolution with a tetraethylene glycol (PG4) molecule bound in an hydrophobic cleft between B-strands in the B-sheet jelly fold roll of the Hcn sub-domain. The molecule is completely engulfed in the cleft, making numerous hydrophobic (Y932, S959, W966, and D1042) and hydrophilic (S935, W977, L979, N1013, and I1066) contacts with the protein’s side chain and backbone that may mimic in vivo interactions with the phospholipid membranes on neuronal cell surfaces. A sulfate ion was also observed bound to residues T1176, D1177, K1196, and R1243 in the Hcc sub-domain of BoNT/CD-HCR. In the crystal structure of a similar protein, BoNT/D-HCR, a sialic acid

  13. Structure of N-Terminal Domain of NPC1 Reveals Distinct Subdomains for Binding and Transfer of Cholesterol

    SciTech Connect (OSTI)

    Kwon, Hyock Joo; Abi-Mosleh, Lina; Wang, Michael L.; Deisenhofer, Johann; Goldstein, Joseph L.; Brown, Michael S.; Infante, Rodney E.

    2010-09-21

    LDL delivers cholesterol to lysosomes by receptor-mediated endocytosis. Exit of cholesterol from lysosomes requires two proteins, membrane-bound Niemann-Pick C1 (NPC1) and soluble NPC2. NPC2 binds cholesterol with its isooctyl side chain buried and its 3{beta}-hydroxyl exposed. Here, we describe high-resolution structures of the N-terminal domain (NTD) of NPC1 and complexes with cholesterol and 25-hydroxycholesterol. NPC1(NTD) binds cholesterol in an orientation opposite to NPC2: 3{beta}-hydroxyl buried and isooctyl side chain exposed. Cholesterol transfer from NPC2 to NPC1(NTD) requires reorientation of a helical subdomain in NPC1(NTD), enlarging the opening for cholesterol entry. NPC1 with point mutations in this subdomain (distinct from the binding subdomain) cannot accept cholesterol from NPC2 and cannot restore cholesterol exit from lysosomes in NPC1-deficient cells. We propose a working model wherein after lysosomal hydrolysis of LDL-cholesteryl esters, cholesterol binds NPC2, which transfers it to NPC1(NTD), reversing its orientation and allowing insertion of its isooctyl side chain into the outer lysosomal membranes.

  14. A Generalized Deletion Machine

    E-Print Network [OSTI]

    Indranil Chakrabarty; Satyabrata Adhikari

    2005-11-22

    In this work we prescribe a more generalized quantum-deleting machine (input state dependent). The fidelity of deletion is dependent on some machine parameters such that on alteration of machine parameters we get back to standard deleting machines. We also carried out a various comparative study of various kinds of quantum deleting machines. We also plotted graphs, making a comparative study of fidelity of deletion of the deletion machines, obtained as particular cases on changing the machine parameters of our machine.

  15. Identification of High Affinity Polo-like Kinase 1 (Plk1) Polo-box Domain Binding Peptides Using Oxime-Based Diversification

    E-Print Network [OSTI]

    Liu, Fa

    In an effort to develop improved binding antagonists of the polo-like kinase 1 (Plk1) polo-box domain (PBD), we optimized interactions of the known high affinity 5-mer peptide PLHSpT using oxime-based post solid-phase ...

  16. Structure of trigger factor binding domain in biologically homologous complex with eubacterial ribosome reveals its chaperone action

    SciTech Connect (OSTI)

    Baram, David; Pyetan, Erez; Sittner, Assa; Auerbach-Nevo, Tamar; Bashan, Anat; Yonath, Ada (WIS-I)

    2010-07-13

    Trigger factor (TF), the first chaperone in eubacteria to encounter the emerging nascent chain, binds to the large ribosomal subunit in the vicinity of the protein exit tunnel opening and forms a sheltered folding space. Here, we present the 3.5-{angstrom} crystal structure of the physiological complex of the large ribosomal subunit from the eubacterium Deinococcus radiodurans with the N-terminal domain of TF (TFa) from the same organism. For anchoring, TFa exploits a small ribosomal surface area in the vicinity of proteins L23 and L29, by using its 'signature motif' as well as additional structural elements. The molecular details of TFa interactions reveal that L23 is essential for the association of TF with the ribosome and may serve as a channel of communication with the nascent chain progressing in the tunnel. L29 appears to induce a conformational change in TFa, which results in the exposure of TFa hydrophobic patches to the opening of the ribosomal exit tunnel, thus increasing its affinity for hydrophobic segments of the emerging nascent polypeptide. This observation implies that, in addition to creating a protected folding space for the emerging nascent chain, TF association with the ribosome prevents aggregation by providing a competing hydrophobic environment and may be critical for attaining the functional conformation necessary for chaperone activity.

  17. Structural dynamics and ssDNA binding activity of the three N-terminal domains of the large subunit of Replication Protein A from small angle X-ray scattering

    SciTech Connect (OSTI)

    Pretto, Dalyir I.; Tsutakawa, Susan; Brosey, Chris A.; Castillo, Amalchi; Chagot, Marie-Eve; Smith, Jarrod A.; Tainer, John A.; Chazin, Walter J.

    2010-03-11

    Replication Protein A (RPA) is the primary eukaryotic ssDNA binding protein utilized in diverse DNA transactions in the cell. RPA is a heterotrimeric protein with seven globular domains connected by flexible linkers, which enable substantial inter-domain motion that is essential to its function. Small angle X-ray scattering (SAXS) experiments on two multi-domain constructs from the N-terminus of the large subunit (RPA70) were used to examine the structural dynamics of these domains and their response to the binding of ssDNA. The SAXS data combined with molecular dynamics simulations reveal substantial interdomain flexibility for both RPA70AB (the tandem high affinity ssDNA binding domains A and B connected by a 10-residue linker) and RPA70NAB (RPA70AB extended by a 70-residue linker to the RPA70N protein interaction domain). Binding of ssDNA to RPA70NAB reduces the interdomain flexibility between the A and B domains, but has no effect on RPA70N. These studies provide the first direct measurements of changes in orientation of these three RPA domains upon binding ssDNA. The results support a model in which RPA70N remains structurally independent of RPA70AB in the DNA bound state and therefore freely available to serve as a protein recruitment module.

  18. Structure of the vesicular stomatitis virus nucleocapsid in complex with the nucleocapsid-binding domain of the small polymerase cofactor, P

    SciTech Connect (OSTI)

    Green, Todd J.; Luo, Ming

    2009-10-05

    The negative-strand RNA viruses (NSRVs) are unique because their nucleocapsid, not the naked RNA, is the active template for transcription and replication. The viral polymerase of nonsegmented NSRVs contains a large polymerase catalytic subunit (L) and a nonenzymatic cofactor, the phosphoprotein (P). Insight into how P delivers the polymerase complex to the nucleocapsid has long been pursued by reverse genetics and biochemical approaches. Here, we present the X-ray crystal structure of the C-terminal domain of P of vesicular stomatitis virus, a prototypic nonsegmented NSRV, bound to nucleocapsid-like particles. P binds primarily to the C-terminal lobe of 2 adjacent N proteins within the nucleocapsid. This binding mode is exclusive to the nucleocapsid, not the nucleocapsid (N) protein in other existing forms. Localization of phosphorylation sites within P and their proximity to the RNA cavity give insight into how the L protein might be oriented to access the RNA template.

  19. The PD-1/PD-L1 complex resembles the antigen-binding Fv domains of antibodies and T cell receptors

    SciTech Connect (OSTI)

    Lin, David Yin-wei; Tanaka, Yoshimasa; Iwasaki, Masashi; Gittis, Apostolos G.; Su, Hua-Poo; Mikami, Bunzo; Okazaki, Taku; Honjo, Tasuku; Minato, Nagahiro; Garboczi, David N. (NIH); (Kyoto)

    2008-07-29

    Signaling through the programmed death 1 (PD-1) inhibitory receptor upon binding its ligand, PD-L1, suppresses immune responses against autoantigens and tumors and plays an important role in the maintenance of peripheral immune tolerance. Release from PD-1 inhibitory signaling revives 'exhausted' virus-specific T cells in chronic viral infections. Here we present the crystal structure of murine PD-1 in complex with human PD-L1. PD-1 and PD-L1 interact through the conserved front and side of their Ig variable (IgV) domains, as do the IgV domains of antibodies and T cell receptors. This places the loops at the ends of the IgV domains on the same side of the PD-1/PD-L1 complex, forming a surface that is similar to the antigen-binding surface of antibodies and T cell receptors. Mapping conserved residues allowed the identification of residues that are important in forming the PD-1/PD-L1 interface. Based on the structure, we show that some reported loss-of-binding mutations involve the PD-1/PD-L1 interaction but that others compromise protein folding. The PD-1/PD-L1 interaction described here may be blocked by antibodies or by designed small-molecule drugs to lower inhibitory signaling that results in a stronger immune response. The immune receptor-like loops offer a new surface for further study and potentially the design of molecules that would affect PD-1/PD-L1 complex formation and thereby modulate the immune response.

  20. The Escherichia coli RhaS Transcriptional Activator: Transcriptional Activation by the DNA-Binding Domain, The Interdomain Effector Response, and Negative Autoregulation

    E-Print Network [OSTI]

    Skredenske, Jeffrey M.

    2012-05-31

    : The AraC/XylS family activator RhaS negatively 78 autoregulates rhaSR expression by preventing cyclic AMP receptor protein activation 1 CHAPTER 1 Transcription Activation by the DNA-Binding Domain of the AraC Family Protein Rha... encodes a second L-rhamnose responsive transcription activator, RhaR (37). RhaR activates transcription of the operon that encodes the two activator proteins, rhaSR (37, 38). All three operons in the L-rhamnose regulon also require a second activator...

  1. Structure of the unique SEFIR domain from human interleukin 17 receptor A reveals a composite ligand-binding site containing a conserved ?-helix for Act1 binding and IL-17 signaling

    SciTech Connect (OSTI)

    Zhang, Bing [Oklahoma State University, Stillwater, OK 74078 (United States); Liu, Caini; Qian, Wen [Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195 (United States); Han, Yue [Oklahoma State University, Stillwater, OK 74078 (United States); Li, Xiaoxia, E-mail: lix@ccf.org [Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195 (United States); Deng, Junpeng, E-mail: lix@ccf.org [Oklahoma State University, Stillwater, OK 74078 (United States)

    2014-05-01

    Crystal structure of the SEFIR domain from human IL-17 receptor A provides new insights into IL-17 signaling. Interleukin 17 (IL-17) cytokines play a crucial role in mediating inflammatory and autoimmune diseases. A unique intracellular signaling domain termed SEFIR is found within all IL-17 receptors (IL-17Rs) as well as the key adaptor protein Act1. SEFIR-mediated protein–protein interaction is a crucial step in IL-17 cytokine signaling. Here, the 2.3 Å resolution crystal structure of the SEFIR domain of IL-17RA, the most commonly shared receptor for IL-17 cytokine signaling, is reported. The structure includes the complete SEFIR domain and an additional ?-helical C-terminal extension, which pack tightly together to form a compact unit. Structural comparison between the SEFIR domains of IL-17RA and IL-17RB reveals substantial differences in protein topology and folding. The uniquely long insertion between strand ?C and helix ?C in IL-17RA SEFIR is mostly well ordered, displaying a helix (?CC?{sub ins}) and a flexible loop (CC?). The DD? loop in the IL-17RA SEFIR structure is much shorter; it rotates nearly 90° with respect to the counterpart in the IL-17RB SEFIR structure and shifts about 12 Å to accommodate the ?CC?{sub ins} helix without forming any knots. Helix ?C was identified as critical for its interaction with Act1 and IL-17-stimulated gene expression. The data suggest that the heterotypic SEFIR–SEFIR association via helix ?C is a conserved and signature mechanism specific for IL-17 signaling. The structure also suggests that the downstream motif of IL-17RA SEFIR together with helix ?C could provide a composite ligand-binding surface for recruiting Act1 during IL-17 signaling.

  2. Identification of new functions for BRCT domains

    E-Print Network [OSTI]

    Mohammad, Duaa H

    2008-01-01

    Our lab identified the tandem BRCT domains of PTIP function as a DNA damage responsive phospho binding domain that recognizes proteins phosphorylated by ATM and ATR after DNA damage. The PTIP tandem BRCT domains are ...

  3. Instruction Guide Deleting Personalizations on

    E-Print Network [OSTI]

    Sin, Peter

    Reconciliation 20. On the Internet Options pop-up page, under Browsing History, click the Delete button: 21 to the upgrade will not cause problems when approving PCard transactions. These instructions are for Internet. Clear your cookies and cache. In Internet Explorer, select Tools, then Internet Options. Updated May 1

  4. A Cysteine-Rich CCG Domain Contains a Novel [4Fe-4S] Cluster Binding Motif As Deduced From Studies With Subunit B of Heterodisulfide Reductase From Methanothermobacter Marburgensis

    SciTech Connect (OSTI)

    Hamann, N.; Mander, G.J.; Shokes, J.E.; Scott, R.A.; Bennati, M.; Hedderich, R.

    2009-06-01

    Heterodisulfide reductase (HDR) of methanogenic archaea with its active-site [4Fe-4S] cluster catalyzes the reversible reduction of the heterodisulfide (CoM-S-S-CoB) of the methanogenic coenzyme M (CoM-SH) and coenzyme B (CoB-SH). CoM-HDR, a mechanistic-based paramagnetic intermediate generated upon half-reaction of the oxidized enzyme with CoM-SH, is a novel type of [4Fe-4S]{sup 3+} cluster with CoM-SH as a ligand. Subunit HdrB of the Methanothermobacter marburgensis HdrABC holoenzyme contains two cysteine-rich sequence motifs (CX{sub 31-39}CCX{sub 35-36}CXXC), designated as CCG domain in the Pfam database and conserved in many proteins. Here we present experimental evidence that the C-terminal CCG domain of HdrB binds this unusual [4Fe-4S] cluster. HdrB was produced in Escherichia coli, and an iron-sulfur cluster was subsequently inserted by in vitro reconstitution. In the oxidized state the cluster without the substrate exhibited a rhombic EPR signal (g{sub zyx} = 2.015, 1.995, and 1.950) reminiscent of the CoM-HDR signal. {sup 57}Fe ENDOR spectroscopy revealed that this paramagnetic species is a [4Fe-4S] cluster with {sup 57}Fe hyperfine couplings very similar to that of CoM-HDR. CoM-{sup 33}SH resulted in a broadening of the EPR signal, and upon addition of CoM-SH the midpoint potential of the cluster was shifted to values observed for CoM-HDR, both indicating binding of CoM-SH to the cluster. Site-directed mutagenesis of all 12 cysteine residues in HdrB identified four cysteines of the C-terminal CCG domain as cluster ligands. Combined with the previous detection of CoM-HDR-like EPR signals in other CCG domain-containing proteins our data indicate a general role of the C-terminal CCG domain in coordination of this novel [4Fe-4S] cluster. In addition, Zn K-edge X-ray absorption spectroscopy identified an isolated Zn site with an S{sub 3}(O/N){sub 1} geometry in HdrB and the HDR holoenzyme. The N-terminal CCG domain is suggested to provide ligands to the Zn site.

  5. Policy-based Secure Deletion Christian Cachin

    E-Print Network [OSTI]

    International Association for Cryptologic Research (IACR)

    Sorniotti February 28, 2013 Abstract Securely deleting data from storage systems has become difficult today in storage systems, whose security relies on the proper erasure of cryptographic keys. Deletion operations storage systems do not include operations to reliably destroy stored information. Common deletion

  6. Policy-based Secure Deletion Christian Cachin

    E-Print Network [OSTI]

    Cachin, Christian

    Sorniotti August 26, 2013 Abstract Securely deleting data from storage systems has become difficult today are typically not foreseen, particularly not in networked and cloud-storage systems. This paper introduces a general cryptographic model for policy-based secure deletion of data in storage systems, whose security

  7. Synthetic heparin-binding growth factor analogs

    DOE Patents [OSTI]

    Pena, Louis A.; Zamora, Paul; Lin, Xinhua; Glass, John D.

    2007-01-23

    The invention provides synthetic heparin-binding growth factor analogs having at least one peptide chain that binds a heparin-binding growth factor receptor, covalently bound to a hydrophobic linker, which is in turn covalently bound to a non-signaling peptide that includes a heparin-binding domain. The synthetic heparin-binding growth factor analogs are useful as soluble biologics or as surface coatings for medical devices.

  8. Crystal structures of the reverse transcriptase-associated ribonuclease H domain of xenotropic murine leukemia-virus related virus

    SciTech Connect (OSTI)

    Zhou, Dongwen; Chung, Suhman; Miller, Maria; Le Grice, Stuart F.J.; Wlodawer, Alexander

    2012-06-19

    The ribonuclease H (RNase H) domain of retroviral reverse transcriptase (RT) plays a critical role in the life cycle by degrading the RNA strands of DNA/RNA hybrids. In addition, RNase H activity is required to precisely remove the RNA primers from nascent (-) and (+) strand DNA. We report here three crystal structures of the RNase H domain of xenotropic murine leukemia virus-related virus (XMRV) RT, namely (i) the previously identified construct from which helix C was deleted, (ii) the intact domain, and (iii) the intact domain complexed with an active site {alpha}-hydroxytropolone inhibitor. Enzymatic assays showed that the intact RNase H domain retained catalytic activity, whereas the variant lacking helix C was only marginally active, corroborating the importance of this helix for enzymatic activity. Modeling of the enzyme-substrate complex elucidated the essential role of helix C in binding a DNA/RNA hybrid and its likely mode of recognition. The crystal structure of the RNase H domain complexed with {beta}-thujaplicinol clearly showed that coordination by two divalent cations mediates recognition of the inhibitor.

  9. Method for introducing unidirectional nested deletions

    DOE Patents [OSTI]

    Dunn, John J. (Bellport, NY); Quesada, Mark A. (Horseheads, NY); Randesi, Matthew (New York, NY)

    2001-01-01

    Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment in the context of a cloning vector which contains an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment. Also disclosed is a method for producing single-stranded DNA probes utilizing the same cloning vector. An optimal vector, PZIP is described. Methods for introducing unidirectional deletions into a terminal location of a cloned DNA sequence which is inserted into the vector of the present invention are also disclosed. These methods are useful for introducing deletions into either or both ends of a cloned DNA insert, for high throughput sequencing of any DNA of interest.

  10. Synthetic heparin-binding factor analogs

    DOE Patents [OSTI]

    Pena, Louis A. (Poquott, NY); Zamora, Paul O. (Gaithersburg, MD); Lin, Xinhua (Plainview, NY); Glass, John D. (Shoreham, NY)

    2010-04-20

    The invention provides synthetic heparin-binding growth factor analogs having at least one peptide chain, and preferably two peptide chains branched from a dipeptide branch moiety composed of two trifunctional amino acid residues, which peptide chain or chains bind a heparin-binding growth factor receptor and are covalently bound to a non-signaling peptide that includes a heparin-binding domain, preferably by a linker, which may be a hydrophobic linker. The synthetic heparin-binding growth factor analogs are useful as pharmaceutical agents, soluble biologics or as surface coatings for medical devices.

  11. 1.15?Å resolution structure of the proteasome-assembly chaperone Nas2 PDZ domain

    E-Print Network [OSTI]

    Singh, Chingakham R.; Lovell, Scott; Mehzabeen, Nurjahan; Chowdhury, Wasimul Q.; Geanes, Eric S.; Battaile, Kevin P.; Roelofs, Jeroen

    2014-04-01

    , binds to the proteasomal AAA-ATPase subunit Rpt5. The PDZ domain of Nas2 binds to the C-terminal tail of Rpt5; however, it does not require the C-terminus of Rpt5 for binding. Here, the 1.15 Å resolution structure of the PDZ domain of Nas2 is reported...

  12. Method for introducing unidirectional nested deletions

    DOE Patents [OSTI]

    Dunn, J.J.; Quesada, M.A.; Randesi, M.

    1999-07-27

    Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment. More specifically, the method comprises providing a recombinant DNA construct comprising a DNA segment of interest inserted in a cloning vector. The cloning vector has an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment of interest. The recombinant DNA construct is then contacted with the protein pII encoded by gene II of phage f1 thereby generating a single-stranded nick. The nicked DNA is then contacted with E. coli Exonuclease III thereby expanding the single-stranded nick into a single-stranded gap. The single-stranded gapped DNA is then contacted with a single-strand-specific endonuclease thereby producing a linearized DNA molecule containing a double-stranded deletion corresponding in size to the single-stranded gap. The DNA treated in this manner is then incubated with DNA ligase under conditions appropriate for ligation. Also disclosed is a method for producing single-stranded DNA probes. In this embodiment, single-stranded gapped DNA, produced as described above, is contacted with a DNA polymerase in the presence of labeled nucleotides to fill in the gap. This DNA is then linearized by digestion with a restriction enzyme which cuts outside the DNA segment of interest. The product of this digestion is then denatured to produce a labeled single-stranded nucleic acid probe. 1 fig.

  13. DMBC: Domain Names & Web Hosting Domain Names

    E-Print Network [OSTI]

    Stowell, Michael

    DMBC: Domain Names & Web Hosting Domain Names Top Level Domains .com .net .org .edu .gov .mil professional or personal life Always aim for a .com Top Level Domain as it is what 99.9% of the web or underscores in the domain name unless there is no other option Web Hosting Web Hosting Providers Web

  14. ?-Tubulin and the C-terminal motor domain kinesin-like protein, KLPA, function in the establishment of spindle bipolarity in Aspergillus nidulans

    E-Print Network [OSTI]

    Prigozhina, Natalie L.; Walker, Richard A.; Oakley, C. Elizabeth; Oakley, Berl R.

    2001-10-01

    Previous research has found that a ?-tubulin mutation inSchizosaccharomyces pombe is synthetically lethal with a deletion of the C-terminal motor domain kinesin-like protein genepkl1, but the lethality of the double mutant ...

  15. Conformational instability of the MARK3 UBA domain compromises ubiquitin recognition and promotes interaction with the adjacent kinase domain

    SciTech Connect (OSTI)

    Murphy, James M.; Korzhnev, Dmitry M.; Ceccarelli, Derek F.; Briant, Douglas J.; Zarrine-Afsar, Arash; Sicheri, Frank; Kay, Lewis E.; Pawson, Tony (Mount Sinai Hospital); (Toronto)

    2012-10-23

    The Par-1/MARK protein kinases play a pivotal role in establishing cellular polarity. This family of kinases contains a unique domain architecture, in which a ubiquitin-associated (UBA) domain is located C-terminal to the kinase domain. We have used a combination of x-ray crystallography and NMR dynamics experiments to understand the interaction of the human (h) MARK3 UBA domain with the adjacent kinase domain as compared with ubiquitin. The x-ray crystal structure of the linked hMARK3 kinase and UBA domains establishes that the UBA domain forms a stable intramolecular interaction with the N-terminal lobe of the kinase domain. However, solution-state NMR studies of the isolated UBA domain indicate that it is highly dynamic, undergoing conformational transitions that can be explained by a folding-unfolding equilibrium. NMR titration experiments indicated that the hMARK3 UBA domain has a detectable but extremely weak affinity for mono ubiquitin, which suggests that conformational instability of the isolated hMARK3 UBA domain attenuates binding to ubiquitin despite the presence of residues typically involved in ubiquitin recognition. Our data identify a molecular mechanism through which the hMARK3 UBA domain has evolved to bind the kinase domain, in a fashion that stabilizes an open conformation of the N- and C-terminal lobes, at the expense of its capacity to engage ubiquitin. These results may be relevant more generally to the 30% of UBA domains that lack significant ubiquitin-binding activity, and they suggest a unique mechanism by which interaction domains may evolve new binding properties.

  16. DMBC: Domain Names & Web Hosting Domain Names

    E-Print Network [OSTI]

    Stowell, Michael

    DMBC: Domain Names & Web Hosting Domain Names Top Level Domains · .com · .net · .org · .edu · .gov.9% of the web-viewing audience is used to typing in. Chances are, a visitor will type in ".com" even if you tell and simple · Try to avoid dashes or underscores in the domain name unless there is no other option Web

  17. Dual chain synthetic heparin-binding growth factor analogs

    DOE Patents [OSTI]

    Zamora, Paul O. (Gaithersburg, MD); Pena, Louis A. (Poquott, NY); Lin, Xinhua (Plainview, NY)

    2012-04-24

    The invention provides synthetic heparin-binding growth factor analogs having two peptide chains each branched from a branch moiety, such as trifunctional amino acid residues, the branch moieties separated by a first linker of from 3 to about 20 backbone atoms, which peptide chains bind a heparin-binding growth factor receptor and are covalently bound to a non-signaling peptide that includes a heparin-binding domain, preferably by a second linker, which may be a hydrophobic second linker. The synthetic heparin-binding growth factor analogs are useful as pharmaceutical agents, soluble biologics or as surface coatings for medical devices.

  18. Dual chain synthetic heparin-binding growth factor analogs

    DOE Patents [OSTI]

    Zamora, Paul O. (Gaithersburg, MD); Pena, Louis A. (Poquott, NY); Lin, Xinhua (Plainview, NY)

    2009-10-06

    The invention provides synthetic heparin-binding growth factor analogs having two peptide chains each branched from a branch moiety, such as trifunctional amino acid residues, the branch moieties separated by a first linker of from 3 to about 20 backbone atoms, which peptide chains bind a heparin-binding growth factor receptor and are covalently bound to a non-signaling peptide that includes a heparin-binding domain, preferably by a second linker, which may be a hydrophobic second linker. The synthetic heparin-binding growth factor analogs are useful as pharmaceutical agents, soluble biologics or as surface coatings for medical devices.

  19. PH domains, FYVE domains, ENTH domains, C2 do-mains, Tubby domains, and PX domains, and the list

    E-Print Network [OSTI]

    domain and the second SH3 domain (yellow), while the Selected Reading C-terminal tail interacts with the first SH3 domain. Phosphorylation of serine and threonine residues in the C-terminal tail liberates., Tempst, P., Thuring, J.W., Cooper,space and time, and thereby prevent inadvertent dam- M.A., Lim, Z

  20. Find It. Delete It. Protect It. Information Technology Security Strategy

    E-Print Network [OSTI]

    Sheridan, Jennifer

    Find It. Delete It. Protect It. Information Technology Security Strategy Executive Summary The general proposed strategy is to optimize risk management for information security incrementally and over that security will be a process rather than project. Achievement of the goal, optimized risk management

  1. RESEARCH ARTICLE Deletion of Chromosomal Region 8p21

    E-Print Network [OSTI]

    Yanikoglu, Berrin

    of Aging, Vaccine and Gene Therapy Institute of Florida, Port St. Lucie, Florida, United States of America:10.1371/journal.pone.0138248 Editor: Sumitra Deb, Virginia Commonwealth University, UNITED STATES patients without the deletion had a response rate of 90%. In vitro analysis revealed a higher resistance

  2. Stochastic Chemical Reactions in Micro-domains

    E-Print Network [OSTI]

    D. Holcman; Z. Schuss

    2004-12-25

    Traditional chemical kinetics may be inappropriate to describe chemical reactions in micro-domains involving only a small number of substrate and reactant molecules. Starting with the stochastic dynamics of the molecules, we derive a master-diffusion equation for the joint probability density of a mobile reactant and the number of bound substrate in a confined domain. We use the equation to calculate the fluctuations in the number of bound substrate molecules as a function of initial reactant distribution. A second model is presented based on a Markov description of the binding and unbinding and on the mean first passage time of a molecule to a small portion of the boundary. These models can be used for the description of noise due to gating of ionic channels by random binding and unbinding of ligands in biological sensor cells, such as olfactory cilia, photo-receptors, hair cells in the cochlea.

  3. Quantum Fusion of Domain Walls with Fluxes

    E-Print Network [OSTI]

    S. Bolognesi; M. Shifman; M. B. Voloshin

    2009-07-20

    We study how fluxes on the domain wall world volume modify quantum fusion of two distant parallel domain walls into a composite wall. The elementary wall fluxes can be separated into parallel and antiparallel components. The parallel component affects neither the binding energy nor the process of quantum merger. The antiparallel fluxes, instead, increase the binding energy and, against naive expectations, suppress quantum fusion. In the small flux limit we explicitly find the bounce solution and the fusion rate as a function of the flux. We argue that at large (antiparallel) fluxes there exists a critical value of the flux (versus the difference in the wall tensions), which switches off quantum fusion altogether. This phenomenon of flux-related wall stabilization is rather peculiar: it is unrelated to any conserved quantity. Our consideration of the flux-related all stabilization is based on substantiated arguments that fall short of complete proof.

  4. Discovery and Characterization of a Cell-Permeable, Small-Molecule c-Abl Kinase Activator that Binds to the Myristoyl Binding Site

    SciTech Connect (OSTI)

    Yang, Jingsong; Campobasso, Nino; Biju, Mangatt P.; Fisher, Kelly; Pan, Xiao-Qing; Cottom, Josh; Galbraith, Sarah; Ho, Thau; Zhang, Hong; Hong, Xuan; Ward, Paris; Hofmann, Glenn; Siegfried, Brett; Zappacosta, Francesca; Washio, Yoshiaki; Cao, Ping; Qu, Junya; Bertrand, Sophie; Wang, Da-Yuan; Head, Martha S.; Li, Hu; Moores, Sheri; Lai, Zhihong; Johanson, Kyung; Burton, George; Erickson-Miller, Connie; Simpson, Graham; Tummino, Peter; Copeland, Robert A.; Oliff, Allen

    2014-10-02

    c-Abl kinase activity is regulated by a unique mechanism involving the formation of an autoinhibited conformation in which the N-terminal myristoyl group binds intramolecularly to the myristoyl binding site on the kinase domain and induces the bending of the {alpha}I helix that creates a docking surface for the SH2 domain. Here, we report a small-molecule c-Abl activator, DPH, that displays potent enzymatic and cellular activity in stimulating c-Abl activation. Structural analyses indicate that DPH binds to the myristoyl binding site and prevents the formation of the bent conformation of the {alpha}I helix through steric hindrance, a mode of action distinct from the previously identified allosteric c-Abl inhibitor, GNF-2, that also binds to the myristoyl binding site. DPH represents the first cell-permeable, small-molecule tool compound for c-Abl activation.

  5. Cell, Vol. 94, 181191, July 24, 1998, Copyright 1998 by Cell Press Crystal Structure of the Signal Sequence Binding

    E-Print Network [OSTI]

    Walter, Peter

    Cell, Vol. 94, 181­191, July 24, 1998, Copyright ©1998 by Cell Press Crystal Structure). During targeting, the Ffh- The crystal structure of the signal sequence binding 4.5S RNA complex binds domain is a four-helix to the structural plasticity necessary for SRP to bind bundle that is closely

  6. An Investigation on the Roles of Insertion and Deletion Operators in Tree Adjoining Grammar Guided Genetic Programming

    E-Print Network [OSTI]

    McKay, Robert Ian

    An Investigation on the Roles of Insertion and Deletion Operators in Tree Adjoining Grammar Guided programming [5, 6]. In this paper, we empirically investigate the use of insertion and deletion operators as the insertion and deletion operators. The experiments to investigate the roles of insertion and deletion in TAG3

  7. DNA binding specificity of the p73 DNA-binding domain

    E-Print Network [OSTI]

    Tse, Pui Wah

    2011-01-01

    of DNA recognition by p53 tetramers. Mol Cell 22, 741-753.site as a self-assembled tetramer. Structure 18, 246- Chene,structure of a p53 core tetramer bound to DNA. Oncogene 28,

  8. Help:Sysop deleting and undeleting | Open Energy Information

    Open Energy Info (EERE)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page on QA:QA J-E-1 SECTION J APPENDIXsource History View NewGuam: Energyarea, California |Sysop deleting and undeleting Jump

  9. Expression and subcellular localisation of poly(A)-binding proteins 

    E-Print Network [OSTI]

    Burgess, Hannah

    2010-11-24

    Poly(A)-binding proteins (PABPs) are important regulators of mRNA translation and stability. In mammals four cytoplasmic PABPs with a similar domain structure have been described - PABP1, tPABP, PABP4 and ePABP. The ...

  10. Analysis of the Vertebrate Insulator Protein CTCF-Binding

    E-Print Network [OSTI]

    D. Green,4 Michael Q. Zhang,3 Victor V. Lobanenkov,2 and Bing Ren1, * 1 Ludwig Institute for Cancer by preventing the spread of heterochromatin and restricting transcriptional enhancers from acti- vation ex- pressed nuclear protein with 11-zinc finger (ZF) DNA- binding domain (Filippova et al., 1996

  11. Time Domain Reflectometry Theory

    E-Print Network [OSTI]

    Palermo, Sam

    Time Domain Reflectometry Theory Application Note 1304-2 For Use with Agilent 86100 Infiniium DCA #12;2 The most general approach to evaluating the time domain response of any electromagnetic system a concise presentation of the fundamentals of TDR and then relates these fundamentals to the parameters

  12. Nucleic acid sequences encoding D1 and D1/D2 domains of human coxsackievirus and adenovirus receptor (CAR)

    DOE Patents [OSTI]

    Freimuth, Paul I.

    2010-04-06

    The invention provides recombinant human CAR (coxsackievirus and adenovirus receptor) polypeptides which bind adenovirus. Specifically, polypeptides corresponding to adenovirus binding domain D1 and the entire extracellular domain of human CAR protein comprising D1 and D2 are provided. In another aspect, the invention provides nucleic acid sequences encoding these domains and expression vectors for producing the domains and bacterial cells containing such vectors. The invention also includes an isolated fusion protein comprised of the D1 polypeptide fused to a polypeptide which facilitates folding of D1 when expressed in bacteria. The functional D1 domain finds application in a therapeutic method for treating a patient infected with a CAR D1-binding virus, and also in a method for identifying an antiviral compound which interferes with viral attachment. The invention also provides a method for specifically targeting a cell for infection by a virus which binds to D1.

  13. Structural Basis for p300 Taz2-p53 TAD1 Binding and Modulation by Phosphorylation

    E-Print Network [OSTI]

    Laboratory of Biochemistry and Molecular Biology 2Laboratory of Cell Biology National Cancer Institute, NIH, Bethesda, MD 20892, USA 3Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick. Among those domains are two transcriptional adaptor zinc-binding (Taz) domains, Taz1 (C/H1) and Taz2 (C

  14. MCM ring hexamerization is a prerequisite for DNA-binding

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Froelich, Clifford A.; Nourse, Amanda; Enemark, Eric J.

    2015-09-13

    The hexameric Minichromosome Maintenance (MCM) protein complex forms a ring that unwinds DNA at the replication fork in eukaryotes and archaea. Our recent crystal structure of an archaeal MCM N-terminal domain bound to single-stranded DNA (ssDNA) revealed ssDNA associating across tight subunit interfaces but not at the loose interfaces, indicating that DNA-binding is governed not only by the DNA-binding residues of the subunits (MCM ssDNA-binding motif, MSSB) but also by the relative orientation of the subunits. We now extend these findings to show that DNA-binding by the MCM N-terminal domain of the archaeal organism Pyrococcus furiosus occurs specifically in themore »hexameric oligomeric form. We show that mutants defective for hexamerization are defective in binding ssDNA despite retaining all the residues observed to interact with ssDNA in the crystal structure. One mutation that exhibits severely defective hexamerization and ssDNA-binding is at a conserved phenylalanine that aligns with the mouse Mcm4(Chaos3) mutation associated with chromosomal instability, cancer, and decreased intersubunit association.« less

  15. Perfect Completion and Deletion in Random Graphs Assaf Natanzon \\Lambda Ron Shamir \\Lambda y

    E-Print Network [OSTI]

    Shamir, Ron

    Perfect Completion and Deletion in Random Graphs Assaf Natanzon \\Lambda Ron Shamir \\Lambda y Abstract In the Perfect Completion problem one wishes to add the fewest possible edges to a graph in order Introduction Edge Completion/Deletion problems call for making minimum changes to the edge set of an input

  16. Substrate binding by a bacterial ABC transporter involved in polysaccharide export

    SciTech Connect (OSTI)

    Cuthbertson, Leslie; Kimber, Matthew S.; Whitfield, Chris (Guelph)

    2008-04-02

    ATP-binding-cassette (ABC) transporters are responsible for the export of a wide variety of cell-surface glycoconjugates in both Gram-positive and Gram-negative bacteria. These include the O-antigenic polysaccharide (O-PS) portion of lipopolysaccharide, a crucial virulence determinant in Gram-negative pathogens. O-PSs are synthesized by one of two fundamentally different pathways. Escherichia coli O serotypes O8 and O9a provide the prototype systems for studying O-PS export via ABC transporters. The transporter is composed of the transmembrane component Wzm and the nucleotide-binding component Wzt. Although the N-terminal domain of Wzt is a conventional ABC protein, the C-terminal domain of Wzt (C-Wzt) is a unique structural element that determines the specificity of the transporter for either the O8 or O9a O-PS. We show here that the two domains of Wzt can function when expressed as separate polypeptides; both are essential for export. In vitro, C-Wzt binds its cognate O-PS by recognizing a residue located at the nonreducing end of the polymer. The crystal structure of C-WztO9a is reported here and reveals a {beta} sandwich with an immunoglobulin-like topology that contains the O-PS-binding pocket. Substrate interactions with nucleotide-binding domains have been demonstrated in an ABC exporter previously. However, to our knowledge substrate binding by a discrete, cytoplasmic accessory domain in an extended nucleotide-binding domain polypeptide has not previously been demonstrated. Elucidation of the substrate-recognition system involved in O-PS export provides insight into the mechanism that coordinates polymer biosynthesis, termination, and export.

  17. Structure and function of the deleted in azoospermia gene 

    E-Print Network [OSTI]

    Sprague, David Chase Cameron

    2009-05-15

    ............................................... 74 25 Graph of 2h Exposure to Phosphorimage Screen............................................ 75 26 Graph of 4h Exposure to Phosphorimage Screen............................................ 76 27 Polyacrylamide Gel Shift of DAZL and CDC25C...) at the N terminus and a 24 amino acid motif repeated 9 to15 times at the C-terminus (DAZ-repeat domain). Researchers in Taiwan described a cohort of patients with reduced fertility whose RRMs in DAZL 6 contained a point mutation within the RRM...

  18. Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model

    SciTech Connect (OSTI)

    Knott, Michael [Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW (United Kingdom)] [Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW (United Kingdom); Best, Robert B., E-mail: robertbe@helix.nih.gov [Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW (United Kingdom); Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520 (United States)

    2014-05-07

    Many proteins undergo a conformational transition upon binding to their cognate binding partner, with intrinsically disordered proteins (IDPs) providing an extreme example in which a folding transition occurs. However, it is often not clear whether this occurs via an “induced fit” or “conformational selection” mechanism, or via some intermediate scenario. In the first case, transient encounters with the binding partner favour transitions to the bound structure before the two proteins dissociate, while in the second the bound structure must be selected from a subset of unbound structures which are in the correct state for binding, because transient encounters of the incorrect conformation with the binding partner are most likely to result in dissociation. A particularly interesting situation involves those intrinsically disordered proteins which can bind to different binding partners in different conformations. We have devised a multi-state coarse-grained simulation model which is able to capture the binding of IDPs in alternate conformations, and by applying it to the binding of nuclear coactivator binding domain (NCBD) to either ACTR or IRF-3 we are able to determine the binding mechanism. By all measures, the binding of NCBD to either binding partner appears to occur via an induced fit mechanism. Nonetheless, we also show how a scenario closer to conformational selection could arise by choosing an alternative non-binding structure for NCBD.

  19. Genomic rearrangements by LINE-1 insertion-mediated deletion in the human

    E-Print Network [OSTI]

    Richard, Cordaux,

    for the correlation of L1 element size and the corres- ponding deletion size. In addition, we show that internal by a 30 -UTR ending in a poly(A) tail. The L1-encoded proteins predominantly exhibit cis

  20. How to recreate a table after deletion | OpenEI Community

    Open Energy Info (EERE)

    0 Get to look at the code it seems like some DboTableMeta row is not deleted which causes creation to be forbid. Is it intended or is it some kind of bug ? Dbinder on 25...

  1. Enhanced Hydrogen Production in Escherichia coli Through Chemical Mutagenesis, Gene Deletion, and Transposon Mutagenesis 

    E-Print Network [OSTI]

    Garzon Sanabria, Andrea Juliana

    2011-08-08

    -1 ENHANCED HYDROGEN PRODUCTION IN ESCHERICHIA COLI THROUGH CHEMICAL MUTAGENESIS, GENE DELETION, AND TRANSPOSON MUTAGENESIS A Thesis by ANDREA JULIANA GARZON SANABRIA Submitted to the Office of Graduate Studies of Texas A&M University... in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE May 2010 Major Subject: Chemical Engineering ENHANCED HYDROGEN PRODUCTION IN ESCHERICHIA COLI THROUGH CHEMICAL MUTAGENESIS, GENE DELETION, AND TRANSPOSON...

  2. Human HLTF mediates postreplication repair by its HIRAN domain-dependent replication fork remodelling

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Achar, Yathish Jagadheesh; Balogh, David; Neculai, Dante; Juhasz, Szilvia; Morocz, Monika; Gali, Himabindu; Dhe-Paganon, Sirano; Venclovas, ?eslovas; Haracska, Lajos

    2015-09-08

    Defects in the ability to respond properly to an unrepaired DNA lesion blocking replication promote genomic instability and cancer. Human HLTF, implicated in error-free replication of damaged DNA and tumour suppression, exhibits a HIRAN domain, a RING domain, and a SWI/SNF domain facilitating DNA-binding, PCNA-polyubiquitin-ligase, and dsDNA-translocase activities, respectively. Here, we investigate the mechanism of HLTF action with emphasis on its HIRAN domain. We found that in cells HLTF promotes the filling-in of gaps left opposite damaged DNA during replication, and this postreplication repair function depends on its HIRAN domain. Our biochemical assays show that HIRAN domain mutant HLTF proteinsmore »retain their ubiquitin ligase, ATPase and dsDNA translocase activities but are impaired in binding to a model replication fork. These data and our structural study indicate that the HIRAN domain recruits HLTF to a stalled replication fork, and it also provides the direction for the movement of the dsDNA translocase motor domain for fork reversal. We suggest functional similarities between the HIRAN, the OB, the HARP2, and other domains found in certain motor proteins, which may explain why only a subset of DNA translocases can carry out fork reversal.« less

  3. Structural and dynamic changes associated with beneficial engineered single-amino-acid deletion mutations in enhanced green fluorescent protein

    SciTech Connect (OSTI)

    Arpino, James A. J. [Cardiff University, Park Place, Cardiff CF10 3AT Wales (United Kingdom); Rizkallah, Pierre J., E-mail: rizkallahp@cardiff.ac.uk [Cardiff University, Heath Park, Cardiff CF14 4XN Wales (United Kingdom); Jones, D. Dafydd, E-mail: rizkallahp@cardiff.ac.uk [Cardiff University, Park Place, Cardiff CF10 3AT Wales (United Kingdom)

    2014-08-01

    The beneficial engineered single-amino-acid deletion variants EGFP{sup D190?} and EGFP{sup A227?} have been studied. Single-amino-acid deletions are a common part of the natural evolutionary landscape but are rarely sampled during protein engineering owing to limited and prejudiced molecular understanding of mutations that shorten the protein backbone. Single-amino-acid deletion variants of enhanced green fluorescent protein (EGFP) have been identified by directed evolution with the beneficial effect of imparting increased cellular fluorescence. Biophysical characterization revealed that increased functional protein production and not changes to the fluorescence parameters was the mechanism that was likely to be responsible. The structure EGFP{sup D190?} containing a deletion within a loop revealed propagated changes only after the deleted residue. The structure of EGFP{sup A227?} revealed that a ‘flipping’ mechanism was used to adjust for residue deletion at the end of a ?-strand, with amino acids C-terminal to the deletion site repositioning to take the place of the deleted amino acid. In both variants new networks of short-range and long-range interactions are generated while maintaining the integrity of the hydrophobic core. Both deletion variants also displayed significant local and long-range changes in dynamics, as evident by changes in B factors compared with EGFP. Rather than being detrimental, deletion mutations can introduce beneficial structural effects through altering core protein properties, folding and dynamics, as well as function.

  4. Pinkbar is an epithelial-specific BAR domain protein that generates planar membrane structures

    SciTech Connect (OSTI)

    Pykäläinen, Anette; Boczkowska, Malgorzata; Zhao, Hongxia; Saarikangas, Juha; Rebowski, Grzegorz; Jansen, Maurice; Hakanen, Janne; Koskela, Essi V.; Peränen, Johan; Vihinen, Helena; Jokitalo, Eija; Salminen, Marjo; Ikonen, Elina; Dominguez, Roberto; Lappalainen, Pekka

    2013-05-29

    Bin/amphipysin/Rvs (BAR)-domain proteins sculpt cellular membranes and have key roles in processes such as endocytosis, cell motility and morphogenesis. BAR domains are divided into three subfamilies: BAR- and F-BAR-domain proteins generate positive membrane curvature and stabilize cellular invaginations, whereas I-BAR-domain proteins induce negative curvature and stabilize protrusions. We show that a previously uncharacterized member of the I-BAR subfamily, Pinkbar, is specifically expressed in intestinal epithelial cells, where it localizes to Rab13-positive vesicles and to the plasma membrane at intercellular junctions. Notably, the BAR domain of Pinkbar does not induce membrane tubulation but promotes the formation of planar membrane sheets. Structural and mutagenesis analyses reveal that the BAR domain of Pinkbar has a relatively flat lipid-binding interface and that it assembles into sheet-like oligomers in crystals and in solution, which may explain its unique membrane-deforming activity.

  5. Utilization of I-domain of LFA-1 to Target Drug and Marker Molecules to Leukocytes

    E-Print Network [OSTI]

    Manikwar, Prakash; Tejo, Bimo A.; Shinogle, Heather; Moore, David S.; Zimmerman, Tahl; Blanco, Francisco; Siahaan, Teruna J.

    2010-05-10

    to deliver drugs to cells with upregulated ICAM-1. Anti-ICAM-1-coated nanopar- ticles successfully delivered lysosomal enzyme into cells obtained from patients suffering from lysosomal storage disorder [34]. These nanoparticles are endo- cytosed via a non... blocks the I-domain binding site to ICAM-1 (Fig. 4). A similar effect of the mAb was observed in the binding of a GST-tagged I-domain (I-GST) to a surface-coated ICAM-1Fc using a solid-phase ELISA assay [29]. The antibody blocking studies indicate...

  6. The PDZ-binding motif of Yes-associated protein is required for its co-activation of TEAD-mediated CTGF transcription and oncogenic cell transforming activity

    SciTech Connect (OSTI)

    Shimomura, Tadanori; Miyamura, Norio; Hata, Shoji; Miura, Ryota; Hirayama, Jun, E-mail: hirayama.dbio@mri.tmd.ac.jp; Nishina, Hiroshi, E-mail: nishina.dbio@mri.tmd.ac.jp

    2014-01-17

    Highlights: •Loss of the PDZ-binding motif inhibits constitutively active YAP (5SA)-induced oncogenic cell transformation. •The PDZ-binding motif of YAP promotes its nuclear localization in cultured cells and mouse liver. •Loss of the PDZ-binding motif inhibits YAP (5SA)-induced CTGF transcription in cultured cells and mouse liver. -- Abstract: YAP is a transcriptional co-activator that acts downstream of the Hippo signaling pathway and regulates multiple cellular processes, including proliferation. Hippo pathway-dependent phosphorylation of YAP negatively regulates its function. Conversely, attenuation of Hippo-mediated phosphorylation of YAP increases its ability to stimulate proliferation and eventually induces oncogenic transformation. The C-terminus of YAP contains a highly conserved PDZ-binding motif that regulates YAP’s functions in multiple ways. However, to date, the importance of the PDZ-binding motif to the oncogenic cell transforming activity of YAP has not been determined. In this study, we disrupted the PDZ-binding motif in the YAP (5SA) protein, in which the sites normally targeted by Hippo pathway-dependent phosphorylation are mutated. We found that loss of the PDZ-binding motif significantly inhibited the oncogenic transformation of cultured cells induced by YAP (5SA). In addition, the increased nuclear localization of YAP (5SA) and its enhanced activation of TEAD-dependent transcription of the cell proliferation gene CTGF were strongly reduced when the PDZ-binding motif was deleted. Similarly, in mouse liver, deletion of the PDZ-binding motif suppressed nuclear localization of YAP (5SA) and YAP (5SA)-induced CTGF expression. Taken together, our results indicate that the PDZ-binding motif of YAP is critical for YAP-mediated oncogenesis, and that this effect is mediated by YAP’s co-activation of TEAD-mediated CTGF transcription.

  7. A Stochastic Model for the Evolution of the Web Allowing Link Deletion

    E-Print Network [OSTI]

    Trevor Fenner; Mark Levene; George Loizou

    2004-03-25

    Recently several authors have proposed stochastic evolutionary models for the growth of the web graph and other networks that give rise to power-law distributions. These models are based on the notion of preferential attachment leading to the ``rich get richer'' phenomenon. We present a generalisation of the basic model by allowing deletion of individual links and show that it also gives rise to a power-law distribution. We derive the mean-field equations for this stochastic model and show that by examining a snapshot of the distribution at the steady state of the model, we are able to tell whether any link deletion has taken place and estimate the link deletion probability. Our model enables us to gain some insight into the distribution of inlinks in the web graph, in particular it suggests a power-law exponent of approximately 2.15 rather than the widely published exponent of 2.1.

  8. Domain walls in gapped graphene

    E-Print Network [OSTI]

    Semenoff, G W; Zhou, Fei

    2015-01-01

    The electronic properties of a particular class of domain walls in gapped graphene are investigated. We show that they can support mid-gap states which are localized in the vicinity of the domain wall and propagate along its length. With a finite density of domain walls, these states can alter the electronic properties of gapped graphene significantly. If the mid-gap band is partially filled,the domain wall can behave like a one-dimensional metal embedded in a semi-conductor, and could potentially be used as a single-channel quantum wire.

  9. Domain walls in gapped graphene

    E-Print Network [OSTI]

    G. W. Semenoff; V. Semenoff; Fei Zhou

    2008-05-31

    The electronic properties of a particular class of domain walls in gapped graphene are investigated. We show that they can support mid-gap states which are localized in the vicinity of the domain wall and propagate along its length. With a finite density of domain walls, these states can alter the electronic properties of gapped graphene significantly. If the mid-gap band is partially filled,the domain wall can behave like a one-dimensional metal embedded in a semi-conductor, and could potentially be used as a single-channel quantum wire.

  10. Binding kinetics of membrane-anchored receptors and ligands: molecular dynamics simulations and theory

    E-Print Network [OSTI]

    Jinglei Hu; Guang-Kui Xu; Reinhard Lipowsky; Thomas R. Weikl

    2015-11-24

    The adhesion of biological membranes is mediated by the binding of membrane-anchored receptor and ligand proteins. Central questions are how the binding kinetics of these proteins is affected by the membranes and by the membrane anchoring of the proteins. In this article, we (i) present detailed data for the binding of membrane-anchored proteins from coarse-grained molecular dynamics simulations, and (ii) provide a theory that describes how the binding kinetics depends on the average separation and thermal roughness of the adhering membranes, and on the anchoring, lengths, and length variations of the proteins. An important element of our theory is the tilt of bound receptor-ligand complexes and transition-state complexes relative to the membrane normals. This tilt results from an interplay of the anchoring energy and rotational entropy of the complexes and facilitates the formation of receptor-ligand bonds at membrane separations smaller than the preferred separation for binding. In our simulations, we have considered both lipid-anchored and transmembrane receptor and ligand proteins. We find that the binding equilibrium constant and binding on-rate constant of lipid-anchored proteins are considerably smaller than the binding constant and on-rate constant of rigid transmembrane proteins with identical binding domains.

  11. Structurally Similar but Functionally Diverse ZU5 Domains in Human Erythrocyte Ankyrin

    SciTech Connect (OSTI)

    Yasunaga, Mai; Ipsaro, Jonathan J.; Mondragón, Alfonso (NWU)

    2014-10-02

    The metazoan cell membrane is highly organized. Maintaining such organization and preserving membrane integrity under different conditions are accomplished through intracellular tethering to an extensive, flexible protein network. Spectrin, the principal component of this network, is attached to the membrane through the adaptor protein ankyrin, which directly bridges the interaction between {beta}-spectrin and membrane proteins. Ankyrins have a modular structure that includes two tandem ZU5 domains. The first domain, ZU5A, is directly responsible for binding {beta}-spectrin. Here, we present a structure of the tandem ZU5 repeats of human erythrocyte ankyrin. Structural and biophysical experiments show that the second ZU5 domain, ZU5B, does not participate in spectrin binding. ZU5B is structurally similar to the ZU5 domain found in the netrin receptor UNC5b supramodule, suggesting that it could interact with other domains in ankyrin. Comparison of several ZU5 domains demonstrates that the ZU5 domain represents a compact and versatile protein interaction module.

  12. Ligand binding and activation of the Ah receptor Michael S. Denison a,

    E-Print Network [OSTI]

    Baldwin, Enoch

    receptor; 2,3,7,8-Tetrachlorodibenzo-p-dioxin; TCDD; Dioxin; Homology model; Ligand binding domain; PAH, polycyclic aromatic hydrocarbon; PAS, PerÁ/ArntÁ/Sim; PCDD, polychlorinated dibenzo-p-dioxin; PGG2, prostaglandin G2 PYP, photoactive yellow protein; TCDD, 2,3,7,8-tetrachlorodibenzo-p-dioxin; TRP

  13. Deleting species from model food webs Christopher Quince, Paul G. Higgs and Alan J. McKane

    E-Print Network [OSTI]

    McKane, Alan

    Deleting species from model food webs Christopher Quince, Paul G. Higgs and Alan J. McKane Quince, C., Higgs, P. G. and McKane, A. J. 2005. Deleting species from model food webs. Á/ Oikos 110: 283Á causing extinction of further species from the food web. To investigate these effects we used

  14. Crystal Structure of the HP1-EMSY Complex Reveals an Unusual Mode of HP1 Binding

    SciTech Connect (OSTI)

    Huang,Y.; Myers, M.; Xu, R.

    2006-01-01

    Heterochromatin protein-1 (HP1) plays an essential role in both the assembly of higher-order chromatin structure and epigenetic inheritance. The C-terminal chromo shadow domain (CSD) of HP1 is responsible for homodimerization and interaction with a number of chromatin-associated nonhistone proteins, including EMSY, which is a BRCA2-interacting protein that has been implicated in the development of breast and ovarian cancer. We have determined the crystal structure of the HP1{beta} CSD in complex with the N-terminal domain of EMSY at 1.8 Angstroms resolution. Surprisingly, the structure reveals that EMSY is bound by two HP1 CSD homodimers, and the binding sequences differ from the consensus HP1 binding motif PXVXL. This structural information expands our understanding of HP1 binding specificity and provides insights into interactions between HP1 homodimers that are likely to be important for heterochromatin formation.

  15. A Secure Cloud Backup System with Assured Deletion and Version Control

    E-Print Network [OSTI]

    Lui, John C.S.

    A Secure Cloud Backup System with Assured Deletion and Version Control Arthur Rahumed, Henry C. H at a low cost. However, cloud clients must enforce security guarantees of their outsourced data backups. We present FadeVersion, a secure cloud backup system that serves as a security layer on top of today's cloud

  16. MHC Class II Tetramers and the Pursuit of Antigen-specific T cells: Define, Deviate, Delete

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    1 MHC Class II Tetramers and the Pursuit of Antigen-specific T cells: Define, Deviate, Delete Class II tetramers Corresponding Author: Roberto Mallone, MD Benaroya Research Institute at Virginia secretion and proliferation. The advent of MHC Class II tetramers has added a pivotal tool to our research

  17. Localization of the Serine Protease-binding Sites in the Collagen-like Domain of Mannose-binding Protein

    E-Print Network [OSTI]

    of microorganisms and thus forms the pathogen recognition component of the lectin pathway of complement activation

  18. Retention of Conformational Entropy upon Calmodulin Binding to Target Peptides is Driven by Transient Salt Bridges

    SciTech Connect (OSTI)

    Smith, Dayle MA; Straatsma, TP; Squier, Thomas C.

    2012-10-03

    Calmodulin (CaM) is a highly flexible calcium-binding protein that mediates signal transduction through an ability to differentially bind to highly variable binding sequences in target proteins. To identify how binding affects CaM motions, and its relationship to conformational entropy and target peptide sequence, we have employed fully atomistic, explicit solvent molecular dynamics simulations of unbound CaM and CaM bound to five different target peptides. The calculated CaM conformational binding entropies correlate with experimentally derived conformational entropies with a correlation coefficient R2 of 0.95. Selected side-chain interactions with target peptides restrain interhelical loop motions, acting to tune the conformational entropy of the bound complex via widely distributed CaM motions. In the complex with the most conformational entropy retention (CaM in complex with the neuronal nitric oxide synthase binding sequence), Lys-148 at the C-terminus of CaM forms transient salt bridges alternating between Glu side chains in the N-domain, the central linker, and the binding target. Additional analyses of CaM structures, fluctuations, and CaM-target interactions illuminate the interplay between electrostatic, side chain, and backbone properties in the ability of CaM to recognize and discriminate against targets by tuning its conformational entropy, and suggest a need to consider conformational dynamics in optimizing binding affinities.

  19. Cross-domain self organizing maps

    E-Print Network [OSTI]

    Fidelholtz, Estanislao L

    2006-01-01

    In this thesis, I present a method for organizing and relating events represented in two domains: the transition-space domain, which focuses on change and the trajectory-space domain, which focuses on movement along paths. ...

  20. Cross Domain Mathematical Concept Formation 

    E-Print Network [OSTI]

    Steel, Graham; Colton, Simon; Bundy, Alan; Walsh, Toby

    2000-01-01

    Many interesting concepts in mathematics are essentially "cross-domain" in nature, relating objects from more than one area of mathematics, e.g. prime order groups. These concepts are often vital to the formation of a ...

  1. Structure determination and analysis of a haemolytic gingipain adhesin domain from Porphyromonas gingivalis

    SciTech Connect (OSTI)

    Li, N.; Yun, P.; Nadkarni, M.A.; Ghadikolaee, N.B.; Nguyen, K.A.; Lee, M.; Hunter, N.; Collyer, C.A. (Sydney)

    2010-08-27

    Porphyromonas gingivalis is an obligately anaerobic bacterium recognized as an aetiological agent of adult periodontitis. P. gingivalis produces cysteine proteinases, the gingipains. The crystal structure of a domain within the haemagglutinin region of the lysine gingipain (Kgp) is reported here. The domain was named K2 as it is the second of three homologous structural modules in Kgp. The K2 domain structure is a 'jelly-roll' fold with two anti-parallel {beta}-sheets. This fold topology is shared with adhesive domains from functionally diverse receptors such as MAM domains, ephrin receptor ligand binding domains and a number of carbohydrate binding modules. Possible functions of K2 were investigated. K2 induced haemolysis of erythrocytes in a dose-dependent manner that was augmented by the blocking of anion transport. Further, cysteine-activated arginine gingipain RgpB, which degrades glycophorin A, sensitized erythrocytes to the haemolytic effect of K2. Cleaved K2, similar to that found in extracted Kgp, lacks the haemolytic activity indicating that autolysis of Kgp may be a staged process which is artificially enhanced by extraction of the protein. The data indicate a functional role for K2 in the integrated capacity conferred by Kgp to enable the porphyrin auxotroph P. gingivalis to capture essential haem from erythrocytes.

  2. Membrane adhesion and domain formation

    E-Print Network [OSTI]

    Thomas R. Weikl; Reinhard Lipowsky

    2007-09-23

    We review theoretical results for the adhesion-induced phase behavior of biomembranes. The focus is on models in which the membranes are represented as discretized elastic sheets with embedded adhesion molecules. We present several mechanism that lead to the formation of domains during adhesion, and discuss the time-dependent evolution of domain patterns obtained in Monte-Carlo simulations. The simulated pattern dynamics has striking similarities to the pattern evolution observed during T cell adhesion.

  3. Slow Dynamics of Orbital Domains in Manganite

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    characterized by the competition between a pinned orbital domain topology that remains static and mobile domain boundaries that exhibit slow, temporal fluctuations. Speckles in...

  4. The N-terminus of TDP-43 promotes its oligomerization and enhances DNA binding affinity

    SciTech Connect (OSTI)

    Chang, Chung-ke [Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan (China)] [Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan (China); Wu, Tzong-Huah [Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan (China) [Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan (China); Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of Biochemistry, Academia Sinica, Taipei 115, Taiwan (China); Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan (China); Wu, Chu-Ya [Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan (China) [Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan (China); Graduate Institute of Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan (China); Chiang, Ming-hui; Toh, Elsie Khai-Woon [Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan (China)] [Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan (China); Hsu, Yin-Chih; Lin, Ku-Feng [Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan (China)] [Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan (China); Liao, Yu-heng [Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan (China)] [Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan (China); Huang, Tai-huang, E-mail: bmthh@gate.sinica.edu.tw [Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan (China) [Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan (China); Department of Physics, National Taiwan Normal University, Taipei 106, Taiwan (China); Huang, Joseph Jen-Tse, E-mail: jthuang@chem.sinica.edu.tw [Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan (China)

    2012-08-24

    Highlights: Black-Right-Pointing-Pointer The N-terminus of TDP-43 contains an independently folded structural domain (NTD). Black-Right-Pointing-Pointer The structural domains of TDP-43 are arranged in a beads-on-a-string fashion. Black-Right-Pointing-Pointer The NTD promotes TDP-43 oligomerization in a concentration-dependent manner. Black-Right-Pointing-Pointer The NTD may assist nucleic acid-binding activity of TDP-43. -- Abstract: TDP-43 is a DNA/RNA-binding protein associated with different neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD-U). Here, the structural and physical properties of the N-terminus on TDP-43 have been carefully characterized through a combination of nuclear magnetic resonance (NMR), circular dichroism (CD) and fluorescence anisotropy studies. We demonstrate for the first time the importance of the N-terminus in promoting TDP-43 oligomerization and enhancing its DNA-binding affinity. An unidentified structural domain in the N-terminus is also disclosed. Our findings provide insights into the N-terminal domain function of TDP-43.

  5. Amplifications and deletions in clinical ovarian cancer detected by Comparative Genomic Hybridization (CGH)

    SciTech Connect (OSTI)

    Sakunaga, H.; Sakamoto, M.; Kallioniemi, A.; Kallioniemi, O.; Sudar, D.; Pinkel, D.; Gray, I.W. ); Yang-Feng, T. )

    1993-01-01

    CGH is a new powerful method for surveying the whole genome for DNA sequence copy number changes in a single hybridization. The method is based on the competition between biotinylated total tumor DNA and a digoxigenin-labeled normal genomic reference DNA during hybridization to normal metaphase chromosomes. After immunofluorescent staining with avidin-FITC and antidigoxigenin Rhodamine, variation of DNA sequence copy numbers in the tumor are detected as variations in the ratios of green and red fluorescence along each chromosome. The authors applied CGH analysis to DNA extracted from surgically removed ovarian cancer specimens (27 cases). Seven amplified regions were identified by CGH analysis. Three loci, 1p32-p34 (most likely, MYCL), 8q23-q24 (MYC), 12q12 (KRAS2), were known to be amplified in solid tumors and four other loci (3q26, 6p22, 9q31-q33, 17q22) were previously unknown to be amplified. Many regions indicating physical deletions were also identified by the analysis. Chromosomal regions showing frequent deletion were 1p, 3p, 17p, 17q, 19p, 19q and Xp. There were also significant similarities of the regions with amplifications and deletions between bilateral ovarian tumors or among several different tumors form the same ovarian cancer cases, suggesting that the genetic changes observed might be relatively early events during the progression of ovarian cancer.

  6. Domain architecture and oligomerization properties of the paramyxovirus PIV 5 hemagglutinin-neuraminidase (HN) protein

    SciTech Connect (OSTI)

    Yuan Ping [Department of Structural Biology, Stanford University, Palo Alto, CA 94305-5126 (United States); Leser, George P. [Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, IL 60208-3500 (United States); Demeler, Borries [Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229-3901 (United States); Lamb, Robert A. [Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, IL 60208-3500 (United States); Howard Hughes Medical Institute, Northwestern University, Evanston, IL 60208-3500 (United States); Jardetzky, Theodore S. [Department of Structural Biology, Stanford University, Palo Alto, CA 94305-5126 (United States)], E-mail: tjardetz@stanford.edu

    2008-09-01

    The mechanism by which the paramyxovirus hemagglutinin-neuraminidase (HN) protein couples receptor binding to activation of virus entry remains to be fully understood, but the HN stalk is thought to play an important role in the process. We have characterized ectodomain constructs of the parainfluenza virus 5 HN to understand better the underlying architecture and oligomerization properties that may influence HN functions. The PIV 5 neuraminidase (NA) domain is monomeric whereas the ectodomain forms a well-defined tetramer. The HN stalk also forms tetramers and higher order oligomers with high {alpha}-helical content. Together, the data indicate that the globular NA domains form weak intersubunit interactions at the end of the HN stalk tetramer, while stabilizing the stalk and overall oligomeric state of the ectodomain. Electron microscopy of the HN ectodomain reveals flexible arrangements of the NA and stalk domains, which may be important for understanding how these two HN domains impact virus entry.

  7. Copyright 2000 by the Genetics Society of America Deletion of an Insulator Element by the Mutation facet-strawberry

    E-Print Network [OSTI]

    Schedl, Paul

    by the Mutation facet-strawberry in Drosophila melanogaster Julio Vazquez* and Paul Schedl *Department mutation, facet-strawberry (faswb ), suggest that this small deletion disrupts such a boundary element

  8. 2.1.14 a) Let G be a graph all of whose vertex-deleted subgraphs ...

    E-Print Network [OSTI]

    gcavigli

    2015-04-30

    Feb 1, 2014 ... b) Let G be a graph all of whose edge-deleted subgraphs are isomorphic. Is G necessarily edge-transitive? 2.1.15 Using Theorem 2.2 and the ...

  9. Ads-Portal Domains: Identification and Measurements

    E-Print Network [OSTI]

    Yang, Xiaowei

    4 Ads-Portal Domains: Identification and Measurements MISHARI ALMISHARI University of California, Irvine and XIAOWEI YANG Duke University An ads-portal domain refers to a Web domain that shows only develop a machine-learning- based classifier to identify ads-portal domains, which has 96% accuracy. We

  10. Evaluation of a modified-live, gene deletion mutant pseudorabies virus vaccine for field use in swine 

    E-Print Network [OSTI]

    Lawhorn, Donald Bruce

    1989-01-01

    EVALUATION OF A MODIFIED-LIVE, GENE DELETION MUTANT PSEUDORABIES VIRUS VACCINE FOR FIELD USE IN SWINE A Thesis by DONALD BRUCE LAWHORN Submitted to the Office of Graduate Studies of Texas ASM University in partial fulfillment... of the requirements for the degree of MASTER OF SCIENCE August 1989 Major Subject: Veterinary Microbiblogy EVALUATION OF A MODIFIED-LIVE, GENE DELETION MUTANT PSEUDORABIES VIRUS VACCINE FOR FIELD USE IN SWINE A Thesis by DONALD BRUCE LAWHORN Approved...

  11. WIKIPEDIA AS DOMAIN KNOWLEDGE NETWORKS: Domain Extraction and Statistical Measurement

    E-Print Network [OSTI]

    Liu, Benyuan

    networks on, respectively, mathematics, physics, biology, and chemistry. We compare the mathematics domain, has developed and evolved rapidly into the most comprehensive online encyclopedia. While people enjoy of the target knowledge network with a trusted knowledge source, such as paper-based encyclopedia. Restricted

  12. Expression levels of MHC class I molecules are inversely correlated with promiscuity of peptide binding

    E-Print Network [OSTI]

    Chappell, Paul E.; Meziane, El Kahina; Harrison, Michael; Magiera, ?ukasz; Hermann, Clemens; Mears, Laura; Wrobel, Antoni G.; Durant, Charlotte; Nielsen, Lise Lotte; Buus, Søren; Ternette, Nicola; Mwangi, William; Butter, Colin; Nair, Venugopal; Ahyee, Trudy; Duggleby, Richard; Madrigal, Alejandro; Roversi, Pietro; Lea, Susan M.; Kaufman, Jim

    2015-04-10

    in and around the beginning of the groove and reveals Figure 4. Structures of BF2*2101 with different peptides show several modes of promiscuous binding through remodelling of the binding site. Left panels, top down view with peptide as sticks (N... residues. Upper panels, side view from ?2 domain side with peptide as sticks (N-terminus of peptide to the left; carbon atoms of peptide, yellow; carbon atoms of class I molecule, white; nitrogen atoms, blue; oxygen atoms, red; hydrogen bonds, dotted lines...

  13. Allostery Is an Intrinsic Property of the Protease Domain of DegS Implications for Enzyme Function and Evolution

    SciTech Connect (OSTI)

    Sohn, Jungsan; Grant, Robert A.; Sauer, Robert T. (MIT)

    2010-12-02

    DegS is a periplasmic Escherichia coli protease, which functions as a trimer to catalyze the initial rate-limiting step in a proteolytic cascade that ultimately activates transcription of stress response genes in the cytoplasm. Each DegS subunit consists of a protease domain and a PDZ domain. During protein folding stress, DegS is allosterically activated by peptides exposed in misfolded outer membrane porins, which bind to the PDZ domain and stabilize the active protease. It is not known whether allostery is conferred by the PDZ domains or is an intrinsic feature of the trimeric protease domain. Here, we demonstrate that free DegS{sup {Delta}PDZ} equilibrates between active and inactive trimers with the latter species predominating. Substrate binding stabilizes active DegS{sup {Delta}PDZ} in a positively cooperative fashion. Mutations can also stabilize active DegS{sup {Delta}PDZ} and produce an enzyme that displays hyperbolic kinetics and degrades substrate with a maximal velocity within error of that for fully activated, intact DegS. Crystal structures of multiple DegS{sup {Delta}PDZ} variants, in functional and non-functional conformations, support a two-state model in which allosteric switching is mediated by changes in specific elements of tertiary structure in the context of an invariant trimeric base. Overall, our results indicate that protein substrates must bind sufficiently tightly and specifically to the functional conformation of DegS{sup {Delta}PDZ} to assist their own degradation. Thus, substrate binding alone may have regulated the activities of ancestral DegS trimers with subsequent fusion of the protease domain to a PDZ domain, resulting in ligand-mediated regulation.

  14. Critical role of the SPAK protein kinase CCT domain in controlling blood pressure

    E-Print Network [OSTI]

    Zhang, Jinwei; Siew, Keith; Macartney, Thomas; O'Shaughnessy, Kevin M.; Alessi, Dario R.

    2015-05-20

    -target effects of agents like thiazide diuretics (16,35). One approachwould be to elaborate smallmolecule compounds that directly inhibit SPAK/OSR1 protein kinase activity (36). However, to our knowledge, no highly selective and potent ki- nase inhibitors of SPAK... -binding enzymes and causing in- tolerable off-target effects. An alternative strategy to suppress SPAK/OSR1 function would be to target the docking domain within the non-catalytic C-terminal region of SPAK/OSR1 called the CCT (conserved C-Terminal) domain...

  15. Coexistence of dilute and densely packed domains of ligand-receptor bonds in membrane adhesion

    E-Print Network [OSTI]

    Daniel Schmidt; Timo Bihr; Udo Seifert; Ana-Sun?ana Smith

    2012-07-11

    We analyze the stability of micro-domains of ligand-receptor bonds that mediate the adhesion of biological model membranes. After evaluating the effects of membrane fluctuations on the binding affinity of a single bond, we characterize the organization of bonds within the domains by theoretical means. In a large range of parameters, we find the commonly suggested dense packing to be separated by a free energy barrier from a regime in which bonds are sparsely distributed. If bonds are mobile, a coexistence of the two regimes should emerge, which agrees with recent experimental observations.

  16. Mutation of the Fiber Shaft Heparan Sulphate Binding Site of a 5/3 Chimeric Adenovirus Reduces Liver Tropism

    E-Print Network [OSTI]

    Hemminki, Akseli

    Mutation of the Fiber Shaft Heparan Sulphate Binding Site of a 5/3 Chimeric Adenovirus Reduces and to cellular heparan sulphate proteoglycans via the fiber shaft KKTK domain are suggested to cause liver. Citation: Koski A, Karli E, Kipar A, Escutenaire S, Kanerva A, et al. (2013) Mutation of the Fiber Shaft

  17. Erythropoietin binding protein from mammalian serum

    DOE Patents [OSTI]

    Clemons, Gisela K. (Berkeley, CA)

    1997-01-01

    Purified mammalian erythropoietin binding-protein is disclosed, and its isolation, identification, characterization, purification, and immunoassay are described. The erythropoietin binding protein can be used for regulation of erythropoiesis by regulating levels and half-life of erythropoietin. A diagnostic kit for determination of level of erythropoietin binding protein is also described.

  18. Erythropoietin binding protein from mammalian serum

    DOE Patents [OSTI]

    Clemons, G.K.

    1997-04-29

    Purified mammalian erythropoietin binding-protein is disclosed, and its isolation, identification, characterization, purification, and immunoassay are described. The erythropoietin binding protein can be used for regulation of erythropoiesis by regulating levels and half-life of erythropoietin. A diagnostic kit for determination of level of erythropoietin binding protein is also described. 11 figs.

  19. A Rare Earth-DOTA-Binding Antibody: Probe Properties and Binding Affinity across the Lanthanide Series

    E-Print Network [OSTI]

    Fisher, Andrew J.

    1) binds transition metals and rare earths with extreme stability under physiological conditionsA Rare Earth-DOTA-Binding Antibody: Probe Properties and Binding Affinity across the Lanthanide affinity and exquisite specificity.1 An antibody that binds rare earth complexes selectively could be used

  20. Supplemental Data S1 The SRA Methyl-Cytosine-Binding Domain

    E-Print Network [OSTI]

    Jacobsen, Steve

    of 4 CG, 7 CNG, and 33 CNN residues. Ten to twelve independent clones were sequenced, and the average number of methylated CG, CNG, or CNN was deter- mined (see Table S1 for all primer sequences). At AtCOPIA4, there are a total of 25 CG, 18 CNG, and 116 CNN residues. Seven to twelve independent clones were

  1. LINC Complexes Form by Binding of Three KASH Peptides to Domain Interfaces of Trimeric SUN Proteins

    E-Print Network [OSTI]

    Sosa, Brian A.

    Linker of nucleoskeleton and cytoskeleton (LINC) complexes span the nuclear envelope and are composed of KASH and SUN proteins residing in the outer and inner nuclear membrane, respectively. LINC formation relies on direct ...

  2. Conserved SMP domains of the ERMES complex bind phospholipids and mediate tether assembly

    E-Print Network [OSTI]

    2015-01-01

    stars) are highlighted and agree with the EM class averages obtained using MBP-Mmm1 or Mdm12-GFP fusion-

  3. Topoisomerase II? Binding Domains of Adenomatous Polyposis Coli Influence Cell Cycle Progression and Aneuploidy

    E-Print Network [OSTI]

    Wang, Yang; Coffey, Robert J.; Osheroff, Neil; Neufeld, Kristi L.

    2010-04-02

    acid repeat region of APC (M2-APC) in the regulation of the G2/M cell cycle transition through interaction with topoisomerase II? (topo II?). Methodology/Principal Findings We now demonstrate that the 20-amino acid repeat region of APC (M3-APC) also...

  4. Evolution and Functional Diversification of the Paired Box (Rzx) DNA-Binding Domains

    E-Print Network [OSTI]

    Kumar, Sudhir

    associated with a number of disease phenotypes, e.g., vertebral column malformation (Pa-l, Balling, Deutsch in vertebrates. Our evolutionary analyses indicate that the vertebrate Pax gene family consists of four well,III),(II,IV)). These four major groups arose before the divergence of Drosophila and vertebrates prior to the Cambrian

  5. Evaluating the sensitivity of hybridization-based epigenotyping using a methyl binding domain protein

    E-Print Network [OSTI]

    Shatova, Tatyana A.

    Hypermethylation of CpG islands in gene promoter regions has been shown to be a predictive biomarker for certain diseases. Most current methods for methylation profiling are not well-suited for clinical analysis. Here, we ...

  6. Whole-Cell Immobilization Using Cell Surface-Exposed Cellulose-Binding Domain

    E-Print Network [OSTI]

    Chen, Wilfred

    processes, ranging from the production of ethanol (1) to the degradation of phenol (2). Industrial methods

  7. Structure of Human Toll-like Receptor 3 (TLR3) Ligand-binding Domain

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power AdministrationRobust,Field-effect PhotovoltaicsStructure and Receptor Specificity ofHuman Toll-like Receptor 3

  8. Multi-PAS domain-mediated protein oligomerization of PpsR from Rhodobacter sphaeroides

    SciTech Connect (OSTI)

    Heintz, Udo; Meinhart, Anton; Winkler, Andreas, E-mail: andreas.winkler@mpimf-heidelberg.mpg.de [Max Planck Institute for Medical Research, Heidelberg (Germany)

    2014-03-01

    Crystal structures of two truncated variants of the transcription factor PpsR from R. sphaeroides are presented that enabled the phasing of a triple PAS domain construct. Together, these structures reveal the importance of ?-helical PAS extensions for multi-PAS domain-mediated protein oligomerization and function. Per–ARNT–Sim (PAS) domains are essential modules of many multi-domain signalling proteins that mediate protein interaction and/or sense environmental stimuli. Frequently, multiple PAS domains are present within single polypeptide chains, where their interplay is required for protein function. Although many isolated PAS domain structures have been reported over the last decades, only a few structures of multi-PAS proteins are known. Therefore, the molecular mechanism of multi-PAS domain-mediated protein oligomerization and function is poorly understood. The transcription factor PpsR from Rhodobacter sphaeroides is such a multi-PAS domain protein that, in addition to its three PAS domains, contains a glutamine-rich linker and a C-terminal helix–turn–helix DNA-binding motif. Here, crystal structures of two N-terminally and C-terminally truncated PpsR variants that comprise a single (PpsR{sub Q-PAS1}) and two (PpsR{sub N-Q-PAS1}) PAS domains, respectively, are presented and the multi-step strategy required for the phasing of a triple PAS domain construct (PpsR{sub ?HTH}) is illustrated. While parts of the biologically relevant dimerization interface can already be observed in the two shorter constructs, the PpsR{sub ?HTH} structure reveals how three PAS domains enable the formation of multiple oligomeric states (dimer, tetramer and octamer), highlighting that not only the PAS cores but also their ?-helical extensions are essential for protein oligomerization. The results demonstrate that the long helical glutamine-rich linker of PpsR results from a direct fusion of the N-cap of the PAS1 domain with the C-terminal extension of the N-domain that plays an important role in signal transduction.

  9. Performance Assessment Report Domain CHP System

    E-Print Network [OSTI]

    Oak Ridge National Laboratory

    Performance Assessment Report for the Domain CHP System November 2005 By Burns & McDonnell Engineering #12;Domain CHP System Performance Assessment Report for the Packaged Cooling, Heating and Power

  10. Slow Dynamics of Orbital Domains in Manganite

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    is shown in purple and red, emphasizing the anti-phase domain wall. Any points where the wave functions are out of phase with each other can act as an orbital domain boundary. To...

  11. Structures of Adnectin/Protein Complexes Reveal an Expanded Binding Footprint

    SciTech Connect (OSTI)

    Ramamurthy, Vidhyashankar; Krystek, Jr., Stanley R.; Bush, Alexander; Wei, Anzhi; Emanuel, Stuart L.; Gupta, Ruchira Das; Janjua, Ahsen; Cheng, Lin; Murdock, Melissa; Abramczyk, Bozena; Cohen, Daniel; Lin, Zheng; Morin, Paul; Davis, Jonathan H.; Dabritz, Michael; McLaughlin, Douglas C.; Russo, Katie A.; Chao, Ginger; Wright, Martin C.; Jenny, Victoria A.; Engle, Linda J.; Furfine, Eric; Sheriff, Steven

    2014-10-02

    Adnectins are targeted biologics derived from the tenth type III domain of human fibronectin ({sup 10}Fn3), a member of the immunoglobulin superfamily. Target-specific binders are selected from libraries generated by diversifying the three {sup 10}Fn3 loops that are analogous to the complementarity determining regions of antibodies. The crystal structures of two Adnectins were determined, each in complex with its therapeutic target, EGFR or IL-23. Both Adnectins bind different epitopes than those bound by known monoclonal antibodies. Molecular modeling suggests that some of these epitopes might not be accessible to antibodies because of the size and concave shape of the antibody combining site. In addition to interactions from the Adnectin diversified loops, residues from the N terminus and/or the {beta} strands interact with the target proteins in both complexes. Alanine-scanning mutagenesis confirmed the calculated binding energies of these {beta} strand interactions, indicating that these nonloop residues can expand the available binding footprint.

  12. X-ray survival characteristics and genetic analysis for nine saccharomyces deletion mutants that show altered radiation sensitivity

    SciTech Connect (OSTI)

    Game, John C.; Williamson, Marsha S.; Baccari, Clelia

    2004-01-07

    The availability of a genome-wide set of Saccharomyces deletion mutants provides a chance to identify all the yeast genes involved in DNA repair. Using X-rays, we are screening these mutants to identify additional genes that show increased sensitivity to the lethal effects of ionizing radiation. For each mutant identified as sensitive, we are confirming that the sensitivity phenotype co-segregates with the deletion allele and are obtaining multipoint survival-versus-dose assays in at least two haploid and one homozygous diploid strains. We present data for deletion mutants involving the genes DOT1, MDM20, NAT3, SPT7, SPT20, GCN5, HFI1, DCC1 and VID21/EAF1, and discuss their potential roles in repair. Eight of these genes have a clear radiation-sensitive phenotype when deleted, but the ninth, GCN5, has at most a borderline phenotype. None of the deletions confer substantial sensitivity to ultra-violet radiation, although one or two may confer marginal sensitivity. The DOT1 gene is of interest because its only known function is to methylate one lysine residue in the core of the histone H3 protein. We find that histone H3 mutants (supplied by K. Struhl) in which this residue is replaced by other amino-acids are also X-ray sensitive, seeming to confirm that methylation of the lysine-79 residue is required for effective repair of radiation damage.

  13. Effective Supergravity for Supergravity Domain Walls

    E-Print Network [OSTI]

    M. Cvetic; N. D. Lambert

    2002-05-23

    We discuss the low energy effective action for the Bosonic and Fermionic zero-modes of a smooth BPS Randall-Sundrum domain wall, including the induced supergravity on the wall. The result is a pure supergravity in one lower dimension. In particular, and in contrast to non-gravitational domain walls or domain walls in a compact space, the zero-modes representing transverse fluctuations of domain wall have vanishing action.

  14. Probing the Impact of the EchinT C-Terminal Domain on Structure and Catalysis

    SciTech Connect (OSTI)

    S Bardaweel; J Pace; T Chou; V Cody; C Wagner

    2011-12-31

    Histidine triad nucleotide binding protein (Hint) is considered as the ancestor of the histidine triad protein superfamily and is highly conserved from bacteria to humans. Prokaryote genomes, including a wide array of both Gram-negative bacteria and Gram-positive bacteria, typically encode one Hint gene. The cellular function of Hint and the rationale for its evolutionary conservation in bacteria have remained a mystery. Despite its ubiquity and high sequence similarity to eukaryote Hint1 [Escherichia coli Hint (echinT) is 48% identical with human Hint1], prokaryote Hint has been reported in only a few studies. Here we report the first conformational information on the full-length N-terminal and C-terminal residues of Hint from the E. coli complex with GMP. Structural analysis of the echinT-GMP complex reveals that it crystallizes in the monoclinic space group P2{sub 1} with four homodimers in the asymmetric unit. Analysis of electron density for both the N-terminal residues and the C-terminal residues of the echinT-GMP complex indicates that the loops in some monomers can adopt more than one conformation. The observation of conformational flexibility in terminal loop regions could explain the presence of multiple homodimers in the asymmetric unit of this structure. To explore the impact of the echinT C-terminus on protein structure and catalysis, we conducted a series of catalytic radiolabeling and kinetic experiments on the C-terminal deletion mutants of echinT. In this study, we show that sequential deletion of the C-terminus likely has no effect on homodimerization and a modest effect on the secondary structure of echinT. However, we observed a significant impact on the folding structure, as reflected by a significant lowering of the T{sub m} value. Kinetic analysis reveals that the C-terminal deletion mutants are within an order of magnitude less efficient in catalysis compared to wild type, while the overall kinetic mechanism that proceeds through a fast step, followed by a rate-limiting hydrolysis step, was conserved. Nevertheless, the ability of the C-terminal deletion mutants to hydrolyze lysyl-AMP generated by LysU was greatly impaired. Taken together, our results highlight the emerging role of the C-terminus in governing the catalytic function of Hints.

  15. Poster: Measuring the Lifecycles of Malicious Domains

    E-Print Network [OSTI]

    Li, Kang

    the lifecycles of malicious domain names will provide insight into the many classes of criminal networks- measures such as blacklisting. Fast-flux is characterized by domain name records with low (time other types of criminal networks abuse the DNS and leverage domain names to provide agility

  16. Domain embedding preconditioners for mixed systems 1

    E-Print Network [OSTI]

    Winther, Ragnar

    Domain embedding preconditioners for mixed systems 1 Torgeir Rusten SINTEF, P. O. Box 124 Blindern preconditioners for the corresponding discrete linear systems where an embedding of the domain papers discussing domain embedding as a tool for solving discrete systems we refer to Astrakhantsev [4

  17. Labelling Heuristics for CSP Application Domains

    E-Print Network [OSTI]

    Rossi, Francesca

    Labelling Heuristics for CSP Application Domains Zeynep K#16;z#16;ltan Computer Science Division an application domain as a family of CSP models, so as to exhibit the generic constraint store for all models store and the domain propagation during search is analysed, so as to infer | before modelling any CSP

  18. Domain architecture evolution of pattern-recognition receptors

    E-Print Network [OSTI]

    Zhang, Qing; Zmasek, Christian M.; Godzik, Adam

    2010-01-01

    1 ORIGINAL PAPER Domain architecture evolution of pattern-in the same domain architectures evolving independentlythe choices of domain architectures for new members in the

  19. Nonlinear Time Domain Modeling and Simulation of Surface and...

    Office of Environmental Management (EM)

    Nonlinear Time Domain Modeling and Simulation of Surface and Embedded NPPS Nonlinear Time Domain Modeling and Simulation of Surface and Embedded NPPS Nonlinear Time Domain Modeling...

  20. C-Terminal Titin Deletions Cause a Novel Early-Onset Myopathy with Fatal

    E-Print Network [OSTI]

    Campbell, Kevin P.

    and suggest that titin segments downstream of the kinase domain are dispensable for skeletal and cardiac, muscle weakness, and delayed motor develop- ment. From clinical features and particularly muscle bi- opsy

  1. Word Domain Disambiguation via Word Sense Disambiguation

    SciTech Connect (OSTI)

    Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.

    2006-06-04

    Word subject domains have been widely used to improve the perform-ance of word sense disambiguation al-gorithms. However, comparatively little effort has been devoted so far to the disambiguation of word subject do-mains. The few existing approaches have focused on the development of al-gorithms specific to word domain dis-ambiguation. In this paper we explore an alternative approach where word domain disambiguation is achieved via word sense disambiguation. Our study shows that this approach yields very strong results, suggesting that word domain disambiguation can be ad-dressed in terms of word sense disam-biguation with no need for special purpose algorithms.

  2. Antigen-specific blocking of immunological synapse formation using bifunctional peptide, Utilization of I-domain of LFA-1 to Target Drug and Marker Molecules to Leukocytes

    E-Print Network [OSTI]

    Manikwar, Prakash; Tejo, Bimo A.; Shinogle, Heather; Moore, David S.; Zimmerman, Tahl; Blanco, Francisco; Siahaan, Teruna J.

    2011-05-01

    to deliver drugs to cells with upregulated ICAM-1. Anti-ICAM-1-coated nanopar- ticles successfully delivered lysosomal enzyme into cells obtained from patients suffering from lysosomal storage disorder [34]. These nanoparticles are endo- cytosed via a non... blocks the I-domain binding site to ICAM-1 (Fig. 4). A similar effect of the mAb was observed in the binding of a GST-tagged I-domain (I-GST) to a surface-coated ICAM-1Fc using a solid-phase ELISA assay [29]. The antibody blocking studies indicate...

  3. Domain Bubbles of Extra Dimensions

    E-Print Network [OSTI]

    Morris, J R

    2003-01-01

    ``Dimension bubbles'' of the type previously studied by Blau and Guendelman [S.K. Blau and E.I. Guendelman, Phys. Rev. D40, 1909 (1989)], which effectively enclose a region of 5d spacetime and are surrounded by a region of 4d spacetime, can arise in a 5d theory with a compact extra dimension that is dimensionally reduced to give an effective 4d theory. These bubbles with thin domain walls can be stabilized against total collapse in a rather natural way by a scalar field which, as in the case with ``ordinary'' nontopological solitons, traps light scalar particles inside the bubble.

  4. Domain Bubbles of Extra Dimensions

    E-Print Network [OSTI]

    J. R. Morris

    2002-11-19

    ``Dimension bubbles'' of the type previously studied by Blau and Guendelman [S.K. Blau and E.I. Guendelman, Phys. Rev. D40, 1909 (1989)], which effectively enclose a region of 5d spacetime and are surrounded by a region of 4d spacetime, can arise in a 5d theory with a compact extra dimension that is dimensionally reduced to give an effective 4d theory. These bubbles with thin domain walls can be stabilized against total collapse in a rather natural way by a scalar field which, as in the case with ``ordinary'' nontopological solitons, traps light scalar particles inside the bubble.

  5. Radiative transfer in decomposed domains

    E-Print Network [OSTI]

    T. Heinemann; W. Dobler; A. Nordlund; A. Brandenburg

    2005-11-09

    An efficient algorithm for calculating radiative transfer on massively parallel computers using domain decomposition is presented. The integral formulation of the transfer equation is used to divide the problem into a local but compute-intensive part for calculating the intensity and optical depth integrals, and a nonlocal part for communicating the intensity between adjacent processors. The waiting time of idle processors during the nonlocal communication part does not have a severe impact on the scaling. The wall clock time thus scales nearly linearly with the inverse number of processors.

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

    SciTech Connect (OSTI)

    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; Forlinoi, Antonella; Cabral, Wayne A.; Barnes, Aileen M.; Marini, Joan C.; San Antonio, James D.

    2008-07-18

    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.

  7. Domain wall conduction in multiaxial ferroelectrics

    SciTech Connect (OSTI)

    Eliseev, E. A.; Morozovska, A. N.; Svechnikov, S. V.; Maksymovych, Petro; Kalinin, Sergei V

    2012-01-01

    The conductance of domain wall structures consisting of either stripes or cylindrical domains in multiaxial ferroelectric-semiconductors is analyzed. The effects of the flexoelectric coupling, domain size, wall tilt, and curvature on charge accumulation are analyzed using the Landau-Ginsburg Devonshire theory for polarization vector combined with the Poisson equation for charge distributions. The proximity and size effect of the electron and donor accumulation/depletion by thin stripe domains and cylindrical nanodomains are revealed. In contrast to thick domain stripes and wider cylindrical domains, in which the carrier accumulation (and so the static conductivity) sharply increases at the domain walls only, small nanodomains of radii less than 5-10 correlation lengths appeared conducting across the entire cross-section. Implications of such conductive nanosized channels may be promising for nanoelectronics.

  8. Engineering Deletions in the Mg1-Pk1 Gene Cluster of Streptomyces sp. Mg1 to Abolish Production of the Mg1-Pk1 Metabolite 

    E-Print Network [OSTI]

    Moisan, Sabrina

    2013-09-25

    when challenged with Bacillus subtilis. When the biosynthetic genes of the Mg1-Pk1 gene cluster are deleted, the resulting mutant strain, S. Mg1-?37, is hypersensitive to growth inhibition by B. subtilis. However, deletion of the Mg1-Pk1 biosynthetic...

  9. Net light-induced oxygen evolution in photosystem I deletion mutants of the cyanobacterium Synechocystis sp. PCC 6803

    E-Print Network [OSTI]

    Govindjee

    Net light-induced oxygen evolution in photosystem I deletion mutants of the cyanobacterium of net light-induced O2 evo- lution in vivo. The net light-induced O2 evolution requires glucose and can assimilate more CO2 in the light compared to the dark. However, the rate of the light-minus-dark CO2

  10. Time domain electromagnetic metal detectors

    SciTech Connect (OSTI)

    Hoekstra, P.

    1996-04-01

    This presentation focuses on illustrating by case histories the range of applications and limitations of time domain electromagnetic (TDEM) systems for buried metal detection. Advantages claimed for TDEM metal detectors are: independent of instrument response (Geonics EM61) to surrounding soil and rock type; simple anomaly shape; mitigation of interference by ambient electromagnetic noise; and responsive to both ferrous and non-ferrous metallic targets. The data in all case histories to be presented were acquired with the Geonics EM61 TDEM system. Case histories are a test bed site on Molokai, Hawaii; Fort Monroe, Virginia; and USDOE, Rocky Flats Plant. The present limitations of this technology are: discrimination capabilities in terms of type of ordnance, and depth of burial is limited, and ability of resolving targets with small metallic ambient needs to be improved.

  11. The structure of the SBP-Tag–streptavidin complex reveals a novel helical scaffold bridging binding pockets on separate subunits

    SciTech Connect (OSTI)

    Barrette-Ng, Isabelle H.; Wu, Sau-Ching; Tjia, Wai-Mui; Wong, Sui-Lam; Ng, Kenneth K. S.

    2013-05-01

    The structure of the SBP-Tag–streptavidin complex reveals a novel mode of peptide recognition in which a single peptide binds simultaneously to biotin-binding pockets from adjacent subunits of streptavidin. The molecular details of peptide recognition suggest how the SBP-Tag can be further modified to become an even more useful tag for a wider range of biotechnological applications. The 38-residue SBP-Tag binds to streptavidin more tightly (K{sub d} ? 2.5–4.9 nM) than most if not all other known peptide sequences. Crystallographic analysis at 1.75 Å resolution shows that the SBP-Tag binds to streptavidin in an unprecedented manner by simultaneously interacting with biotin-binding pockets from two separate subunits. An N-terminal HVV peptide sequence (residues 12–14) and a C-terminal HPQ sequence (residues 31–33) form the bulk of the direct interactions between the SBP-Tag and the two biotin-binding pockets. Surprisingly, most of the peptide spanning these two sites (residues 17–28) adopts a regular ?-helical structure that projects three leucine side chains into a groove formed at the interface between two streptavidin protomers. The crystal structure shows that residues 1–10 and 35–38 of the original SBP-Tag identified through in vitro selection and deletion analysis do not appear to contact streptavidin and thus may not be important for binding. A 25-residue peptide comprising residues 11–34 (SBP-Tag2) was synthesized and shown using surface plasmon resonance to bind streptavidin with very similar affinity and kinetics when compared with the SBP-Tag. The SBP-Tag2 was also added to the C-terminus of ?-lactamase and was shown to be just as effective as the full-length SBP-Tag in affinity purification. These results validate the molecular structure of the SBP-Tag–streptavidin complex and establish a minimal bivalent streptavidin-binding tag from which further rational design and optimization can proceed.

  12. Docking Small Ligands in Flexible Binding Sites

    E-Print Network [OSTI]

    Caflisch, Amedeo

    binding site. For all three systems the best minima in terms of free energy have a root mean square 3100-043423.95 Contractrgrant sponsor: Swiss Federal Office of Public Health; contractrgrant number the conformational space that has to be searched. There are known examples where the empty receptor cannot bind

  13. Detecting Networks Employing Algorithmically Generated Domain Names 

    E-Print Network [OSTI]

    Ashwath Kumar Krishna Reddy

    2011-10-21

    , current botnets use simple pseudo-random generators which may not preserve the distribution of alphabets or bigrams (two consecutive alphabets) as usually occur in legitimate domain name strings. In this regards, we propose several metrics to classify a... generates. For instance, in the extreme scenario that a botnet generates 50 domains mapped to the same TLD, we show that KL-divergence over unigrams achieves 100% detection accuracy albeit at 15% false positive rate (legitimate domain groups clas- 7 si ed...

  14. Charm physics with Moebius Domain Wall Fermions

    E-Print Network [OSTI]

    Andreas Jüttner; Francesco Sanfilippo; Justus Tobias Tsang; Peter Boyle; Marina Marinkovic; Shoji Hashimoto; Takashi Kaneko; Yong-Gwi Cho

    2015-01-04

    We present results showing that Domain Wall fermions are a suitable discretisation for the simulation of heavy quarks. This is done by a continuum scaling study of charm quarks in a M\\"obius Domain Wall formalism using a quenched set-up. We find that discretisation effects remain well controlled by the choice of Domain Wall parameters preparing the ground work for the ongoing dynamical $2+1f$ charm program of RBC/UKQCD.

  15. Charm physics with Moebius Domain Wall Fermions

    E-Print Network [OSTI]

    Jüttner, Andreas; Tsang, Justus Tobias; Boyle, Peter; Marinkovic, Marina; Hashimoto, Shoji; Kaneko, Takashi; Cho, Yong-Gwi

    2015-01-01

    We present results showing that Domain Wall fermions are a suitable discretisation for the simulation of heavy quarks. This is done by a continuum scaling study of charm quarks in a M\\"obius Domain Wall formalism using a quenched set-up. We find that discretisation effects remain well controlled by the choice of Domain Wall parameters preparing the ground work for the ongoing dynamical $2+1f$ charm program of RBC/UKQCD.

  16. Hidden Rotational Symmetries in Magnetic Domain Patterns

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    California, San Diego, have recently used coherent soft x-ray scattering with angular Fourier analysis to discover that the disordered domain patterns do, in fact, exhibit...

  17. Development of Nonlinear SSI Time Domain Methodology

    Broader source: Energy.gov [DOE]

    Development of Nonlinear SSI Time Domain Methodology Justin Coleman, P.E. Nuclear Science and Technology Idaho National Laboratory October 22, 2014

  18. Integral Domains Inside Noetherian Power Series Rings ...

    E-Print Network [OSTI]

    2015-05-21

    Another theme is an analysis of extensions of integral domains R ?? S ...... TOOLS. Flatness is preserved by several standard ring constructions as we record in.

  19. Regional characteristics, tilt domains, and extensional history...

    Open Energy Info (EERE)

    Report Number 303 DOI Not Provided Check for DOI availability: http:crossref.org Online Internet link for Regional characteristics, tilt domains, and extensional history of the...

  20. Unfurling of the band 4.1, ezrin, radixin, moesin (FERM) domain of the merlin tumor suppressor

    SciTech Connect (OSTI)

    Yogesha, S.D.; Sharff, Andrew J.; Giovannini, Marco; Bricogne, Gerard; Izard, Tina (House Ear); (Globel Phasing); (Scripps)

    2014-10-02

    The merlin-1 tumor suppressor is encoded by the Neurofibromatosis-2 (Nf2) gene and loss-of-function Nf2 mutations lead to nervous system tumors in man and to several tumor types in mice. Merlin is an ERM (ezrin, radixin, moesin) family cytoskeletal protein that interacts with other ERM proteins and with components of cell-cell adherens junctions (AJs). Merlin stabilizes the links of AJs to the actin cytoskeleton. Thus, its loss destabilizes AJs, promoting cell migration and invasion, which in Nf2{sup +/-} mice leads to highly metastatic tumors. Paradoxically, the 'closed' conformation of merlin-1, where its N-terminal four-point-one, ezrin, radixin, moesin (FERM) domain binds to its C-terminal tail domain, directs its tumor suppressor functions. Here we report the crystal structure of the human merlin-1 head domain when crystallized in the presence of its tail domain. Remarkably, unlike other ERM head-tail interactions, this structure suggests that binding of the tail provokes dimerization and dynamic movement and unfurling of the F2 motif of the FERM domain. We conclude the 'closed' tumor suppressor conformer of merlin-1 is in fact an 'open' dimer whose functions are disabled by Nf2 mutations that disrupt this architecture.

  1. DLEU2, frequently deleted in malignancy, functions as a critical host gene of the cell cycle inhibitory microRNAs miR-15a and miR-16-1

    SciTech Connect (OSTI)

    Lerner, Mikael; Harada, Masako; Loven, Jakob; Castro, Juan; Davis, Zadie; Oscier, David; Henriksson, Marie; Sangfelt, Olle; Grander, Dan; Corcoran, Martin M.

    2009-10-15

    The microRNAs miR-15a and miR-16-1 are downregulated in multiple tumor types and are frequently deleted in chronic lymphocytic leukemia (CLL), myeloma and mantle cell lymphoma. Despite their abundance in most cells the transcriptional regulation of miR-15a/16-1 remains unclear. Here we demonstrate that the putative tumor suppressor DLEU2 acts as a host gene of these microRNAs. Mature miR-15a/miR-16-1 are produced in a Drosha-dependent process from DLEU2 and binding of the Myc oncoprotein to two alterative DLEU2 promoters represses both the host gene transcript and levels of mature miR-15a/miR-16-1. In line with a functional role for DLEU2 in the expression of the microRNAs, the miR-15a/miR-16-1 locus is retained in four CLL cases that delete both promoters of this gene and expression analysis indicates that this leads to functional loss of mature miR-15a/16-1. We additionally show that DLEU2 negatively regulates the G1 Cyclins E1 and D1 through miR-15a/miR-16-1 and provide evidence that these oncoproteins are subject to miR-15a/miR-16-1-mediated repression under normal conditions. We also demonstrate that DLEU2 overexpression blocks cellular proliferation and inhibits the colony-forming ability of tumor cell lines in a miR-15a/miR-16-1-dependent way. Together the data illuminate how inactivation of DLEU2 promotes cell proliferation and tumor progression through functional loss of miR-15a/miR-16-1.

  2. Mechanosensing by the Primary Cilium: Deletion of Kif3A Reduces Bone Formation Due to Loading

    E-Print Network [OSTI]

    Stearns, Tim

    of America, 9 Energy Biosciences Institute, University of California, Berkeley, California, United States and extend into the extracellular space, have increasingly been implicated as sensors of a variety lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication

  3. Improved flow cytometer measurement of binding assays

    DOE Patents [OSTI]

    Saunders, G.C.

    1984-05-30

    The invention relates to a method of measuring binding assays carried out with different size particles wherein the binding assay sample is run through a flow cytometer without separating the sample from the marking agent. The amount of a binding reactant present in a sample is determined by providing particles with a coating of binder and also a known quantity of smaller particles with a coating of binder reactant. The binding reactant is the same as the binding reactant present in the sample. The smaller particles also contain a fluorescent chemical. The particles are combined with the sample and the binding reaction is allowed to occur for a set length of time followed by combining the smaller particles with the mixture of the particles and the sample produced and allowing the binding reactions to proceed to equilibrium. The fluorescence and light scatter of the combined mixture is then measured as the combined mixture passes through a flow cytometer equipped with a laser to bring about fluorescence, and the number and strength of fluorescent events are compared. A similar method is also provided for determining the amount of antigen present in the sample by providing spheres with an antibody coating and some smaller spheres with an antigen coating. (LEW)

  4. Diary of a domain analyst: a domain analysis case-study from avionics

    E-Print Network [OSTI]

    Kelly, Tim

    . In this paper, we describe a domain analysis case-study in the domain of aero-engine systems. The principle-STUDY: AERO-ENGINE STARTING SYSTEMS We chose aero-engine starting systems as the domain to be analysed, taking

  5. NATIONAL PLAN TO ACHIEVE MARITIME DOMAIN AWARENESS

    E-Print Network [OSTI]

    Huang, Wei

    NATIONAL PLAN TO ACHIEVE MARITIME DOMAIN AWARENESS FOR THE NATIONAL STRATEGY FOR MARITIME SECURITY OCTOBER 2005 #12;National Strategy for Maritime Security: National Plan to Achieve Maritime Domain Awareness i FOREWORD By signing National Security Presidential Directive-41/Homeland Security Presidential

  6. Optical coherence domain reflectometry guidewire

    DOE Patents [OSTI]

    Colston, Billy W. (Livermore, CA); Everett, Matthew (Pleasanton, CA); Da Silva, Luiz B. (Danville, CA); Matthews, Dennis (Moss Beach, CA)

    2001-01-01

    A guidewire with optical sensing capabilities is based on a multiplexed optical coherence domain reflectometer (OCDR), which allows it to sense location, thickness, and structure of the arterial walls or other intra-cavity regions as it travels through the body during minimally invasive medical procedures. This information will be used both to direct the guidewire through the body by detecting vascular junctions and to evaluate the nearby tissue. The guidewire contains multiple optical fibers which couple light from the proximal to distal end. Light from the fibers at the distal end of the guidewire is directed onto interior cavity walls via small diameter optics such as gradient index lenses and mirrored corner cubes. Both forward viewing and side viewing fibers can be included. The light reflected or scattered from the cavity walls is then collected by the fibers, which are multiplexed at the proximal end to the sample arm of an optical low coherence reflectometer. The guidewire can also be used in nonmedical applications.

  7. Bipolaron and N-Polaron Binding Energies

    SciTech Connect (OSTI)

    Frank, Rupert L. [Department of Mathematics, Princeton University, Washington Road, Princeton, New Jersey 08544 (United States); Lieb, Elliott H. [Department of Mathematics, Princeton University, Washington Road, Princeton, New Jersey 08544 (United States); Department of Physics, Princeton University, P.O. Box 708, Princeton, New Jersey 08542 (United States); Seiringer, Robert [Department of Physics, Princeton University, P.O. Box 708, Princeton, New Jersey 08542 (United States); Thomas, Lawrence E. [Department of Mathematics, University of Virginia, Charlottesville, Virginia 22904 (United States)

    2010-05-28

    The binding of polarons, or its absence, is an old and subtle topic. Here we prove two things rigorously. First, the transition from many-body collapse to the existence of a thermodynamic limit for N polarons occurs precisely at U=2{alpha}, where U is the electronic Coulomb repulsion and {alpha} is the polaron coupling constant. Second, if U is large enough, there is no multipolaron binding of any kind. Considering the known fact that there is binding for some U>2{alpha}, these conclusions are not obvious and their proof has been an open problem for some time.

  8. Automotion of domain walls for spintronic interconnects

    SciTech Connect (OSTI)

    Nikonov, Dmitri E.; Manipatruni, Sasikanth; Young, Ian A.

    2014-06-07

    We simulate “automotion,” the transport of a magnetic domain wall under the influence of demagnetization and magnetic anisotropy, in nanoscale spintronic interconnects. In contrast to spin transfer driven magnetic domain wall motion, the proposed interconnects operate without longitudinal charge current transfer, with only a transient current pulse at domain wall creation and have favorable scaling down to the 20?nm dimension. Cases of both in-plane and out-of-plane magnetization are considered. Analytical dependence of the velocity of domain walls on the angle of magnetization are compared with full micromagnetic simulations. Deceleration, attenuation and disappearance, and reflection of domain walls are demonstrated through simulation. Dependences of the magnetization angle on the current pulse parameters are studied. The energy and delay analysis suggests that automotion is an attractive option for spintronic logic interconnects.

  9. Insights into substrate specificity of NlpC/P60 cell wall hydrolases containing bacterial SH3 domains

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Xu, Qingping; Mengin-Lecreulx, Dominique; Liu, Xueqian W.; Patin, Delphine; Farr, Carol L.; Grant, Joanna C.; Chiu, Hsiu -Ju; Jaroszewski, Lukasz; Knuth, Mark W.; Godzik, Adam; et al

    2015-09-15

    Bacterial SH3 (SH3b) domains are commonly fused with papain-like Nlp/P60 cell wall hydrolase domains. To understand how the modular architecture of SH3b and NlpC/P60 affects the activity of the catalytic domain, three putative NlpC/P60 cell wall hydrolases were biochemically and structurally characterized. In addition, these enzymes all have ?-d-Glu-A2pm (A2pm is diaminopimelic acid) cysteine amidase (ordl-endopeptidase) activities but with different substrate specificities. One enzyme is a cell wall lysin that cleaves peptidoglycan (PG), while the other two are cell wall recycling enzymes that only cleave stem peptides with an N-terminall-Ala. Their crystal structures revealed a highly conserved structure consisting ofmore »two SH3b domains and a C-terminal NlpC/P60 catalytic domain, despite very low sequence identity. Interestingly, loops from the first SH3b domain dock into the ends of the active site groove of the catalytic domain, remodel the substrate binding site, and modulate substrate specificity. Two amino acid differences at the domain interface alter the substrate binding specificity in favor of stem peptides in recycling enzymes, whereas the SH3b domain may extend the peptidoglycan binding surface in the cell wall lysins. Remarkably, the cell wall lysin can be converted into a recycling enzyme with a single mutation.Peptidoglycan is a meshlike polymer that envelops the bacterial plasma membrane and bestows structural integrity. Cell wall lysins and recycling enzymes are part of a set of lytic enzymes that target covalent bonds connecting the amino acid and amino sugar building blocks of the PG network. These hydrolases are involved in processes such as cell growth and division, autolysis, invasion, and PG turnover and recycling. To avoid cleavage of unintended substrates, these enzymes have very selective substrate specificities. Our biochemical and structural analysis of three modular NlpC/P60 hydrolases, one lysin, and two recycling enzymes, show that they may have evolved from a common molecular architecture, where the substrate preference is modulated by local changes. These results also suggest that new pathways for recycling PG turnover products, such as tracheal cytotoxin, may have evolved in bacteria in the human gut microbiome that involve NlpC/P60 cell wall hydrolases.« less

  10. Sequestering Uranium from Seawater: Binding Strength and Modes...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Sequestering Uranium from Seawater: Binding Strength and Modes of Uranyl Complexes with Glutarimidedioxime Sequestering Uranium from Seawater: Binding Strength and Modes of Uranyl...

  11. Ligand-induced conformational changes in a thermophilic ribose-binding protein

    SciTech Connect (OSTI)

    Cuneo, Matthew J.; Beese, Lorena S.; Hellinga, Homme W.

    2009-05-21

    Members of the periplasmic binding protein (PBP) superfamily are involved in transport and signaling processes in both prokaryotes and eukaryotes. Biological responses are typically mediated by ligand-induced conformational changes in which the binding event is coupled to a hinge-bending motion that brings together two domains in a closed form. In all PBP-mediated biological processes, downstream partners recognize the closed form of the protein. This motion has also been exploited in protein engineering experiments to construct biosensors that transduce ligand binding to a variety of physical signals. Understanding the mechanistic details of PBP conformational changes, both global (hinge bending, twisting, shear movements) and local (rotamer changes, backbone motion), therefore is not only important for understanding their biological function but also for protein engineering experiments. Here we present biochemical characterization and crystal structure determination of the periplasmic ribose-binding protein (RBP) from the hyperthermophile Thermotoga maritima in its ribose-bound and unliganded state. The T. maritima RBP (tmRBP) has 39% sequence identity and is considerably more resistant to thermal denaturation (appTm value is 108 C) than the mesophilic Escherichia coli homolog (ecRBP) (appTm value is 56 C). Polar ligand interactions and ligand-induced global conformational changes are conserved among ecRBP and tmRBP; however local structural rearrangements involving side-chain motions in the ligand-binding site are not conserved. Although the large-scale ligand-induced changes are mediated through similar regions, and are produced by similar backbone movements in tmRBP and ecRBP, the small-scale ligand-induced structural rearrangements differentiate the mesophile and thermophile. This suggests there are mechanistic differences in the manner by which these two proteins bind their ligands and are an example of how two structurally similar proteins utilize different mechanisms to form a ligand-bound state.

  12. Deletion mapping of a locus on human chromosome 22 involved in the oncogenesis of meningioma

    SciTech Connect (OSTI)

    Dumanski, J.P.; Carlbom, E.; Collins, V.P.; Nordenskjoeld, M.

    1987-12-01

    The genotypes were analyzed at 11 polymorphic DNA loci (restriction fragment length alleles) on chromosome 22 in tumor and normal tissues from 35 unrelated patients with meningiomas. Sixteen tumors retained the constitutional genotype along chromosome 22, while 14 tumors (40%) showed loss of one constitutional allele at all informative loci, consistent with monosomy 22 in the tumor DNA. The remaining 5 tumors (14%) showed loss of heterozygosity in the tumor DNA at one or more chromosome 22 loci and retained heterozygosity at other loci, consistent with variable terminal deletions of one chromosome 22 in the tumor DNA. The results suggest that a meningioma locus is located distal to the myoglobin locus, within 22q12.3-qter. Multiple loci on their chromosomes also were studied, and 12 of the 19 tumors with losses of chromosome 22 alleles showed additional losses of heterozygosity at loci on one to three other chromosomes. All tumors that retained the constitutional genotype on chromosome 22 also retained heterozygosity at all informative loci on other chromosomes analyzed, suggesting that the rearrangement of chromosome 22 is a primary event in the tumorigenesis of meningioma.

  13. Metal-binding polymesr as chelating agents

    E-Print Network [OSTI]

    Mohammadi, Zahra

    2011-04-11

    , high affinity binding of toxic metals by these functionalized hydrogels offers potential applications in waste water treatment and may enable applications in acute metal poisoning. Finally, a unique synthetic methodology using similar metal chelating...

  14. Hardware device binding and mutual authentication

    DOE Patents [OSTI]

    Hamlet, Jason R; Pierson, Lyndon G

    2014-03-04

    Detection and deterrence of device tampering and subversion by substitution may be achieved by including a cryptographic unit within a computing device for binding multiple hardware devices and mutually authenticating the devices. The cryptographic unit includes a physically unclonable function ("PUF") circuit disposed in or on the hardware device, which generates a binding PUF value. The cryptographic unit uses the binding PUF value during an enrollment phase and subsequent authentication phases. During a subsequent authentication phase, the cryptographic unit uses the binding PUF values of the multiple hardware devices to generate a challenge to send to the other device, and to verify a challenge received from the other device to mutually authenticate the hardware devices.

  15. RNA binding protein and binding site useful for expression of recombinant molecules

    DOE Patents [OSTI]

    Mayfield, Stephen (Cardiff, CA)

    2000-01-01

    The present invention relates to a gene expression system in eukaryotic and prokaryotic cells, preferably plant cells and intact plants. In particular, the invention relates to an expression system having a RB47 binding site upstream of a translation initiation site for regulation of translation mediated by binding of RB47 protein, a member of the poly(A) binding protein family. Regulation is further effected by RB60, a protein disulfide isomerase. The expression system is capable of functioning in the nuclear/cytoplasm of cells and in the chloroplast of plants. Translation regulation of a desired molecule is enhanced approximately 100 fold over that obtained without RB47 binding site activation.

  16. RNA binding protein and binding site useful for expression of recombinant molecules

    DOE Patents [OSTI]

    Mayfield, Stephen P.

    2006-10-17

    The present invention relates to a gene expression system in eukaryotic and prokaryotic cells, preferably plant cells and intact plants. In particular, the invention relates to an expression system having a RB47 binding site upstream of a translation initiation site for regulation of translation mediated by binding of RB47 protein, a member of the poly(A) binding protein family. Regulation is further effected by RB60, a protein disulfide isomerase. The expression system is capable of functioning in the nuclear/cytoplasm of cells and in the chloroplast of plants. Translation regulation of a desired molecule is enhanced approximately 100 fold over that obtained without RB47 binding site activation.

  17. Localized Domains of Disoriented Chiral Condensates

    E-Print Network [OSTI]

    B. K. Nandi; T. K. Nayak; B. Mohanty; D. P. Mahapatra; Y. P. Viyogi

    1999-03-12

    A new method to search for localized domains of disoriented chiral condensates (DCC) has been proposed by utilising the (eta-phi) phase space distributions of charged particles and photons. Using the discrete wavelet transformation (DWT) analysis technique, it has been found that the presence of DCC domains broadens the distribution of wavelet coefficients in comparison to that of normal events. Strength contours have been derived from the differences in rms deviations of these distributions by taking into account the size of DCC domains and the probability of DCC production in ultra-relativistic heavy ion collisions. This technique can be suitably adopted to experiments measuring multiplicities of charged particles and photons.

  18. Use of Cre/loxP recombination to swap cell binding motifs on the adenoviral capsid protein IX

    SciTech Connect (OSTI)

    Poulin, Kathy L.; Tong, Grace; Vorobyova, Olga; Pool, Madeline; Kothary, Rashmi; Parks, Robin J.

    2011-11-25

    We used Cre/loxP recombination to swap targeting ligands present on the adenoviral capsid protein IX (pIX). A loxP-flanked sequence encoding poly-lysine (pK-binds heparan sulfate proteoglycans) was engineered onto the 3'-terminus of pIX, and the resulting fusion protein allowed for routine virus propagation. Growth of this virus on Cre-expressing cells removed the pK coding sequence, generating virus that could only infect through alternative ligands, such as a tyrosine kinase receptor A (TrkA)-binding motif engineered into the capsid fibre protein for enhanced infection of neuronal cells. We used a similar approach to swap the pK motif on pIX for a sequence encoding a single-domain antibody directed towards CD66c for targeted infection of cancer cells; Cre-mediated removal of the pK-coding sequence simultaneously placed the single-domain antibody coding sequence in frame with pIX. Thus, we have developed a simple method to propagate virus lacking native viral tropism but containing cell-specific binding ligands. - Highlights: > We describe a method to grow virus lacking native tropism but containing novel cell-binding ligands. > Cre/loxP recombination was used to modify the adenovirus genome. > A targeting ligand present on capsid protein IX was removed or replaced using recombination. > Cre-loxP was also used to 'swap' the identity of the targeting ligand present on pIX.

  19. Binding and Recognition in the Assembly of an Active BRCA1/BARD1 Ubiquitin-Ligase Complex

    SciTech Connect (OSTI)

    Brzovic, Peter S.; Keeffe, Jennifer R.; Nishikawa, Hiroyuki; Miyamoto, Keiko; Fox, David; Fukuda, Mamoru; Ohta, Tomohiko; Klevit, Rachel E.

    2003-05-13

    BRCA1 is a breast and ovarian cancer tumor suppressor protein that associates with BARD1 to form a RING/RING heterodimer. The BRCA1/BARD1 RING complex functions as an ubiquitin (Ub) ligase with activity substantially greater than individual BRCA1 or BARD1 subunits. By using NMR spectroscopy and site-directed mutagenesis, we have mapped the binding site on the BRCA1/BARD1 heterodimer for the Ub-conjugating enzyme UbcH5c. The results demonstrate that UbcH5c binds only to the BRCA1 RING domain and not the BARD1 RING. The binding interface is formed by the first and second Zn2+-loops and central -helix of the BRCA1 RING domain, a region disrupted by cancer-predisposing mutations. Unexpectedly, a second Ub-conjugating enzyme, UbcH7, also interacts with the BRCA1/BARD1 complex with similar affinity, although it is not active in Ub-ligase activity assays. Thus, binding alone is not sufficient for BRCA1-dependent Ub-ligase activity.

  20. Q550 Sports Bursary Application 2014-15 Year: 1st / 2nd / 3rd / 4th / postgraduate (delete as applicable)

    E-Print Network [OSTI]

    Sengun, Mehmet Haluk

    Q550 Sports Bursary Application 2014-15 Name: Year: 1st / 2nd / 3rd / 4th / postgraduate (delete to personally incur participating in University level sport during the academic year 2014-15. Details of expense

  1. Learning Energy Demand Domain Knowledge via Feature Transformation

    E-Print Network [OSTI]

    Povinelli, Richard J.

    -- Domain knowledge is an essential factor for forecasting energy demand. This paper introduces a method knowledge substantially improves energy demand forecasting accuracy. However, domain knowledge may differ. The first stage automatically captures energy demand forecasting domain knowledge through nonlinear

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

    SciTech Connect (OSTI)

    J Ipsaro; S Harper; T Messick; R Marmorstein; A Mondragon; D Speicher

    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 spectrin 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.

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

    SciTech Connect (OSTI)

    Ipsaro, Jonathan J.; Harper, Sandra L.; Messick, Troy E.; Marmorstein, Ronen; Mondragón, Alfonso; Speicher, David W. (Wistar); (NWU)

    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 spectrin 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.

  4. The pilus usher controls protein interactions via domain masking and is functional as an oligomer

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Werneburg, Glenn T.; Li, Huilin; Henderson, Nadine S.; Portnoy, Erica B.; Sarowar, Samema; Hultgren, Scott J.; Thanassi, David G.

    2015-06-08

    The chaperone/usher (CU) pathway is responsible for biogenesis of organelles termed pili or fimbriae in Gram-negative bacteria. Type 1 pili expressed by uropathogenic Escherichia coli are prototypical structures assembled by the CU pathway. Assembly and secretion of pili by the CU pathway requires a dedicated periplasmic chaperone and a multidomain outer membrane protein termed the usher (FimD). We show that the FimD C-terminal domains provide the high-affinity substrate binding site, but that these domains are masked in the resting usher. Domain masking requires the FimD plug domain, which served as a central switch controlling usher activation. In addition, we demonstratemore »that usher molecules can act in trans for pilus biogenesis, providing conclusive evidence for a functional usher oligomer. These results reveal mechanisms by which molecular machines such as the usher regulate and harness protein-protein interactions, and suggest that ushers may interact in a cooperative manner during pilus assembly in bacteria.« less

  5. The protein tyrosine phosphatases PTPRZ and PTPRG bind to distinct members of the contactin family of neural recognition molecules

    SciTech Connect (OSTI)

    Bouyain, Samuel; Watkins, Dara J. (UMKC)

    2010-04-05

    The receptor protein tyrosine phosphatases gamma (PTPRG) and zeta (PTPRZ) are expressed primarily in the nervous system and mediate cell adhesion and signaling events during development. We report here the crystal structures of the carbonic anhydrase-like domains of PTPRZ and PTPRG and show that these domains interact directly with the second and third immunoglobulin repeats of the members of the contactin (CNTN) family of neural recognition molecules. Interestingly, these receptors exhibit distinct specificities: PTPRZ binds only to CNTN1, whereas PTPRG interacts with CNTN3, 4, 5, and 6. Furthermore, we present crystal structures of the four N-terminal immunoglobulin repeats of mouse CNTN4 both alone and in complex with the carbonic anhydrase-like domain of mouse PTPRG. In these structures, the N-terminal region of CNTN4 adopts a horseshoe-like conformation found also in CNTN2 and most likely in all CNTNs. This restrained conformation of the second and third immunoglobulin domains creates a binding site that is conserved among CNTN3, 4, 5, and 6. This site contacts a discrete region of PTPRG composed primarily of an extended {beta}-hairpin loop found in both PTPRG and PTPRZ. Overall, these findings implicate PTPRG, PTPRZ and CNTNs as a group of receptors and ligands involved in the manifold recognition events that underlie the construction of neural networks.

  6. Domain Decomposition Methods for a Complementarity Problem

    E-Print Network [OSTI]

    Cai, Xiao-Chuan

    Domain Decomposition Methods for a Complementarity Problem Haijian Yang1 and Xiao-Chuan Cai2 1 under grants CCF-0634894 and CNS-0722023. 1 #12;2 Haijian Yang and Xiao-Chuan Cai with partial

  7. Slow Dynamics of Orbital Domains in Manganite

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    technique with photons of light that have wavelengths a billion times smaller than radio waves in order to study their domain motion. By using these soft x rays generated at...

  8. Transmission eigenvalues for strictly concave domains

    E-Print Network [OSTI]

    Georgi Vodev

    2015-01-05

    We prove that for strictly concave domains much larger transmission eigenvalue-free regions exist. As a consequence, we get Weyl asymptotics for the total counting function with an almost optimal remainder term.

  9. Antiferromagnetic domain size and exchange bias 

    E-Print Network [OSTI]

    Fitzsimmons, M. R.; Lederman, D.; Cheon, M.; Shi, H.; Olamit, J.; Roshchin, Igor V.; Schuller, Ivan K.

    2008-01-01

    Using neutron diffraction, we measured the sizes of antiferromagnetic domains in three ferromagnet/antiferromagnet bilayer samples as a function of the magnitude and sign of exchange bias, temperature, and antiferromagnet composition. Neutron...

  10. Frequency domain design of interval controller 

    E-Print Network [OSTI]

    Park, Wunyong

    1993-01-01

    Subject: Electrical Engineering FREQUENCY DOMAIN DFSIGN OF INTERVAL CONTROLLER A Thesis by WUNYONG PARK Approved as to style and content by: S. P. Bhattacharyyd (Chair of Committee) C. N. Georghiades (Member) A. Datta (Member) S. Jayasuriya... (Member) . H. Keel (Member) A. Patton (Head of Department) May 1993 111 ABSTRACT Frequency Domain Design of Interval Controller. (May 1993) Wunyong Park, B. S. , Yon Sei University; M. S. , Yon Sei University Chair of Advisory Committee: Dr. S...

  11. Structured hints : extracting and abstracting domain expertise.

    SciTech Connect (OSTI)

    Hereld, M.; Stevens, R.; Sterling, T.; Gao, G. R.; Mathematics and Computer Science; California Inst. of Tech.; Louisiana State Univ.; Univ. of Delaware

    2009-03-16

    We propose a new framework for providing information to help optimize domain-specific application codes. Its design addresses problems that derive from the widening gap between the domain problem statement by domain experts and the architectural details of new and future high-end computing systems. The design is particularly well suited to program execution models that incorporate dynamic adaptive methodologies for live tuning of program performance and resource utilization. This new framework, which we call 'structured hints', couples a vocabulary of annotations to a suite of performance metrics. The immediate target is development of a process by which a domain expert describes characteristics of objects and methods in the application code that would not be readily apparent to the compiler; the domain expert provides further information about what quantities might provide the best indications of desirable effect; and the interactive preprocessor identifies potential opportunities for the domain expert to evaluate. Our development of these ideas is progressing in stages from case study, through manual implementation, to automatic or semi-automatic implementation. In this paper we discuss results from our case study, an examination of a large simulation of a neural network modeled after the neocortex.

  12. Direct Visualization of Magnetoelectric Domains | U.S. DOE Office...

    Office of Science (SC) Website

    image of ferroelectric domains in hexagonal erbium manganite. Image size: 16 x 16 m2. Blue (red) color denotes domains with up (down) electric polarization. Right:...

  13. Time-Domain Electromagnetics At Glass Mountain Area (Cumming...

    Open Energy Info (EERE)

    Time-Domain Electromagnetics At Glass Mountain Area (Cumming And Mackie, 2007) Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Exploration Activity: Time-Domain...

  14. Estrophilin immunoreactivity versus estrogen receptor binding activity in meningiomas: evidence for multiple estrogen binding sites

    SciTech Connect (OSTI)

    Lesch, K.P.; Schott, W.; Gross, S.

    1987-09-01

    The existence of estrogen receptors in human meningiomas has long been a controversial issue. This may be explained, in part, by apparent heterogeneity of estrogen binding sites in meningioma tissue. In this study, estrogen receptors were determined in 58 meningiomas with an enzyme immunoassay using monoclonal antibodies against human estrogen receptor protein (estrophilin) and with a sensitive radioligand binding assay using /sup 125/I-labeled estradiol (/sup 125/I-estradiol) as radioligand. Low levels of estrophilin immunoreactivity were found in tumors from 62% of patients, whereas radioligand binding activity was demonstrated in about 46% of the meningiomas examined. In eight (14%) tissue samples multiple binding sites for estradiol were observed. The immunoreactive binding sites correspond to the classical, high affinity estrogen receptors: the Kd for /sup 125/I-estradiol binding to the receptor was approximately 0.2 nM and the binding was specific for estrogens. The second, low affinity class of binding sites considerably influenced measurement of the classical receptor even at low ligand concentrations. The epidemiological and clinical data from patients with meningiomas, and the existence of specific estrogen receptors confirmed by immunochemical detection, may be important factors in a theory of oncogenesis.

  15. Structural basis of substrate discrimination and integrin binding by autotaxin

    SciTech Connect (OSTI)

    Hausmann, Jens; Kamtekar, Satwik; Christodoulou, Evangelos; Day, Jacqueline E.; Wu, Tao; Fulkerson, Zachary; Albers, Harald M.H.G.; van Meeteren, Laurens A.; Houben, Anna J.S.; van Zeijl, Leonie; Jansen, Silvia; Andries, Maria; Hall, Troii; Pegg, Lyle E.; Benson, Timothy E.; Kasiem, Mobien; Harlos, Karl; Vander Kooi, Craig W.; Smyth, Susan S.; Ovaa, Huib; Bollen, Mathieu; Morris, Andrew J.; Moolenaar, Wouter H.; Perrakis, Anastassis (Pfizer); (Leuven); (Oxford); (NCI-Netherlands); (Kentucky)

    2013-09-25

    Autotaxin (ATX, also known as ectonucleotide pyrophosphatase/phosphodiesterase-2, ENPP2) is a secreted lysophospholipase D that generates the lipid mediator lysophosphatidic acid (LPA), a mitogen and chemoattractant for many cell types. ATX-LPA signaling is involved in various pathologies including tumor progression and inflammation. However, the molecular basis of substrate recognition and catalysis by ATX and the mechanism by which it interacts with target cells are unclear. Here, we present the crystal structure of ATX, alone and in complex with a small-molecule inhibitor. We have identified a hydrophobic lipid-binding pocket and mapped key residues for catalysis and selection between nucleotide and phospholipid substrates. We have shown that ATX interacts with cell-surface integrins through its N-terminal somatomedin B-like domains, using an atypical mechanism. Our results define determinants of substrate discrimination by the ENPP family, suggest how ATX promotes localized LPA signaling and suggest new approaches for targeting ATX with small-molecule therapeutic agents.

  16. Dual-domain point diffraction interferometer

    DOE Patents [OSTI]

    Naulleau, Patrick P. (5239 Miles Ave., Apt. A, Oakland, CA 94618); Goldberg, Kenneth Alan (1195 Keeler Ave., Berkeley, CA 94708)

    2000-01-01

    A hybrid spatial/temporal-domain point diffraction interferometer (referred to as the dual-domain PS/PDI) that is capable of suppressing the scattered-reference-light noise that hinders the conventional PS/PDI is provided. The dual-domain PS/PDI combines the separate noise-suppression capabilities of the widely-used phase-shifting and Fourier-transform fringe pattern analysis methods. The dual-domain PS/PDI relies on both a more restrictive implementation of the image plane PS/PDI mask and a new analysis method to be applied to the interferograms generated and recorded by the modified PS/PDI. The more restrictive PS/PDI mask guarantees the elimination of spatial-frequency crosstalk between the signal and the scattered-light noise arising from scattered-reference-light interfering with the test beam. The new dual-domain analysis method is then used to eliminate scattered-light noise arising from both the scattered-reference-light interfering with the test beam and the scattered-reference-light interfering with the "true" pinhole-diffracted reference light. The dual-domain analysis method has also been demonstrated to provide performance enhancement when using the non-optimized standard PS/PDI design. The dual-domain PS/PDI is essentially a three-tiered filtering system composed of lowpass spatial-filtering the test-beam electric field using the more restrictive PS/PDI mask, bandpass spatial-filtering the individual interferogram irradiance frames making up the phase-shifting series, and bandpass temporal-filtering the phase-shifting series as a whole.

  17. JAB1 regulates unphosphorylated STAT3 DNA-binding activity through protein–protein interaction in human colon cancer cells

    SciTech Connect (OSTI)

    Nishimoto, Arata, E-mail: anishimo@yamaguchi-u.ac.jp [Department of Surgery and Clinical Science, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-Kogushi, Ube, Yamaguchi 755-8505 (Japan)] [Department of Surgery and Clinical Science, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-Kogushi, Ube, Yamaguchi 755-8505 (Japan); Kugimiya, Naruji; Hosoyama, Toru; Enoki, Tadahiko [Department of Surgery and Clinical Science, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-Kogushi, Ube, Yamaguchi 755-8505 (Japan)] [Department of Surgery and Clinical Science, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-Kogushi, Ube, Yamaguchi 755-8505 (Japan); Li, Tao-Sheng [Department of Stem Cell Biology, Nagasaki University Graduate School of Biomedical Sciences, 1-12-4 Sakamoto, Nagasaki 852-8523 (Japan)] [Department of Stem Cell Biology, Nagasaki University Graduate School of Biomedical Sciences, 1-12-4 Sakamoto, Nagasaki 852-8523 (Japan); Hamano, Kimikazu [Department of Surgery and Clinical Science, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-Kogushi, Ube, Yamaguchi 755-8505 (Japan)] [Department of Surgery and Clinical Science, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-Kogushi, Ube, Yamaguchi 755-8505 (Japan)

    2013-08-30

    Highlights: •JAB1 interacted with unphosphorylated STAT3 in the nucleus. •JAB1 knockdown tended to increase nuclear STAT3 expression. •JAB1 knockdown significantly decreased unphosphorylated STAT3 DNA-binding activity. •JAB1 knockdown significantly decreased MDR1, NANOG, and VEGF expressions. •Nuclear JAB1, but not nuclear STAT3, correlated with STAT3 DNA-binding activity. -- Abstract: Recent studies have revealed that unphosphorylated STAT3 forms a dimer, translocates to the nucleus, binds to the STAT3 binding site, and activates the transcription of STAT3 target genes, thereby playing an important role in oncogenesis in addition to phosphorylated STAT3. Among signaling steps of unphosphorylated STAT3, nuclear translocation and target DNA-binding are the critical steps for its activation. Therefore, elucidating the regulatory mechanism of these signaling steps of unphosphorylated STAT3 is a potential step in the discovery of a novel cancer drug. However, the mechanism of unphosphorylated STAT3 binding to the promoter of target genes remains unclear. In this study, we focused on Jun activation domain-binding protein 1 (JAB1) as a candidate protein that regulates unphosphorylated STAT3 DNA-binding activity. Initially, we observed that both unphosphorylated STAT3 and JAB1 existed in the nucleus of human colon cancer cell line COLO205 at the basal state (no cytokine stimulation). On the other hand, phosphorylated STAT3 did not exist in the nucleus of COLO205 cells at the basal state. Immunoprecipitation using nuclear extract of COLO205 cells revealed that JAB1 interacted with unphosphorylated STAT3. To investigate the effect of JAB1 on unphosphorylated STAT3 activity, RNAi studies were performed. Although JAB1 knockdown tended to increase nuclear STAT3 expression, it significantly decreased unphosphorylated STAT3 DNA-binding activity. Subsequently, JAB1 knockdown significantly decreased the expression levels of MDR1, NANOG, and VEGF, which are STAT3 target genes. Furthermore, the expression level of nuclear JAB1, but not nuclear STAT3, correlated with unphosphorylated STAT3 DNA-binding activity between COLO205 and LoVo cells. Taken together, these results suggest that nuclear JAB1 positively regulates unphosphorylated STAT3 DNA-binding activity through protein–protein interaction in human colon cancer cell line COLO205.

  18. Domain Assignment to Transcription FactorsDomain Assignment to Transcription Factors 412 Proteins with

    E-Print Network [OSTI]

    Babu, M. Madan

    Domain Assignment to Transcription FactorsDomain Assignment to Transcription Factors 412 Proteins with at least one SCOP DBD assignment 412 Proteins with at least one SCOP DBD assignment 7 proteins with PFAM DBD assignment 7 proteins with PFAM DBD assignment 419 proteins with DBD assignment419 proteins

  19. Rings & Arithmetic 2: Integral domains Thursday, 13 October 2005

    E-Print Network [OSTI]

    Flynn, E. Victor

    Rings & Arithmetic 2: Integral domains and fields Thursday, 13 October 2005 Lectures for Part A of Oxford FHS in Mathematics and Joint Schools · Units in a ring · Integral domains; examples · Fields; examples · Characteristic of an integral domain · Field of fractions of an integral domain 0 #12;Units

  20. Binding Energies in Nonrelativistic Field Theories

    E-Print Network [OSTI]

    Andreas S. Kronfeld

    1996-08-26

    Relativistic corrections communicate the binding energy of a bound state to its kinetic mass. This mechanism is reviewed and used to explain anomalous results of Collins, Edwards, Heller, and Sloan (hep-lat/9512026), which compared rest and kinetic masses of heavy-light mesons and quarkonia.

  1. BOUND SYSTEMS 4.A Binding Energy

    E-Print Network [OSTI]

    Boal, David

    CHAPTER 4 BOUND SYSTEMS 4.A Binding Energy The mass-energy equation (3.2) is valid for a single linear momentum and its energy. While we introduced the equation in order to describe the energy is measurable. The implication of (4.1) taken with (3.2) is that the mass energy of a bound state is less than

  2. Thermodynamics of free Domain Wall fermions

    E-Print Network [OSTI]

    R. V. Gavai; Sayantan Sharma

    2008-11-19

    Studying various thermodynamic quantities for the free domain wall fermions for both finite and infinite fifth dimensional extent N_5, we find that the lattice corrections are minimum for $N_T\\geq10$ for both energy density and susceptibility, for its irrelevant parameter M in the range 1.45-1.50. The correction terms are, however, quite large for small lattice sizes of $N_T\\leq8$. We propose modifications of the domain wall operator, as well as the overlap operator, to reduce the finite cut-off effects to within 10% of the continuum results of the thermodynamic quantities for the currently used N_T=6-8 lattices. Incorporating chemical potential, we show that \\mu^2 divergences are absent for a large class of such domain wall fermion actions although the chiral symmetry is broken for $\\mu\

  3. Perforation of domain wall by point mass

    E-Print Network [OSTI]

    D. V. Gal'tsov; E. Yu. Melkumova; P. A. Spirin

    2013-12-30

    We investigate collision of a point particle and an infinitely thin planar domain wall interacting gravitationally within the linearized gravity in Minkowski space-time of arbitrary dimension. In this setting we are able to describe analytically the perforation of the wall by an impinging particle, showing that it is accompanied by excitation of the spherical shock branon wave propagating outwards with the speed of light. Formally, the shock wave is a free solution of the branon wave equation which has to be added to ensure the validity of the retarded solution at the perforation point. Physically, the domain wall gets excited due to the shake caused by an instantaneous change of sign of the repulsive gravitational force. This effect is shown to hold, in particular, in four space-time dimensions, being applicable to the problem of cosmological domain walls.

  4. Perforation of domain wall by point mass

    E-Print Network [OSTI]

    Gal'tsov, D V; Spirin, P A

    2013-01-01

    We investigate collision of a point particle and an infinitely thin planar domain wall interacting gravitationally within the linearized gravity in Minkowski space-time of arbitrary dimension. In this setting we are able to describe analytically the perforation of the wall by an impinging particle, showing that it is accompanied by excitation of the spherical shock branon wave propagating outwards with the speed of light. Formally, the shock wave is a free solution of the branon wave equation which has to be added to ensure the validity of the retarded solution at the perforation point. Physically, the domain wall gets excited due to the shake caused by an instantaneous change of sign of the repulsive gravitational force. This effect is shown to hold, in particular, in four space-time dimensions, being applicable to the problem of cosmological domain walls.

  5. Gravitational Effects in Supersymmetric Domain Wall Backgrounds

    E-Print Network [OSTI]

    M. Cvetic; S. Griffies

    1992-04-13

    A recent study of supersymmetric domain walls in $N=1$ supergravity theories revealed a new class of domain walls interpolating between supersymmetric vacua with different non-positive cosmological constants. We classify three classes of domain wall configurations and study the geodesic structure of the induced space-time. Motion of massive test particles in such space-times shows that these walls are always repulsive from the anti-deSitter (AdS) side, while on the Minkowski side test particles feel no force. Freely falling particles far away from a wall in an AdS vacuum experience a constant proper acceleration, \\ie\\ they are Rindler particles. A new coordinate system for discussing AdS space-time is presented which eliminates the use of a periodic time-like coordinate.

  6. Standing gravitational waves from domain walls

    E-Print Network [OSTI]

    Merab Gogberashvili; Shynaray Myrzakul; Douglas Singleton

    2009-07-19

    We construct a plane symmetric, standing gravitational wave for a domain wall plus a massless scalar field. The scalar field can be associated with a fluid which has the properties of `stiff' matter, i.e. matter in which the speed of sound equals the speed of light. Although domain walls are observationally ruled out in the present era the solution has interesting features which might shed light on the character of exact non-linear wave solutions to Einstein's equations. Additionally this solution may act as a template for higher dimensional 'brane-world' model standing waves.

  7. Structures of the Porphyromonas gingivalis OxyR regulatory domain explain differences in expression of the OxyR regulon in Escherichia coli and P. gingivalis

    SciTech Connect (OSTI)

    Svintradze, David V. [Virginia Commonwealth University, Richmond, VA 23298-0566 (United States); Virginia Commonwealth University, Richmond, VA 23219-1540 (United States); Peterson, Darrell L. [Virginia Commonwealth University, Richmond, VA 23219-1540 (United States); Virginia Commonwealth University, Richmond, VA 23298-0614 (United States); Collazo-Santiago, Evys A.; Lewis, Janina P. [Virginia Commonwealth University, Richmond, VA 23298-0566 (United States); Wright, H. Tonie, E-mail: xrdproc@vcu.edu [Virginia Commonwealth University, Richmond, VA 23219-1540 (United States); Virginia Commonwealth University, Richmond, VA 23298-0614 (United States); Virginia Commonwealth University, Richmond, VA 23298-0566 (United States)

    2013-10-01

    Differences in OxyR regulated expression of oxidative stress genes between Escherichia coli and Porphyromonas gingivalis are explained by very minor differences in structure and amino-acid sequence of the respective oxidized and reduced OxyR regulatory domains. These differences affect OxyR quaternary structures and are predicted from model building of full length OxyR–DNA complexes to confer distinct modes of DNA binding on this transcriptional regulator. OxyR transcriptionally regulates Escherichia coli oxidative stress response genes through a reversibly reducible cysteine disulfide biosensor of cellular redox status. Structural changes induced by redox changes in these cysteines are conformationally transmitted to the dimer subunit interfaces, which alters dimer and tetramer interactions with DNA. In contrast to E. coli OxyR regulatory-domain structures, crystal structures of Porphyromonas gingivalis OxyR regulatory domains show minimal differences in dimer configuration on changes in cysteine disulfide redox status. This locked configuration of the P. gingivalis OxyR regulatory-domain dimer closely resembles the oxidized (activating) form of the E. coli OxyR regulatory-domain dimer. It correlates with the observed constitutive activation of some oxidative stress genes in P. gingivalis and is attributable to a single amino-acid insertion in P. gingivalis OxyR relative to E. coli OxyR. Modelling of full-length P. gingivalis, E. coli and Neisseria meningitidis OxyR–DNA complexes predicts different modes of DNA binding for the reduced and oxidized forms of each.

  8. Homozygous deletions on the short arm of chromosome 9 in ovarian adenocarcinoma cell lines and loss of heterozygosity in sporadic tumors

    SciTech Connect (OSTI)

    Chenevix-Trench, G.; Kerr, J.; Hurst, T.; Sanderson, B.; Coglan, M.; Ward, B.; Khoo, S.K. ); Friedlander, M.; Leary, J.

    1994-07-01

    Rat ovarian surface epithelial cells transformed spontaneously in vitro have been found to have homozygous deletions of the interferon alpha (IFNA) gene. This suggests that inactivation of a tumor-suppressor gene in this region may be crucial for the development of ovarian cancer. The authors therefore used microsatellite markers and Southern analysis to examine the homologous region in humans - the short arm of chromosome 9 - for deletions in sporadic ovarian adenocarcinomas and ovarian tumor cell lines. Loss of heterozygosity occurred in 34 (37%) of 91 informative sporadic tumors, including some benign, low-malignant-potential and early-stage tumors, suggesting that it is an early event in the development of ovarian adenocarcinoma. Furthermore, homozygous deletions on 9p were found in 2 of 10 independent cell lines. Deletion mapping of the tumors and lines indicates that the candidate suppressor gene inactivated as a consequence lies between D9S171 and the IFNA locus, a region that is also deleted in several other tumors and that contains the melanoma predisposition gene, MLM. 52 refs., 4 figs., 1 tab.

  9. Large power grid analysis using domain decomposition

    E-Print Network [OSTI]

    Mohanram, Kartik

    Large power grid analysis using domain decomposition Quming Zhou, Kai Sun, Kartik Mohanram, Danny C referred to as the power grid. The power grid for a modern integrated circuit may consist of several grid is traditionally described as a large-scale linear system. Simulation of power grids usually

  10. Solitons and Domain Walls in Odd Dimensions

    E-Print Network [OSTI]

    N. D. Lambert; G. W. Gibbons

    2000-07-04

    We discuss the existance of smooth soliton solutions which interpolate between supersymmetric vacua in odd-dimensional theories. In particular we apply this analysis to a wide class of supergravities to argue against the existence of smooth domain walls interpolating between supersymmetric vacua. We find that if the superpotential changes sign then any Goldstino modes will diverge.

  11. Domain switching in polycrystalline ferroelectric ceramics

    E-Print Network [OSTI]

    Li, Jiangyu

    ARTICLES Domain switching in polycrystalline ferroelectric ceramics J. Y. LI1, R. C. ROGAN2,3, E:10.1038/nmat1485 Ferroelectric ceramics are widely used as sensors and actuators for their electro collective process in commercially used polycrystalline ceramics that are agglomerations of a very large

  12. Reduction of Economic Inequality in Combinatorial Domains

    E-Print Network [OSTI]

    Koolen, Marijn

    for assessing the fairness of a mechanism is the level of economic equality it can ensure. If it producesReduction of Economic Inequality in Combinatorial Domains Ulle Endriss Institute for Logic economic inequality, such as the Lorenz curve and the Gini index, are widely used in the social sciences

  13. Structure of the SH3 domain of human osteoclast-stimulating factor at atomic resolution

    SciTech Connect (OSTI)

    Chen, Liqing Wang, Yujun; Wells, David; Toh, Diana; Harold, Hunt; Zhou, Jing; DiGiammarino, Enrico; Meehan, Edward J.

    2006-09-01

    The crystal structure of the SH3 domain of human osteoclast-stimulating factor has been determined and refined to the ultrahigh resolution of 1.07 Å. The structure at atomic resolution provides an accurate framework for structure-based design of its inhibitors. Osteoclast-stimulating factor (OSF) is an intracellular signaling protein, produced by osteoclasts themselves, that enhances osteoclast formation and bone resorption. It is thought to act via an Src-related signaling pathway and contains SH3 and ankyrin-repeat domains which are involved in protein–protein interactions. As part of a structure-based anti-bone-loss drug-design program, the atomic resolution X-ray structure of the recombinant human OSF SH3 domain (hOSF-SH3) has been determined. The domain, residues 12–72, yielded crystals that diffracted to the ultrahigh resolution of 1.07 Å. The overall structure shows a characteristic SH3 fold consisting of two perpendicular ?-sheets that form a ?-barrel. Structure-based sequence alignment reveals that the putative proline-rich peptide-binding site of hOSF-SH3 consists of (i) residues that are highly conserved in the SH3-domain family, including residues Tyr21, Phe23, Trp49, Pro62, Asn64 and Tyr65, and (ii) residues that are less conserved and/or even specific to hOSF, including Thr22, Arg26, Thr27, Glu30, Asp46, Thr47, Asn48 and Leu60, which might be key to designing specific inhibitors for hOSF to fight osteoporosis and related bone-loss diseases. There are a total of 13 well defined water molecules forming hydrogen bonds with the above residues in and around the peptide-binding pocket. Some of those water molecules might be important for drug-design approaches. The hOSF-SH3 structure at atomic resolution provides an accurate framework for structure-based design of its inhibitors.

  14. Factor IX[sub Madrid 2]: A deletion/insertion in Facotr IX gene which abolishes the sequence of the donor junction at the exon IV-intron d splice site

    SciTech Connect (OSTI)

    Solera, J. (Unidades de Genetica Molecular, Madrid (Spain)); Magallon, M.; Martin-Villar, J. (Hemofilia Hospital, Madrid (Spain)); Coloma, A. (Departamento deBioquimica de la Facultad de Medicina de la Universidad Autonoma, Madrid (Spain))

    1992-02-01

    DNA from a patient with severe hemophilia B was evaluated by RFLP analysis, producing results which suggested the existence of a partial deletion within the factor IX gene. The deletion was further localized and characterized by PCR amplification and sequencing. The altered allele has a 4,442-bp deletion which removes both the donor splice site located at the 5[prime] end of intron d and the two last coding nucleotides located at the 3[prime] end of exon IV in the normal factor IX gene; this fragment has been inserted in inverted orientation. Two homologous sequences have been discovered at the ends of the deleted DNA fragment.

  15. A fraction of Crm1 locates at centrosomes by its CRIME domain and regulates the centrosomal localization of pericentrin

    SciTech Connect (OSTI)

    Liu, Qinying; Jiang, Qing [The MOE Key Laboratory of Cell Proliferation and Differentiation and The State Key Laboratory of Bio-membrane and Membrane Bio-engineering, College of Life Sciences, Peking University, Beijing 100871 (China)] [The MOE Key Laboratory of Cell Proliferation and Differentiation and The State Key Laboratory of Bio-membrane and Membrane Bio-engineering, College of Life Sciences, Peking University, Beijing 100871 (China); Zhang, Chuanmao, E-mail: zhangcm@pku.edu.cn [The MOE Key Laboratory of Cell Proliferation and Differentiation and The State Key Laboratory of Bio-membrane and Membrane Bio-engineering, College of Life Sciences, Peking University, Beijing 100871 (China)] [The MOE Key Laboratory of Cell Proliferation and Differentiation and The State Key Laboratory of Bio-membrane and Membrane Bio-engineering, College of Life Sciences, Peking University, Beijing 100871 (China)

    2009-07-03

    Crm1 plays a role in exporting proteins containing nuclear export signals (NESs) from the nucleus to the cytoplasm. Some proteins that are capable of interacting with Ran/Crm1 were reported to be localized at centrosomes and to function as centrosome checkpoints. But it remains unclear how Crm1 locates at centrosomes. In this study, we found that a fraction of Crm1 is located at centrosomes through its N-terminal CRM1, importin {beta} etc. (CRIME) domain, which is responsible for interacting with RanGTP, suggesting that Crm1 might target to centrosomes through binding centrosomal RanGTP. Moreover, overexpression of the CRIME domain, which is free of NES binding domain, resulted in the dissociation of pericentrin and {gamma}-tubulin complex from centrosomes and the disruption of microtubule nucleation. Deficiency of Crm1 provoked by RNAi also decreased the spindle poles localization of pericentrin and {gamma}-tubulin complex, coupled with mitotic defects. Since pericentrin was sensitive to Crm1 specific inhibitor leptomycin B, we propose that the centrosomal Crm1 might interact with pericentrin and regulate the localization and function of pericentrin at centrosomes.

  16. Study of fragmentation using clusterization algorithm with realistic binding energies

    E-Print Network [OSTI]

    Yogesh K. Vermani; Jatinder K. Dhawan; Supriya Goyal; Rajeev K. Puri; J. Aichelin

    2009-12-28

    We here study fragmentation using \\emph{simulated annealing clusterization algorithm} (SACA) with binding energy at a microscopic level. In an earlier version, a constant binding energy (4 MeV/nucleon) was used. We improve this binding energy criterion by calculating the binding energy of different clusters using modified Bethe-Weizs\\"{a}cker mass (BWM) formula. We also compare our calculations with experimental data of ALADiN group. Nearly no effect is visible of this modification.

  17. Predicting Metal-Binding Sites from Protein Sequence

    E-Print Network [OSTI]

    Passerini, Andrea

    Predicting Metal-Binding Sites from Protein Sequence Andrea Passerini, Marco Lippi, and Paolo algorithmic ideas based on structured- output learning for determining transition-metal-binding sites coordinate more than one metal ion, we prove that metal binding has the algebraic structure of a matroid

  18. The role of the N domain in substrate binding, oligomerization, and allosteric regulation of the AAA+ Lon protease

    E-Print Network [OSTI]

    Wohlever, Matthew L

    2013-01-01

    For cells and organisms to survive, they must maintain protein homeostasis in varied and often harsh environments. Cells utilize proteases and chaperones to maintain their proteomes. In bacteria, most cytosolic proteolysis ...

  19. Volume 139, number 1 FEBS LETTER? March 1982 DNA BINDING OF CAMP RECEPTOR PROTEIN AND ITS N-TERMJNAL CORE STABILIZES

    E-Print Network [OSTI]

    Clore, G. Marius

    the initiation of mBNA synthesis in the presence of CAMP[l-7]. The smaller carboxy- terminal domain of both of binding and of initiation of mBNA synthesis by RNA polymerase [8]. This model was suggested on the basis on the 2.9 A resolution crystal structure of the CAMP-CBP complex [8]. If this hypothesis is correct, the N

  20. UNC-45/CRO1/She4p (UCS) Protein Forms Elongated Dimer and Joins Two Myosin Heads Near Their Actin Binding Region

    SciTech Connect (OSTI)

    H Shi; G Blobel

    2011-12-31

    UNC-45/CRO1/She4p (UCS) proteins have variously been proposed to affect the folding, stability, and ATPase activity of myosins. They are the only proteins known to interact directly with the motor domain. To gain more insight into UCS function, we determined the atomic structure of the yeast UCS protein, She4p, at 2.9 {angstrom} resolution. We found that 16 helical repeats are organized into an L-shaped superhelix with an amphipathic N-terminal helix dangling off the short arm of the L-shaped molecule. In the crystal, She4p forms a 193-{angstrom}-long, zigzag-shaped dimer through three distinct and evolutionary conserved interfaces. We have identified She4p's C-terminal region as a ligand for a 27-residue-long epitope on the myosin motor domain. Remarkably, this region consists of two adjacent, but distinct, binding epitopes localized at the nucleotide-responsive cleft between the nucleotide- and actin-filament-binding sites. One epitope is situated inside the cleft, the other outside the cleft. After ATP hydrolysis and Pi ejection, the cleft narrows at its base from 20 to 12 {angstrom} thereby occluding the inside the cleft epitope, while leaving the adjacent, outside the cleft binding epitope accessible to UCS binding. Hence, one cycle of higher and lower binding affinity would accompany one ATP hydrolysis cycle and a single step in the walk on an actin filament rope. We propose that a UCS dimer links two myosins at their motor domains and thereby functions as one of the determinants for step size of myosin on actin filaments.

  1. Inflationary power asymmetry from primordial domain walls

    E-Print Network [OSTI]

    Jazayeri, Sadra; Firouzjahi, Hassan; Solomon, Adam R; Wang, Yi

    2014-01-01

    We study the asymmetric primordial fluctuations in a model of inflation in which translational invariance is broken by a domain wall. We calculate the corrections to the power spectrum of curvature perturbations; they are anisotropic and contain dipole, quadrupole, and higher multipoles with non-trivial scale-dependent amplitudes. Inspired by observations of these multipole asymmetries in terms of two-point correlations and variance in real space, we demonstrate that this model can explain the observed anomalous power asymmetry of the cosmic microwave background (CMB) sky, including its characteristic feature that the dipole dominates over higher multipoles. We test the viability of the model and place approximate constraints on its parameters by using observational values of dipole, quadrupole, and octopole amplitudes of the asymmetry measured by a local-variance estimator. We find that a configuration of the model in which the CMB sphere does not intersect the domain wall during inflation provides a good fi...

  2. LHC RF System Time-Domain Simulation

    SciTech Connect (OSTI)

    Mastorides, T.; Rivetta, C.

    2010-09-14

    Non-linear time-domain simulations have been developed for the Positron-Electron Project (PEP-II) and the Large Hadron Collider (LHC). These simulations capture the dynamic behavior of the RF station-beam interaction and are structured to reproduce the technical characteristics of the system (noise contributions, non-linear elements, and more). As such, they provide useful results and insight for the development and design of future LLRF feedback systems. They are also a valuable tool for the study of diverse longitudinal beam dynamics effects such as coupled-bunch impedance driven instabilities and single bunch longitudinal emittance growth. Results from these studies and related measurements from PEP-II and LHC have been presented in multiple places. This report presents an example of the time-domain simulation implementation for the LHC.

  3. Light quark masses using domain wall fermions

    E-Print Network [OSTI]

    Tom Blum; Amarjit Soni; Matthew Wingate

    1998-09-10

    We compute the one-loop self-energy correction to the massive domain wall quark propagator. Combining this calculation with simulations at several gauge couplings, we estimate the strange quark mass in the continuum limit. The perturbative one-loop mass renormalization is comparable to that for Wilson quarks and considerably smaller than that for Kogut-Susskind quarks. Also, scaling violations appear mild in comparison to other errors at present. Given their good chiral behavior and these features, domain wall quarks are attractive for evaluating the light quark masses. Our preliminary quenched result is m_s(2 GeV) = 82(15) MeV in the ${\\bar{MS}}$ scheme.

  4. Antibodies Purification Using ELP-zz Domain Fusions

    E-Print Network [OSTI]

    CHAUDHARY, GARIMA

    2011-01-01

    Engineered Elastin-Protein A Fusion as a Universal Platformtoxin T domain-ZZ fusion protein as a pH sensitive membraneUsing ELP-zz Domain Fusions A Thesis submitted in partial

  5. Time-Domain Electromagnetics At Kilauea East Rift Geothermal...

    Open Energy Info (EERE)

    mapping, line-loop time-domain inductive sounding, galvanic sounding, and loop-loop frequency-domain sounding. Surveys were conducted across the East Rift Zone and along the...

  6. Frequent intragenic deletion of the P gene in Tanzanian patients with Type II oculocutaneous albinism (OCA2)

    SciTech Connect (OSTI)

    Spritz, R.; Fukai, K.; Holmes, S.A.

    1995-06-01

    Type II oculocutaneous albinism (OCA2) is an autosomal recessive disorder in which the biosynthesis of melanin pigment is reduced in the skin, hair, and eyes. OCA2, which results from mutations of the P gene, is the most frequent type of albinism in African and African-American patients. OCA2 is especially frequent in Tanzania, where it occurs with an incidence of {approximately}1/1,400. We have identified abnormalities of the P gene in each of 13 unrelated patients with OCA2 from Tanzania. One of these, a deletion of exon 7, is strongly predominant, accounting for {approximately}77% of mutant alleles in this group of patients. 20 refs., 2 figs.

  7. Integral Closures of Ideals in Completions of Regular Local Domains

    E-Print Network [OSTI]

    Integral Closures of Ideals in Completions. of Regular Local Domains. WILLIAM HEINZER, Department of Mathematics, Purdue University,. West Lafayette, IN ...

  8. Edinburgh Research Explorer Cartesian closed categories of separable Scott domains

    E-Print Network [OSTI]

    Millar, Andrew J.

    domains' Theoretical Computer Science, vol 546, pp. 17-29., 10.1016/j.tcs.2014.02.042 Digital Object of the category of separable Scott domains. The classification employs a notion of coherence degree de- termined by the possible inconsistency patterns of sets of finite elements of a domain. Using the classification, we

  9. Defaults in Domain Theory GuoQiang Zhang

    E-Print Network [OSTI]

    Zhang, Guo-Qiang

    intelligence? Our basic observation is that partial information 1 #12; is a fundamental concept shared by both areas. Essentially, domain theory is about partial information: elements of domains are partial objects default reasoning in AI. We are, however, not claiming that domain theory can be so applied without much

  10. ON COMPLETE INTEGRAL CLOSURE AND ARCHIMEDEAN VALUATION DOMAINS

    E-Print Network [OSTI]

    ON COMPLETE INTEGRAL CLOSURE AND ARCHIMEDEAN VALUATION DOMAINS ROBERT GILMER Abstract Suppose D is an integral domain with quotient field K and that L is an extension field of K. We show in Theorem 4 that if the complete integral closure of D is an intersection of Archimedean valuation domains on K, then the complete

  11. Parameter Estimation for the Heat Equation on Perforated Domains

    E-Print Network [OSTI]

    Parameter Estimation for the Heat Equation on Perforated Domains H.T. Banks1 , D. Cioranescu2 , A: Inverse problems, parameter estimation, perforated domains, homogeniza- tion, thermal diffusion, ordinary porous samples by use of solutions of a heat equation on a randomly perforated domain. As noted

  12. Polynucleotides encoding TRF1 binding proteins

    DOE Patents [OSTI]

    Campisi, Judith (Berkeley, CA); Kim, Sahn-Ho (Albany, CA)

    2002-01-01

    The present invention provides a novel telomere associated protein (Trf1-interacting nuclear protein 2 "Tin2") that hinders the binding of Trf1 to its specific telomere repeat sequence and mediates the formation of a Tin2-Trf1-telomeric DNA complex that limits telomerase access to the telomere. Also included are the corresponding nucleic acids that encode the Tin2 of the present invention, as well as mutants of Tin2. Methods of making, purifying and using Tin2 of the present invention are described. In addition, drug screening assays to identify drugs that mimic and/or complement the effect of Tin2 are presented.

  13. Insights into Regulated Ligand Binding Sites from the Structure of ZO-1 Src Homology 3-Guanylate Kinase Module

    SciTech Connect (OSTI)

    Lye, Ming F.; Fanning, Alan S.; Su, Ying; Anderson, James M.; Lavie, Arnon (UNC); (UIC)

    2010-11-09

    Tight junctions are dynamic components of epithelial and endothelial cells that regulate the paracellular transport of ions, solutes, and immune cells. The assembly and permeability of these junctions is dependent on the zonula occludens (ZO) proteins, members of the membrane-associated guanylate kinase homolog (MAGUK) protein family, which are characterized by a core Src homology 3 (SH3)-GUK module that coordinates multiple protein-protein interactions. The structure of the ZO-1 SH3-GUK domain confirms that the interdependent folding of the SH3 and GUK domains is a conserved feature of MAGUKs, but differences in the orientation of the GUK domains in three different MAGUKs reveal interdomain flexibility of the core unit. Using pull-down assays, we show that an effector loop, the U6 region in ZO-1, forms a novel intramolecular interaction with the core module. This interaction is divalent cation-dependent and overlaps with the binding site for the regulatory molecule calmodulin on the GUK domain. These findings provide insight into the previously observed ability of the U6 region to regulate TJ assembly in vivo and the structural basis for the complex protein interactions of the MAGUK family.

  14. ANDERSON-TEIXEIRA FINAL PROOF.DOCX (DO NOT DELETE) 3/7/2011 9:29 AM DO BIOFUELS LIFE CYCLE

    E-Print Network [OSTI]

    DeLucia, Evan H.

    ANDERSON-TEIXEIRA FINAL PROOF.DOCX (DO NOT DELETE) 3/7/2011 9:29 AM 589 DO BIOFUELS LIFE CYCLE ANALYSES ACCURATELY QUANTIFY THE CLIMATE IMPACTS OF BIOFUELS-RELATED LAND USE CHANGE? Kristina J. Anderson in determining the sustainability of biofuels. To ensure that legal standards are effective in limiting climate

  15. Structural analysis of a 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase with an N-terminal chorismate mutase-like regulatory domain

    SciTech Connect (OSTI)

    Light, Samuel H.; Halavaty, Andrei S.; Minasov, George; Shuvalova, Ludmilla; Anderson, Wayne F. (NWU)

    2012-06-27

    3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAHPS) catalyzes the first step in the biosynthesis of a number of aromatic metabolites. Likely because this reaction is situated at a pivotal biosynthetic gateway, several DAHPS classes distinguished by distinct mechanisms of allosteric regulation have independently evolved. One class of DAHPSs contains a regulatory domain with sequence homology to chorismate mutase - an enzyme further downstream of DAHPS that catalyzes the first committed step in tyrosine/phenylalanine biosynthesis - and is inhibited by chorismate mutase substrate (chorismate) and product (prephenate). Described in this work, structures of the Listeria monocytogenes chorismate/prephenate regulated DAHPS in complex with Mn{sup 2+} and Mn{sup 2+} + phosphoenolpyruvate reveal an unusual quaternary architecture: DAHPS domains assemble as a tetramer, from either side of which chorismate mutase-like (CML) regulatory domains asymmetrically emerge to form a pair of dimers. This domain organization suggests that chorismate/prephenate binding promotes a stable interaction between the discrete regulatory and catalytic domains and supports a mechanism of allosteric inhibition similar to tyrosine/phenylalanine control of a related DAHPS class. We argue that the structural similarity of chorismate mutase enzyme and CML regulatory domain provides a unique opportunity for the design of a multitarget antibacterial.

  16. Long-range Fourier domain optical coherence tomography of the pediatric subglottis

    E-Print Network [OSTI]

    2015-01-01

    cat e/ijp o r l Long-range Fourier domain optical coherencechild remains intubated. Fourier domain optical coherencesec). Frequency, or ‘‘Fourier’’, domain swept source OCT (

  17. Atypical Response Regulator ChxR from Chlamydia trachomatis Is Structurally Poised for DNA Binding

    E-Print Network [OSTI]

    Barta, Michael L.; Hickey, John Michael; Anbanandam, Asokan; Dyer, Kevin; Hammel, Michal; Hefty, P. Scott

    2014-03-19

    ] and are as follows: PhoB (1QQI); YycF (2D1V); HP1043 (2HQR); OmpR (2JPB); PhoP (2PMU); KdpE (3ZQ7) for effector domains and DrrD (1KGS); DrrB (1P2F); PrrA (1YS6); MtrA (2GWR); HP1043 (2HQR); RegX3 (2OQR); PhoP (3R0J) for full-length structures. Representations of all... in the chxR promoter with a dissociation constant (Kd) of approximately 44 nM [17]. To determine if ChxREff (residues 115–227) alone can to bind to DNA, an electrophoretic mobility Table 2. SAXS Parameters for Data Validation and Interpretation. SAXS...

  18. Melting Instantons, Domain Walls, and Large N

    E-Print Network [OSTI]

    H. B. Thacker

    2008-10-22

    Monte Carlo studies of $CP^{N-1}$ sigma models have shown that the structure of topological charge in these models undergoes a sharp transition at $N=N_c\\approx 4$. For $NN_c$ it is dominated by extended, thin, 1-dimensionally coherent membranes of topological charge, which can be interpreted as domain walls between discrete quasi-stable vacua. These vacua differ by a unit of background electric flux. The transition can be identified as the delocalization of topological charge, or "instanton melting," a phenomenon first suggested by Witten to resolve the conflict between instantons and large $N$ behavior. Implications for $QCD$ are discussed.

  19. Hardware device to physical structure binding and authentication

    SciTech Connect (OSTI)

    Hamlet, Jason R.; Stein, David J.; Bauer, Todd M.

    2013-08-20

    Detection and deterrence of device tampering and subversion may be achieved by including a cryptographic fingerprint unit within a hardware device for authenticating a binding of the hardware device and a physical structure. The cryptographic fingerprint unit includes an internal physically unclonable function ("PUF") circuit disposed in or on the hardware device, which generate an internal PUF value. Binding logic is coupled to receive the internal PUF value, as well as an external PUF value associated with the physical structure, and generates a binding PUF value, which represents the binding of the hardware device and the physical structure. The cryptographic fingerprint unit also includes a cryptographic unit that uses the binding PUF value to allow a challenger to authenticate the binding.

  20. Crown Ethers Flatten in Graphene for Strong, Specific Binding...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    2011 2010 News Home | ORNL | News | Features | 2014 SHARE Crown Ethers Flatten in Graphene for Strong, Specific Binding ORNL discovery holds potential for separations, sensors,...

  1. Inflationary power asymmetry from primordial domain walls

    E-Print Network [OSTI]

    Sadra Jazayeri; Yashar Akrami; Hassan Firouzjahi; Adam R. Solomon; Yi Wang

    2014-11-29

    We study the asymmetric primordial fluctuations in a model of inflation in which translational invariance is broken by a domain wall. We calculate the corrections to the power spectrum of curvature perturbations; they are anisotropic and contain dipole, quadrupole, and higher multipoles with non-trivial scale-dependent amplitudes. Inspired by observations of these multipole asymmetries in terms of two-point correlations and variance in real space, we demonstrate that this model can explain the observed anomalous power asymmetry of the cosmic microwave background (CMB) sky, including its characteristic feature that the dipole dominates over higher multipoles. We test the viability of the model and place approximate constraints on its parameters by using observational values of dipole, quadrupole, and octopole amplitudes of the asymmetry measured by a local-variance estimator. We find that a configuration of the model in which the CMB sphere does not intersect the domain wall during inflation provides a good fit to the data. We further derive analytic expressions for the corrections to the CMB temperature covariance matrix, or angular power spectra, which can be used in future statistical analysis of the model in spherical harmonic space.

  2. Inflationary power asymmetry from primordial domain walls

    SciTech Connect (OSTI)

    Jazayeri, Sadra; Akrami, Yashar; Firouzjahi, Hassan; Solomon, Adam R.; Wang, Yi E-mail: yashar.akrami@astro.uio.no E-mail: a.r.solomon@damtp.cam.ac.uk

    2014-11-01

    We study the asymmetric primordial fluctuations in a model of inflation in which translational invariance is broken by a domain wall. We calculate the corrections to the power spectrum of curvature perturbations; they are anisotropic and contain dipole, quadrupole, and higher multipoles with non-trivial scale-dependent amplitudes. Inspired by observations of these multipole asymmetries in terms of two-point correlations and variance in real space, we demonstrate that this model can explain the observed anomalous power asymmetry of the cosmic microwave background (CMB) sky, including its characteristic feature that the dipole dominates over higher multipoles. We test the viability of the model and place approximate constraints on its parameters by using observational values of dipole, quadrupole, and octopole amplitudes of the asymmetry measured by a local-variance estimator. We find that a configuration of the model in which the CMB sphere does not intersect the domain wall during inflation provides a good fit to the data. We further derive analytic expressions for the corrections to the CMB temperature covariance matrix, or angular power spectra, which can be used in future statistical analysis of the model in spherical harmonic space.

  3. Frequency domain and time domain analysis of thermoacoustic oscillations with wave-based acoustics

    E-Print Network [OSTI]

    Orchini, A.; Illingworth, S. J.; Juniper, M. P.

    2015-05-14

    Many thermoacoustic systems exhibit rich nonlinear behaviour. Recent studies show that this nonlinear dynamics can be well captured by low-order time domain models that couple a level set kinematic model for a laminar flame, the G-equation, with a...

  4. Neptunium Binding Kinetics with Arsenazo(III)

    SciTech Connect (OSTI)

    Leigh R. Martin; Aaron T. Johnson; Stephen P. Mezyk

    2014-08-01

    This document has been prepared to meet FCR&D level 2 milestone M2FT-14IN0304021, “Report on the results of actinide binding kinetics with aqueous phase complexants” This work was carried out under the auspices of the Thermodynamics and Kinetics of Advanced Separations Systems FCR&D work package. The report details kinetics experiments that were performed to measure rates of aqueous phase complexation for pentavalent neptunium with the chromotropic dye Arsenazo III (AAIII). The studies performed were designed to determine how pH, ionic strength and AAIII concentration may affect the rate of the reaction. A brief comparison with hexavalent neptunium is also made. It was identified that as pH was increased the rate of reaction also increased, however increasing the ionic strength and concentration of AAIII had the opposite effect. Interestingly, the rate of reaction of Np(VI) with AAIII was found to be slower than that of the Np(V) reaction.

  5. Cloning, purification and preliminary X-ray analysis of the C-terminal domain of Helicobacter pylori MotB

    SciTech Connect (OSTI)

    Roujeinikova, Anna, E-mail: anna.roujeinikova@manchester.ac.uk [Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN (United Kingdom)

    2008-04-01

    The cloning, overexpression, purification, crystallization and preliminary X-ray diffraction analysis of a putative peptidoglycan-binding domain of H. pylori MotB, a stator component of the bacterial flagellar motor, are reported. The C-terminal domain of MotB (MotB-C) contains a putative peptidoglycan-binding motif and is believed to anchor the MotA/MotB stator unit of the bacterial flagellar motor to the cell wall. Crystals of Helicobacter pylori MotB-C (138 amino-acid residues) were obtained by the hanging-drop vapour-diffusion method using polyethylene glycol as a precipitant. These crystals belong to space group P2{sub 1}, with unit-cell parameters a = 50.8, b = 89.5, c = 66.3 Å, ? = 112.5°. The crystals diffract X-rays to at least 1.6 Å resolution using a synchrotron-radiation source. Self-rotation function and Matthews coefficient calculations suggest that the asymmetric unit contains one tetramer with 222 point-group symmetry. The anomalous difference Patterson maps calculated for an ytterbium-derivative crystal using diffraction data at a wavelength of 1.38 Å showed significant peaks on the v = 1/2 Harker section, suggesting that ab initio phase information could be derived from the MAD data.

  6. Cancer-associated p53 tetramerization domain mutants: quantitative analysis reveals a low threshold for tumor suppressor inactivation

    SciTech Connect (OSTI)

    Kamada, R.; Anderson, C.; Nomura, T.; Sakaguchi, K.

    2011-01-07

    The tumor suppressor p53, a 393-amino acid transcription factor, induces cell cycle arrest and apoptosis in response to genotoxic stress. Its inactivation via the mutation of its gene is a key step in tumor progression, and tetramer formation is critical for p53 post-translational modification and its ability to activate or repress the transcription of target genes vital in inhibiting tumor growth. About 50% of human tumors have TP53 gene mutations; most are missense ones that presumably lower the tumor suppressor activity of p53. In this study, we explored the effects of known tumor-derived missense mutations on the stability and oligomeric structure of p53; our comprehensive, quantitative analyses encompassed the tetramerization domain peptides representing 49 such substitutions in humans. Their effects on tetrameric structure were broad, and the stability of the mutant peptides varied widely ({Delta}T{sub m} = 4.8 {approx} -46.8 C). Because formation of a tetrameric structure is critical for protein-protein interactions, DNA binding, and the post-translational modification of p53, a small destabilization of the tetrameric structure could result in dysfunction of tumor suppressor activity. We suggest that the threshold for loss of tumor suppressor activity in terms of the disruption of the tetrameric structure of p53 could be extremely low. However, other properties of the tetramerization domain, such as electrostatic surface potential and its ability to bind partner proteins, also may be important.

  7. Cosmic Microwave Background anisotropies generated by domain wall networks

    E-Print Network [OSTI]

    Sousa, L

    2015-01-01

    We develop a numerical tool for the fast computation of the temperature and polarization power spectra generated by domain wall networks, by extending the publicly available CMBACT code --- that calculates the CMB signatures generated by active sources --- to also describe domain wall networks. In order to achieve this, we adapt the Unconnected Segment model for cosmic strings to also describe domain wall networks, and use it to model the energy-momentum of domain wall networks throughout their cosmological history. We use this new tool to compute and study the TT, EE, TE and BB power spectra generated by standard domain wall networks, and derive a conservative constraint on the energy scale of the domain wall-forming phase transition of $\\upeta <0.92\\,\\,{\\rm MeV}$ (which is a slight improvement over the original Zel'dovich bound of $1\\,\\,{\\rm MeV}$).

  8. Birefringence insensitive optical coherence domain reflectometry system

    DOE Patents [OSTI]

    Everett, Matthew J. (Livermore, CA); Davis, Joseph G. (Lafayette, CA)

    2002-01-01

    A birefringence insensitive fiber optic optical coherence domain reflectometry (OCDR) system is provided containing non-polarization maintaining (non-PM) fiber in the sample arm and the reference arm without suffering from signal degradation caused by birefringence. The use of non-PM fiber significantly reduces the cost of the OCDR system and provides a disposable or multiplexed section of the sample arm. The dispersion in the reference arm and sample arm of the OCDR system are matched to achieve high resolution imaging. This system is useful in medical applications or for non-medical in situ probes. The disposable section of non-PM fiber in the sample arm can be conveniently replaced when contaminated by a sample or a patient.

  9. Chemomechanical mapping of ligandreceptor binding kinetics on cells

    E-Print Network [OSTI]

    Van Vliet, Krystyn J.

    Chemomechanical mapping of ligand­receptor binding kinetics on cells Sunyoung Lee, Jelena Mandic, Providence, RI, April 23, 2007 (received for review January 2, 2007) The binding kinetics between cell activity. Modeling and prediction of receptor-mediated cell func- tions are facilitated by measurement

  10. Water at biomolecular binding interfaces Zheng Li and Themis Lazaridis*

    E-Print Network [OSTI]

    Lazaridis, Themis

    Water at biomolecular binding interfaces Zheng Li and Themis Lazaridis* Received 29th August 2006.1039/b612449f Water molecules are often found at the binding interface of biomolecular complexes Waals interactions. Recent studies have demonstrated the importance of taking such water molecules

  11. Hydrogen Bonding Penalty upon Ligand Binding Hongtao Zhao, Danzhi Huang*

    E-Print Network [OSTI]

    Caflisch, Amedeo

    Hydrogen Bonding Penalty upon Ligand Binding Hongtao Zhao, Danzhi Huang* Department of Biochemistry, University of Zurich, Zurich, Switzerland Abstract Ligand binding involves breakage of hydrogen bonds with water molecules and formation of new hydrogen bonds between protein and ligand. In this work, the change

  12. ORIGINAL ARTICLE Analysis of RUNX1 binding site and RAPTOR

    E-Print Network [OSTI]

    Abecasis, Goncalo

    ORIGINAL ARTICLE Analysis of RUNX1 binding site and RAPTOR polymorphisms in psoriasis: no evidence psoriasis and single nucleotide polymorphisms (SNPs) mapping to distal chromosome 17q, including a disease for the previously identified RUNX1 binding site or for the RAPTOR locus as genetic determinants of psoriasis

  13. Performance-Guided Character Bind Pose for Deformations 

    E-Print Network [OSTI]

    Pena, Benito

    2011-08-08

    Current production methods for creating a motion system for a deformable digital character model involve providing an underlying joint structure based o of a T-Pose, A-Pose or another arbitrary bind pose of the character. A bind pose is required...

  14. NUCLEAR FISSION AND FUSION 6.A Nuclear Binding Energies

    E-Print Network [OSTI]

    Boal, David

    CHAPTER 6 NUCLEAR FISSION AND FUSION 6.A Nuclear Binding Energies A nucleus is characterized emphasis on the nuclear charge, the mass number of a nucleus plays a large role in its binding energy, and is denoted by 7Li. Some further items from the nuclear lexicon: nuclei with the same Z and differing N

  15. Structure and Mutagenesis of the Parainfluenza Virus 5 Hemagglutinin-Neuraminidase Stalk Domain Reveals a Four-Helix Bundle and the Role of the Stalk in Fusion Promotion

    SciTech Connect (OSTI)

    Bose, Sayantan; Welch, Brett D.; Kors, Christopher A.; Yuan, Ping; Jardetzky, Theodore S.; Lamb, Robert A.

    2014-10-02

    Paramyxovirus entry into cells requires the fusion protein (F) and a receptor binding protein (hemagglutinin-neuraminidase [HN], H, or G). The multifunctional HN protein of some paramyxoviruses, besides functioning as the receptor (sialic acid) binding protein (hemagglutinin activity) and the receptor-destroying protein (neuraminidase activity), enhances F activity, presumably by lowering the activation energy required for F to mediate fusion of viral and cellular membranes. Before or upon receptor binding by the HN globular head, F is believed to interact with the HN stalk. Unfortunately, until recently none of the receptor binding protein crystal structures have shown electron density for the stalk domain. Parainfluenza virus 5 (PIV5) HN exists as a noncovalent dimer-of-dimers on the surface of cells, linked by a single disulfide bond in the stalk. Here we present the crystal structure of the PIV5-HN stalk domain at a resolution of 2.65 {angstrom}, revealing a four-helix bundle (4HB) with an upper (N-terminal) straight region and a lower (C-terminal) supercoiled part. The hydrophobic core residues are a mix of an 11-mer repeat and a 3- to 4-heptad repeat. To functionally characterize the role of the HN stalk in F interactions and fusion, we designed mutants along the PIV5-HN stalk that are N-glycosylated to physically disrupt F-HN interactions. By extensive study of receptor binding, neuraminidase activity, oligomerization, and fusion-promoting functions of the mutant proteins, we found a correlation between the position of the N-glycosylation mutants on the stalk structure and their neuraminidase activities as well as their abilities to promote fusion.

  16. Visualizing the Behavior of Polar Domains and Screening Charges...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Visualizing the Behavior of Polar Domains and Screening Charges Under Electric and Mechanical Fields Event Sponsor: Mathematics and Computing Science - LANS Seminar Start Date: Sep...

  17. Domain architecture evolution of pattern-recognition receptors

    E-Print Network [OSTI]

    Zhang, Qing; Zmasek, Christian M.; Godzik, Adam

    2010-01-01

    PRRs, the intracel- lular NOD-like receptors (NLRs) and theexpansion . Domain shuffling . NOD-like receptor . Toll-likecontaining proteins NLRs NOD-like receptors PAMPs pathogen-

  18. Controlled Source Frequency-Domain Magnetics At Salt Wells Area...

    Open Energy Info (EERE)

    Controlled Source Frequency-Domain Magnetics At Salt Wells Area (Montgomery, Et Al., 2005) Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Exploration Activity:...

  19. Stochastic Domain-Wall Depinning in Magnetic Nanowires

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    of magnetic-domain walls and opens a path to further technological developments in spintronics applications. Magnetic Data Storage "Rats My disk drive has crashed. How will I...

  20. Time-Domain Electromagnetics At Kilauea Southwest Rift And South...

    Open Energy Info (EERE)

    Details Location Kilauea Southwest Rift And South Flank Area Exploration Technique Time-Domain Electromagnetics Activity Date Usefulness useful DOE-funding Unknown Notes The...

  1. Time-Domain Electromagnetics At Mauna Loa Northeast Rift Area...

    Open Energy Info (EERE)

    Activity Details Location Mauna Loa Northeast Rift Area Exploration Technique Time-Domain Electromagnetics Activity Date Usefulness useful DOE-funding Unknown Notes The...

  2. Time-Domain Electromagnetics At Hualalai Northwest Rift Area...

    Open Energy Info (EERE)

    Activity Details Location Hualalai Northwest Rift Area Exploration Technique Time-Domain Electromagnetics Activity Date Usefulness useful DOE-funding Unknown Notes Three...

  3. Structure and Dynamics of Domains in Ferroelectric Nanostructures...

    Office of Scientific and Technical Information (OSTI)

    of ferroelectric domains in ferroelectric thin films and nanostructures by advanced transmission electron microscopy (TEM) techniques in close collaboration with phase field...

  4. Examples of integral domains inside power series rings

    E-Print Network [OSTI]

    Abstract. We present examples of Noetherian and non-Noetherian integral do- ... over a Noetherian integral domain R and given a subfield L of the total quotient.

  5. Ultrabroadband coherence-domain imaging using parametric downconversion and

    E-Print Network [OSTI]

    Teich, Malvin C.

    Ultrabroadband coherence-domain imaging using parametric downconversion and superconducting single lithium tantalate (chirped-PPSLT) structure, in conjunction with a niobium nitride superconducting single

  6. Configuration of ripple domains and their topological defects...

    Office of Scientific and Technical Information (OSTI)

    their topological defects formed under local mechanical stress on hexagonal monolayer graphene Citation Details In-Document Search Title: Configuration of ripple domains and their...

  7. National Geothermal Data System (NGDS) Geothermal Data Domain...

    Open Energy Info (EERE)

    National Geothermal Data System (NGDS) Geothermal Data Domain: Assessment of Geothermal Community Data Needs Jump to: navigation, search OpenEI Reference LibraryAdd to library...

  8. Organic Solar Cells: Absolute Measurement of Domain Composition...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Organic Solar Cells: Absolute Measurement of Domain Composition and Nanoscale Size Distribution Explains Performance in Solar Cells Organic Solar Cells: Absolute Measurement of...

  9. Hamilton-Jacobi method for Domain Walls and Cosmologies

    E-Print Network [OSTI]

    Kostas Skenderis; Paul K. Townsend

    2006-12-07

    We use Hamiltonian methods to study curved domain walls and cosmologies. This leads naturally to first order equations for all domain walls and cosmologies foliated by slices of maximal symmetry. For Minkowski and AdS-sliced domain walls (flat and closed FLRW cosmologies) we recover a recent result concerning their (pseudo)supersymmetry. We show how domain-wall stability is consistent with the instability of adS vacua that violate the Breitenlohner-Freedman bound. We also explore the relationship to Hamilton-Jacobi theory and compute the wave-function of a 3-dimensional closed universe evolving towards de Sitter spacetime.

  10. Dual Transform Domain Echo Canceller for Discrete Multitone Systems

    E-Print Network [OSTI]

    Champagne, Benoît

    Dual Transform Domain Echo Canceller for Discrete Multitone Systems Neda Ehtiati and Beno Email:{neda.ehtiati,benoit.champagne}@mcgill.ca Abstract--In communication systems where full

  11. Time-Domain Electromagnetics At Kilauea East Rift Geothermal...

    Open Energy Info (EERE)

    Thomas, 1986) Exploration Activity Details Location Kilauea East Rift Geothermal Area Exploration Technique Time-Domain Electromagnetics Activity Date 1978 - 1987 Usefulness useful...

  12. Time-Domain Electromagnetics At Kilauea East Rift Geothermal...

    Open Energy Info (EERE)

    ENERGYGeothermal Home Exploration Activity: Time-Domain Electromagnetics At Kilauea East Rift Geothermal Area (Skokan, 1974) Exploration Activity Details Location Kilauea East...

  13. 'Escherichia Coli' MutS Tetramerization Domain Structure Reveals That Stable Dimers But Not Tetramers are Essential for DNA Mismatch Repair in Vivo

    SciTech Connect (OSTI)

    Mendillo, M.L.; Putnam, C.D.; Kolodner, R.D.; /UC, San Diego

    2007-07-10

    The E. coli mispair binding protein MutS forms dimers and tetramers in vitro, although the functional form in vivo is under debate. Here we demonstrate that the MutS tetramer is extended in solution using small angle x-ray scattering (SAXS) and the crystal structure of the C-terminal 34 amino acids of MutS containing the tetramer-forming domain fused to maltose binding protein (MBP). Wild-type C-terminal MBP fusions formed tetramers and could bind MutS and MutS-MutL-DNA complexes. In contrast, Asp835Arg and Arg840Glu mutations predicted to disrupt tetrameric interactions only allowed dimerization of MBP. A chromosomal MutS truncation mutation eliminating the dimerization/tetramerization domain eliminated mismatch repair, whereas the tetramer-disrupting MutS Asp835Arg and Arg840Glu mutations only modestly affected MutS function. These results demonstrate that dimerization but not tetramerization of the MutS C- terminus is essential for mismatch repair.

  14. Atomic structure of the nuclear pore complex targeting domain of a Nup116 homologue from the yeast, Candida glabrata

    SciTech Connect (OSTI)

    Sampathkumar, Parthasarathy; Kim, Seung Joong; Manglicmot, Danalyn; Bain, Kevin T.; Gilmore, Jeremiah; Gheyi, Tarun; Phillips, Jeremy; Pieper, Ursula; Fernandez-Martinez, Javier; Franke, Josef D.; Matsui, Tsutomu; Tsuruta, Hiro; Atwell, Shane; Thompson, Devon A.; Emtage, J. Spencer; Wasserman, Stephen R.; Rout, Michael P.; Sali, Andrej; Sauder, J. Michael; Almo, Steven C.; Burley, Stephen K. (Einstein); (SLAC); (Rockefeller); (UCSF); (Lilly)

    2012-10-23

    The nuclear pore complex (NPC), embedded in the nuclear envelope, is a large, dynamic molecular assembly that facilitates exchange of macromolecules between the nucleus and the cytoplasm. The yeast NPC is an eightfold symmetric annular structure composed of {approx}456 polypeptide chains contributed by {approx}30 distinct proteins termed nucleoporins. Nup116, identified only in fungi, plays a central role in both protein import and mRNA export through the NPC. Nup116 is a modular protein with N-terminal 'FG' repeats containing a Gle2p-binding sequence motif and a NPC targeting domain at its C-terminus. We report the crystal structure of the NPC targeting domain of Candida glabrata Nup116, consisting of residues 882-1034 [CgNup116(882-1034)], at 1.94 {angstrom} resolution. The X-ray structure of CgNup116(882-1034) is consistent with the molecular envelope determined in solution by small-angle X-ray scattering. Structural similarities of CgNup116(882-1034) with homologous domains from Saccharomyces cerevisiae Nup116, S. cerevisiae Nup145N, and human Nup98 are discussed.

  15. Characterization of the Carbohydrate Binding Module 18 gene family in the amphibian pathogen Batrachochytrium dendrobatidis.

    E-Print Network [OSTI]

    Liu, Peng; Stajich, Jason E

    2015-01-01

    a! chitin9binding! module. ! Appl! Microbiol! Biotechnol. !Species9specific! chitin9binding! module! 18! expansion! in!of the Carbohydrate Binding Module 18 gene family in the

  16. Page 1 A dedicated binding mechanism for the visual control of movement

    E-Print Network [OSTI]

    Diedrichsen, Jörn

    Page 1 A dedicated binding mechanism for the visual control of movement results therefore suggest the existence of a dedicated visuo-motor binding mechanism visual target information · A dedicated visuo-motor binding mechanism links visual

  17. PPRODO: Prediction of Protein Domain Boundaries Using Neural Networks

    E-Print Network [OSTI]

    Lee, Jooyoung

    PPRODO: Prediction of Protein Domain Boundaries Using Neural Networks Jaehyun Sim, Seung-Yeon Kim-BLAST. A 10-fold cross-validation technique is performed to obtain the parameters of neural networks using; neural network INTRODUCTION Domains are semi-independent 3-dimensional (3D) units in proteins, and often

  18. Characterizing Inter-domain Rerouting after Japan Earthquake

    E-Print Network [OSTI]

    Chang, Rocky Kow-Chuen

    Characterizing Inter-domain Rerouting after Japan Earthquake Yujing Liu1 , Xiapu Luo2 , Rocky K- domain rerouting as a result of the massive earthquake in Japan on March 2011. Moreover by unstable routing state caused by a cable fault after the earthquake. Our work provides a new method

  19. Three NASA Application Domains for Integrated Planning, Scheduling and Execution

    E-Print Network [OSTI]

    Kortenkamp, David

    Three NASA Application Domains for Integrated Planning, Scheduling and Execution David Kortenkamp. NASA Johnson Space Center { ER2 Houston, TX 77058 kortenkamp@jsc.nasa.gov Abstract This paper describes three application domains for in- tegrating planning, scheduling and execution at NASA Johnson Space

  20. A Cloud-Oriented Cross-Domain Security Architecture

    E-Print Network [OSTI]

    A Cloud-Oriented Cross-Domain Security Architecture Thuy D. Nguyen, Mark A. Gondree, David J to support a cloud of cross-domain services, hosted within a federation of multilevel secure (MLS) MYSEA}@nps.edu Abstract--The Monterey Security Architecture addresses the need to share high-value data across multiple

  1. Lipid Domain Order and the Algebra of Morphology

    E-Print Network [OSTI]

    Tristan Ursell; Rob Phillips

    2009-05-09

    Lipid membranes regulate the flow of materials and information between cells and their organelles. Further, lipid composition and morphology can play a key role in regulating a variety of biological processes. For example, viral uptake, plasma membrane tension regulation, and the formation of caveolae all require the creation and control of groups of lipids that adopt specific morphologies. In this paper, we use a simplified model mixture of lipids and cholesterol to examine the interplay between lipid phase-separation and bilayer morphology. We observe and theoretically analyze three main features of phase-separated giant unilamellar vesicles. First, by tracking the motion of `dimpled' domains, we measure repulsive, elastic interactions that create short--range translational and orientational order, leading to a stable distribution of domain sizes, and hence maintaining lateral heterogeneity on relatively short length scales and long time scales. Second, we examine the transition to `budded' domain morphologies, showing that the transition is size-selective, and has two kinetic regimes, as revealed by a calculated phase diagram. Finally, using observations of the interactions between dimpled and budded domains, we build a theoretical framework with an elastic model that maps the free energies and allowed transitions in domain morphology upon coalescence, to serve as an interpretive tool for understanding the algebra of domain morphology. In all three cases, the two major factors that regulate domain morphology and morphological transitions are the domain size and membrane tension.

  2. Scaling reinforcement learning to the unconstrained multi-agent domain 

    E-Print Network [OSTI]

    Palmer, Victor

    2009-06-02

    - MENT LEARNING . . . . . . . . . . . . . . . . . . . . . . . . . 76 A. Sample Complexity and Reinforcement Learning . . . . . . 78 B. Domain Knowledge and Fuzzy Rules . . . . . . . . . . . . 79 C. Potential Negative Effects of Added Domain Knowledge... . . 80 1. Derivation . . . . . . . . . . . . . . . . . . . . . . . . 80 2. Interpretation . . . . . . . . . . . . . . . . . . . . . . 84 D. Fuzzy Reward Shaping . . . . . . . . . . . . . . . . . . . . 86 E. Integrating Fuzzy Knowledge...

  3. Surface effect on domain wall width in ferroelectrics

    E-Print Network [OSTI]

    2009-10-26

    Oct 26, 2009 ... the domain wall thickness and gradient coefficients in typical ... phase transitions or u. 0 for the second ... tained from the surface energy in the form12. P3 ? 1 ..... Calculated width solid curves of domain wall at level. 0.76 as a ...

  4. On Some Constructions in Quantitative Domain Theory (Extended Abstract)

    E-Print Network [OSTI]

    Spreen, Dieter

    On Some Constructions in Quantitative Domain Theory (Extended Abstract) Dieter Spreen Theoretische of an approximation, the theory of approximation based on domains was mainly of a qualitative nature. The situation introduced by K. Martin in his thesis [7]. They are strongly intertwined with the topological structure

  5. Expanded polyglutamine domain possesses nuclear export activity which modulates subcellular

    E-Print Network [OSTI]

    Higgins, Darren

    experiments, were ana- lyzed. Mammalian cell culture HEK293 cells were cultured at 378C with 5% CO2 in high,16). To investigate the nuclear transport property of expanded polyQ domain per se, we initially took advantage then focused on elucidating the nuclear export property of an expanded polyQ domain and its associated

  6. ORIGINAL ARTICLE Single ferroelectric-domain photovoltaic switch based

    E-Print Network [OSTI]

    Jo, Moon-Ho

    ORIGINAL ARTICLE Single ferroelectric-domain photovoltaic switch based on lateral BiFeO3 cells Ji serves as a basis for solid-state memory. This phenomenon can also yield an interesting photovoltaic imposed by the ferroelectric polarization vectors. Here, we demonstrate a single-domain photovoltaic

  7. SIMMODEL: A DOMAIN DATA MODEL FOR WHOLE BUILDING ENERGY SIMULATION

    E-Print Network [OSTI]

    LBNL-5566E SIMMODEL: A DOMAIN DATA MODEL FOR WHOLE BUILDING ENERGY SIMULATION Author(s), James O;SIMMODEL: A DOMAIN DATA MODEL FOR WHOLE BUILDING ENERGY SIMULATION James O'Donnell1 Richard See2 , Cody exist within industry-standard data models as used by present-day whole-building energy simulation

  8. Parameter Estimation for the Heat Equation on Perforated Domains

    E-Print Network [OSTI]

    Parameter Estimation for the Heat Equation on Perforated Domains H.T. Banks1 , D. Cioranescu2 , A for simulated data for heat flow in a porous medium. We consider data simulated from a model on a perforated Words: Inverse problems, parameter estimation, perforated domains, homogeniza- tion, thermal diffusion

  9. Important Cognitive Components of Domain-Specific Search Knowledge

    E-Print Network [OSTI]

    Bhavnani, Suresh K.

    the subject-specific terms to enter in a query. For example, many university students often buy electronicImportant Cognitive Components of Domain-Specific Search Knowledge Suresh K. Bhavnani School Many users have acquired a sophisticated understanding of searching the Web in specific domains

  10. Extending OpenStack Access Control with Domain Trust

    E-Print Network [OSTI]

    Sandhu, Ravi

    Stack identity service Keystone has introduced several entities, such as domains and projects in addition-of-concept prototype of this trust extension based on Keystone. The authorization delay introduced by the domain trustsStack.2 The identity service in OpenStack, called Keystone, is used to manage users as globally available

  11. Stabilizing the cystic fibrosis transmembrane conductance regulator (CFTR) by nucleotide derivative binding to promote proper folding 

    E-Print Network [OSTI]

    Smith, Ryan Craig

    2013-02-22

    Seventy percent of people who suffer from cystic fibrosis have a cystic fibrosis transmembrane conductance regulator gene on chromosome 7 that contains a three base-pair deletion of phenylalanine at position 508, in a ...

  12. How Swift is redefining Time Domain Astronomy

    E-Print Network [OSTI]

    Gehrels, Neil

    2015-01-01

    NASA's Swift satellite has completed ten years of amazing discoveries in time domain astronomy. Its primary mission is to chase gamma-ray bursts (GRBs), but due to its scheduling flexibility it has subsequently become a prime discovery machine for new types of behavior. The list of major discoveries in GRBs and other transients includes the long-lived X-ray afterglows and flares from GRBs, the first accurate localization of short GRBs, the discovery of GRBs at high redshift (z>8), supernova shock break-out from SN Ib, a jetted tidal disruption event, an ultra-long class of GRBs, high energy emission from flare stars, novae and supernovae with unusual characteristics, magnetars with glitches in their spin periods, and a short GRB with evidence of an accompanying kilonova. Swift has developed a dynamic synergism with ground based observatories. In a few years gravitational wave observatories will come on-line and provide exciting new transient sources for Swift to study.

  13. Catheter guided by optical coherence domain reflectometry

    DOE Patents [OSTI]

    Everett, Matthew (Pleasanton, CA); Colston, Billy W. (Livermore, CA); Da Silva, Luiz B. (Danville, CA); Matthews, Dennis (Moss Beach, CA)

    2002-01-01

    A guidance and viewing system based on multiplexed optical coherence domain reflectometry is incorporated into a catheter, endoscope, or other medical device to measure the location, thickness, and structure of the arterial walls or other intra-cavity regions at discrete points on the medical device during minimally invasive medical procedures. The information will be used both to guide the device through the body and to evaluate the tissue through which the device is being passed. Multiple optical fibers are situated along the circumference of the device. Light from the distal end of each fiber is directed onto the interior cavity walls via small diameter optics (such as gradient index lenses and mirrored corner cubes). Both forward viewing and side viewing fibers can be included. The light reflected or scattered from the cavity walls is then collected by the fibers and multiplexed at the proximal end to the sample arm of an optical low coherence reflectometer. The system may also be implemented in a nonmedical inspection device.

  14. Pedestrian flows in bounded domains with obstacles

    E-Print Network [OSTI]

    Benedetto Piccoli; Andrea Tosin

    2008-12-23

    In this paper we systematically apply the mathematical structures by time-evolving measures developed in a previous work to the macroscopic modeling of pedestrian flows. We propose a discrete-time Eulerian model, in which the space occupancy by pedestrians is described via a sequence of Radon positive measures generated by a push-forward recursive relation. We assume that two fundamental aspects of pedestrian behavior rule the dynamics of the system: On the one hand, the will to reach specific targets, which determines the main direction of motion of the walkers; on the other hand, the tendency to avoid crowding, which introduces interactions among the individuals. The resulting model is able to reproduce several experimental evidences of pedestrian flows pointed out in the specialized literature, being at the same time much easier to handle, from both the analytical and the numerical point of view, than other models relying on nonlinear hyperbolic conservation laws. This makes it suitable to address two-dimensional applications of practical interest, chiefly the motion of pedestrians in complex domains scattered with obstacles.

  15. Dual-domain lateral shearing interferometer

    DOE Patents [OSTI]

    Naulleau, Patrick P.; Goldberg, Kenneth Alan

    2004-03-16

    The phase-shifting point diffraction interferometer (PS/PDI) was developed to address the problem of at-wavelength metrology of extreme ultraviolet (EUV) optical systems. Although extremely accurate, the fact that the PS/PDI is limited to use with coherent EUV sources, such as undulator radiation, is a drawback for its widespread use. An alternative to the PS/PDI, with relaxed coherence requirements, is lateral shearing interferometry (LSI). The use of a cross-grating, carrier-frequency configuration to characterize a large-field 4.times.-reduction EUV lithography optic is demonstrated. The results obtained are directly compared with PS/PDI measurements. A defocused implementation of the lateral shearing interferometer in which an image-plane filter allows both phase-shifting and Fourier wavefront recovery. The two wavefront recovery methods can be combined in a dual-domain technique providing suppression of noise added by self-interference of high-frequency components in the test-optic wavefront.

  16. Domain wall QCD with physical quark masses

    E-Print Network [OSTI]

    RBC,; Blum, T; Boyle, P A; Christ, N H; Frison, J; Garron, N; Hudspith, R J; Izubuchi, T; Janowski, T; Jung, C; Juettner, A; Kelly, C; Kenway, R D; Lehner, C; Marinkovic, M; Mawhinney, R D; McGlynn, G; Murphy, D J; Ohta, S; Portelli, A; Sachrajda, C T; Soni, A

    2014-01-01

    We present results for several light hadronic quantities ($f_\\pi$, $f_K$, $B_K$, $m_{ud}$, $m_s$, $t_0^{1/2}$, $w_0$) obtained from simulations of 2+1 flavor domain wall lattice QCD with large physical volumes and nearly-physical pion masses at two lattice spacings. We perform a short, O(3)%, extrapolation in pion mass to the physical values by combining our new data in a simultaneous chiral/continuum `global fit' with a number of other ensembles with heavier pion masses. We use the physical values of $m_\\pi$, $m_K$ and $m_\\Omega$ to determine the two quark masses and the scale - all other quantities are outputs from our simulations. We obtain results with sub-percent statistical errors and negligible chiral and finite-volume systematics for these light hadronic quantities, including: $f_\\pi$ = 130.2(9) MeV; $f_K$ = 155.5(8) MeV; the average up/down quark mass and strange quark mass in the $\\overline {\\rm MS}$ scheme at 3 GeV, 2.997(49) and 81.64(1.17) MeV respectively; and the neutral kaon mixing parameter, ...

  17. Domain wall QCD with physical quark masses

    E-Print Network [OSTI]

    RBC; UKQCD collaborations; :; T. Blum; P. A. Boyle; N. H. Christ; J. Frison; N. Garron; R. J. Hudspith; T. Izubuchi; T. Janowski; C. Jung; A. Juettner; C. Kelly; R. D. Kenway; C. Lehner; M. Marinkovic; R. D. Mawhinney; G. McGlynn; D. J. Murphy; S. Ohta; A. Portelli; C. T. Sachrajda; A. Soni

    2014-11-25

    We present results for several light hadronic quantities ($f_\\pi$, $f_K$, $B_K$, $m_{ud}$, $m_s$, $t_0^{1/2}$, $w_0$) obtained from simulations of 2+1 flavor domain wall lattice QCD with large physical volumes and nearly-physical pion masses at two lattice spacings. We perform a short, O(3)%, extrapolation in pion mass to the physical values by combining our new data in a simultaneous chiral/continuum `global fit' with a number of other ensembles with heavier pion masses. We use the physical values of $m_\\pi$, $m_K$ and $m_\\Omega$ to determine the two quark masses and the scale - all other quantities are outputs from our simulations. We obtain results with sub-percent statistical errors and negligible chiral and finite-volume systematics for these light hadronic quantities, including: $f_\\pi$ = 130.2(9) MeV; $f_K$ = 155.5(8) MeV; the average up/down quark mass and strange quark mass in the $\\overline {\\rm MS}$ scheme at 3 GeV, 2.997(49) and 81.64(1.17) MeV respectively; and the neutral kaon mixing parameter, $B_K$, in the RGI scheme, 0.750(15) and the $\\overline{\\rm MS}$ scheme at 3 GeV, 0.530(11).

  18. Thermal effects on transverse domain wall dynamics in magnetic nanowires

    SciTech Connect (OSTI)

    Leliaert, J.; Van de Wiele, B.; Vandermeulen, J.; Coene, A.; Dupré, L.; Vansteenkiste, A.; Waeyenberge, B. Van; Laurson, L.; Durin, G.

    2015-05-18

    Magnetic domain walls are proposed as data carriers in future spintronic devices, whose reliability depends on a complete understanding of the domain wall motion. Applications based on an accurate positioning of domain walls are inevitably influenced by thermal fluctuations. In this letter, we present a micromagnetic study of the thermal effects on this motion. As spin-polarized currents are the most used driving mechanism for domain walls, we have included this in our analysis. Our results show that at finite temperatures, the domain wall velocity has a drift and diffusion component, which are in excellent agreement with the theoretical values obtained from a generalized 1D model. The drift and diffusion component are independent of each other in perfect nanowires, and the mean square displacement scales linearly with time and temperature.

  19. Contribution of domain wall networks to the CMB power spectrum

    E-Print Network [OSTI]

    Lazanu, A; Shellard, E P S

    2015-01-01

    We use three domain wall simulations from the radiation era to the late time dark energy domination era based on the PRS algorithm to calculate the energy-momentum tensor components of domain wall networks in an expanding universe. Unequal time correlators in the radiation, matter and cosmological constant epochs are calculated using the scaling regime of each of the simulations. The CMB power spectrum of a network of domain walls is determined. The first ever quantitative constraint for the domain wall surface tension is obtained using a Markov chain Monte Carlo method; an energy scale of domain walls of 0.93 MeV, which is close but below the Zel'dovich bound, is determined.

  20. X-ray Crystallographic Studies of Substrate Binding to Aristolochene Synthase Suggest a Metal Ion Binding Sequence for Catalysis

    SciTech Connect (OSTI)

    Shishova,E.; Yu, F.; Miller, D.; Faraldos, J.; Zhao, Y.; Coates, R.; Allemann, R.; Cane, D.; Christianson, D.

    2008-01-01

    The universal sesquiterpene precursor, farnesyl diphosphate (FPP), is cyclized in an Mg2+-dependent reaction catalyzed by the tetrameric aristolochene synthase from Aspergillus terreus to form the bicyclic hydrocarbon aristolochene and a pyrophosphate anion (PPi) coproduct. The 2.1- Angstroms resolution crystal structure determined from crystals soaked with FPP reveals the binding of intact FPP to monomers A-C, and the binding of PPi and Mg2+B to monomer D. The 1.89- Angstroms resolution structure of the complex with 2-fluorofarnesyl diphosphate (2F-FPP) reveals 2F-FPP binding to all subunits of the tetramer, with Mg2+Baccompanying the binding of this analogue only in monomer D. All monomers adopt open activesite conformations in these complexes, but slight structural changes in monomers C and D of each complex reflect the very initial stages of a conformational transition to the closed state. Finally, the 2.4- Angstroms resolution structure of the complex with 12,13-difluorofarnesyl diphosphate (DF-FPP) reveals the binding of intact DF-FPP to monomers A-C in the open conformation and the binding of PPi, Mg2+B, and Mg2+C to monomer D in a predominantly closed conformation. Taken together, these structures provide 12 independent 'snapshots' of substrate or product complexes that suggest a possible sequence for metal ion binding and conformational changes required for catalysis.

  1. Cellulose Binding Protein from the Parasitic Nematode Heterodera schachtii Interacts with Arabidopsis Pectin

    E-Print Network [OSTI]

    Hussey, Richard S.

    Cellulose Binding Protein from the Parasitic Nematode Heterodera schachtii Interacts Heterodera glycines also produces a cellulose binding protein (Hg CBP) secretory protein. To determine

  2. Blimp-1{delta}exon7: A naturally occurring Blimp-1 deletion mutant with auto-regulatory potential

    SciTech Connect (OSTI)

    Schmidt, Doris; Nayak, Arnab; Schumann, Julia E.; Schimpl, Anneliese; Berberich, Ingolf Berberich-Siebelt, Friederike

    2008-12-10

    Blimp-1 is a master regulator of terminal B cell differentiation and plays a pivotal role in various developmental processes. In addition to full length Blimp-1, a Blimp-1 mRNA lacking exon 7 (Blimp-1{delta}7) has been described to occur in murine B cells. The activity and function of the mutant mRNA-encoded protein (Blimp-1{delta}7), lacking three crucial zinc fingers necessary for DNA interaction, is completely unknown. Since isoforms of other prdm family proteins affect each other's functions, we wondered whether Blimp-1{delta}7 still plays a role in B cells, independent of direct DNA binding. In this study, we found that Blimp-1{delta}7 is preferentially expressed in naive CD19{sup +} B cells. A fraction of Blimp-1{delta}7 migrates to the nucleus, colocalizes with HDAC2 and is found at sites of repressed chromatin, although it does not bind to the Blimp-1 DNA consensus site. Unexpectedly, Blimp-1 and Blimp-1{delta}7 homodimerize as well as heterodimerize with each other. Ectopic expression of Blimp-1{delta}7 in WEHI 231 cells, a Blimp-1-negative murine lymphoma line, leads to cessation of proliferation and enhancement of apoptosis. Importantly, LPS-induced differentiation is suppressed in the presence of Blimp-1{delta}7. This is in agreement with our finding that Blimp-1{delta}7 interferes with endogenous Blimp-1 expression. Thus, our data suggest an auto-regulatory mechanism of Blimp-1 activation.

  3. Post-transcriptional coordination by an RNA-binding protein

    E-Print Network [OSTI]

    Wolf, Joshua Jaeger

    2010-01-01

    RNA-binding proteins can regulate the stability, localization, and translation of their target mRNAs. Post-transcriptional regulation can orchestrate dynamic changes in gene expression, and can coordinate multiple cellular ...

  4. Original article Distribution of endogenous retinoids, retinoid binding

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    of specific retinoid-binding proteins was investigated; these are involved in vitamin A transport, metabolism is induced by a concentration gradient (high posteri- orly) of all-trans-RA along the anterior-p

  5. Metal binding proteins, recombinant host cells and methods

    DOE Patents [OSTI]

    Summers, Anne O.; Caguiat, Jonathan J.

    2004-06-15

    The present disclosure provides artificial heavy metal binding proteins termed chelons by the inventors. These chelons bind cadmium and/or mercuric ions with relatively high affinity. Also disclosed are coding sequences, recombinant DNA molecules and recombinant host cells comprising those recombinant DNA molecules for expression of the chelon proteins. In the recombinant host cells or transgenic plants, the chelons can be used to bind heavy metals taken up from contaminated soil, groundwater or irrigation water and to concentrate and sequester those ions. Recombinant enteric bacteria can be used within the gastrointestinal tracts of animals or humans exposed to toxic metal ions such as mercury and/or cadmium, where the chelon recombinantly expressed in chosen in accordance with the ion to be rededicated. Alternatively, the chelons can be immobilized to solid supports to bind and concentrate heavy metals from a contaminated aqueous medium including biological fluids.

  6. Linear Scaling of the Exciton Binding Energy versus the Band...

    Office of Scientific and Technical Information (OSTI)

    Linear Scaling of the Exciton Binding Energy versus the Band Gap of Two-Dimensional Materials This content will become publicly available on August 6, 2016 Prev Next Title:...

  7. Second-order susceptibility from a tight-binding Hamiltonian 

    E-Print Network [OSTI]

    Dumitrica, T.; Graves, JS; Allen, Roland E.

    1998-01-01

    Using a new formalism that modifies a tight-binding Hamiltonian to include interaction with a time-dependent electromagnetic field, we have obtained an analytical expression for the second-order susceptibility. This expression has been used...

  8. Aberrant Alternative Splicing of Thyroid Hormone Receptor in a TSH-Secreting Pituitary Tumor Is

    E-Print Network [OSTI]

    Aberrant Alternative Splicing of Thyroid Hormone Receptor in a TSH-Secreting Pituitary Tumor that encodes the ligand-binding domain of TR 2. This deletion was caused by alternative splicing of TR 2 m. These findings strongly suggest that aberrant alternative splicing of TR 2 mRNA generated an abnormal TR protein

  9. Structure of a Glomulin-RBX1-CUL1 Complex: Inhibition of a RING E3 Ligase through Masking of Its E2-Binding Surface

    SciTech Connect (OSTI)

    Duda, David M.; Olszewski, Jennifer L.; Tron, Adriana E.; Hammel, Michal; Lambert, Lester J.; Waddell, M. Brett; Mittag, Tanja; DeCaprio, James A.; Schulman, Brenda A. (BWH); (LBNL); (SJCH); (DFCI)

    2012-11-01

    The approximately 300 human cullin-RING ligases (CRLs) are multisubunit E3s in which a RING protein, either RBX1 or RBX2, recruits an E2 to catalyze ubiquitination. RBX1-containing CRLs also can bind Glomulin (GLMN), which binds RBX1's RING domain, regulates the RBX1-CUL1-containing SCF{sup FBW7} complex, and is disrupted in the disease Glomuvenous Malformation. Here we report the crystal structure of a complex between GLMN, RBX1, and a fragment of CUL1. Structural and biochemical analyses reveal that GLMN adopts a HEAT-like repeat fold that tightly binds the E2-interacting surface of RBX1, inhibiting CRL-mediated chain formation by the E2 CDC34. The structure explains the basis for GLMN's selectivity toward RBX1 over RBX2, and how disease-associated mutations disrupt GLMN-RBX1 interactions. Our study reveals a mechanism for RING E3 ligase regulation, whereby an inhibitor blocks E2 access, and raises the possibility that other E3s are likewise controlled by cellular proteins that mask E2-binding surfaces to mediate inhibition.

  10. Dimer Dissociation and Unfolding Mechanism of Coagulation Factor XI Apple 4 Domain: Spectroscopic

    E-Print Network [OSTI]

    Roder, Heinrich

    Dimer Dissociation and Unfolding Mechanism of Coagulation Factor XI Apple 4 Domain: Spectroscopic of disulfide- linked chains each containing four apple domains and a catalytic domain. The apple 4 domain (A4; A4, apple 4 domain of factor XI; DLS, dynamic light scattering; FXI, factor XI; FXIa, factor FXIa

  11. Evolution of domain compositions in the metabolic networks of human and Escherichia coli

    E-Print Network [OSTI]

    Yeang, Chen-Hsiang

    Evolution of domain compositions in the metabolic networks of human and Escherichia coli C.H. Yeang and recombination of enzyme protein domains. However, varia- tions of the domain evolution mechanisms among heterogeneity of domain evolution mechanisms by comparing the domain composi- tions of the metabolic networks

  12. Ore Extensions and V -domains S. K. Jain, T. Y. Lam and A. Leroy

    E-Print Network [OSTI]

    Jain, Surender K.

    and PCI-domain (A domain such that each proper cyclic right module is injective is called right PCI, the question whether the property of being V -domain or PCI-domain is left-right symmetric remains open obtain necessary and sufficient conditions for K[t; , ] to be a left V -domain (equivalently, left PCI

  13. Gapped Domain Walls, Gapped Boundaries and Topological Degeneracy

    E-Print Network [OSTI]

    Tian Lan; Juven Wang; Xiao-Gang Wen

    2014-11-26

    Gapped domain walls, as topological line defects between 2+1D topologically ordered states, are examined. We provide simple criteria to determine the existence of gapped domain walls, which apply to both Abelian and non-Abelian topological orders. Our criteria also determine which 2+1D topological orders must have gapless edge modes, namely which 1+1D global gravitational anomalies ensure gaplessness. Furthermore, we introduce a new mathematical object, the tunneling matrix $\\mathcal W$, whose entries are the fusion-space dimensions $\\mathcal W_{ia}$, to label different types of gapped domain walls. By studying many examples, we find evidence that the tunneling matrices are powerful quantities to classify different types of gapped domain walls. Since a gapped boundary is a gapped domain wall between a bulk topological order and the vacuum, regarded as the trivial topological order, our theory of gapped domain walls inclusively contains the theory of gapped boundaries. In addition, we derive a topological ground state degeneracy formula, applied to arbitrary orientable spatial 2-manifolds with gapped domain walls, including closed 2-manifolds and open 2-manifolds with gapped boundaries.

  14. Topography influence on the Lake equations in bounded domains

    E-Print Network [OSTI]

    Christophe Lacave; Toan T. Nguyen; Benoit Pausader

    2013-06-10

    We investigate the influence of the topography on the lake equations which describe the two-dimensional horizontal velocity of a three-dimensional incompressible flow. We show that the lake equations are structurally stable under Hausdorff approximations of the fluid domain and $L^p$ perturbations of the depth. As a byproduct, we obtain the existence of a weak solution to the lake equations in the case of singular domains and rough bottoms. Our result thus extends earlier works by Bresch and M\\'etivier treating the lake equations with a fixed topography and by G\\'erard-Varet and Lacave treating the Euler equations in singular domains.

  15. Calculation of the strange quark mass using domain wall fermions

    E-Print Network [OSTI]

    Tom Blum; Amarjit Soni; Matthew Wingate

    2000-09-18

    We present a first calculation of the strange quark mass using domain wall fermions. This paper contains an overview of the domain wall discretization and a pedagogical presentation of the perturbative calculation necessary for computing the mass renormalization. We combine the latter with numerical simulations to estimate the strange quark mass. Our final result in the quenched approximation is 95(26) MeV in the ${\\bar{MS}}$ scheme at a scale of 2 GeV. We find that domain wall fermions have a small perturbative mass renormalization, similar to Wilson quarks, and exhibit good scaling behavior.

  16. Asymmetric domain walls of small angle in soft ferromagnetic films

    E-Print Network [OSTI]

    Lukas Döring; Radu Ignat

    2014-12-07

    We focus on a special type of domain walls appearing in the Landau-Lifshitz theory for soft ferromagnetic films. These domain walls are divergence-free $S^2$-valued transition layers that connect two directions in $S^2$ (differing by an angle $2\\theta$) and minimize the Dirichlet energy. Our main result is the rigorous derivation of the asymptotic structure and energy of such "asymmetric" domain walls in the limit $\\theta \\to 0$. As an application, we deduce that a supercritical bifurcation causes the transition from symmetric to asymmetric walls in the full micromagnetic model.

  17. The importance of domain-domain interactions in the regulation and activity of neuronal nitric oxide synthase 

    E-Print Network [OSTI]

    Welland, Andrew David

    2008-01-01

    Nitric oxide synthases (NOSs) catalyse the production of the physiological messenger molecule NO from L-arginine in a unique two step oxygenation reaction. Constitutive forms of NOS are activated by the binding of ...

  18. Effect of the deletion of qmoABC and the promoter distal gene encoding a hypothetical protein on sulfate-reduction in Desulfovibrio vulgaris Hildenborough

    SciTech Connect (OSTI)

    Zane, Grant M.; Yen, Huei-chi Bill; Wall, Judy D.

    2010-03-18

    The pathway of electrons required for the reduction of sulfate in sulfate-reducing bacteria (SRB) is not yet fully characterized. In order to determine the role of a transmembrane protein complex suggested to be involved in this process, a deletion of Desulfovibrio vulgaris Hildenborough was created by marker exchange mutagenesis that eliminated four genes putatively encoding the QmoABC complex and a hypothetical protein (DVU0851). The Qmo complex (quinone-interacting membrane-bound oxidoreductase) is proposed to be responsible for transporting electrons to the dissimilatory adenosine-5?phosphosulfate (APS) reductase in SRB. In support of the predicted role of this complex, the deletion mutant was unable to grow using sulfate as its sole electron acceptor with a range of electron donors. To explore a possible role for the hypothetical protein in sulfate reduction, a second mutant was constructed that had lost only the gene that codes for DVU0851. The second constructed mutant grew with sulfate as the sole electron acceptor; however, there was a lag that was not present with the wild-type or complemented strain. Neither deletion strain was significantly impaired for growth with sulfite or thiosulfate as terminal electron acceptor. Complementation of the D(qmoABC-DVU0851) mutant with all four genes or only the qmoABC genes restored its ability to grow by sulfate respiration. These results confirmed the prediction that the Qmo complex is in the electron pathway for sulfate-reduction and revealed that no other transmembrane complex could compensate when Qmo was lacking.

  19. MANAGING TIGHT BINDING RECEPTORS FOR NEW SPEARATIONS TECHNOLOGIES

    SciTech Connect (OSTI)

    DARYLE H BUSCH RICHARD S GIVENS

    2004-12-10

    Much of the earth's pollution involves compounds of the metallic elements, including actinides, strontium, cesium, technetium, and RCRA metals. Metal ions bind to molecules called ligands, which are the molecular tools that can manipulate the metal ions under most conditions. This DOE-EMSP sponsored program strives (1) to provide the foundations for using the most powerful ligands in transformational separations technologies and (2) to produce seminal examples of their applications to separations appropriate to the DOE EM mission. These ultra tight-binding ligands can capture metal ions in the most competitive of circumstances (from mineralized sites, lesser ligands, and even extremely dilute solutions), but they react so slowly that they are useless in traditional separations methodologies. Two attacks on this problem are underway. The first accommodates to the challenging molecular lethargy by developing a seminal slow separations methodology termed the soil poultice. The second designs ligands that are only tight-binding while wrapped around the targeted metal ion, but can be put in place by switch-binding and removed by switch-release. We envision a kind of molecular switching process to accelerate the union between metal ion and tight-binding ligand. Molecular switching processes are suggested for overcoming the slow natural equilibration rate with which ultra tight-binding ligands combine with metal ions. Ligands that bind relatively weakly combine with metal ions rapidly, so the trick is to convert a ligand from a weak, rapidly binding species to a powerful, slow releasing ligand--during the binding of the ligand to the metal ion. Such switch-binding ligands must react with themselves, and the reaction must take place under the influence of the metal ion. For example, our generation 1 ligands showed that a well-designed linear ligand with ends that readily combine, forms a cyclic molecule when it wraps around a metal ion. Our generation 2 ligands are even more interesting. They convert from rings to structures that wrap around a metal ion to form a cage. These ligands are called cryptands. Switch release is accomplished by photolytic cleavage of a bond to convert a cyclic ligand into a linear ligand or to break similar bonds in a cryptate. Our studies have demonstrated switch binding and switch release with cryptates of calcium. These remarkable cyclic ligands and cage-like ligands are indeed tight-binding and may, in principle, be incorporated in various separations methodologies, including the soil poultice. The soil poultice mimics the way in which microbes secrete extremely powerful ligands into the soil in order to harvest iron. The cellular membrane of the microbe recognizes the iron/ligand complex and admits it into the cell. The soil poultice uses molecularly imprinted polymers (MIPs) to play the role of the cellular membrane. Imprinting involves creation of the polymer in the presence of the metal/ligand complex. In principle, a well design ligand/MIP combination can be highly selective toward almost any targeted metal ion. The principles for that design are the focus of these investigations. An imprinting molecule can interact with the polymer through any, some, or all of the so-called supramolecular modes; e.g., hydrogen bonding, electrostatic charge, minor ligand bonding, Pi-Pi stacking, and hydrophobic and van der Waals interactions. Historically these modes of binding have given MIPs only small re-binding capacities and very limited selectivities. This program has shown that each mode of interaction can be made more powerful than previously suspected and that combinations of different supramolecular interaction modes can produce remarkable synergisms. The results of this systematic study provide a firm foundation for tailoring molecular imprinted polymers for reclamation of specific metal ion, including those important to the DOE EM mission.

  20. An Overlapping Domain Decomposition Method for Parameter Identification Problems

    E-Print Network [OSTI]

    Cai, Xiao-Chuan

    An Overlapping Domain Decomposition Method for Parameter Identification Problems Xiao-Chuan Cai1 by the Hong Kong RGC grant, Project 404105. #12;2 Xiao-Chuan Cai, Si Liu, and Jun Zou which is usually

  1. Nonlinear Overlapping Domain Decomposition Xiao-Chuan Cai1

    E-Print Network [OSTI]

    Cai, Xiao-Chuan

    Nonlinear Overlapping Domain Decomposition Methods Xiao-Chuan Cai1 Department of Computer Science, and CNS-0722023. #12;2 Xiao-Chuan Cai the following steps: first find an inexact Newton direction p

  2. Gerhard Fischer 1 Domain-Oriented Design Environments

    E-Print Network [OSTI]

    Fischer, Gerhard

    architecture (the multifaceted architecture) and a process model (the seeding, evolutionary growth, reseeding, Science and Technology Center, and (4) U S WEST Advanced Technologies. #12;Gerhard Fischer 2 Table.......................................................................................... 6 The Multifaceted Architecture: A Domain-Independent Architecture for DODEs

  3. Analytical and micromagnetic study of a Neel domain wall 

    E-Print Network [OSTI]

    Rivkin, K.; Romanov, K.; Abanov, Artem; Adamov, Y.; Saslow, W. M.

    2008-01-01

    For ferromagnets with exchange, dipolar interaction, and uniaxial anisotropy, by both analytic methods and micromagnetic simulations we study Neel domain walls in thin ferromagnetic strips of finite width. Comparison of the numerical results...

  4. Domain-level rocking motion within a polymerase that translocates...

    Office of Scientific and Technical Information (OSTI)

    nucleic acid An X-ray crystallographic structure is described for unliganded Vaccinia virus poly(A) polymerase monomer (VP55), showing the first domain-level structural isoforms...

  5. Domain wall displacement by remote spin-current injection

    E-Print Network [OSTI]

    Skirdkov, P. N.

    We demonstrate numerically the ability to displace a magnetic domain wall (DW) by remote spin current injection. We consider a long and narrow magnetic nanostripe with a single DW. The spin-polarized current is injected ...

  6. Domain-specific Web Service Discovery with Service Class Descriptions

    SciTech Connect (OSTI)

    Rocco, D; Caverlee, J; Liu, L; Critchlow, T J

    2005-02-14

    This paper presents DynaBot, a domain-specific web service discovery system. The core idea of the DynaBot service discovery system is to use domain-specific service class descriptions powered by an intelligent Deep Web crawler. In contrast to current registry-based service discovery systems--like the several available UDDI registries--DynaBot promotes focused crawling of the Deep Web of services and discovers candidate services that are relevant to the domain of interest. It uses intelligent filtering algorithms to match services found by focused crawling with the domain-specific service class descriptions. We demonstrate the capability of DynaBot through the BLAST service discovery scenario and describe our initial experience with DynaBot.

  7. Digital Frequency Domain Multiplexer for mm-Wavelength Telescopes

    E-Print Network [OSTI]

    Dobbs, Matt

    2008-01-01

    for Large Scale Bolometer Arrays”, Monterey Far-IR, Sub-mmand mm Detector Technology Workshop proceedings, 2002, pp.Domain Multiplexer for mm-Wavelength Telescopes Matt Dobbs,

  8. Dynein Motor Domain Shows Ring-Shaped Motor, Buttress

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Dynein Motor Domain Shows Ring-Shaped Motor, Buttress Print Movement is fundamental to life. It takes place even at the cellular level where cargo is continually being transported...

  9. Crystalline Protein Domains and Lipid Bilayer Vesicle Shape Transformations

    E-Print Network [OSTI]

    Gast, Alice Petry

    Cellular membranes can take on a variety of shapes to assist biological processes including endocytosis. Membrane-associated protein domains provide a possible mechanism for determining membrane curvature. We study the ...

  10. A multi-domain process design and improvement framework

    E-Print Network [OSTI]

    Nicol, Robert A. (Robert Arthur), 1969-

    2010-01-01

    Processes in manufacturing, services, and healthcare are complex socio-technical systems composed of intricately sequenced activities supported by elements drawn from multiple domains. While many of these processes offer ...

  11. An Axiomatisation of Computationally Adequate Domain Theoretic Models of FPC 

    E-Print Network [OSTI]

    Fiore, Marcelo P; Plotkin, Gordon

    1994-01-01

    Categorical models of the metalanguage FPC (a type theory with sums, products, exponentials and recursive types) are defined. Then, domain-theoretic models of FPC are axiomatised and a wide subclass of them —the ...

  12. Signal statistics of phase dependent optical time domain reflectometry 

    E-Print Network [OSTI]

    Wojcik, Aleksander Karol

    2007-04-25

    The statistics of the phase dependent optical time-domain reflectometer have been analyzed. The optical fiber is modeled by the use of a discrete set of reflectors positioned randomly along the fiber. The statistics of the ...

  13. Induction, Domains, Calculi: Strachey's Contributions to ProgrammingLanguage

    E-Print Network [OSTI]

    Schmidt, David A.

    Induction, Domains, Calculi: Strachey's Contributions to Programming­Language Engineering David A pioneered the analysis of programming languages in terms of semantic features. Three of Strachey programming languages designed by programming­language experts? Sometimes they are, but the requirements

  14. Characterization of Nanoscale Objects and Domains with Massive Cluster SIMS 

    E-Print Network [OSTI]

    Liang, Chao-Kai

    2014-07-31

    . These observations point out the necessity of accurate data interpretation when dealing with nano-scaled objects. The capability of nano-domain analysis was demonstrated with fuel cell cathode materials consisting of pyrolized catalyst/carbon black mixtures...

  15. Log-domain circuit models of chemical reactions

    E-Print Network [OSTI]

    Mandal, Soumyajit

    We exploit the detailed similarities between electronics and chemistry to develop efficient, scalable bipolar or subthreshold log-domain circuits that are dynamically equivalent to networks of chemical reactions. Our ...

  16. A time and frequency domain analysis of contrarian trading strategies/

    E-Print Network [OSTI]

    Chaudhuri, Shomesh E

    2014-01-01

    This thesis applies time and frequency domain analyses to a high-frequency market making strategy to study the profitability of liquidity provision over multiple time horizons from 1964 to 2013. Using daily returns and ...

  17. Dual Domain Echo Cancellers for Multirate Discrete Multitone Systems

    E-Print Network [OSTI]

    Champagne, Benoît

    Dual Domain Echo Cancellers for Multirate Discrete Multitone Systems Neda Ehtiati and Beno Email:{neda.ehtiati, benoit.champagne}@mcgill.ca Abstract--Digital echo cancellers are used in duplex

  18. Axiomatic Domain Theory in Categories of Partial Maps 

    E-Print Network [OSTI]

    Fiore, Marcelo P

    This thesis is an investigation into axiomatic categorical domain theory as needed for the denotational semantics of deterministic programming languages. To provide a direct semantic treatment of non-terminating ...

  19. Collapse of Axionic Domain Wall and Axion Emission

    E-Print Network [OSTI]

    Michiyasu Nagasawa; Masahiro Kawasaki

    1994-05-09

    We examine the collapse of an axion domain wall bounded by an axionic string. It is found that the collapse proceeds quickly and axion domain walls disappear. However axions are emitted in the collapse and its energy density increases during radiation dominated era and contributes significantly to the present mass density of the universe. In particular the axion emitted from the wall can account for the dark matter in the universe for $F_a\\gsim 10^{10}\\GeV$.

  20. Antiferromagnetism and domain effects in UPdSn

    SciTech Connect (OSTI)

    Nakotte, H. [Manual Lujan Jr. Neutron Scattering Center, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)] [Manual Lujan Jr. Neutron Scattering Center, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); [Department of Physics, New Mexico State University, Las Cruces, New Mexico 88003 (United States); Robinson, R.A.; Purwanto, A. [Manuel Lujan Jr. Neutron Scattering Center, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)] [Manuel Lujan Jr. Neutron Scattering Center, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Tun, Z. [Chalk River Laboratories, Atomic Energy of Canada Limited, Chalk River, Ontario, K0J 1J0 (CANADA)] [Chalk River Laboratories, Atomic Energy of Canada Limited, Chalk River, Ontario, K0J 1J0 (CANADA); Prokes, K.; Brueck, E.; de Boer, F.R. [Van der Waals-Zeeman Institute, University of Amsterdam, 1018 XE Amsterdam (The Netherlands)] [Van der Waals-Zeeman Institute, University of Amsterdam, 1018 XE Amsterdam (The Netherlands)

    1998-10-01

    Neutron-diffraction experiments have been performed on a single crystal of the hexagonal noncollinear antiferromagnetic compound UPdSn as a function of temperature and magnetic field. The use of a special horizontal-field magnet (with very wide horizontal access to the neutron beams) has allowed the study of the principal magnetic Bragg reflections in all three antiferromagnetic domain pairs throughout the magnetic phase diagram for B{lt}3thinspT and T{gt}6thinspK. The data confirm a picture in which one domain pair (1) grows at the expense of the other two domain pairs (2 and 3), for fields along the [100] axis for domain 1. On the other hand, if the field is applied along the perpendicular axis, [010] for domain 1, the other two domains are preferred. These results are consistent with the picture given in a previous vertical-field study of only one magnetic reflection from one domain, in which the 3-T field-induced transition is viewed as a spin-flop transition. There is, however, a small amount of irreversible moment rotation (from {theta}=43{degree} to 48{degree}, where {theta} is the moment canting angle within the hexagonal basal plane), on passing through the spin-flop transition. This seems to be connected with whether the sample is single or multidomain. In addition, the field independence of the N{acute e}el temperature (T{sub N}=37thinspK) has been measured up to 3 T, and data on the domain kinetics are presented. {copyright} {ital 1998} {ital The American Physical Society}

  1. Critical Ising interfaces in multiply-connected domains

    E-Print Network [OSTI]

    Konstantin Izyurov

    2015-03-13

    We prove a general result on convergence of interfaces in the critical planar Ising model to conformally invariant curves absolutely continuous with respect to SLE(3). Our setup includes multiple interfaces on arbitrary finitely connected domains, and we also treat the radial SLE case. In the case of simply and doubly connected domains, the limiting processes are described explicitly in terms of rational and elliptic functions, respectively.

  2. Acid Gas Capture Using CO2-Binding Organic Liquids

    SciTech Connect (OSTI)

    Heldebrant, David J.; Koech, Phillip K.; Rainbolt, James E.; Zheng, Feng

    2010-11-10

    Current chemical CO2 scrubbing technology is primarily aqueous alkanolamine based. These systems rapidly bind CO2 (forming water-soluble carbamate and bicarbonate salts) however, the process has serious disadvantages. The concentration of monoethanolamine rarely exceeds 30 wt % due to the corrosive nature of the solution, and this reduces the maximum CO2 volumetric (?108 g/L) and gravimetric capacity (?7 wt%) of the CO2 scrubber. The ?30 wt % loading of ethanolamine also means that a large excess of water must be pumped and heated during CO2 capture and release, and this greatly increases the energy requirements especially considering the high specific heat of water (4 j/g-1K-1). Our approach is to switch to organic systems that chemically bind CO2 as liquid alkylcarbonate salts. Our CO2-binding organic liquids have higher CO2 solubility, lower specific heats, potential for less corrosion and lower binding energies for CO2 than aqueous systems. CO2BOLs also reversibly bind and release mixed sulfur oxides. Furthermore the CO2BOL system can be direct solvent replacements for any solvent based CO2 capture systems because they are commercially available reagents and because they are fluids they would not require extensive process re-engineering.

  3. Dynamic Structural Rearrangements Between DNA Binding Modes of E. coli SSB Protein

    E-Print Network [OSTI]

    Lohman, Timothy M.

    an oligonucleotide/oligosaccharide bind- ing (OB) fold,5,7­9 hence the tetramer has four po- tential ssDNA binding sites. The SSB tetramer can bind long ssDNA in a variety of binding modes depending on solutionCl) and high protein to DNA ratios, an SSB tetramer binds to ssDNA with high inter-tetramer cooperativity using

  4. Impact on the steam electric power industry of deleting Section 316(a) of the Clean Water Act: Energy and environmental impacts

    SciTech Connect (OSTI)

    Veil, J.A.; VanKuiken, J.C.; Folga, S.; Gillette, J.L.

    1993-01-01

    Many power plants discharge large volumes of cooling water. In some cases, the temperature of the discharge exceeds state thermal requirements. Section 316(a) of the Clean Water Act (CWA) allows a thermal discharger to demonstrate that less stringent thermal effluent limitations would still protect aquatic life. About 32% of the total steam electric generating capacity in the United States operates under Section 316(a) variances. In 1991, the US Senate proposed legislation that would delete Section 316(a) from the CWA. This study, presented in two companion reports, examines how this legislation would affect the steam electric power industry. This report quantitatively and qualitatively evaluates the energy and environmental impacts of deleting the variance. No evidence exists that Section 316(a) variances have caused any widespread environmental problems. Conversion from once-through cooling to cooling towers would result in a loss of plant output of 14.7-23.7 billion kilowatt-hours. The cost to make up the lost energy is estimated at $12.8-$23.7 billion (in 1992 dollars). Conversion to cooling towers would increase emission of pollutants to the atmosphere and water loss through evaporation. The second report describes alternatives available to plants that currently operate under the variance and estimates the national cost of implementing such alternatives. Little justification has been found for removing the 316(a) variance from the CWA.

  5. Crystal structure of dimeric cardiac L-type calcium channel regulatory domains bridged by Ca[superscript 2+]·calmodulins

    SciTech Connect (OSTI)

    Fallon, Jennifer L.; Baker, Mariah R.; Xiong, Liangwen; Loy, Ryan E.; Yang, Guojun; Dirksen, Robert T.; Hamilton, Susan L.; Quiocho, Florante A.; (Baylor); (Rochester-Med)

    2009-11-10

    Voltage-dependent calcium channels (Ca(V)) open in response to changes in membrane potential, but their activity is modulated by Ca(2+) binding to calmodulin (CaM). Structural studies of this family of channels have focused on CaM bound to the IQ motif; however, the minimal differences between structures cannot adequately describe CaM's role in the regulation of these channels. We report a unique crystal structure of a 77-residue fragment of the Ca(V)1.2 alpha(1) subunit carboxyl terminus, which includes a tandem of the pre-IQ and IQ domains, in complex with Ca(2+).CaM in 2 distinct binding modes. The structure of the Ca(V)1.2 fragment is an unusual dimer of 2 coiled-coiled pre-IQ regions bridged by 2 Ca(2+).CaMs interacting with the pre-IQ regions and a canonical Ca(V)1-IQ-Ca(2+).CaM complex. Native Ca(V)1.2 channels are shown to be a mixture of monomers/dimers and a point mutation in the pre-IQ region predicted to abolish the coiled-coil structure significantly reduces Ca(2+)-dependent inactivation of heterologously expressed Ca(V)1.2 channels.

  6. Orientation-dependent binding energy of graphene on palladium

    SciTech Connect (OSTI)

    Kappes, Branden B.; Ebnonnasir, Abbas; Ciobanu, Cristian V. [Department of Mechanical Engineering and Materials Science Program, Colorado School of Mines, Golden, Colorado 80401 (United States)] [Department of Mechanical Engineering and Materials Science Program, Colorado School of Mines, Golden, Colorado 80401 (United States); Kodambaka, Suneel [Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, California 90095 (United States)] [Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, California 90095 (United States)

    2013-02-04

    Using density functional theory calculations, we show that the binding strength of a graphene monolayer on Pd(111) can vary between physisorption and chemisorption depending on its orientation. By studying the interfacial charge transfer, we have identified a specific four-atom carbon cluster that is responsible for the local bonding of graphene to Pd(111). The areal density of such clusters varies with the in-plane orientation of graphene, causing the binding energy to change accordingly. Similar investigations can also apply to other metal substrates and suggests that physical, chemical, and mechanical properties of graphene may be controlled by changing its orientation.

  7. Pathogenicity of the BRCA1 Missense Variant M1775K is Determined by the Disruption of the BRCT Phosphopeptide-Binding Pocket: a Multi-Modal Approach

    SciTech Connect (OSTI)

    Tischkowitz,M.; Hamel, N.; Carvalho, M.; Birrane, G.; Soni, A.; van Beers, E.; Joosse, S.; Wong, N.; Novak, D.; et al

    2008-01-01

    A number of germ-line mutations in the BRCA1 gene confer susceptibility to breast and ovarian cancer. However, it remains difficult to determine whether many single amino-acid (missense) changes in the BRCA1 protein that are frequently detected in the clinical setting are pathologic or not. Here, we used a combination of functional, crystallographic, biophysical, molecular and evolutionary techniques, and classical genetic segregation analysis to demonstrate that the BRCA1 missense variant M1775K is pathogenic. Functional assays in yeast and mammalian cells showed that the BRCA1 BRCT domains carrying the amino-acid change M1775K displayed markedly reduced transcriptional activity, indicating that this variant represents a deleterious mutation. Importantly, the M1775K mutation disrupted the phosphopeptide-binding pocket of the BRCA1 BRCT domains, thereby inhibiting the BRCA1 interaction with the proteins BRIP1 and CtIP, which are involved in DNA damage-induced checkpoint control. These results indicate that the integrity of the BRCT phosphopeptide-binding pocket is critical for the tumor suppression function of BRCA1. Moreover, this study demonstrates that multiple lines of evidence obtained from a combination of functional, structural, molecular and evolutionary techniques, and classical genetic segregation analysis are required to confirm the pathogenicity of rare variants of disease-susceptibility genes and obtain important insights into the underlying pathogenetic mechanisms.

  8. Sampling Approaches for Multi-Domain Internet Performance Measurement Infrastructures

    SciTech Connect (OSTI)

    Calyam, Prasad

    2014-09-15

    The next-generation of high-performance networks being developed in DOE communities are critical for supporting current and emerging data-intensive science applications. The goal of this project is to investigate multi-domain network status sampling techniques and tools to measure/analyze performance, and thereby provide “network awareness” to end-users and network operators in DOE communities. We leverage the infrastructure and datasets available through perfSONAR, which is a multi-domain measurement framework that has been widely deployed in high-performance computing and networking communities; the DOE community is a core developer and the largest adopter of perfSONAR. Our investigations include development of semantic scheduling algorithms, measurement federation policies, and tools to sample multi-domain and multi-layer network status within perfSONAR deployments. We validate our algorithms and policies with end-to-end measurement analysis tools for various monitoring objectives such as network weather forecasting, anomaly detection, and fault-diagnosis. In addition, we develop a multi-domain architecture for an enterprise-specific perfSONAR deployment that can implement monitoring-objective based sampling and that adheres to any domain-specific measurement policies.

  9. Frequency-domain multiscale quantum mechanics/electromagnetics simulation method

    SciTech Connect (OSTI)

    Meng, Lingyi; Yin, Zhenyu; Yam, ChiYung E-mail: ghc@everest.hku.hk; Koo, SiuKong; Chen, GuanHua E-mail: ghc@everest.hku.hk; Chen, Quan; Wong, Ngai

    2013-12-28

    A frequency-domain quantum mechanics and electromagnetics (QM/EM) method is developed. Compared with the time-domain QM/EM method [Meng et al., J. Chem. Theory Comput. 8, 1190–1199 (2012)], the newly developed frequency-domain QM/EM method could effectively capture the dynamic properties of electronic devices over a broader range of operating frequencies. The system is divided into QM and EM regions and solved in a self-consistent manner via updating the boundary conditions at the QM and EM interface. The calculated potential distributions and current densities at the interface are taken as the boundary conditions for the QM and EM calculations, respectively, which facilitate the information exchange between the QM and EM calculations and ensure that the potential, charge, and current distributions are continuous across the QM/EM interface. Via Fourier transformation, the dynamic admittance calculated from the time-domain and frequency-domain QM/EM methods is compared for a carbon nanotube based molecular device.

  10. Spherical Domain Wall Collapse in a Dust Universe

    E-Print Network [OSTI]

    Norihiro Tanahashi; Chul-Moon Yoo

    2015-05-13

    To clarify observational consequence of bubble nucleations in inflationary era, we analyse dynamics of a spherical domain wall in an expanding universe. We consider a spherical shell of the domain wall with tension $\\sigma$ collapsing in a spherically-symmetric dust universe, which is initially separated into the open Friedmann-Lema\\^itre-Robertson-Walker universe inside the shell and the Einstein-de Sitter universe outside. The domain wall shell collapses due to the tension, and sweeps the dust fluid. The universe after the collapse becomes inhomogeneous and is described by the Lema\\^itre-Tolman-Bondi model. We construct solutions describing this inhomogeneous universe by solving dynamical equations obtained from Israel's junction conditions applied to this system. We find that a black hole forms after the domain wall collapse for any initial condition, and that the black hole mass at the moment of its formation is universally given by $M_{\\rm BH}\\simeq 17 \\sigma/H_{\\rm hc}$, where $H_{\\rm hc}$ is the Hubble parameter at the time when the shell radius becomes equal to the Hubble radius. We also find that the dust fluid is distributed as $\\rho\\propto R^{3/2}$ near the central region after the collapse, where $R$ is the area radius. These features would provide observable signatures of a spherical domain wall generated in the early universe.

  11. Cross-Domain Sentiment Classification Using a Two-Stage Kang Liu, Jun Zhao

    E-Print Network [OSTI]

    Zong, Chengqing

    Cross-Domain Sentiment Classification Using a Two-Stage Method Kang Liu, Jun Zhao Institute knowledge between different domains. Through these common topics, the features in the source domain different domains. In the second step, we use the classifier trained on the labeled examples in the source

  12. A Learning Approach for Word Sense Disambiguation in the Biomedical Domain

    E-Print Network [OSTI]

    Al-Mubaid, Hisham

    A Learning Approach for Word Sense Disambiguation in the Biomedical Domain Hisham Al investigated extensively within the natural language processing domain. In the biomedical domain, word sense in the biomedical domain will help lessen this limitation. Our approach has been evaluated with the benchmark

  13. Assessment of current cybersecurity practices in the public domain : cyber indications and warnings domain.

    SciTech Connect (OSTI)

    Hamlet, Jason R.; Keliiaa, Curtis M.

    2010-09-01

    This report assesses current public domain cyber security practices with respect to cyber indications and warnings. It describes cybersecurity industry and government activities, including cybersecurity tools, methods, practices, and international and government-wide initiatives known to be impacting current practice. Of particular note are the U.S. Government's Trusted Internet Connection (TIC) and 'Einstein' programs, which are serving to consolidate the Government's internet access points and to provide some capability to monitor and mitigate cyber attacks. Next, this report catalogs activities undertaken by various industry and government entities. In addition, it assesses the benchmarks of HPC capability and other HPC attributes that may lend themselves to assist in the solution of this problem. This report draws few conclusions, as it is intended to assess current practice in preparation for future work, however, no explicit references to HPC usage for the purpose of analyzing cyber infrastructure in near-real-time were found in the current practice. This report and a related SAND2010-4766 National Cyber Defense High Performance Computing and Analysis: Concepts, Planning and Roadmap report are intended to provoke discussion throughout a broad audience about developing a cohesive HPC centric solution to wide-area cybersecurity problems.

  14. Domain wall and isocurvature perturbation problems in axion models

    SciTech Connect (OSTI)

    Kawasaki, Masahiro; Yoshino, Kazuyoshi; Yanagida, Tsutomu T. E-mail: tsutomu.tyanagida@ipmu.jp

    2013-11-01

    Axion models have two serious cosmological problems, domain wall and isocurvature perturbation problems. In order to solve these problems we investigate the Linde's model in which the field value of the Peccei-Quinn (PQ) scalar is large during inflation. In this model the fluctuations of the PQ field grow after inflation through the parametric resonance and stable axionic strings may be produced, which results in the domain wall problem. We study formation of axionic strings using lattice simulations. It is found that in chaotic inflation the axion model is free from both the domain wall and the isocurvature perturbation problems if the initial misalignment angle ?{sub a} is smaller than O(10{sup ?2}). Furthermore, axions can also account for the dark matter for the breaking scale v ? 10{sup 12?16} GeV and the Hubble parameter during inflation H{sub inf}?<10{sup 11?12} GeV in general inflation models.

  15. Study of interdomain boundary in diamagnetic domain structure in beryllium

    E-Print Network [OSTI]

    Philip Lykov

    2002-11-21

    At low temperatures, in strong magnetic fields, the formation of a non-uniform magnetisation is possible in a single-crystal metal sample whose demagnetising factor along the field is close to unity. Namely, so-called Condon diamagnetic domain structure arises and disappears periodically with magnetic field. In this paper, the diamagnetic domain structure in beryllium single crystalis analysed. Directly, existence of diamagnetic domains in that sample was observed earlier by the muon spin precession (mSR) resonance peak splitting. A method is described that allows to calculate quantitative characteristics of the interdomain boundary using the muon histograms. The technique is based on the Marquardt minimisation procedure that has been modified in order to reduce the influence of noise on iterations convergence. Boundary volume fraction was calculated.

  16. Molecular Cell High-Affinity Binding of Chp1 Chromodomain

    E-Print Network [OSTI]

    Halazonetis, Thanos

    Molecular Cell Article High-Affinity Binding of Chp1 Chromodomain to K9 Methylated Histone H3, Chp1, and siRNAs derived from centro- meric repeats. Recruitment of RITS to centromeres has been establishment. Our crystal structure of Chp1's chromodomain in complex with a trimethylated lysine 9 H3 peptide

  17. Telomeres and telomere binding proteins in Arabidopsis thaliana 

    E-Print Network [OSTI]

    Shakirov, Yevgeniy Vitalievich

    2004-09-30

    . Additionally, two Arabidopsis genes, AtPot1 and AtPot2, were identified and characterized. The genes encode two single-strand telomeric DNA binding proteins. AtPot1 and AtPot2 proteins can homo- and heterodimerize in vitro. Pot1 protein predominantly localizes...

  18. CAR2 Displays Unique Ligand Binding and RXR Heterodimerization Characteristics

    E-Print Network [OSTI]

    Omiecinski, Curtis

    CAR2 Displays Unique Ligand Binding and RXR Heterodimerization Characteristics Scott S. Auerbach ABSTRACT: The constitutive androstane receptor (CAR; NR1I3) regulates the expression of genes involved in xenobiotic metabolism. Alternative splicing of the human CAR gene yields an array of mRNAs that encode

  19. Binding of Harvested Bacterial Exopolymers to the Surface of

    E-Print Network [OSTI]

    of the EPS showed that binding strength to calcite depended on the chemical nature of the polymer. Introduction Dissolution of calcium carbonate (calcite) affects global carbon cycling (1), the chemistry of calcium carbonate in the form of limestone or marble. Retardation of deterioration is important

  20. A probabilistic approach to microRNA-target binding

    SciTech Connect (OSTI)

    Ogul, Hasan; Umu, Sinan U.; Bioinformatics Program, Informatics Institute, Middle East Technical University, Cankaya TR-06800, Ankara ; Tuncel, Y. Yener; Akkaya, Mahinur S.

    2011-09-16

    Highlights: {yields} A new probabilistic model is introduced for microRNA-target binding. {yields} The new model significantly outperforms RNAHybrid and miRTif. {yields} The experiments can unveil the effects of the type and directions of distinct base pairings. -- Abstract: Elucidation of microRNA activity is a crucial step in understanding gene regulation. One key problem in this effort is how to model the pairwise interactions of microRNAs with their targets. As this interaction is strongly mediated by their sequences, it is desired to set-up a probabilistic model to explain the binding preferences between a microRNA sequence and the sequence of a putative target. To this end, we introduce a new model of microRNA-target binding, which transforms an aligned duplex to a new sequence and defines the likelihood of this sequence using a Variable Length Markov Chain. It offers a complementary representation of microRNA-mRNA pairs for microRNA target prediction tools or other probabilistic frameworks of integrative gene regulation analysis. The performance of present model is evaluated by its ability to predict microRNA-target mRNA interaction given a mature microRNA sequence and a putative mRNA binding site. In regard to classification accuracy, it outperforms two recent methods based on thermodynamic stability and sequence complementarity. The experiments can also unveil the effects of base pairing types and non-seed region in duplex formation.

  1. Compilation as Metacomputation: Binding Time Separation in Modular Compilers

    E-Print Network [OSTI]

    Kamin, Sam

    Compilation as Metacomputation: Binding Time Separation in Modular Compilers (Extended Abstract­ ings. Metacomputation­style specification lends itself to semantics­directed compilation, which we demonstrate by creating a modular compiler for a higher­order, imperative, Algol­like language. Keywords

  2. Workshop on gate valve pressure locking and thermal binding

    SciTech Connect (OSTI)

    Brown, E.J.

    1995-07-01

    The purpose of the Workshop on Gate Valve Pressure Locking and Thermal Binding was to discuss pressure locking and thermal binding issues that could lead to inoperable gate valves in both boiling water and pressurized water reactors. The goal was to foster exchange of information to develop the technical bases to understand the phenomena, identify the components that are susceptible, discuss actual events, discuss the safety significance, and illustrate known corrective actions that can prevent or limit the occurrence of pressure locking or thermal binding. The presentations were structured to cover U.S. Nuclear Regulatory Commission staff evaluation of operating experience and planned regulatory activity; industry discussions of specific events, including foreign experience, and efforts to determine causes and alleviate the affects; and valve vendor experience and recommended corrective action. The discussions indicated that identifying valves susceptible to pressure locking and thermal binding was a complex process involving knowledge of components, systems, and plant operations. The corrective action options are varied and straightforward.

  3. Host Cell Responses Induced by Hepatitis C Virus Binding

    E-Print Network [OSTI]

    Timmer, Jens

    Host Cell Responses Induced by Hepatitis C Virus Binding Xinhua Fang,1 Mirjam B. Zeisel,1 Jochen. Blum,1 and Thomas F. Baumert1,5 Initiation of hepatitis C virus (HCV) infection is mediated by docking nitiation of hepatitis C virus (HCV) infection is me- diated by docking of the viral envelope to the hepa

  4. Inhibition Of Call-Cell Binding By Kipid Assemblies

    DOE Patents [OSTI]

    Nagy, Jon O. (Rodeo, CA), Bargatze, Robert F. (Bozeman, MT)

    2003-12-16

    This invention relates generally to the field of therapeutic compounds designed to interfere between the binding of ligands and their receptors on cell surface. More specifically, it provides products and methods for inhibiting cell migration and activation using lipid assemblies with surface recognition elements that are specific for the receptors involved in cell migration and activation.

  5. Inhibition of cell-cell binding by lipid assemblies

    DOE Patents [OSTI]

    Nagy, Jon O. (Rodeo, CA); Bargatze, Robert F. (Bozeman, MT)

    2001-05-22

    This invention relates generally to the field of therapeutic compounds designed to interfere between the binding of ligands and their receptors on cell surface. More specifically, it provides products and methods for inhibiting cell migration and activation using lipid assemblies with surface recognition elements that are specific for the receptors involved in cell migration and activation.

  6. Automatic Generation of Tcl Bindings for C and C++ Libraries

    E-Print Network [OSTI]

    Heidrich, Wolfgang

    functions. This facility has been used to create a variety of language bindings for C libraries, ranging++ library functions to Tcl, is that they do not normally receive their arguments using this argc public member function, but since C(++) data can not be addressed directly from Tcl, string handles need

  7. The peanut lectin-binding glycoproteins of human epidermal keratinocytes

    SciTech Connect (OSTI)

    Morrison, A.I. (Max-Planck-Institute fuer Systemphysiologie, Dortmund (West Germany)); Keeble, S.; Watt, F.M. (Imperial Cancer Research Fund, London (England))

    1988-08-01

    The peanut lectin (PNA) is known to bind more strongly to keratinocytes that are undergoing terminal differentiation than to proliferating keratinocytes. In order to investigate the significance of this change in cell-surface carbohydrate authors have identified the PNA-binding glycoproteins of cultured human keratinocytes and antibodies against them. Two heavily glycosylated bands of 110 and 250 kDa were resolved by PAGE of ({sup 14}C)galactose- or ({sup 14}C)mannose- and ({sup 14}C)glucosamine-labeled cell extracts eluted with galactose from PNA affinity columns. The higher molecular weight band was also detected on PNA blots of unlabeled cell extracts transferred to nitrocellulose. Both bands were sensitive to pronase digestion, but only the 250-kDa band was digested with trypsin. A rabbit antiserum that we prepared (anti-PNA-gp) immunoprecipitated both bands from cell extracts. In contrast to PNA, anti-PNA-gp bound equally to proliferating and terminally differentiating cells, indicating that some epitope(s) of the PNA-binding glycoproteins is present on the cell surface prior to terminal differentiation. When keratinocytes grown as a monolayer in low-calcium medium were switched to medium containing 2 mM calcium ions in order to induce desmosome formation and stratification, there was a dramatic redistribution of the PNA-binding glycoproteins, which became concentrated at the boundaries between cells. This may suggest a role for the glycoproteins in cell-cell interactions during stratification.

  8. The crystal structure of the mycobacterium tuberculosis Rv3019c-Rv3020c ESX complex reveals a domain-swapped heterotetramer

    SciTech Connect (OSTI)

    Arbing, Mark A.; Kaufmann, Markus; Phan, Tung; Chan, Sum; Cascio, Duilio; Eisenberg, David (UCLA)

    2010-11-15

    Mycobacterium tuberculosis encodes five gene clusters (ESX-1 to ESX-5) for Type VII protein secretion systems that are implicated in mycobacterial pathogenicity. Substrates for the secretion apparatus are encoded within the gene clusters and in additional loci that lack the components of the secretion apparatus. The best characterized substrates are the ESX complexes, 1:1 heterodimers of ESAT-6 and CFP-10, the prototypical member that has been shown to be essential for Mycobacterium tuberculosis pathogenesis. We have determined the structure of EsxRS, a homolog of EsxGH of the ESX-3 gene cluster, at 1.91 {angstrom} resolution. The EsxRS structure is composed of two four-helix bundles resulting from the 3D domain swapping of the C-terminal domain of EsxS, the CFP-10 homolog. The four-helix bundles at the extremities of the complex have a similar architecture to the structure of ESAT-6 {center_dot} CFP-10 (EsxAB) of ESX-1, but in EsxRS a hinge loop linking the {alpha}-helical domains of EsxS undergoes a loop-to-helix transition that creates the domain swapped EsxRS tetramer. Based on the atomic structure of EsxRS and existing biochemical data on ESX complexes, we propose that higher order ESX oligomers may increase avidity of ESX binding to host receptor molecules or, alternatively, the conformational change that creates the domain swapped structure may be the basis of ESX complex dissociation that would free ESAT-6 to exert a cytotoxic effect.

  9. A common region of deletion on chromosome 17q in both sporadic and familial epithelial ovarian tumors distal to BRCA1

    SciTech Connect (OSTI)

    Godwin, A.K.; Vanderveer, L.; Schultz, D.C.; Altomare, D.A.; Buetow, K.H.; Daly, M.; Getts, L.A.; Masny, A.; Rosenblum, N.

    1994-10-01

    Linkage analysis in familial breast and ovarian cancer and studies of allelic deletion in sporadic ovarian tumors have identified a region on chromosome 17q containing a candidate tumor-suppressor gene (referred to as BRCA1) of likely importance in ovarian carcinogenesis. We have examined normal and tumor DNA samples from 32 patients with sporadic and 8 patients with familial forms of the disease, for loss of heterozygosity (LOH) at 21 loci on chromosome 17 (7 on 17p and 14 on 17q). LOH on 17p was 55% (22/40) for informative 17p13.1 and 17p13.3 markers. When six polymorphic markers flanking the familial breast/ovarian cancer susceptibility locus on 17q12-q21 were used, LOH was 58% (23/40), with one tumor showing telomeric retention. Evaluation of a set of markers positioned telomeric to BRCA1 resulted in the highest degree of LOH, 73% (29/40), indicating that a candidate locus involved in ovarian cancer may reside distal to BRCA1. Five of the tumors demonstrating allelic loss for 17q markers were from individuals with a strong family history of breast and ovarian cancer. More important, two of these tumors (unique patient number [UPN] 57 and UPN 79) retained heterozygosity for all informative markers spanning the BRCA1 locus but showed LOH at loci distal to but not including the anonymous markers CMM86 (D17S74) and 42D6 (D17S588), respectively. Deletion mapping of seven cases (two familial and five sporadic) showing limited LOH on 17q revealed a common region of deletion, distal to GH and proximal to D17S4, that spans {approximately} 25 cM. These results suggest that a potential tumor-suppressor gene involved in both sporadic and familial ovarian cancer may reside on the distal portion of chromosome 17q and is distinct from the BRCA1 gene. 58 refs., 3 figs., 4 tabs.

  10. The binding affinity of a soluble TCR-Fc fusion protein is significantly improved by crosslinkage with an anti-C{beta} antibody

    SciTech Connect (OSTI)

    Ozawa, Tatsuhiko; Horii, Masae; Kobayashi, Eiji [Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194 (Japan)] [Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194 (Japan); Jin, Aishun [Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194 (Japan) [Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194 (Japan); Department of Immunology, College of Basic Medical Sciences, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin 150081 (China); Kishi, Hiroyuki, E-mail: immkishi@med.u-toyama.ac.jp [Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194 (Japan)] [Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194 (Japan); Muraguchi, Atsushi [Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194 (Japan)] [Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194 (Japan)

    2012-06-01

    Highlights: Black-Right-Pointing-Pointer A novel soluble TCR composed of TCR V and C regions with Ig Fc region is generated. Black-Right-Pointing-Pointer TCR-Fc protein immobilized by an anti-C{beta} antibody bound to a p/MHC tetramer. Black-Right-Pointing-Pointer Binding affinity of TCR-Fc was markedly increased by binding with anti-C{beta} antibody. -- Abstract: The identification and cloning of tumor antigen-specific T cell receptors (TCRs) and the production of the soluble form of the TCR (sTCR) contributed to the development of diagnostic and therapeutic tools for cancer. Recently, several groups have reported the development of technologies for the production of sTCRs. The native sTCR has a very low binding affinity for the antigenic peptide/MHC (p/MHC) complex. In this study, we established a technology to produce high affinity, functional sTCRs. We generated a novel sTCR-Fc fusion protein composed of the TCR V and C regions of the TCR linked to the immunoglobulin (Ig) Fc region. A Western blot analysis revealed that the molecular weight of the fusion protein was approximately 60 kDa under reducing conditions and approximately 100-200 kDa under non-reducing conditions. ELISAs using various antibodies showed that the structure of each domain of the TCR-Fc protein was intact. The TCR-Fc protein immobilized by an anti-C{beta} antibody effectively bound to a p/MHC tetramer. An SPR analysis showed that the TCR-Fc protein had a low binding affinity (KD; 1.1 Multiplication-Sign 10{sup -5} M) to the p/MHC monomer. Interestingly, when the TCR-Fc protein was pre-incubated with an anti-C{beta} antibody, its binding affinity for p/MHC increased by 5-fold (2.2 Multiplication-Sign 10{sup -6} M). We demonstrated a novel method for constructing a functional soluble TCR using the Ig Fc region and showed that the binding affinity of the functional sTCR-Fc was markedly increased by an anti-C{beta} antibody, which is probably due to the stabilization of the V{alpha}/V{beta} region of the TCR. These findings provide new insights into the binding of sTCRs to p/MHCs and will hopefully be instrumental in establishing functional sTCR as a diagnostic and therapeutic tool for cancer.

  11. REPRESENTING GEO-SCIENTIFIC DOMAIN CONCEPTS Boyan Brodaric

    E-Print Network [OSTI]

    Bennett, Brandon

    1 REPRESENTING GEO-SCIENTIFIC DOMAIN CONCEPTS Boyan Brodaric Penn State Geography and Geological Survey of Canada brodaric@NRCan.gc.ca 1. Introduction The geo-sciences, including geology, ecology, soil accumulate and change, and (3) are characterized by degrees of uncertainty and granularity. This suggests

  12. Harmonic maps on domains with piecewise Lipschitz continuous metrics

    E-Print Network [OSTI]

    Wang, Changyou

    Harmonic maps on domains with piecewise Lipschitz continuous metrics Haigang Li , Changyou Wang consider harmonic map from (, g) to a compact Rie- mannian manifold (N, h) Rk without boundary. We generalize the notion of stationary harmonic maps and prove their partial regularity. We also discuss

  13. Domain-Driven Data Mining: Challenges and Prospects

    E-Print Network [OSTI]

    Cao, Longbing

    in real- world smart decision making. To this end, domain-driven data mining (D3 M) has been proposed, which is supposed to enable smart business intelligence for smart decisions in production. If we by business people for seamless decision making. To bridge the gap and enhance real-world problem- solving

  14. A CHARACTERIZATION OF BOUNDED SYMMETRIC DOMAINS OF TYPE IV

    E-Print Network [OSTI]

    Geatti, Laura

    A CHARACTERIZATION OF BOUNDED SYMMETRIC DOMAINS OF TYPE IV L. GEATTI, A. IANNUZZI, AND J.-J. LOEB with the compact-open topology is a topological group. We say that X is characterized by its automorphism group to Aut(X) is biholomorphic to X. Most manifolds are not characterized by their automorphism group. For in

  15. Nonlinear magnetoinductive waves and domain walls in composite metamaterials

    E-Print Network [OSTI]

    Nonlinear magnetoinductive waves and domain walls in composite metamaterials Ilya V. Shadrivov a-handed composite metamaterials. We derive the coupled equations for describing the propagation of magnetoinductive waves, and show that in the nonlinear regime the magnetic response of a metamaterial may become bistable

  16. ADAPTIVE FINITE ELEMENT FREQUENCY DOMAIN METHOD FOR EDDY CURRENT PROBLEMS

    E-Print Network [OSTI]

    Zheng, Weiying

    ADAPTIVE FINITE ELEMENT FREQUENCY DOMAIN METHOD FOR EDDY CURRENT PROBLEMS WEIYING ZHENG-harmonic eddy current problems in the case of three-dimensional isotropic and linear materials. We adopt. Time-harmonic Maxwell's equations, eddy current, adaptive finite element method, multiply connected

  17. Databases on the Web: national web domain survey Denis Shestakov

    E-Print Network [OSTI]

    Hammerton, James

    , Aalto University Konemiehentie 2, Espoo, 02150 Finland denis.shestakov@aalto.fi ABSTRACT The deep Web of the deep Web by sampling one national web domain. We report some of our results ob- tained when surveying the Russian Web. The survey find- ings, namely the size estimates of the deep Web, could be useful for further

  18. SUMTIME: KA For Weather Domain Page 1 of 20

    E-Print Network [OSTI]

    Sripada, Yaji

    News Inc, Aberdeen, UK) and gas turbine diagnosis (in collaboration with Intelligent Applications on a third (yet to be chosen) domain. In the case of gas turbine diagnosis, as is the case with the doctors of Aberdeen Aberdeen, UK {ssripada,ereiter,jhunter,jyu}@csd.abdn.ac.uk Abstract SUMTIME (http://www.csd.abdn.ac.in

  19. Analytic design and solutions for resonance domain diffractive optical elements

    E-Print Network [OSTI]

    Friesem, Asher A.

    Analytic design and solutions for resonance domain diffractive optical elements Michael A. Golub. INTRODUCTION Diffractive optical elements (DOEs) are usually designed and characterized with scalar diffraction, 2006 (Doc. ID 72721); published February 14, 2007 A model for designing and analyzing complicated

  20. Hybrid Powertrain Design Using a Domain-Specific Modeling Environment

    E-Print Network [OSTI]

    Gray, Jeffrey G.

    of design tools that are used in the electronics industry. Widely accepted automotive powertrain design industry has demonstrated that similar tools in the automotive domain still lack the power, sophistication--State of the art design tools in automotive engineering still lack the power, sophistication, and automation

  1. TIME DOMAIN REFLECTOMETRY MEASUREMENT AND HIGHLY PLASTIC CLAYS

    E-Print Network [OSTI]

    Zornberg, Jorge G.

    1 TIME DOMAIN REFLECTOMETRY MEASUREMENT AND HIGHLY PLASTIC CLAYS By: J. A. Kuhn1 and J. G. Zornberg for use in highly plastic clay. The clay used for experimentation was taken locally from the Eagle Ford Ford Clay is determined. INTRODUCTION The progression of wetting and drying fronts in highly plastic

  2. Time domain analog circuit simulation J.G. Fijnvandraat

    E-Print Network [OSTI]

    Eindhoven, Technische Universiteit

    of circuits in the electronics industry. Keywords: transient analysis, modified nodal analysis, differential be applied such as DC or steady­state anal­ ysis, Transient Analysis, AC­analysis (linear frequency domain analysis, after linearization around a DC­solution), Noise Analysis, Harmonic Balance (non­linear frequency

  3. Time domain analog circuit simulation J.G. Fijnvandraat

    E-Print Network [OSTI]

    Eindhoven, Technische Universiteit

    of circuits in the electronics industry. Keywords: transient analysis, modified nodal analysis, differential be applied such as DC or steady-state anal- ysis, Transient Analysis, AC-analysis (linear frequency domain analysis, after linearization around a DC-solution), Noise Analysis, Harmonic Balance (non-linear frequency

  4. A Domain Wall Model for Hysteresis in Piezoelectric Materials

    E-Print Network [OSTI]

    A Domain Wall Model for Hysteresis in Piezoelectric Materials Ralph C. Smith Center for Research to attain the full potential of the materials as sensors and actuators in high performance applications design. i #12; 1 Introduction Piezoelectric materials provide the capability for designing actuators

  5. Optimal risk allocation for convex risk functionals in general domains

    E-Print Network [OSTI]

    Rüschendorf, Ludger

    Optimal risk allocation for convex risk functionals in general domains Swen Kiesel and Ludger R of cash invariant, strictly convex risk functionals on Ed the uniqueness of Pareto optimal allocations up¨uschendorf University of Freiburg Abstract In this paper we extend the classical optimal risk allocation problem

  6. Analyzing Parallelism and Domain Similarities in the MAREC Patent Corpus

    E-Print Network [OSTI]

    Riezler, Stefan

    Analyzing Parallelism and Domain Similarities in the MAREC Patent Corpus Katharina W}@cl.uni-heidelberg.de Abstract. Statistical machine translation of patents requires large a- mounts of sentence-parallel data. Translations of patent text often exist for parts of the patent document, namely title, abstract and claims

  7. RADON TRANSFORM ON SYMMETRIC MATRIX DOMAINS GENKAI ZHANG

    E-Print Network [OSTI]

    Zhang, Genkai

    RADON TRANSFORM ON SYMMETRIC MATRIX DOMAINS GENKAI ZHANG Abstract. Let K = R; C ; H be the #12;eld space. We consider the Radon transform Rf(y) for functions f 2 C 1 0 (X) de#12;ned by integration of f 0 Radon transform, namely MR t Rf = cf . This generalizes

  8. Time Domain Maxwell Equations Solved with Schwarz Waveform

    E-Print Network [OSTI]

    Gander, Martin J.

    with Dirichlet boundary conditions and was analyzed for the heat equation by Gander and Stuart [1998]. Giladi transmission conditions for the time domain Maxwell equations is given by -tEi,n + Ã? Hi,n - Ei,n = J, i is called the characteristic transmission condition, establishes how the subdomains communicate with each

  9. Merging Applicability Domains for in Silico Assessment of Chemical Mutagenicity

    E-Print Network [OSTI]

    , Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, 2405 structure-activity relationship (QSAR) models and defining applicability domains with two machine To date, thousands of chemicals have been evaluated using the Ames test, and it has become a standard

  10. Catalytic Domain of Phosphoinositide-specific Phospholipase C (PLC)

    E-Print Network [OSTI]

    Williams, Roger L.

    Catalytic Domain of Phosphoinositide-specific Phospholipase C (PLC) MUTATIONAL ANALYSIS OF RESIDUES WITHIN THE ACTIVE SITE AND HYDROPHOBIC RIDGE OF PLC 1* (Received for publication, November 20, 1997 Institute, University of Dundee, Dundee DD1 4HN, United Kingdom Structural studies of phospholipase C 1 (PLC

  11. Revised, final form, July 1994 Domain Decomposition, Parallel Computing and

    E-Print Network [OSTI]

    Bjørstad, Petter E.

    reservoir flow problem, we are given the reservoir conditions (pressure and saturation) and the well flow. The simulator has a domain­based data structure whereby the reservoir is represented by a possibly large number of smaller reservoirs each having a complete local data structure. This design is essential for effective use

  12. A New Grid Structure for Domain Extension Stanford University

    E-Print Network [OSTI]

    Fedkiw, Ron

    reflecting off of grid boundaries thus allowing for a large amount of detail and grid resolution nearA New Grid Structure for Domain Extension Bo Zhu Stanford University Wenlong Lu Stanford University Stanford University Industrial Light + Magic Figure 1: Our far-field grid structure provides an extended

  13. Assignment 3 Objective: Signal processing through simple time domain operations.

    E-Print Network [OSTI]

    Naik, Naren

    Assignment 3 Objective: Signal processing through simple time domain operations. Part 1 : Q1. Play millisecond and alpha = 0.2 . Compare your output with signal generated by an audio processing software. Audacity Software: It is a open source software to do basic signal processing operations over audio

  14. Cellular pattern formation in circular domains Antonio Palacios,a)

    E-Print Network [OSTI]

    Cellular pattern formation in circular domains Antonio Palacios,a) Gemunu H. Gunaratne 1997; accepted for publication 24 June 1997 An analysis of stationary and nonstationary cellular. Motivated by the observa- tion of novel stationary and nonstationary cellular states on a flame front, we

  15. Classification: Biological Sciences / Biophysics Domain Compliance and Elastic Power Transmission

    E-Print Network [OSTI]

    Junge, Wolfgang

    in Rotary FOF1-ATPase Hendrik Sielaff1 , Henning Rennekamp1 , André Wächter1,2 , Hao Xie1 , Florian Hilbers1 of rotary ATP synthase, ionmotive FO and chemically active F1, are mechanically coupled by a central rotor. The compliance of certain domains was restricted by engineered disulfide bridges between rotor and stator

  16. Domains and Expressions: An Interface Between Two Approaches

    E-Print Network [OSTI]

    Watt, Stephen M.

    Domains and Expressions: An Interface Between Two Approaches to Computer Algebra Cosmin E. Oancea- proach to structuring computer algebra software: using an efficient, compiled language, designed for writing large com- plex mathematical libraries, together with a top-level system based on user

  17. DDDM2007: Domain Driven Data Mining Longbing Cao

    E-Print Network [OSTI]

    Cao, Longbing

    DDDM2007: Domain Driven Data Mining Longbing Cao University of Technology Sydney, Australia lbcao of Technology Sydney, Australia {chengqi,yczhao}@it.uts.edu.au Graham Williams Australian Taxation Office, Australia Graham.Williams@togaware.com ABSTRACT Real-world data mining generally must consider and in- volve

  18. Condorcet Domains; A Geometric Perspective Donald G. Saari

    E-Print Network [OSTI]

    Saari, Don

    of the area. To explain "Condorcet Domains" and why they are of interest, start with the fact that when making identifies what is called a fundamental conflict between individual and societal decisions. (For different], Monjardet [10], and Monjardet's survey [11] that appears in this volume. Indeed, it was Monjardet's clear

  19. Glucose oxidation in heart-type fatty acid binding protein null mice 

    E-Print Network [OSTI]

    Adhikari, Sean

    2006-10-30

    Heart-type fatty acid binding protein (H-FABP) is a major fatty acid binding factor in skeletal muscles. Genetic lack of H-FABP severely impairs the esterification and oxidation of exogenous fatty acids in soleus muscles ...

  20. Insight into Ligand Diversity and Novel Biological Roles for Family 32 Carbohydrate-Binding Modules

    E-Print Network [OSTI]

    Eirin Lopez, Jose Maria

    a new platform for the prediction of CBM binding specificity and highlight significant new targets et al. 2007). For example, Yersinia enterocolitica contains a family 32 car- bohydrate-binding module

  1. Expression and characterisation of a novel poly(A)-binding protein, PABP5 

    E-Print Network [OSTI]

    Anderson, Ross Calley

    2010-11-24

    The poly(A)-binding proteins (PABPs) are a family of eukaryotic RNA-binding proteins with key roles in mRNA translation and stability. The molecular function of PABPs have been largely revealed through study of the ...

  2. Common binding by redundant group B Sox proteins is evolutionarily conserved in Drosophila.

    E-Print Network [OSTI]

    Carl, Sarah H.; Russell, Steven

    2015-04-13

    Three-way comparison of Dichaete binding. (A) Pie chart showin present in one species (47%), two species (23%) or all three species (30%). in D. melanogaster, D. simulans and D. yakuba clustered by binding affinity key and histogram shows...

  3. Syntax-driven bindings of Spanish clitic pronoun Ivan V. Meza Ruiz

    E-Print Network [OSTI]

    Pineda, Luis

    ´on con la teor´ia de binding. Los pronombres cl´iticos del espa~nol presentan un comportamiento dual dado control de objeto. Palabras clave: Pronombres cl´iticos, Teor´ia de Binding, Reflexividad, HPSG Abstract

  4. The TLR4 agonist fibronectin extra domain A is cryptic, exposed by elastase-2; use in a fibrin matrix cancer vaccine

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Julier, Ziad; Martino, Mikaël M.; de Titta, Alexandre; Jeanbart, Laura; Hubbell, Jeffrey A.

    2015-02-24

    Fibronectin (FN) is an extracellular matrix (ECM) protein including numerous fibronectin type III (FNIII) repeats with different functions. The alternatively spliced FN variant containing the extra domain A (FNIII EDA), located between FNIII 11 and FNIII 12, is expressed in sites of injury, chronic inflammation, and solid tumors. Although its function is not well understood, FNIII EDA is known to agonize Toll-like receptor 4 (TLR4). Here, by producing various FN fragments containing FNIII EDA, we found that FNIII EDA's immunological activity depends upon its local intramolecular context within the FN chain. N-terminal extension of the isolated FNIII EDA with itsmore »neighboring FNIII repeats (FNIII 9-10-11) enhanced its activity in agonizing TLR4, while C-terminal extension with the native FNIII 12-13-14 heparin-binding domain abrogated it. We reveal that an elastase 2 cleavage site is present between FNIII EDA and FNIII 12. Activity of the C-terminally extended FNIII EDA could be restored after cleavage of the FNIII 12-13-14 domain by elastase 2. FN being naturally bound to the ECM, we immobilized FNIII EDA-containing FN fragments within a fibrin matrix model along with antigenic peptides. Such matrices were shown to stimulate cytotoxic CD8+ T cell responses in two murine cancer models.« less

  5. The Crystal Structure of Escherichia coli Group 4 Capsule Protein GfcC Reveals a Domain Organization Resembling That of Wza

    SciTech Connect (OSTI)

    Sathiyamoorthy, Karthik; Mills, Erez; Franzmann, Titus M.; Rosenshine, Ilan; Saper, Mark A. (Michigan); (Hebrew)

    2012-03-15

    We report the 1.9 {angstrom} resolution crystal structure of enteropathogenic Escherichia coli GfcC, a periplasmic protein encoded by the gfc operon, which is essential for assembly of group 4 polysaccharide capsule (O-antigen capsule). Presumed gene orthologs of gfcC are present in capsule-encoding regions of at least 29 genera of Gram-negative bacteria. GfcC, a member of the DUF1017 family, is comprised of tandem {beta}-grasp (ubiquitin-like) domains (D2 and D3) and a carboxyl-terminal amphipathic helix, a domain arrangement reminiscent of that of Wza that forms an exit pore for group 1 capsule export. Unlike the membrane-spanning C-terminal helix from Wza, the GfcC C-terminal helix packs against D3. Previously unobserved in a {beta}-grasp domain structure is a 48-residue helical hairpin insert in D2 that binds to D3, constraining its position and sequestering the carboxyl-terminal amphipathic helix. A centrally located and invariant Arg115 not only is essential for proper localization but also forms one of two mostly conserved pockets. Finally, we draw analogies between a GfcC protein fused to an outer membrane {beta}-barrel pore in some species and fusion proteins necessary for secreting biofilm-forming exopolysaccharides.

  6. The role of cooperative binding on noise expression

    E-Print Network [OSTI]

    P. S. Gutierrez; D. Monteoliva; L. Diambra

    2009-08-02

    The origin of stochastic fluctuations in gene expression has received considerable attention recently. Fluctuations in gene expression are particularly pronounced in cellular systems because of the small copy number of species undergoing transitions between discrete chemical states and the small size of biological compartments. In this paper, we propose a stochastic model for gene expression regulation including several binding sites, considering elementary reactions only. The model is used to investigate the role of cooperativity on the intrinsic fluctuations of gene expression, by means of master equation formalism. We found that the Hill coefficient and the level of noise increases as the interaction energy between activators increases. Additionally, we show that the model allows to distinguish between two cooperative binding mechanisms.

  7. Improved value for the silicon free exciton binding energy

    SciTech Connect (OSTI)

    Green, Martin A., E-mail: m.green@unsw.edu.au [Australian Centre for Advanced Photovoltaics, School of Photovoltaic and Renewable Energy Engineering, University of New South Wales, Sydney, Australia 2052 (Australia)

    2013-11-15

    The free exciton binding energy is a key parameter in silicon material and device physics. In particular, it provides the necessary link between the energy threshold for valence to conduction band optical absorption and the bandgap determining electronic properties. The long accepted low temperature binding energy value of 14.7 ± 0.4 meV is reassessed taking advantage of developments subsequent to its original determination, leading to the conclusion that this value is definitely an underestimate. Using three largely independent experimental data sets, an improved low temperature value of 15.01 ± 0.06 meV is deduced, in good agreement with the most comprehensive theoretical calculations to date.

  8. Syntheses and DNA binding of new cationic porphyrintetrapeptide conjugates Gbor Mez a

    E-Print Network [OSTI]

    Langowski, Jörg

    shifts and hypochromicities. Decomposition of absorption spectra suggested the formation of two of di- and tricationic porphyrins bind to DNA by two distinct binding modes which can be identi ed agents [6,7]. The binding of cationic porphyrin derivatives to nucleic acids has been the subject

  9. Promiscuous binding of extracellular peptides to cell surface class I MHC protein

    E-Print Network [OSTI]

    Eisen, Herman N.

    Algorithms derived from measurements of short-peptide (8–10 mers) binding to class I MHC proteins suggest that the binding groove of a class I MHC protein, such as K[superscript b], can bind well over 1 million different ...

  10. SFmap: a web server for motif analysis and prediction of splicing factor binding sites

    E-Print Network [OSTI]

    Mandel-Gutfreund, Yael

    SFmap: a web server for motif analysis and prediction of splicing factor binding sites Inbal Paz1) that bind to sequence elements on the RNA. SFmap is a web server for predicting putative SF binding sites by the user. SFmap results are provided both as a text file and as a graphical web interface. INTRODUCTION

  11. Ultrastrong Optical Binding of Metallic Nanoparticles Vassili Demergis and Ernst-Ludwig Florin*

    E-Print Network [OSTI]

    Texas at Austin. University of

    Ultrastrong Optical Binding of Metallic Nanoparticles Vassili Demergis and Ernst-Ludwig Florin the optical binding force, which has been assumed to be weak compared to the optical gradient and scattering forces. We show that trapping by the optical binding force can be over 20 times stronger than

  12. Theory of Free Energy and Entropy in Noncovalent Binding Huan-Xiang Zhou*,

    E-Print Network [OSTI]

    Weston, Ken

    Theory of Free Energy and Entropy in Noncovalent Binding Huan-Xiang Zhou*, and Michael K. Gilson, Rockville, Maryland 20850 Received December 23, 2008 Contents 1. Introduction 4092 2. Free Energy, Partition.4. Solvation and a Temperature-Dependent Energy Function 4096 3. Binding Free Energy and Binding Constant 4096

  13. Metal binding in proteins: machine learning complements X-ray absorption spectroscopy

    E-Print Network [OSTI]

    Passerini, Andrea

    Metal binding in proteins: machine learning complements X-ray absorption spectroscopy Marco Lippi1 for the identification of metalloproteins and metal binding sites on a genome scale. An extensive evaluation conducted in combination with X- ray absorption spectroscopy shows the great potentiality of the approach. 1 Metal binding

  14. Efficient Evaluation of Binding Free Energy Using Continuum Electrostatics Danzhi Huang and Amedeo Caflisch*

    E-Print Network [OSTI]

    Caflisch, Amedeo

    Efficient Evaluation of Binding Free Energy Using Continuum Electrostatics Solvation Danzhi Huang of the absolute free energy of binding. A predictive accuracy of about 1.0 kcal/mol is obtained for 13 and 29 into proteins of known structure require fast and accurate methods for the evaluation of binding free energies.1

  15. Non-binding of Flavor-Singlet Hadrons to Nuclei

    E-Print Network [OSTI]

    Glennys R. Farrar; Gabrijela Zaharijas

    2003-02-20

    Strongly attractive color forces in the flavor singlet channel may lead to a stable H dibaryon. Here we show that an H or other compact, flavor singlet hadron is unlikely to bind to nuclei, so that bounds on exotic isotopes do not exclude their stability. Remarkably, a stable H appears to evade other experimental constraints as well, when account is taken of its expected compact spatial wavefunction.

  16. Reversible Acid Gas Capture Using CO2-Binding Organic Liquids

    SciTech Connect (OSTI)

    Heldebrant, David J.; Koech, Phillip K.; Yonker, Clement R.; Rainbolt, James E.; Zheng, Feng

    2010-08-31

    Acid gas scrubbing technology is predominantly aqueous alkanolamine based. Of the acid gases, CO2, H2S and SO2 have been shown to be reversible, however there are serious disadvantages with corrosion and high regeneration costs. The primary scrubbing system composed of monoethanolamine is limited to 30% by weight because of the highly corrosive solution. This gravimetric limitation limits the CO2 volumetric (?108 g/L) and gravimetric capacity (?7 wt%) of the system. Furthermore the scrubbing system has a large energy penalty from pumping and heating the excess water required to dissolve the MEA bicarbonate salt. Considering the high specific heat of water (4 j/g-1K-1), low capacities and the high corrosion we set out to design a fully organic solvent that can chemically bind all acid gases i.e. CO2 as reversible alkylcarbonate ionic liquids or analogues thereof. Having a liquid acid gas carrier improves process economics because there is no need for excess solvent to pump and to heat. We have demonstrated illustrated in Figure 1, that CO2-binding organic liquids (CO2BOLs) have a high CO2 solubility paired with a much lower specific heat (<1.5 J/g-1K-1) than aqueous systems. CO2BOLs are a subsection of a larger class of materials known as Binding Organic Liquids (BOLs). Our BOLs have been shown to reversibly bind and release COS, CS2, and SO2, which we denote COSBOLS, CS2BOLs and SO2BOLs. Our BOLs are highly tunable and can be designed for post or pre-combustion gas capture. The design and testing of the next generation zwitterionic CO2BOLs and SO2BOLs are presented.

  17. Synthesis and Characterization of Polyamine Bicycles for Anion Binding

    E-Print Network [OSTI]

    Morehouse, Paula Kay

    2007-10-09

    ,4,12,15,18,26,31,39-octaazapentacyclo [13.13.13.1.6,101.20,241.33,37] tetratetraconta-6, 7,9,20(43), 21,23,33(42),34,36-nonaene], N(CH2CH2NHCH2-m-xylyl-CH2NHCH2CH2)3N), 12, is readily capable of being protonated at the bridgehead amines. As a result it is also capable of binding anions...

  18. High molecular weight polysaccharide that binds and inhibits virus

    DOE Patents [OSTI]

    Konowalchuk, Thomas W

    2014-01-14

    This invention provides a high molecular weight polysaccharide capable of binding to and inhibiting virus and related pharmaceutical formulations and methods on inhibiting viral infectivity and/or pathogenicity, as well as immunogenic compositions. The invention further methods of inhibiting the growth of cancer cells and of ameliorating a symptom of aging. Additionally, the invention provides methods of detecting and/or quantifying and/or isolating viruses.

  19. Bounds to binding energies from the concavity of thermodynamical functions

    E-Print Network [OSTI]

    B. K. Jennings; B. R. Barrett; B. G. Giraud

    2007-08-22

    Sequences of experimental ground-state energies are mapped onto concave patterns cured from convexities due to pairing and/or shell effects. The same patterns, completed by a list of excitation energies, can be used to give numerical estimates of the grand potential $\\Omega(\\beta,\\mu)$ for a mixture of nuclei at low or moderate temperatures $T=\\beta^{-1}$ and at many chemical potentials $\\mu.$ The average nucleon number $(\\beta,\\mu)$ then becomes a continuous variable, allowing extrapolations towards nuclear masses closer to drip lines. We study the possible concavity of several thermodynamical functions, such as the free energy and the average energy, as functions of $.$ Concavity, when present in such functions, allows trivial interpolations and extrapolations providing upper and lower bounds, respectively, to binding energies. Such bounds define an error bar for the prediction of binding energies. An extrapolation scheme for such concave functions is tested. We conclude with numerical estimates of the binding energies of a few nuclei closer to drip lines.

  20. Binding energy of the $X(3872)$ at unphysical pion masses

    E-Print Network [OSTI]

    Baru, V; Filin, A A; Gegelia, J; Nefediev, A V

    2015-01-01

    Chiral extrapolation of the $X(3872)$ binding energy is investigated using the modified Weinberg formulation of chiral effective field theory for the $D \\bar{D}^*$ scattering. Given its explicit renormalisability, this approach is particularly useful to explore the interplay of the long- and short-range $D \\bar{D}^*$ forces in the $X(3872)$ from studying the light-quark (pion) mass dependence of its binding energy. In particular, the parameter-free leading-order calculation shows that the $X$-pole disappears for unphysical large pion masses. On the other hand, without contradicting the naive dimensional analysis, the higher-order pion-mass-dependent contact interaction can change the slope of the binding energy at the physical point yielding the opposite scenario of a stronger bound $X$ at pion masses larger than its physical value. An important role of the pion dynamics and of the 3-body $D\\bar{D}\\pi$ effects for chiral extrapolations of the $X$-pole is emphasised. The results of the present study should be ...

  1. Gold Binding by Native and Chemically Modified Hops Biomasses

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    López, M. Laura; Gardea-Torresdey, J. L.; Peralta-Videa, J. R.; de la Rosa, G.; Armendáriz, V.; Herrera, I.; Troiani, H.; Henning, J.

    2005-01-01

    Heavy metals from mining, smelting operations and other industrial processing facilities pollute wastewaters worldwide. Extraction of metals from industrial effluents has been widely studied due to the economic advantages and the relative ease of technical implementation. Consequently, the search for new and improved methodologies for the recovery of gold has increased. In this particular research, the use of cone hops biomass ( Humulus lupulus ) was investigated as a new option for gold recovery. The results showed that the gold binding to native hops biomass was pH dependent from pH 2 to pH 6, with a maximum percentage bindingmore »at pH 3. Time dependency studies demonstrated that Au(III) binding to native and modified cone hops biomasses was found to be time independent at pH 2 while at pH 5, it was time dependent. Capacity experiments demonstrated that at pH 2, esterified hops biomass bound 33.4 mg Au/g of biomass, while native and hydrolyzed hops biomasses bound 28.2 and 12.0 mg Au/g of biomass, respectively. However, at pH 5 the binding capacities were 38.9, 37.8 and 11.4 mg of Au per gram of native, esterified and hydrolyzed hops biomasses, respectively. « less

  2. Testing and Evaluation of Routing Robustness in Assurable Inter-domain Networking

    E-Print Network [OSTI]

    2009 2009 Move Data to Ls8 SQL Storage Engine SQL Storage Engine Data Storage Engine (DSE) SQL Storage Engine SQL Storage Engine Data Storage Engine (DSE) Transfer data for Conversion HDD Retrieve data Store Convert Delete MRT Route Converter (MRC) MySQL RIB UPD RIR MySQL RIB UPD RIR to SQL server Converted Data

  3. Sex Hormones Genotypes and Phenotypes and Determinants of Sex Hormone Binding Globulin in relation to Type 2 Diabetes Risk

    E-Print Network [OSTI]

    GOTO, ATSUSHI

    2012-01-01

    Consumption in Relation to Sex Hormone–Binding Globulin andin Relation to Circulating Sex Hormone-binding GlobulinReferences 4. Genes in Sex Hormone Pathways and Diabetes

  4. Engagement of Nucleotide-Binding Oligomerization Domain-Containing Protein 1 (NOD1) by Receptor Interacting Protein 2 (RIP2) is Insufficient for Signal Transduction.

    E-Print Network [OSTI]

    Mayle, Sophie; Boyle, Joseph P.; Sekine, Eiki; Zurek, Birte; Kufer, Thomas A.; Monie, Tom P.

    2014-06-23

    Following activation, the cytoplasmic pattern recognition receptor NOD1 interacts with its adaptor protein RIP2 to propagate immune signalling and initiate a pro-inflammatory immune response. This interaction is mediated by the caspase recruitment...

  5. Towards an understanding of human alpha-7 nicotinic acetylcholine receptor selectivity : the creation and characterization of a soluble ligand binding domain template

    E-Print Network [OSTI]

    Nemecz, Ákos

    2011-01-01

    Rossum-Fikkert, S. E. , van Dijk, W. J. , Brejc, K. , Smit,8808-8816. Brejc, K. , van Dijk, W. J. , Klaassen, R. V. ,Rossum-Fikkert, S. E. , van Dijk, W. J. , Brejc, K. , Smit,

  6. The methyl binding domain 3/nucleosome remodelling and deacetylase complex regulates neural cell fate determination and terminal differentiation in the cerebral cortex

    E-Print Network [OSTI]

    Knock, Erin; Pereira, João; Lombard, Patrick D.; Dimond, Andrew; Leaford, Donna; Livesey, Frederick J.; Hendrich, Brian

    2015-05-02

    Inc. (Newmarket, UK); Alexa-Fluor© - 488 (A21206) or 555 (A31572) conjugated donkey anti- rabbit and Alexa-Fluor© - 488 (A21202), 555 (A31570) or 647 (A31571) conjugated donkey anti-mouse, Life Technologies (Paisley, UK). Image acquisition and analysis...

  7. Domain-independent information extraction in unstructured text

    SciTech Connect (OSTI)

    Irwin, N.H.

    1996-09-01

    Extracting information from unstructured text has become an important research area in recent years due to the large amount of text now electronically available. This status report describes the findings and work done during the second year of a two-year Laboratory Directed Research and Development Project. Building on the first-year`s work of identifying important entities, this report details techniques used to group words into semantic categories and to output templates containing selective document content. Using word profiles and category clustering derived during a training run, the time-consuming knowledge-building task can be avoided. Though the output still lacks in completeness when compared to systems with domain-specific knowledge bases, the results do look promising. The two approaches are compatible and could complement each other within the same system. Domain-independent approaches retain appeal as a system that adapts and learns will soon outpace a system with any amount of a priori knowledge.

  8. Time Domain Partitioning of Electricity Production Cost Simulations

    SciTech Connect (OSTI)

    Barrows, C.; Hummon, M.; Jones, W.; Hale, E.

    2014-01-01

    Production cost models are often used for planning by simulating power system operations over long time horizons. The simulation of a day-ahead energy market can take several weeks to compute. Tractability improvements are often made through model simplifications, such as: reductions in transmission modeling detail, relaxation of commitment variable integrality, reductions in cost modeling detail, etc. One common simplification is to partition the simulation horizon so that weekly or monthly horizons can be simulated in parallel. However, horizon partitions are often executed with overlap periods of arbitrary and sometimes zero length. We calculate the time domain persistence of historical unit commitment decisions to inform time domain partitioning of production cost models. The results are implemented using PLEXOS production cost modeling software in an HPC environment to improve the computation time of simulations while maintaining solution integrity.

  9. Stopbands in the existence domains of acoustic solitons

    SciTech Connect (OSTI)

    Nsengiyumva, F. Hellberg, M. A. Mace, R. L.; Verheest, F.

    2014-10-15

    A fully nonlinear Sagdeev pseudopotential approach is used to study the existence domain of fast mode ion-acoustic solitons in a three-species plasma composed of cold and warm adiabatic positive ion species and Boltzmann electrons. It is shown that for appropriate values of the cold-to-warm ion charge-to-mass ratio, ?, and the effective warm ion-to-electron temperature ratio, ?, there is a range in cold to warm ion charge density ratio, f, over which a stopband in soliton speed exists. Solitons do not propagate in the stopband, although they can occur for both higher and lower speeds. The stopbands are associated with a limiting curve of the existence domain that is double-valued in speed for a range of values of f. Analytical estimates of the upper and lower limits of ? and ? that support stopbands are found. It is suggested that, inter alia, the analysis should be applicable to the solar wind plasma.

  10. Speeding up Domain Wall Fermion Algorithms using QCDLAB

    E-Print Network [OSTI]

    Artan Borici

    2007-03-21

    Simulating lattice QCD with chiral fermions and indeed using Domain Wall Fermions continues to be challenging project however large are concurrent computers. One obvious bottleneck is the slow pace of prototyping using the low level coding which prevails in most, if not all, lattice projects. Recently, we came up with a new proposal, namely QCDLAB, a high level language interface, which we believe will boost our endeavours to rapidly code lattice prototype applications in lattice QCD using MATLAB/OCTAVE language and environment. The first version of the software, QCDLAB 1.0 offers the general framework on how to achieve this goal by simulating set of the lattice Schwinger model {\\tt http://phys.fshn.edu.al/qcdlab.html}. In this talk we introduce QCDLAB 1.1, which extends QCDLAB 1.0 capabilities for real world lattice computations with Wilson and Domain Wall fermions.

  11. End states, ladder compounds, and domain wall fermions

    E-Print Network [OSTI]

    Michael Creutz

    1999-09-01

    A magnetic field applied to a cross linked ladder compound can generate isolated electronic states bound to the ends of the chain. After exploring the interference phenomena responsible, I discuss a connection to the domain wall approach to chiral fermions in lattice gauge theory. The robust nature of the states under small variations of the bond strengths is tied to chiral symmetry and the multiplicative renormalization of fermion masses.

  12. Analysis of ultra-narrow ferromagnetic domain walls

    SciTech Connect (OSTI)

    Jenkins, Catherine; Paul, David

    2012-01-10

    New materials with high magnetic anisotropy will have domains separated by ultra-narrow ferromagnetic walls with widths on the order of a few unit cells, approaching the limit where the elastic continuum approximation often used in micromagnetic simulations is accurate. The limits of this approximation are explored, and the static and dynamic interactions with intrinsic crystalline defects and external driving #12;elds are modeled. The results developed here will be important when considering the stability of ultra-high-density storage media.

  13. Prediction of Protein DomainTypes by Backpropagation

    E-Print Network [OSTI]

    Szepesvari, Csaba

    Prediction of Protein Domain­Types by Backpropagation J'anos Murvai 1 , Csaba Szepesv'ari 1 , Csan'ad Bachrati 4 and S'andor Pongor 2;3 1 MTA­JATE Research Group on Artificial Intelligence, Szeged 6720, Aradi vrt. tere 1. Hungary 2 ABC Institute for Biochemistry and Protein Research, 2100 G¨od¨oll�o, Hungary 3

  14. Structures of pseudechetoxin and pseudecin, two snake-venom cysteine-rich secretory proteins that target cyclic nucleotide-gated ion channels: implications for movement of the C-terminal cysteine-rich domain

    SciTech Connect (OSTI)

    Suzuki, Nobuhiro [Department of Applied Biochemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8572 (Japan); Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602 (Japan); Yamazaki, Yasuo [Department of Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588 (Japan); Brown, R. Lane [Neurological Science Institute, Oregon Health and Science University, Beaverton, Oregon 97006 (United States); Fujimoto, Zui [Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602 (Japan); Morita, Takashi, E-mail: tmorita@my-pharm.ac.jp [Department of Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588 (Japan); Mizuno, Hiroshi, E-mail: tmorita@my-pharm.ac.jp [Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602 (Japan); VALWAY Technology Center, NEC Soft Ltd, Koto-ku, Tokyo 136-8627 (Japan); Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, Central 6, Tsukuba, Ibaraki 305-8566 (Japan); Department of Applied Biochemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8572 (Japan)

    2008-10-01

    The structures of pseudechetoxin and pseudecin suggest that both proteins bind to cyclic nucleotide-gated ion channels in a manner in which the concave surface occludes the pore entrance. Cyclic nucleotide-gated (CNG) ion channels play pivotal roles in sensory transduction by retinal photoreceptors and olfactory neurons. The elapid snake toxins pseudechetoxin (PsTx) and pseudecin (Pdc) are the only known protein blockers of CNG channels. These toxins belong to a cysteine-rich secretory protein (CRISP) family containing an N-terminal pathogenesis-related proteins of group 1 (PR-1) domain and a C-terminal cysteine-rich domain (CRD). PsTx and Pdc are highly homologous proteins, but their blocking affinities on CNG channels are different: PsTx blocks both the olfactory and retinal channels with ?15–30-fold higher affinity than Pdc. To gain further insights into their structure and function, the crystal structures of PsTx, Pdc and Zn{sup 2+}-bound Pdc were determined. The structures revealed that most of the amino-acid-residue differences between PsTx and Pdc are located around the concave surface formed between the PR-1 domain and the CRD, suggesting that the concave surface is functionally important for CNG-channel binding and inhibition. A structural comparison in the presence and absence of Zn{sup 2+} ion demonstrated that the concave surface can open and close owing to movement of the CRD upon Zn{sup 2+} binding. The data suggest that PsTx and Pdc occlude the pore entrance and that the dynamic motion of the concave surface facilitates interaction with the CNG channels.

  15. Characterization of Cardio signals by time-frequency domain analysis

    E-Print Network [OSTI]

    Sayan Mukherjee; Sanjay Kumar Palit; Santo Banerjee; MRK Ariffin; Lamberto Rondoni; Dilip Kumar Bhattacharya

    2014-09-04

    Long term behavior of nonlinear deterministic continuous time signals can be studied in terms of their reconstructed attractors. Reconstructed attractors of a continuous signal are meant to be topologically equivalent representations of the dynamics of the unknown dynamical system which generates the signal. Sometimes, geometry of the attractor or its complexity may give important information on the system of interest. However, if the trajectories of the attractor behave as if they are not coming from continuous system or there exists many spike like structures on the path of the system trajectories, then there is no way to characterize the shape of the attractor. In this article, the traditional attractor reconstruction method is first used for two types of ECG signals: Normal healthy persons (NHP) and Congestive Heart failure patients (CHFP). As common in such a framework, the reconstructed attractors are not at all well formed and hence it is not possible to adequately characterize their geometrical features. Thus, we incorporate frequency domain information to the given time signals. This is done by transforming the signals to a time frequency domain by means of suitable Wavelet transforms (WT). The transformed signal concerns two non homogeneous variables and is still quite difficult to use to reconstruct some dynamics out of it. By applying a suitable mapping, this signal is further converted into integer domain and a new type of 3D plot, called integer lag plot, which characterizes and distinguishes the ECG signals of NHP and CHFP, is finally obtained.

  16. A Time Domain Waveform for Testing General Relativity

    E-Print Network [OSTI]

    Cédric Huwyler; Edward K. Porter; Philippe Jetzer

    2014-10-24

    Gravitational-wave parameter estimation is only as good as the theory the waveform generation models are based upon. It is therefore crucial to test General Relativity (GR) once data becomes available. Many previous works, such as studies connected with the ppE framework by Yunes and Pretorius, rely on the stationary phase approximation (SPA) to model deviations from GR in the frequency domain. As Fast Fourier Transform algorithms have become considerably faster and in order to circumvent possible problems with the SPA, we test GR with corrected time domain waveforms instead of SPA waveforms. Since a considerable amount of work has been done already in the field using SPA waveforms, we establish a connection between leading-order-corrected waveforms in time and frequency domain, concentrating on phase-only corrected terms. In a Markov Chain Monte Carlo study, whose results are preliminary and will only be available later, we will assess the ability of the eLISA detector to measure deviations from GR for signals coming from supermassive black hole inspirals using these corrected waveforms.

  17. The Scanalyzer Domain: Greenhouse Logistics as a Planning Problem Malte Helmert

    E-Print Network [OSTI]

    Vetter, Thomas

    The Scanalyzer Domain: Greenhouse Logistics as a Planning Problem Malte Helmert Albert the problem of automatic greenhouse logistic management. At its mathematical core, the Scanalyzer domain; Finkel 2009). Smart greenhouses (smarthouses in the following) are an important technology

  18. Nonadiabatic Spin Torque Investigated Using Thermally Activated Magnetic Domain Wall Dynamics

    E-Print Network [OSTI]

    Dunin-Borkowski, Rafal E.

    Nonadiabatic Spin Torque Investigated Using Thermally Activated Magnetic Domain Wall Dynamics M microscopy, we investigate the thermally activated motion of domain walls (DWs) between two positions properly analyzed, thermally activated processes at tem- peratures even well below the Curie temperature

  19. 1. An integral extension of integral domains where going-down fails ...

    E-Print Network [OSTI]

    2011-11-10

    An integral extension of integral domains where going-down fails. Definition 1. Let A be a subring of an integral domain B. The conductor of B into A is c = {a ? A ...

  20. SUPPORTING DOMAIN SPECIFIC WEB-BASED SEARCH USING HEURISTIC KNOWLEDGE EXTRACTION 

    E-Print Network [OSTI]

    Gunanathan, Sudharsan

    2010-01-16

    Modern search engines like Google support domain-independent search over the vast information contained in web documents. However domain-specific information access, such as finding less well-known people, locations, and ...

  1. Permissible symmetries of multi-domain configurations in perovskite ferroelectric crystals

    E-Print Network [OSTI]

    Cao, Wenwu

    Permissible symmetries of multi-domain configurations in perovskite ferroelectric crystals Jiri through domain engineering are specified for perovskite ferroelectric crystals having tetragonal walls . Many useful ferroelectric materials have the so-called perovskite structure, which contains

  2. Phenomenological theory of a single domain wall in uniaxial trigonal ferroelectrics: Lithium niobate and lithium tantalate

    E-Print Network [OSTI]

    Gopalan, Venkatraman

    Phenomenological theory of a single domain wall in uniaxial trigonal ferroelectrics: Lithium niobate and lithium tantalate David A. Scrymgeour and Venkatraman Gopalan Department of Materials Science, lithium niobate and lithium tantalate. The contributions to the domain- wall energy from polarization

  3. Cross-domain comparison of quantitative technology improvement using patent derived characteristics

    E-Print Network [OSTI]

    Benson, Christopher Lee

    2014-01-01

    This thesis compares the performance improvement rates of 28 technological domains with characteristics derived from the patents of the domains, seeking to objectively test theories of how and why technologies change over ...

  4. Magnetic behavior of 360° domain walls in patterned magnetic thin films

    E-Print Network [OSTI]

    Mascaro, Mark Daniel

    2012-01-01

    360° transverse domain walls (360DWs), which form readily from transverse 180° domain walls (180DWs) of opposite sense, demonstrate qualitatively distinct behaviors from their constituent 180DWs and are therefore of interest ...

  5. The Neurofascins orchestrate assembly and maintenance of axonal domains in the central nervous system 

    E-Print Network [OSTI]

    Zonta, Barbara

    Close interaction between oligodendrocytes and axons is essential to initiate myelination and to form specialised domains along myelinated fibres. These domains are characterised by the assembly of protein complexes at ...

  6. NEW RESULTS ON THE ASYMPTOTIC BEHAVIOUR OF DIRICHLET PROBLEMS IN PERFORATED DOMAINS

    E-Print Network [OSTI]

    Garroni, Adriana

    NEW RESULTS ON THE ASYMPTOTIC BEHAVIOUR OF DIRICHLET PROBLEMS IN PERFORATED DOMAINS GIANNI DAL MASO behaviour of the solutions of elliptic equations with Dirichlet boundary conditions in perforated domains

  7. A New Methodology for Frequency Domain Analysis of Wave Energy Converters with Periodically Varying Physical Parameters

    E-Print Network [OSTI]

    Victoria, University of

    A New Methodology for Frequency Domain Analysis of Wave Energy Converters with Periodically Varying Methodology for Frequency Domain Analysis of Wave Energy Converters with Periodically Varying Physical of Mechanical Engineering) ABSTRACT Within a wave energy converter's operational bandwidth, device operation

  8. Pedogenic Thresholds and Soil Process Domains in Basalt-Derived Soils

    E-Print Network [OSTI]

    Vitousek, PM; Chadwick, OA

    2013-01-01

    rejuvenation of weathering-derived nutri- ent supply in anProcess Domains in Basalt-Derived Soils Peter M. Vitousekand domains in basalt-derived soils on two rainfall

  9. NS1-binding protein abrogates the elevation of cell viability by the influenza A virus NS1 protein in association with CRKL

    SciTech Connect (OSTI)

    Miyazaki, Masaya [Department of Cancer Pathology, Hokkaido University Graduate School of Medicine, N15W7, Kita-ku, Sapporo 060-8638 (Japan)] [Department of Cancer Pathology, Hokkaido University Graduate School of Medicine, N15W7, Kita-ku, Sapporo 060-8638 (Japan); Nishihara, Hiroshi, E-mail: hnishihara@med.hokudai.ac.jp [Department of Translational Pathology, Hokkaido University Graduate School of Medicine, N15W7, Kita-ku, Sapporo 060-8638 (Japan)] [Department of Translational Pathology, Hokkaido University Graduate School of Medicine, N15W7, Kita-ku, Sapporo 060-8638 (Japan); Hasegawa, Hideki [Department of Pathology, National Institute of Infectious Diseases, Sinjuku-ku, Tokyo (Japan)] [Department of Pathology, National Institute of Infectious Diseases, Sinjuku-ku, Tokyo (Japan); Tashiro, Masato [Influenza Virus Research Center, National Institute of Infectious Diseases, Sinjuku-ku, Tokyo (Japan)] [Influenza Virus Research Center, National Institute of Infectious Diseases, Sinjuku-ku, Tokyo (Japan); Wang, Lei [Department of Translational Pathology, Hokkaido University Graduate School of Medicine, N15W7, Kita-ku, Sapporo 060-8638 (Japan)] [Department of Translational Pathology, Hokkaido University Graduate School of Medicine, N15W7, Kita-ku, Sapporo 060-8638 (Japan); Kimura, Taichi; Tanino, Mishie; Tsuda, Masumi [Department of Cancer Pathology, Hokkaido University Graduate School of Medicine, N15W7, Kita-ku, Sapporo 060-8638 (Japan)] [Department of Cancer Pathology, Hokkaido University Graduate School of Medicine, N15W7, Kita-ku, Sapporo 060-8638 (Japan); Tanaka, Shinya [Department of Cancer Pathology, Hokkaido University Graduate School of Medicine, N15W7, Kita-ku, Sapporo 060-8638 (Japan) [Department of Cancer Pathology, Hokkaido University Graduate School of Medicine, N15W7, Kita-ku, Sapporo 060-8638 (Japan); Department of Translational Pathology, Hokkaido University Graduate School of Medicine, N15W7, Kita-ku, Sapporo 060-8638 (Japan)

    2013-11-29

    Highlights: •NS1 induced excessive phosphorylation of ERK and elevated cell viability. •NS1-BP expression and CRKL knockdown abolished survival effect of NS1. •NS1-BP and NS1 formed the complex through the interaction with CRKL-SH3(N). -- Abstract: The influenza A virus non-structural protein 1 (NS1) is a multifunctional virulence factor consisting of an RNA binding domain and several Src-homology (SH) 2 and SH3 binding motifs, which promotes virus replication in the host cell and helps to evade antiviral immunity. NS1 modulates general host cell physiology in association with various cellular molecules including NS1-binding protein (NS1-BP) and signaling adapter protein CRK-like (CRKL), while the physiological role of NS1-BP during influenza A virus infection especially in association with NS1 remains unclear. In this study, we analyzed the intracellular association of NS1-BP, NS1 and CRKL to elucidate the physiological roles of these molecules in the host cell. In HEK293T cells, enforced expression of NS1 of A/Beijing (H1N1) and A/Indonesia (H5N1) significantly induced excessive phosphorylation of ERK and elevated cell viability, while the over-expression of NS1-BP and the abrogation of CRKL using siRNA abolished such survival effect of NS1. The pull-down assay using GST-fusion CRKL revealed the formation of intracellular complexes of NS1-BP, NS1 and CRKL. In addition, we identified that the N-terminus SH3 domain of CRKL was essential for binding to NS1-BP using GST-fusion CRKL-truncate mutants. This is the first report to elucidate the novel function of NS1-BP collaborating with viral protein NS1 in modulation of host cell physiology. In addition, an alternative role of adaptor protein CRKL in association with NS1 and NS1-BP during influenza A virus infection is demonstrated.

  10. The metalloid arsenite induces nuclear export of Id3 possibly via binding to the N-terminal cysteine residues

    SciTech Connect (OSTI)

    Kurooka, Hisanori, E-mail: hkurooka@u-fukui.ac.jp [Division of Molecular Genetics, Department of Biochemistry and Bioinformative Sciences, School of Medicine, Faculty of Medical Sciences, University of Fukui, Fukui (Japan) [Division of Molecular Genetics, Department of Biochemistry and Bioinformative Sciences, School of Medicine, Faculty of Medical Sciences, University of Fukui, Fukui (Japan); Research and Education Program for Life Science, University of Fukui, Fukui (Japan); Sugai, Manabu [Department of Experimental Therapeutics, Translational Research Center, Kyoto University Hospital, Kyoto (Japan)] [Department of Experimental Therapeutics, Translational Research Center, Kyoto University Hospital, Kyoto (Japan); Mori, Kentaro [Division of Molecular Genetics, Department of Biochemistry and Bioinformative Sciences, School of Medicine, Faculty of Medical Sciences, University of Fukui, Fukui (Japan)] [Division of Molecular Genetics, Department of Biochemistry and Bioinformative Sciences, School of Medicine, Faculty of Medical Sciences, University of Fukui, Fukui (Japan); Yokota, Yoshifumi, E-mail: yokota@u-fukui.ac.jp [Division of Molecular Genetics, Department of Biochemistry and Bioinformative Sciences, School of Medicine, Faculty of Medical Sciences, University of Fukui, Fukui (Japan) [Division of Molecular Genetics, Department of Biochemistry and Bioinformative Sciences, School of Medicine, Faculty of Medical Sciences, University of Fukui, Fukui (Japan); Research and Education Program for Life Science, University of Fukui, Fukui (Japan)

    2013-04-19

    Highlights: •Sodium arsenite induces cytoplasmic accumulation of Id3. •Arsenite binds to closely spaced N-terminal cysteine residues of Id3. •N-terminal cysteines are essential for arsenite-induced nuclear export of Id3. •Nuclear export of Id3 counteracts its transcriptional repression activity. -- Abstract: Ids are versatile transcriptional repressors that regulate cell proliferation and differentiation, and appropriate subcellular localization of the Id proteins is important for their functions. We previously identified distinct functional nuclear export signals (NESs) in Id1 and Id2, but no active NES has been reported in Id3. In this study, we found that treatment with the stress-inducing metalloid arsenite led to the accumulation of GFP-tagged Id3 in the cytoplasm. Cytoplasmic accumulation was impaired by a mutation in the Id3 NES-like sequence resembling the Id1 NES, located at the end of the HLH domain. It was also blocked by co-treatment with the CRM1-specific nuclear export inhibitor leptomycin B (LMB), but not with the inhibitors for mitogen-activated protein kinases (MAPKs). Importantly, we showed that the closely spaced N-terminal cysteine residues of Id3 interacted with the arsenic derivative phenylarsine oxide (PAO) and were essential for the arsenite-induced cytoplasmic accumulation, suggesting that arsenite induces the CRM1-dependent nuclear export of Id3 via binding to the N-terminal cysteines. Finally, we demonstrated that Id3 significantly repressed arsenite-stimulated transcription of the immediate-early gene Egr-1 and that this repression activity was inversely correlated with the arsenite-induced nuclear export. Our results imply that Id3 may be involved in the biological action of arsenite.

  11. Speech perception in noise with a two-sensor frequency-domain minimum-variance (FMV)

    E-Print Network [OSTI]

    Illinois at Urbana-Champaign, University of

    domain [e.g., Griffiths and Jim, 1982; Zurek et al., 1996; Fischer and Simmer, 1996] by its simplified

  12. Model-Based Mediation with Domain Maps Bertram Ludascher? Amarnath Gupta? Maryann E. Martonez

    E-Print Network [OSTI]

    Ludäscher, Bertram

    Model-Based Mediation with Domain Maps Bertram Lud¨ascher? Amarnath Gupta? Maryann E. Martonez ?San

  13. Detection of Botnet Collusion by Degree Distribution of Domains Pieter Burghouwt1

    E-Print Network [OSTI]

    the Internet by DDoS- attacks, spam, information theft and other criminal activities. They are using botnet-traffic. 1. Introduction Malicious botnets are a major threat to the Inter- net. Criminal spam domains. Anomalies are described, like non-existent domains, typo squatter domains, A-records

  14. A New Software Testing Approach Based on Domain Analysis of Specifications and Programs

    E-Print Network [OSTI]

    Lyu, Michael R.

    A New Software Testing Approach Based on Domain Analysis of Specifications and Programs Ruilian of Sciences in Beijing Abstract Partition testing is a well-known software testing technique. This paper shows domain boundary. We present an innovative software testing approach based on input domain analysis

  15. Classifying Domain-Specific Terms Using a Dictionary Dept. of CSSE

    E-Print Network [OSTI]

    with the domain of oil due to their frequent appear- ances in contexts related to oil although they indi- cate- saurus); and with domain concepts (e.g. WordNet, WordNet Domain, Unified Medical Language Sys- tem (UMLS

  16. On-Line Transform Domain LMS Algorithm Implemented with PCA Learning

    E-Print Network [OSTI]

    Slatton, Clint

    On-Line Transform Domain LMS Algorithm Implemented with PCA Learning Chuan Wang, L-K Yen, and Jose University of Florida Gainesville, FL 32611 Abstract An on-line transform domain Least Mean Square (LMS is used as an orthonormalization layer in the transform domain LMS filter. Since PCA learning is an on

  17. Time domain half-space dyadic Green's functions for eddy-current calculations

    E-Print Network [OSTI]

    Bowler, John R.

    Time domain half-space dyadic Green's functions for eddy-current calculations J. R. Bowlera) Centre American Institute of Physics. S0021-8979 99 08422-4 I. TIME DOMAIN INTERACTION The calculation of eddy-current-domain eddy-current scattering problems for cases in which a scat- terer is embedded in an otherwise

  18. Robust and Efficient Covering of Unknown Continuous Domains with Simple, Ant-Like

    E-Print Network [OSTI]

    Bruckstein, Alfred M.

    want to cover (or clean or search or paint) a connected domain in R2 simple robots having effectors (or that a domain was covered by the (team of) robots if each and every point of the domain was swept by a robot effector. In fact, every time we want to build an automatic machine suitable for applications such as floor

  19. In-medium effects for nuclear matter in the Fermi energy domain D. Durand,1

    E-Print Network [OSTI]

    Boyer, Edmond

    In-medium effects for nuclear matter in the Fermi energy domain O. Lopez,1 D. Durand,1 G. Lehaut,1 of nuclear reactions in the Fermi energy domain. I. INTRODUCTION Transport properties in nuclear matter energy domain, transport features should exhibit the in- terplay between mean-field (nuclear degrees

  20. Learning with Augmented Features for Heterogeneous Domain Lixin Duan S080003@ntu.edu.sg

    E-Print Network [OSTI]

    Xu, Dong

    . Copyright 2012 by the author(s)/owner(s). learning (a.k.a., domain adaptation), as a new machine learning data from the target domain by leveraging a large amount of labeled data from other existing domains (a.k.a

  1. Propagating and reflecting of spin wave in permalloy nanostrip with 360° domain wall

    SciTech Connect (OSTI)

    Zhang, Senfu; Mu, Congpu; Zhu, Qiyuan; Zheng, Qi; Liu, Xianyin; Wang, Jianbo; Liu, Qingfang

    2014-01-07

    By micromagnetic simulation, we investigated the interaction between propagating spin wave (or magnonic) and a 360° domain wall in a nanostrip. It is found that propagating spin wave can drive a 360° domain wall motion, and the velocity and direction are closely related to the transmission coefficient of the spin wave of the domain wall. When the spin wave passes through the domain wall completely, the 360° domain wall moves toward the spin wave source. When the spin wave is reflected by the domain wall, the 360° domain wall moves along the spin wave propagation direction. Moreover, when the frequency of the spin wave is coincident with that of the 360° domain wall normal mode, the 360° domain wall velocity will be resonantly enhanced no matter which direction the 360 DW moves along. On the other hand, when the spin wave is reflected from the moving 360° domain wall, we observed the Doppler effect clearly. After passing through a 360° domain wall, the phase of the spin wave is changed, and the phase shift is related to the frequency. Nevertheless, phase shift could be manipulated by the number of 360° domain walls that spin wave passing through.

  2. Domain Engineering for Enhanced Ferroelectric Properties of Epitaxial (001) BiFeO Thin Films

    E-Print Network [OSTI]

    Eom, Chang Beom

    Domain Engineering for Enhanced Ferroelectric Properties of Epitaxial (001) BiFeO Thin Films By Ho of conventional Ti-rich lead zirconia titanate, suggested BiFeO3 as a strong candidate for lead-free nonvolatile are simultaneously improved by domain engineering. For the demonstration of the domain variant selection in BiFeO3

  3. WHEN Cp(X) IS DOMAIN REPRESENTABLE WILLIAM FLEISSNER AND LYNNE YENGULALP

    E-Print Network [OSTI]

    Yengulalp, Lynne

    WHEN Cp(X) IS DOMAIN REPRESENTABLE WILLIAM FLEISSNER AND LYNNE YENGULALP ABSTRACT. Let M corollaries answer open questions. If X is completely regular and Cp(X) is domain representable, then X is discrete. If X is zero-dimensional, T2 , and Cp(X, D) is subcompact, then X is discrete. keywords: Domain

  4. Two-parameter homogenization for a GL problem in a perforated domain

    E-Print Network [OSTI]

    Berlyand, Leonid

    Two-parameter homogenization for a GL problem in a perforated domain Leonid Berlyand(1) , Petru the notations: o = o, i = i so that A = o i. We next define a perforated domain A obtained by "punching" holes, a point x R2 and define Z = {m + x + P A}. Then the perforated domain is defined as follows: A = A \\ m

  5. DNA-Binding Mechanism in Prokaryotic Partition Complex Formation

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would like submit theCovalent Bonding Low-Cost Ground8 GasDEVELOPMENTS E P I IT h itDNA-Binding

  6. Vibrational Softening of a Protein on Ligand Binding

    SciTech Connect (OSTI)

    Balog, Erica [Semmelweis University, Budapest, Hungary; Perahia, David [Ecole Normale Superieure de Cachan, Cachan, France; Smith, Jeremy C [ORNL; Merzel, Franci [National Institute of Chemistry, Solvenia

    2011-01-01

    Neutron scattering experiments have demonstrated that binding of the cancer drug methotrexate softens the low-frequency vibrations of its target protein, dihydrofolate reductase (DHFR). Here, this softening is fully reproduced using atomic detail normal-mode analysis. Decomposition of the vibrational density of states demonstrates that the largest contributions arise from structural elements of DHFR critical to stability and function. Mode-projection analysis reveals an increase of the breathing-like character of the affected vibrational modes consistent with the experimentally observed increased adiabatic compressibility of the protein on complexation.

  7. Towards engineering hormone-binding globulins as drug delivery agents

    E-Print Network [OSTI]

    Chan, Wee Lee; Zhou, Aiwu; Read, Randy J.

    2014-11-26

    (2014) Towards Engineering Hormone-Binding Globulins as Drug Delivery Agents. PLoS ONE 9(11): e113402. doi:10.1371/journal.pone. 0113402 Editor: Ashley M. Buckle, Monash University, Australia Received: June 10, 2014 Accepted: October 24, 2014 Published... stock solution was prepared by dissolving lyophilised cortisol (Sigma Aldrich) in 80% ethanol to make a 500 mM solution, which was then diluted with water to make solutions of 20, 40 and 80 mM, with water being used as a negative control. Aliquots...

  8. Hydroxyapatite-binding peptides for bone growth and inhibition

    DOE Patents [OSTI]

    Bertozzi, Carolyn R. (Berkeley, CA); Song, Jie (Shrewsbury, MA); Lee, Seung-Wuk (Walnut Creek, CA)

    2011-09-20

    Hydroxyapatite (HA)-binding peptides are selected using combinatorial phage library display. Pseudo-repetitive consensus amino acid sequences possessing periodic hydroxyl side chains in every two or three amino acid sequences are obtained. These sequences resemble the (Gly-Pro-Hyp).sub.x repeat of human type I collagen, a major component of extracellular matrices of natural bone. A consistent presence of basic amino acid residues is also observed. The peptides are synthesized by the solid-phase synthetic method and then used for template-driven HA-mineralization. Microscopy reveal that the peptides template the growth of polycrystalline HA crystals .about.40 nm in size.

  9. Climate change: Clinton affirms binding emissions reduction policy

    SciTech Connect (OSTI)

    Fairley, P.

    1996-12-04

    In Australia last month President Clinton called for an international agreement to negotiate {open_quotes}legally binding commitments to fight climate change.{close_quotes} His comments affirmed the line the Administration adopted in July and lent prominence to the effort to bring about a treaty by December 1997. Environmentalists welcomed Clinton`s comments, but industry response is divided. The Global Climate Coalition (Washington), of which CMA is a member, has tried to slow negotiations by questioning the scientific consensus on climate change and suggesting {open_quotes}serious damage to the American economy{close_quotes} could result from emissions reduction.

  10. Functionalized polymers for binding to solutes in aqueous solutions

    DOE Patents [OSTI]

    Smith, Barbara F.; Robison, Thomas W.

    2006-11-21

    A functionalized polymer for binding a dissolved molecule in an aqueous solution is presented. The polymer has a backbone polymer to which one or more functional groups are covalently linked. The backbone polymer can be such polymers as polyethylenimine, polyvinylamine, polyallylamine, and polypropylamine. These polymers are generally water-soluble, but can be insoluble when cross-linked. The functional group can be for example diol derivatives, polyol derivatives, thiol and dithiol derivatives, guest-host groups, affinity groups, beta-diphosphonic acids, and beta-diamides

  11. Characterization of Selective Binding of Alkali Cations with Carboxylate

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 OutreachProductswsicloudwsiclouddenDVA N C E D BGene Network ShapingDate:Characterization of Selective Binding of

  12. Somatic mutational analysis of FAK in breast cancer: A novel gain-of-function mutation due to deletion of exon 33

    SciTech Connect (OSTI)

    Fang, Xu-Qian; Liu, Xiang-Fan; Yao, Ling; Chen, Chang-Qiang; Gu, Zhi-Dong; Ni, Pei-Hua; Zheng, Xin-Min; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY ; Fan, Qi-Shi

    2014-01-10

    Highlights: •A novel FAK splicing mutation identified in breast tumor. •FAK-Del33 mutation promotes cell migration and invasion. •FAK-Del33 mutation regulates FAK/Src signal pathway. -- Abstract: Focal adhesion kinase (FAK) regulates cell adhesion, migration, proliferation, and survival. We identified a novel splicing mutant, FAK-Del33 (exon 33 deletion, KF437463), in both breast and thyroid cancers through colony sequencing. Considering the low proportion of mutant transcripts in samples, this mutation was detected by TaqMan-MGB probes based qPCR. In total, three in 21 paired breast tissues were identified with the FAK-Del33 mutation, and no mutations were found in the corresponding normal tissues. When introduced into a breast cell line through lentivirus infection, FAK-Del33 regulated cell motility and migration based on a wound healing assay. We demonstrated that the expression of Tyr397 (main auto-phosphorylation of FAK) was strongly increased in FAK-Del33 overexpressed breast tumor cells compared to wild-type following FAK/Src RTK signaling activation. These results suggest a novel and unique role of the FAK-Del33 mutation in FAK/Src signaling in breast cancer with significant implications for metastatic potential.

  13. Relativistic Nuclear Energy Density Functionals: adjusting parameters to binding energies

    E-Print Network [OSTI]

    T. Niksic; D. Vretenar; P. Ring

    2008-09-08

    We study a particular class of relativistic nuclear energy density functionals in which only nucleon degrees of freedom are explicitly used in the construction of effective interaction terms. Short-distance (high-momentum) correlations, as well as intermediate and long-range dynamics, are encoded in the medium (nucleon density) dependence of the strength functionals of an effective interaction Lagrangian. Guided by the density dependence of microscopic nucleon self-energies in nuclear matter, a phenomenological ansatz for the density-dependent coupling functionals is accurately determined in self-consistent mean-field calculations of binding energies of a large set of axially deformed nuclei. The relationship between the nuclear matter volume, surface and symmetry energies, and the corresponding predictions for nuclear masses is analyzed in detail. The resulting best-fit parametrization of the nuclear energy density functional is further tested in calculations of properties of spherical and deformed medium-heavy and heavy nuclei, including binding energies, charge radii, deformation parameters, neutron skin thickness, and excitation energies of giant multipole resonances.

  14. Binding and structure of tetramers in the scaling limit

    E-Print Network [OSTI]

    Hadizadeh, M R; Tomio, L; Delfino, A; Frederico, T

    2011-01-01

    The momentum-space structure of the Faddeev-Yakubovsky (FY) components of weakly-bound tetramers is investigated at the unitary limit using a renormalized zero-range two-body interaction. The results, obtained by considering a given trimer level with binding energy $B_3$, provide further support to a universal scaling function relating the binding energies of two successive tetramer states. The correlated scaling between the tetramer energies comes from the sensitivity of the four-boson system to a short-range four-body scale. Each excited $N-$th tetramer energy $B_4^{(N)}$ moves as the short-range four-body scale changes, while the trimer properties are kept fixed, with the next excited tetramer $B_4^{(N+1)}$ emerging from the atom-trimer threshold for a universal ratio $B_4^{(N)}/B_3 = B_4^ {(N)}/B_4^{(N+1)} \\simeq 4.6$, which does not depend on $N$. We show that both channels of the FY decomposition [atom-trimer ($K-$type) and dimer-dimer ($H-$type)] present high momentum tails, which reflect the short-ran...

  15. Binding and structure of tetramers in the scaling limit

    E-Print Network [OSTI]

    M. R. Hadizadeh; M. T. Yamashita; L. Tomio; A. Delfino; T. Frederico

    2012-01-17

    The momentum-space structure of the Faddeev-Yakubovsky (FY)components of weakly-bound tetramers is investigated at the unitary limit using a renormalized zero-range two-body interaction. The results, obtained by considering a given trimer level with binding energy $B_3$, provide further support to a universal scaling function relating the binding energies of two successive tetramer states. The correlated scaling between the tetramer energies comes from the sensitivity of the four-boson system to a short-range four-body scale. Each excited $N-$th tetramer energy $B_4^{(N)}$ moves as the short-range four-body scale changes, while the trimer properties are kept fixed, with the next excited tetramer $B_4^{(N+1)}$ emerging from the atom-trimer threshold for a universal ratio $B_4^{(N)}/B_3 = B_4^ {(N)}/B_4^{(N+1)} \\simeq 4.6$, which does not depend on $N$. We show that both channels of the FY decomposition [atom-trimer ($K-$type) and dimer-dimer ($H-$type)] present high momentum tails, which reflect the short-range four-body scale. We also found that the $H-$channel is favored over $K-$channel at low momentum when the four-body momentum scale largely overcomes the three-body one.

  16. Time-domain simulation of nonlinear radiofrequency phenomena

    SciTech Connect (OSTI)

    Jenkins, Thomas G.; Austin, Travis M.; Smithe, David N.; Loverich, John [Tech-X Corporation, 5621 Arapahoe Avenue, Boulder, Colorado 80303 (United States); Hakim, Ammar H. [Princeton Plasma Physics Laboratory, Princeton, New Jersey 08543 (United States)

    2013-01-15

    Nonlinear effects associated with the physics of radiofrequency wave propagation through a plasma are investigated numerically in the time domain, using both fluid and particle-in-cell (PIC) methods. We find favorable comparisons between parametric decay instability scenarios observed on the Alcator C-MOD experiment [J. C. Rost, M. Porkolab, and R. L. Boivin, Phys. Plasmas 9, 1262 (2002)] and PIC models. The capability of fluid models to capture important nonlinear effects characteristic of wave-plasma interaction (frequency doubling, cyclotron resonant absorption) is also demonstrated.

  17. Castaing Instability and Precessing Domains in Confined Alkali Gases

    E-Print Network [OSTI]

    A. Kuklov; A. E. Meyerovich

    2002-02-05

    We explore analogy between two-component quantum alkali gases and spin-polarized helium systems. Recent experiments in trapped gases are put into the frame of the existing theory for Castaing instability in transverse channel and formation of homogeneous precessing domains in spin-polarized systems. Analogous effects have already been observed in spin-polarized $% ^{3}He$ and $^{3}He- ^{4}He$ mixtures systems. The threshold effect of the confining potential on the instability is analyzed. New experimental possibilities for observation of transverse instability in a trap are discussed.

  18. Energy dissipation in single-domain ferromagnetic nanoparticles: Dynamical approach

    E-Print Network [OSTI]

    T. V. Lyutyy; S. I. Denisov; A. Yu. Peletskyi; C. Binns

    2015-02-14

    We study, both analytically and numerically, the phenomenon of energy dissipation in single-domain ferromagnetic nanoparticles driven by an alternating magnetic field. Our interest is focused on the power loss resulting from the Landau-Lifshitz-Gilbert equation, which describes the precessional motion of the nanoparticle magnetic moment. We determine the power loss as a function of the field amplitude and frequency and analyze its dependence on different regimes of forced precession induced by circularly and linearly polarized magnetic fields. The conditions to maximize the nanoparticle heating are also analyzed.

  19. Stochastic Domain-Wall Depinning in Magnetic Nanowires

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power AdministrationRobust,Field-effect Photovoltaics -7541C.3X-rays3 Prepared by:'! IStochastic Domain-Wall

  20. Dynein Motor Domain Shows Ring-Shaped Motor, Buttress

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would like submit theCovalentLaboratory |Sectorfor $1.14Dynein Motor Domain Shows

  1. Dynein Motor Domain Shows Ring-Shaped Motor, Buttress

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would like submit theCovalentLaboratory |Sectorfor $1.14Dynein Motor Domain ShowsDynein

  2. Dynein Motor Domain Shows Ring-Shaped Motor, Buttress

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would like submit theCovalentLaboratory |Sectorfor $1.14Dynein Motor Domain

  3. Dynein Motor Domain Shows Ring-Shaped Motor, Buttress

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would like submit theCovalentLaboratory |Sectorfor $1.14Dynein Motor DomainDynein Motor

  4. Dynein Motor Domain Shows Ring-Shaped Motor, Buttress

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would like submit theCovalentLaboratory |Sectorfor $1.14Dynein Motor DomainDynein

  5. Binding of transcription factors adapts to resolve information-energy trade-off

    E-Print Network [OSTI]

    Kagan, Yonatan Savir Jacob

    2015-01-01

    We examine the binding of transcription factors to DNA in terms of an information transfer problem. The input of the noisy channel is the biophysical signal of a factor bound to a DNA site, and the output is a distribution of probable DNA sequences at this site. This task involves an inherent tradeoff between the information gain and the energetics of the binding interaction - high binding energies provide higher information gain but hinder the dynamics of the system as factors are bound too tightly. We show that adaptation of the binding interaction towards increasing information transfer under energy constraints implies that the information gain per specific binding energy at each base-pair is maximized. We analyze hundreds of prokaryote and eukaryote transcription factors from various organisms to evaluate the discrimination energies. We find that, in accordance with our theoretical argument, binding energies nearly maximize the information gain per energy. This work suggests the adaptation of information ...

  6. Ranking on Cross Domain Manifold forRanking on Cross-Domain Manifold for Sketch-based 3D model Retrieval

    E-Print Network [OSTI]

    Ohbuchi, Ryutarou

    printers,... ­ User generated. T i bl 3D h· Trimble 3D warehouse... 3D model retrieval is essentialRanking on Cross Domain Manifold forRanking on Cross-Domain Manifold for Sketch-based 3D model Retrieval Takahiko FuruyaRyutarou Ohbuchi University of Yamanashi #12;IntroductionIntroduction 3D models

  7. Ranking on Cross Domain Manifold forRanking on Cross-Domain Manifold for Sketch-based 3D model Retrieval

    E-Print Network [OSTI]

    Ohbuchi, Ryutarou

    printers,... ­ User generated. T i bl 3D h· Trimble 3D warehouse... 3D model retrieval is essential scanners, 3D printers,... ­ User generated. T i bl 3D h· Trimble 3D warehouse... 3D model retrievalRanking on Cross Domain Manifold forRanking on Cross-Domain Manifold for Sketch-based 3D model

  8. Evolutionary patterns of group B Sox binding and function in Drosophila

    E-Print Network [OSTI]

    Carl, Sarah Hamilton

    2015-04-07

    ChIP-seq reads and input reads from three biological replicates in D. pseudoobscura . . . . . . . . . . . . . . . . . . . . 89 4.1 Reproducibility of biological replicate DamID samples . . . . . . . 97 4.2 Translated reads for Sox fusion proteins... ) is to bind DNA and regulate the expression of target genes; however, the complexity of combinatorial binding patterns and the sheer quantity of binding events, even in the model organism Drosophila, which has a smaller and more compact genome than hu- mans...

  9. Crystal Structures of Apo and Metal-Bound Forms of the UreE Protein from Helicobacter pylori: Role of Multiple Metal Binding Sites

    SciTech Connect (OSTI)

    Shi, Rong; Munger, Christine; Asinas, Abdalin; Benoit, Stephane L.; Miller, Erica; Matte, Allan; Maier, Robert J.; Cygler, Miroslaw (McGill); (Georgia); (Biotech Res.)

    2010-10-22

    The crystal structure of the urease maturation protein UreE from Helicobacter pylori has been determined in its apo form at 2.1 {angstrom} resolution, bound to Cu{sup 2+} at 2.7 {angstrom} resolution, and bound to Ni{sup 2+} at 3.1 {angstrom} resolution. Apo UreE forms dimers, while the metal-bound enzymes are arranged as tetramers that consist of a dimer of dimers associated around the metal ion through coordination by His102 residues from each subunit of the tetramer. Comparison of independent subunits from different crystal forms indicates changes in the relative arrangement of the N- and C-terminal domains in response to metal binding. The improved ability of engineered versions of UreE containing hexahistidine sequences at either the N-terminal or C-terminal end to provide Ni{sup 2+} for the final metal sink (urease) is eliminated in the H102A version. Therefore, the ability of the improved Ni{sup 2+}-binding versions to deliver more nickel is likely an effect of an increased local concentration of metal ions that can rapidly replenish transferred ions bound to His102.

  10. Sequestering Uranium from Seawater: Binding Strength and Modes of Uranyl Complexes with Glutarimidedioxime

    E-Print Network [OSTI]

    Tian, Guoxin

    2013-01-01

    binding strength and modes of uranyl complexes withand the coordination modes in the uranyl glutarimidedioximeof the bonding orbitals of uranyl (? u , ? g , ? u and ? g )

  11. Energy landscapes for protein folding, binding, and aggregation : simple funnels and beyond

    E-Print Network [OSTI]

    Cho, Samuel Sung-Il

    2007-01-01

    coordinates capture protein folding on smooth landscapes.in the Prediction of Protein Folding Kinetics. Proc. Natl.Landscapes for Protein Folding, Binding, and Aggregation:

  12. Binding Energies of the Alpha Particle and the A=3 Isobars from a Theoretical Geometric Model

    E-Print Network [OSTI]

    Gustavo R. Gonzalez-Martin

    2008-05-03

    We assume a triple geometric structure for the electromagnetic nuclear interaction. This nuclear electromagnetism is used to calculate the binding energies of the alpha particle and the A=3 isobar nuclides. The approximation for the resultant wave equation which lead to the deuteron binding energy from the modified Mathieu equation for the radial eigenvalue equation also establishes proton-electron-proton magnetic bonds in these nuclides and determines their binding energies. Completely theoretical calculations give 28.5 Mev., 7.64 Mev. and 8.42 Mev. for the binding energies of the alpha particle, the helium 3 isotope and tritium respectively. These values admit correction factors due to the approximations made.

  13. Sequestering Uranium from Seawater: Binding Strength and Modes of Uranyl Complexes with Glutarimidedioxime

    E-Print Network [OSTI]

    Tian, Guoxin

    2013-01-01

    data_request/cif. OECD, Uranium 2009: Resources, Productionthermodynamics of uranium”, (H. Wanner and I. Forest,of California. Sequestering uranium from seawater: binding

  14. Proton decay matrix elements with domain-wall fermions

    E-Print Network [OSTI]

    Y. Aoki; C. Dawson; J. Noaki; A. Soni

    2006-09-18

    Hadronic matrix elements of operators relevant to nucleon decay in grand unified theories are calculated numerically using lattice QCD. In this context, the domain-wall fermion formulation, combined with non-perturbative renormalization, is used for the first time. These techniques bring reduction of a large fraction of the systematic error from the finite lattice spacing. Our main effort is devoted to a calculation performed in the quenched approximation, where the direct calculation of the nucleon to pseudoscalar matrix elements, as well as the indirect estimate of them from the nucleon to vacuum matrix elements, are performed. First results, using two flavors of dynamical domain-wall quarks for the nucleon to vacuum matrix elements are also presented to address the systematic error of quenching, which appears to be small compared to the other errors. Our results suggest that the representative value for the low energy constants from the nucleon to vacuum matrix elements are given as |alpha| simeq |beta| simeq 0.01 GeV^3. For a more reliable estimate of the physical low energy matrix elements, it is better to use the relevant form factors calculated in the direct method. The direct method tends to give smaller value of the form factors, compared to the indirect one, thus enhancing the proton life-time; indeed for the pi^0 final state the difference between the two methods is quite appreciable.

  15. Example Work Domain Analysis for a Reference Sodium Fast Reactor

    SciTech Connect (OSTI)

    Hugo, Jacques; Oxstrand, Johanna

    2015-01-01

    The nuclear industry is currently designing and building a new generation of reactors that will include different structural, functional, and environmental aspects, all of which are likely to have a significant impact on the way these plants are operated. In order to meet economic and safety objectives, these new reactors will all use advanced technologies to some extent, including new materials and advanced digital instrumentation and control systems. New technologies will affect not only operational strategies, but will also require a new approach to how functions are allocated to humans or machines to ensure optimal performance. Uncertainty about the effect of large scale changes in plant design will remain until sound technical bases are developed for new operational concepts and strategies. Up-to-date models and guidance are required for the development of operational concepts for complex socio-technical systems. This report describes how the classical Work Domain Analysis method was adapted to develop operational concept frameworks for new plants. This adaptation of the method is better able to deal with the uncertainty and incomplete information typical of first-of-a-kind designs. Practical examples are provided of the systematic application of the method in the operational analysis of sodium-cooled reactors. Insights from this application and its utility are reviewed and arguments for the formal adoption of Work Domain Analysis as a value-added part of the Systems Engineering process are presented.

  16. Parametric Study of the Frequency-Domain Thermoreflectance Technique

    SciTech Connect (OSTI)

    C. Xing; C. Jensen; Z. Hua; H. Ban; D. H. Hurley; M. Khafizov; J. Rory Kennedy

    2012-11-01

    Without requiring regression for parameter determination, one-dimensional (1D) analytical models are used by many research groups to extract the thermal properties in frequency-domain thermoreflectance measurements. Experimentally, this approach involves heating the sample with a pump laser and probing the temperature response with spatially coincident probe laser. Micron order lateral resolution can be obtained by tightly focusing the pump and probe lasers. However, small laser beam spot sizes necessarily bring into question the assumptions associated with 1D analytical models. In this study, we analyzed the applicability of 1D analytical models by comparing to 2D analytical and fully numerical models. Specifically, we considered a generic nlayer two-dimensional (2D), axisymmetric analytical model including effects of volumetric heat absorption, contact resistance, and anisotropic properties. In addition, a finite element numerical model was employed to consider nonlinear effects caused by temperature dependent thermal conductivity. Nonlinearity is of germane importance to frequency domain approaches because the experimental geometry is such that the probe is always sensing the maximum temperature fluctuation. To quantify the applicability of the 1D model, parametric studies were performed considering the effects of: film thickness, heating laser size, probe laser size, substrate-to-film effusivity ratio, interfacial thermal resistance between layers, volumetric heating, substrate thermal conductivity, nonlinear boundary conditions, and anisotropic and temperature dependent thermal conductivity.

  17. Phylogenomic and functional domain analysis of polyketide synthases in Fusarium

    SciTech Connect (OSTI)

    Brown, Daren W.; Butchko, Robert A.; Baker, Scott E.; Proctor, Robert H.

    2012-02-01

    Fusarium species are ubiquitous in nature, cause a range of plant diseases, and produce a variety of chemicals often referred to as secondary metabolites. Although some fungal secondary metabolites affect plant growth or protect plants from other fungi and bacteria, their presence in grain based food and feed is more often associated with a variety of diseases in plants and in animals. Many of these structurally diverse metabolites are derived from a family of related enzymes called polyketide synthases (PKSs). A search of genomic sequence of Fusarium verticillioides, F. graminearum, F. oxysporum and Nectria haematococca (anamorph F. solani) identified a total of 58 PKS genes. To gain insight into how this gene family evolved and to guide future studies, we conducted a phylogenomic and functional domain analysis. The resulting genealogy suggested that Fusarium PKSs represent 34 different groups responsible for synthesis of different core metabolites. The analyses indicate that variation in the Fusarium PKS gene family is due to gene duplication and loss events as well as enzyme gain-of-function due to the acquisition of new domains or of loss-of-function due to nucleotide mutations. Transcriptional analysis indicate that the 16 F. verticillioides PKS genes are expressed under a range of conditions, further evidence that they are functional genes that confer the ability to produce secondary metabolites.

  18. On the nuclear interaction. Potential, binding energy and fusion reaction

    E-Print Network [OSTI]

    I. Casinos

    2008-05-22

    The nuclear interaction is responsible for keeping neutrons and protons joined in an atomic nucleus. Phenomenological nuclear potentials, fitted to experimental data, allow one to know about the nuclear behaviour with more or less success where quantum mechanics is hard to be used. A nuclear potential is suggested and an expression for the potential energy of two nuclear entities, either nuclei or nucleons, is developed. In order to estimate parameters in this expression, some nucleon additions to nuclei are considered and a model is suggested as a guide of the addition process. Coulomb barrier and energy for the addition of a proton to each one of several nuclei are estimated by taking into account both the nuclear and electrostatic components of energy. Studies on the binding energies of several nuclei and on the fusion reaction of two nuclei are carried out.

  19. Quasielastic electron-deuteron scattering in the weak binding approximation

    SciTech Connect (OSTI)

    Ethier, Jacob J. [William and Mary College, JLAB; Doshi, Nidhi P. [Carnegie Mellon University; Malace, Simona P. [JLAB; Melnitchouk, Wally [JLAB

    2014-06-01

    We perform a global analysis of all available electron-deuteron quasielastic scattering data using Q^2-dependent smearing functions that describe inclusive inelastic e-d scattering within the weak binding approximation. We study the dependence of the cross sections on the deuteron wave function and the off-shell extrapolation of the elastic electron-nucleon cross section, which show particular sensitivity at x >> 1. The excellent overall agreement with data over a large range of Q^2 and x suggest a limited need for effects beyond the impulse approximation, with the exception of the very high-x or very low-Q^2 regions, where short-distance effects in the deuteron become more relevant.

  20. Cell-penetrating DNA-binding protein as a safe and efficient naked DNA delivery carrier in vitro and in vivo

    SciTech Connect (OSTI)

    Kim, Eun-Sung; Yang, Seung-Woo; Hong, Dong-Ki; Kim, Woo-Taek; Kim, Ho-Guen; Lee, Sang-Kyou

    2010-01-29

    Non-viral gene delivery is a safe and suitable alternative to viral vector-mediated delivery to overcome the immunogenicity and tumorigenesis associated with viral vectors. Using the novel, human-origin Hph-1 protein transduction domain that can facilitate the transduction of protein into cells, we developed a new strategy to deliver naked DNA in vitro and in vivo. The new DNA delivery system contains Hph-1-GAL4 DNA-binding domain (DBD) fusion protein and enhanced green fluorescent protein (EGFP) reporter plasmid that includes the five repeats of GAL4 upstream activating sequence (UAS). Hph-1-GAL4-DBD protein formed complex with plasmid DNA through the specific interaction between GAL4-DBD and UAS, and delivered into the cells via the Hph-1-PTD. The pEGFP DNA was successfully delivered by the Hph-1-GAL4 system, and the EGFP was effectively expressed in mammalian cells such as HeLa and Jurkat, as well as in Bright Yellow-2 (BY-2) plant cells. When 10 {mu}g of pEGFP DNA was intranasally administered to mice using Hph-1-GAL4 protein, a high level of EGFP expression was detected throughout the lung tissue for 7 days. These results suggest that an Hph-1-PTD-mediated DNA delivery strategy may be an useful non-viral DNA delivery system for gene therapy and DNA vaccines.